bluuebunny/crossref_metadata_2025 huggingface dataset:
ERBB4Mutant Alleles Found inBRAFWT Melanomas That Drive the Proliferation of aBRAFWT Melanoma Cell Line
Authors: Lucas Lauren M. , Cullum Richard L. , Woggerman Joelle N. , Dwivedi Vipasha , Markham Jessica A. , Kelley Connor M. , Knerr Elizabeth L. , Cook Laura J. , Jacobi Megan A. , Taylor Darby C. , Rael Cristina C. , Lucas Howard C. , Waits Damien S. , Ghosh Taraswi M. , Halanych Kenneth M. , Gupta Ram B. , Riese David J.
Published: June 2022

Metastatic skin cutaneous melanomas that contain wild-typeBRAFalleles (“BRAFWT melanomas”) remain a significant clinical challenge, primarily because of the paucity of targets for therapeutic intervention. In prior work,in silicoanalyses of The Cancer Genome Atlas Skin Cutaneous Melanoma (TCGA-SKCM) dataset suggested that elevated transcription of the gene that encodes the ERBB4 receptor tyrosine kinase may driveBRAFWT melanomas. Moreover, that prior work demonstrated that expression of the wild-type ERBB4 gene (WTERBB4) stimulates clonogenic proliferation by the IPC-298, MEL-JUSO, MeWo, and SK-MEL-2 humanBRAFWT melanoma cell lines. Moreover, expression of a dominant-negative (K751M)ERBB4mutant (ERBB4DN) inhibits clonogenic proliferation by these same cell lines.

Here we have extended these findings by investigating the role ofERBB4mutant alleles inBRAFWT melanomas.In silicoanalyses of the TCGA-SKCMBRAFWT melanoma dataset indicates thatERBB4missense mutant alleles occur in a non-random manner, suggesting that melanomagenesis selects for theERBB4missense mutant alleles. Specifically,ERBB4missense mutant alleles affect amino acid residues that are weakly correlated with residues conserved in the ERBB3 extracellular domains and the EGFR tyrosine kinase domain. The occurrence ofERBB4missense mutant alleles in the TCGA-SKCMBRAFWT melanoma dataset is weakly inversely correlated with events that cause ERBB4-independent PI3K pathway signaling and is strongly correlated with events that cause elevated RAS pathway signaling. Thus, thein silicoanalyses suggest thatERBB4mutant alleles encode proteins that stimulate PI3K signaling, which cooperates with elevated RAS signaling to driveBRAFWT melanomas. Moreover, thein silicoanalyses have prioritized theERBB4mutant alleles as candidate drivers ofBRAFWT melanomas. TwoERBB4mutant alleles (G85S and G741E) found inBRAFWT melanomas stimulate clonogenic proliferation of MEL-JUSOBRAFWT melanoma cells. We discuss these findings in the context of strategies for identifying and treatingERBB4-dependentBRAFWT melanomas.
U.S. state-level COVID-19 transmission insights from a mechanistic mobility-incidence model
Authors: Thommes Edward W. , Mohammadi Zahra , Flynn-Primrose Darren , Smook Sarah , Gomez Gabriela , Chaves Sandra S. , Coudeville Laurent , Van Aalst Robertus , Mahé Cedric , Cojocaru Monica G.
Published: June 2022

Summary

Background

Throughout the COVID-19 pandemic, human mobility has played a central role in shaping disease transmission. In this study, we develop a mechanistic model to calculate disease incidence from commercially-available US mobility data over the course of 2020. We use it to study, at the US state level, the lag between infection and case report. We examine the evolution of per-contact transmission probability, and its dependence on mean air temperature. Finally, we evaluate the potential of the model to produce short-term incidence forecasts from mobility data.

Methods

We develop a mechanistic model that relates COVID-19 incidence to time series contact index (CCI) data collected by mobility data vendor Cuebiq. From this, we perform maximum-likelihood estimates of the transmission probability per CCI event. Finally, we retrospectively conduct forecasts from multiple dates in 2020 forward.

Findings

Across US states, we find a median lag of 19 days between transmission and case report. We find that the median transmission probability from May onward was about 20% lower than it was during March and April. We find a moderate, statistically significant negative correlation between mean state temperature and transmission probability, r = − .57, N = 49, p = 2 × 10−5. We conclude that for short-range forecasting, CCI data would likely have performed best overall during the first few months of the pandemic.

Interpretation

Our results are consistent with associations between colder temperatures and stronger COVID-19 burden reported in previous studies, and suggest that changes in the per-contact transmission probability play an important role. Our model displays good potential as a short-range (2 to 3 week) forecasting tool during the early stages of a future pandemic, before non-pharmaceutical interventions (NPIs) that modify per-contact transmission probability, principally face masks, come into widespread use. Hence, future development should also incorporate time series data of NPI use.
Waterlogging stress induces antioxidant defense responses and aerenchyma formation and alters metabolisms of banana plants
Authors: Teoh Ee Yang , Teo Chee How , Baharum Nadiya Akmal , Pua Teen-Lee , Tan Boon Chin
Published: June 2022

Flooding caused or exacerbated by climate change has threatened plant growth and food production worldwide. The lack of knowledge on how crops respond and adapt to flooding stress imposes a major barrier to enhancing their productivity. Hence, understanding the flooding-responsive mechanisms of crops is indispensable for developing new flooding-tolerant varieties. Here, we examined the banana (Musa acuminata cv. Berangan) responses to soil waterlogging for 1, 3, 5, 7, 14, and 24 days. After waterlogging stress, banana root samples were analyzed for their molecular and biochemical changes. We found that waterlogging treatment induced the formation of adventitious roots and aerenchyma with conspicuous gas spaces. In addition, the antioxidant activities, hydrogen peroxide and malondialdehyde contents of the waterlogged bananas increased in response to waterlogging stress. To assess the initial response of bananas toward waterlogging stress, we analyzed the transcriptome changes of banana roots. A total of 3,508 unigenes were differentially expressed under 1-day waterlogging conditions. These unigenes comprise abiotic stress-related transcription factors, such as ethylene response factors, basic helix-loop-helix, myeloblastosis, plant signal transduction, and carbohydrate metabolisms. The findings of the study provide insight into the complex molecular events of bananas in response to waterlogging stress, which could later help develop waterlogging resilient crops for the future climate.
Convergence of Ras- and Rac-regulated formin pathways is pivotal for phagosome formation and particle uptake in Dictyostelium
Authors: Körber Sarah , Junemann Alexander , Litschko Christof , Winterhoff Moritz , Faix Jan
Published: June 2022

Macroendocytosis comprising phagocytosis and macropinocytosis are actin-driven processes regulated by small GTPases that depend on the dynamic reorganization of the membrane that protrudes and internalizes extracellular material by cup-shaped structures. To effectively capture, enwrap, and internalize their targets, these cups are arranged into a peripheral ring or ruffle of protruding actin sheets emerging from an actin-rich, non-protrusive zone at its base. Despite extensive knowledge of the mechanism driving actin assembly of the branched network at the protrusive cup edge, which is initiated by the actin-related protein (Arp) 2/3 complex downstream of Rac signaling, our understanding of actin assembly in the base is still incomplete. In the Dictyostelium model system, the Ras-regulated formin ForG was previously shown to specifically contribute to actin assembly at the cup base. Loss of ForG is associated with a strongly impaired macroendocytosis and a 50% reduction of F-actin content at the base of phagocytic cups, in turn indicating the presence of additional factors that specifically contribute to actin formation at the base. Here, we show that ForG synergizes with the Rac-regulated formin ForB to form the bulk of linear filaments at the cup base. Consistently, combined loss of both formins virtually abolishes cup formation and leads to severe defects of macroendocytosis, emphasizing the relevance of converging Ras- and Rac-regulated formin pathways in assembly of linear filaments in the cup base, which apparently provide mechanical support to the entire structure. Remarkably, we finally show that active ForB, unlike ForG, additionally drives phagosome rocketing to aid particle internalization.

Significance Statement

Cup formation in macroendocytosis is a decisive, actin-dependent process that relies on distinct actin assembly factors generating the necessary mechanical forces to drive rearrangements of the plasma membrane and engulfment of extracellular material. Hitherto, in Dictyostelium the Arp2/3 complex and VASP were shown to promote actin assembly at the protrusive rim of phagocytic cups, while the Ras-regulated formin ForG generates about half of the actin filament mass at the base. Here, we show that ForG synergizes with the Rac-regulated formin ForB to form the bulk of filaments at the cup base. Loss of both formins virtually abolishes cup formation and leads to dramatic defects in macroendocytosis, illustrating the relevance of converging Ras- and Rac-regulated signaling pathways in this process.
Oxidative stress potentiates the therapeutic action of a mitochondrial complex I inhibitor in MYC-driven B-cell lymphoma
Authors: Donati Giulio , Nicoli Paola , Verrecchia Alessandro , Vallelonga Veronica , Croci Ottavio , Rodighiero Simona , Audano Matteo , Cassina Laura , Ghsein Aya , Binelli Giorgio , Boletta Alessandra , Mitro Nico , Amati Bruno
Published: June 2022

MYC is a key oncogenic driver and an adverse prognostic factor in multiple types of cancer, including diffuse large B-cell lymphoma (DLBCL). Yet, MYC activation also endows cancer cells with a series of metabolic dependencies, which can provide strategic points for targeted pharmacological intervention. We recently reported that targeting the mitochondrial electron transport chain (ETC) complex I with the small molecule inhibitor IACS-010759 selectively killed MYC-overexpressing lymphoid cells. Here, we unravel the mechanistic basis for this synthetic-lethal interaction and exploit it to improve the anti-tumoral effects of ETC inhibition. In a mouse B-cell line, MYC hyperactivation and IACS-010759 treatment added up to induce oxidative stress, with consequent depletion of reduced glutathione and lethal disruption of redox homeostasis. This effect could be enhanced by targeted pharmacological intervention, with either inhibitors of NADPH production through the pentose phosphate pathway, or with ascorbate (vitamin C), known to contribute pro-oxidant effects when administered at high doses. In these conditions, ascorbate synergized with IACS-010759 to kill MYC-overexpressing cells in vitro and reinforced its therapeutic action against human B-cell lymphoma xenografts. Hence, ETC inhibition and high-dose ascorbate might improve the outcome of patients affected by high-grade lymphomas and other MYC-driven cancers.

Key point #1

MYC and the ETC complex I inhibitor IACS-010759 elicit different reactive oxygen species (ROS) that cooperate to disrupt redox homeostasis.

Key point #2

Further boosting of oxidative stress with high doses of ascorbate increases the killing of MYC-driven lymphoma xenografts by IACS-010759.
Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle
Authors: Rahlff Janina , Esser Sarah P. , Plewka Julia , Heinrichs Mara Elena , Soares André , Scarchilli Claudio , Grigioni Paolo , Wex Heike , Giebel Helge-Ansgar , Probst Alexander J.
Published: June 2022

Marine viruses have thoroughly been studied in seawater, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2 % of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols and rain. Viruses detected in rain and aerosols showed a significantly higher percent G/C base content compared to marine viruses, and a genetically distinct rain virome supports that those viruses could inhabit higher air masses. CRISPR spacer matches of marine prokaryotes to “foreign” viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization and long-range atmospheric dispersal implicate virus-mediated carbon turnover in remote areas, viral dispersal mechanisms relevant to human health, and involvement of viruses in atmospheric processes like ice-nucleation.
Dopamine in the Dorsal Bed Nucleus of Stria Terminalis signals Pavlovian sign-tracking and reward violations
Authors: Gyawali Utsav , Martin David A. , Sun Fangmiao , Li Yulong , Calu Donna J.
Published: June 2022

Midbrain and striatal dopamine signals have been extremely well characterized over the past several decades, yet novel dopamine signals and functions in reward learning and motivation continue to emerge. A similar characterization of real-time sub-second dopamine signals in areas outside of the striatum has been limited. Recent advances in fluorescent sensor technology and fiber photometry permit measurement of dopamine binding correlates, which can divulge basic functions of dopamine signaling in non-striatal dopamine terminal regions, like the dorsal bed nucleus of the stria terminalis (dBNST). Here, we record GRABDAsignals in the dBNST during a Pavlovian lever autoshaping task. We observe greater Pavlovian cue-evoked dBNST GRABDAsignals in sign-tracking (ST) compared to goal-tracking/intermediate (GT/INT) rats and the magnitude of cue-evoked dBNST GRABDAsignals decrease immediately following reinforcer-specific satiety. When we deliver unexpected reward or omit expected reward, we find that dBNST dopamine signals encode bidirectional reward prediction errors in GT/INT rats, but only positive prediction errors in ST rats. Since sign- and goal-tracking approach strategies are associated with distinct drug relapse vulnerabilities, we examined the effects of experimenter-administered fentanyl on dBNST dopamine associative encoding. Systemic fentanyl injections do not disrupt dBNST cue discrimination but generally potentiate dBNST dopamine signals. These results reveal multiple dBNST dopamine correlates of learning and motivation that depend on the Pavlovian approach strategy employed.
OrganelX Web Server for Sub-Peroxisomal and Sub-Mitochondrial protein localisation
Authors: Anteghini Marco , Haja Asmaa , Martins dos Santos Vitor AP , Schomaker Lambert , Saccenti Edoardo
Published: June 2022

Computational approaches for sub-organelle protein localisation and identification are often neglected while general methods, not suitable for specific use cases, are promoted instead. In particular, organelle-specific research lacks user-friendly and easily accessible computational tools that allow researchers to perform computational analysis before starting time-consuming and expensive wet-lab experiments. We present the Organelx e-Science Web Server which hosts three sequence localisation predictive algorithms: In-Pero and In-Mito for classifying sub-peroxisomal and sub-mitochondrial protein localisations given their FASTA sequences, as well as the Is-PTS1 algorithm for detecting and validating potential peroxisomal proteins carrying a PTS1 signal. These tools can be used for a fast and accurate screening while looking for new peroxisomal and mitochondrial proteins. To our knowledge, this is the only service that provides these functionalities and can fasten the daily research of the peroxisomal science community.
Differential roles of delta and theta oscillations in understanding semantic gist during natural audiovisual speech perception: Functional and anatomical evidence
Authors: Park Hyojin , Ince Robin A. A. , Gross Joachim
Published: June 2022

Understanding the main topic of naturalistic speech in a multi-speaker environment is demanding though the availability of visual speech can be beneficial for speech comprehension. Recent studies provided evidence that low-frequency brain rhythms play an important role in the processing of acoustic speech features. However, at present, the neural dynamics of brain rhythms implementing a higher-order semantic system during naturalistic audiovisual speech perception is unknown. Here we investigated information processing carried by low-frequency oscillations in delta and theta bands for audiovisual speech integration for high-level semantic gist processing using a representational interaction approach. By manipulating the degree of high-level semantic content (speech chunks with high versus low topic probability) using Latent Dirichlet Allocation (LDA) topic modelling algorithm and complexity of speaker environment (single versus multi-speaker), we first found that delta and theta phase exert distinctive roles in high-level semantic processing where delta phase represents auditory and visual inputs synergistically whereas theta band does so redundantly. Next, we show both forms of representational interaction are observed to be greater for speech with low semantic gist, supported by speech comprehension and white matter tractography. Furthermore, we show that the delta phase-specific synergistic interaction in the right auditory, temporal, and inferior frontal areas is sensitive to the speaker environment, whereas theta band activity showing redundant representations is sensitive to semantic content. Our results shed new light on dynamic neural mechanisms of implementing higher-order semantic systems through representational interactions between audiovisual speech information and differential roles of delta and theta bands depending on the speaker environment.
Arginine methylation of Puf4 drives diverse protein functions
Authors: Kalem Murat C. , Duffy Sean , Shen Shichen , Kaur Jan Naseer , Qu Jun , Panepinto John C.
Published: June 2022

The evolutionarily conserved Pumilio domain-containing RNA binding proteins (RBPs) are involved in many steps of post-transcriptional gene regulation, including RNA stability, polyadenylation, deadenylation, and translation. RBPs are post-translationally modified by methylation of arginine/glycine-rich domains, though the consequences of these modifications are not well known. We determined the arginine methylation and phosphorylation landscape of the Pumilio domain-containing RBP Puf4 from the basidiomycete fungus Cryptococcus neoformans. We found that methyl-deficient Puf4 mutants do not complement critical PUF4 deletion phenotypes, such as resistances to endoplasmic reticulum stress and antifungals, and cell wall remodeling. Methyl-deficient mutants also exhibit unique RNA and protein interactions. Lastly, we identified intra-protein cross talk between post-translationally modified methylated and phosphorylated residues. Overall, we show that post-translational modifications, particularly arginine methylation, of Puf4 regulate the functions of this RBP.
VPS13A and VPS13C influence lipid droplet abundance
Authors: Chen Shuliang , Roberts Melissa A. , Chen Chun-Yuan , Markmiller Sebastian , Wei Hong-Guang , Yeo Gene W. , Granneman James G , Olzmann James A. , Ferro-Novick Susan
Published: June 2022

Lipid transfer proteins mediate the exchange of lipids between closely apposed membranes at organelle contact sites and play key roles in lipid metabolism, membrane homeostasis, and cellular signaling. A recently discovered novel family of lipid transfer proteins, which includes the VPS13 proteins (VPS13A-D), adopt a rod-like bridge conformation with an extended hydrophobic groove that enables the bulk transfer of membrane lipids for membrane growth. Loss of function mutations in VPS13A and VPS13C cause chorea acanthocytosis and Parkinson’s disease, respectively. VPS13A and VPS13C localize to multiple organelle contact sites, including endoplasmic reticulum (ER) – lipid droplet (LD) contact sites, but the functional roles of these proteins in LD regulation remains mostly unexplored. Here, we employ CRISPR-Cas9 genome editing to generate VPS13A and VPS13C knockout cell lines in U-2 OS cells via deletion of exon 2 and introduction of an early frameshift. Analysis of LD content in these cell lines revealed that loss of either VPS13A or VPS13C results in reduced LD abundance under oleate-stimulated conditions. These data implicate VPS13A and VPS13C in LD regulation and raise the intriguing possibility that VPS13A and VPS13C-mediated lipid transfer facilitates LD biogenesis.
Mechanisms ofListeria monocytogenesdisinfection with Benzalkonium chloride: from molecular dynamics to kinetics of time-kill curves
Authors: Pérez-Rodríguez Martín , Cabo Marta L. , Balsa-Canto Eva , R. García Míriam
Published: June 2022

Unravelling the mechanisms of action of disinfectants is essential to optimise dosing regimes and minimise the emergence of antimicrobial resistance. In this work, we examine the mechanisms of action of a commonly used disinfectant - benzalkonium chloride (BAC)-over a significant pathogen -L. monocytogenes- in the food industry. For that purpose, we use modelling at multiple scales, from the cell membrane to the cell population inactivation. Molecular modelling reveals that the integration of the BAC into the membrane requires three phases: (1) the BAC approaches the cellular membrane, (2) the BAC is adsorbed on its surface, and (3) it is rapidly integrated into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilising the membrane. We hypothesise that the equilibrium of adsorption, although fast, is limiting for sufficiently large BAC concentrations, and a kinetic model is derived to describe time-kill curves of a large population of cells. The model is tested and validated with time series data of free BAC decay and time-kill curves ofL. monocytogenesat different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to design novel disinfection processes rationally.
Bacterial profiles of the human placenta from term and preterm deliveries
Authors: Theis Kevin R. , Winters Andrew D. , Romero Roberto , Alhousseini Ali , Greenberg Jonathan M. , Panzer Jonathan , Galaz Jose , Pacora Percy , Shaffer Zachary , Jung Eunjung , Gomez-Lopez Nardhy
Published: June 2022

Whether the human placenta is a sterile organ is under debate. Yet, infection of the amniotic cavity, including the placenta, is causally linked to preterm birth. This study compares the bacterial profiles of term and preterm placentas through culture and 16S rRNA gene sequencing of the amnion, amnion-chorion interface, subchorion, villous tree, and basal plate, while accounting for patient identity, mode of delivery, presence/absence of labor, and potential background DNA contamination. As no evidence of a placental microbiota in term pregnancy was found, these placentas were considered as controls. Placentas from preterm birth cases were more likely to yield bacterial cultures, and their bacterial DNA profiles were less rich than those of term controls, suggesting the predominance of only a few bacteria. Nevertheless, the bacterial DNA profiles of placentas from preterm cases and term controls were not consistently different. The placentas from preterm cases may often have a microbiota but the bacteria constituting these communities varied among the women. Mode of delivery had a pronounced effect on the bacterial profiles of all sampled levels of the placenta. Specifically, the bacterial DNA profiles of vaginally delivered placentas had higher relative abundances of Finegoldia, Gardnerella, Peptoniphilus, and Prevotella (each a common resident of the vaginal microbiota) than the profiles of cesarean-delivered placentas. Collectively, these data indicate that there is a not a placental microbiota in normal term pregnancy, and that although the placentas of some preterm cases were populated by bacteria, the identities of these bacteria varied among women delivering preterm.

IMPORTANCE

If a placental microbiota exists, then current understanding of the roles of microorganisms in pregnancy outcomes need to be reconsidered. For instance, we will need to determine if a placental microbiota is beneficial to pregnancy outcome by excluding potential pathogens from colonizing the placenta and/or effectively priming the fetal immune system, and furthermore which characteristics of the placental microbiota preclude versus promote placental infection, which can result in pregnancy complications such as preterm birth. Our findings here are consistent with prior investigations that have reported that there is not a placental microbiota in typical human pregnancies. Yet, bacteria can be detected in placentas from preterm deliveries. The principal source of microorganisms invading the amniotic cavity, including the placenta, is the vaginal microbiota. Focus should be on elucidating the metabolic and/or virulence characteristics of the subset of bacteria within the vaginal microbiota that commonly invade the amniotic cavity, resulting in infection.
The ESX-1 substrate PPE68 has a key function in the ESX-1 mediated secretion inMycobacterium marinum
Authors: Damen Merel P.M. , Meijers Aniek S. , Keizer Esther M. , Piersma Sander R. , Jiménez Connie R. , Kuijl Coenraad P. , Bitter Wilbert , Houben Edith N. G.
Published: June 2022

Mycobacteria use specialized type VII secretion systems (T7SSs) to secrete proteins across their diderm cell envelope. One of the T7SS subtypes, named ESX-1, is a major virulence determinant in pathogenic species such asMycobacterium tuberculosisand the fish pathogenMycobacterium marinum.ESX-1 secretes a variety of substrates, called Esx, PE, PPE and Esp proteins, at least some of which as folded heterodimers. Investigations into the functions of these substrates is problematic, because of the intricate network of co-dependent secretion between several ESX-1 substrates. Here, we describe that the ESX-1 substrate PPE68 is essential for secretion of the highly immunogenic substrate EsxA and EspE via the ESX-1 system inM. marinum. While secreted PPE68 is processed on the cell surface, the majority of cell-associated PPE68 ofM. marinumandM. tuberculosisis present in a cytosolic complex with its PE partner and the EspG1chaperone. Interfering with the binding of EspG1to PPE68 blocked its export and the secretion of EsxA and EspE. In contrast,esxAis not required for the secretion of PPE68, revealing hierarchy in co-dependent secretion. Remarkably, the final ten residues of PPE68, a negatively charged domain, seem essential for EspE secretion, but not for the secretion of EsxA and PPE68 itself. This indicates that distinctive domains of PPE68 are involved in secretion of the different ESX-1 substrates. Based on these findings, we propose a mechanistic model for the central role of PPE68 in ESX-1 mediated secretion and substrate co-dependence.

Importance

Mycobacterium tuberculosisuse type VII secretion systems (T7SSs) to secrete proteins across its uniquely hydrophobic diderm cell envelope. A T7SS subtype, called ESX-1, is one of its most important virulence determinants by mediating intracellular survival through phagosomal rupture and subsequent translocation of the mycobacterium to the host cytosol. Identifying the ESX-1 substrate that is responsible for this process is problematic because of the intricate network of co-dependent secretion between ESX-1 substrates. Here, we provide mechanistic insight into the central role of the ESX-1 substrate PPE68 for the secretion of ESX-1 substrates, using the model organismMycobacterium marinum. Unravelling the mechanism of co-dependent secretion will aid the functional understanding of T7SSs and will allow the analysis of the individual roles of ESX-1 substrates in the virulence caused by this significant human pathogen.
Neurophysiological consequences of synapse loss in progressive supranuclear palsy
Authors: Adams Natalie E. , Jafarian Amirhossein , Perry Alistair , Rouse Matthew A. , Shaw Alexander D. , Murley Alexander G. , Cope Thomas E. , Bevan-Jones W. Richard , Passamonti Luca , Street Duncan , Holland Negin , Nesbitt David , Hughes Laura E. , Friston Karl J , Rowe James B.
Published: June 2022

Synaptic loss occurs early in many neurodegenerative diseases and contributes to cognitive impairment even in the absence of gross atrophy. Currently, for human disease there are few formal models to explain how cortical networks underlying cognition are affected by synaptic loss. We advocate that biophysical models of neurophysiology offer both a bridge from clinical to preclinical models of pathology, and quantitative assays for experimental medicine. Such biophysical models can also disclose hidden neuronal dynamics generating neurophysiological observations like electro- and magneto-encephalography (MEG). Here, we augment a biophysically informed mesoscale model of human cortical function by inclusion of synaptic density estimates as captured by [11C]UCB-J positron emission tomography, and provide insights into how regional synapse loss affects neurophysiology. We use the primary tauopathy of progressive supranuclear palsy (Richardson’s syndrome) as an exemplar condition, with high clinicopathological correlations. Progressive supranuclear palsy causes a marked change in cortical neurophysiology in the presence of mild atrophy and is associated with a decline in cognitive functions associated with the frontal lobe. Using (parametric empirical) Bayesian inversion of a conductance-based canonical microcircuit model of MEG data, we show that the inclusion of regional synaptic density—as a subject-specific prior on laminar specific neuronal populations—markedly increases model evidence. Specifically, model comparison suggests that a reduction in synaptic density in inferior frontal cortex affects superficial and granular layer glutamatergic excitation. This predicted individual differences in behaviour, demonstrating the link between synaptic loss, neurophysiology, and cognitive deficits. The method we demonstrate is not restricted to progressive supranuclear palsy or the effects of synaptic loss: such pathology-enriched dynamic causal models can be used to assess the mechanisms of other neurological disorders, with diverse non-invasive measures of pathology, and is suitable to test the effects of experimental pharmacology.
Estimating the incubation period of monkeypox virus during the 2022 multi-national outbreak
Authors: Charniga Kelly , Masters Nina B. , Slayton Rachel B. , Gosdin Lucas , Minhaj Faisal S. , Philpott David , Smith Dallas , Gearhart Shannon , Alvarado-Ramy Francisco , Brown Clive , Waltenburg Michelle A. , Hughes Christine M. , Nakazawa Yoshinori
Published: June 2022

Monkeypox is a zoonotic disease endemic in Central and West Africa. In May 2022, an outbreak of monkeypox characterized by human-to-human transmission was detected in multiple non-endemic countries. We estimated the incubation period for monkeypox using information from 22 probable (N = 1) and confirmed (N = 21) monkeypox cases in patients reported in the United States through June 6, 2022. We pooled U.S. patient data with the data from 18 confirmed cases in patients reported from the Netherlands through May 31, 2022. The mean incubation period from exposure to first symptom onset was 7.6 days (95% credible interval: 6.2 – 9.7), and the 95th percentile was 17.1 days (95% CrI: 12.7–24.3). These findings align with current CDC recommendations for monitoring close contacts of people with monkeypox for 21 days after their last exposure.
Automated 360-degree goniophotography with the NIDEK Gonioscope GS-1 for glaucoma
Authors: Madu Chisom T. , Phelps Taylor , Schuman Joel S. , Zambrano Ronald , Lee Ting-Fang , Panarelli Joseph , Al-Aswad Lama , Wollstein Gadi
Published: June 2022

Purpose

To evaluate the reliability of the NIDEK Gonioscope GS-1 when used to grade the iridocorneal angle in a clinical setting.

Methods

A total of 20 participants (37 eyes) who were 18 or older and had glaucoma or were glaucoma suspects were enrolled from the NYU Langone Eye Center and Bellevue Hospital. During their usual ophthalmology visit, they were consented for the study and underwent 360-degree goniophotography using the NIDEK Gonioscope GS-1. Afterwards, the three ophthalmologists separately examined the images obtained and determined the status of the iridocorneal angle in four quadrants using the Shaffer grading system. Physicians were masked to patient names and diagnoses. Inter-observer reproducibility was determined using Fleiss’ kappa statistics.

Results

The interobserver reliability using Fleiss’ statistics was shown to be significant between three glaucoma specialists with fair overall agreement (Fleiss’ kappa: 0.266, p<.0001) in the interpretation of 360-degree goniophotos. Automated 360-degree goniophotography using the NIDEK Gonioscope GS-1 have quality such that they are interpreted similarly by independent expert observers. This indicates that angle investigation may be performed using this automated device and that interpretation by expert observers is likely to be similar.

Conclusion

Images produced from automated 360-degree goniophotography using the NIDEK Gonioscope GS-1 are similarly interpreted amongst glaucoma specialists, thus supporting use of this technique to document and assess the anterior chamber angle in patients with, or suspected of, glaucoma and iridocorneal angle abnormalities.

Précis

Automated 360-degree goniophotography using the NIDEK Gonioscope GS-1 is a reasonable tool for anterior chamber angle assessment.
Dietary Exposure to Oxidized Lipids in US Infants
Authors: Maldonado-Pereira Lisaura , Barnaba Carlo , Medina-Meza Ilce Gabriela
Published: June 2022

Baby Foods (BFs) and Infant formulas (IFs) are the main sources of nutrition for an infant throughout the 1st year of life. A variety of enriched products are commercially available for parents seeking to fulfill their baby’s nutritional needs. Consequently, different bioactive lipids are present in BFs and IFs including dietary oxidative substances (DOxS) whose known toxicity has been associated with mutagenicity, cancer, and other chronic diseases. In this work, we performed an exposure assessment of 25 bioactive lipids on a total of 63 baby food samples (50 – IFs and 13 – BFs) commercially available in the US. To determine the dietary exposure to DOxS, we used EPA’s SHEDS-HT probabilistic model. Even though β-Sitosterol was the most exposed bioactive lipid with 75,4 µg/day, cholesterol was the most absorbed compound during the entire first year (19,320 µg/day). Additionally, we found 7α-hydroxycholesterol (7α-OH) as a potential DOxS biomarker of the BFs manufacturing process. This is the first time that an exposure assessment including DOxS ingested by infants after BFs and IFs consumption is performed, enabling much-needed information regarding these hazardous compounds and their potential effects on infants’ health.
Estimation of time cost of anti-cancer drugs approved based on comparisons to best supportive care: a cross sectional analysis
Authors: Prasad Vinay , Olivier Timothée , Chen Emerson Y , Haslam Alyson
Published: June 2022

Background

Financial costs from cancer treatment are increasingly recognized, but what has historically been underrecognized is the time cost of therapy. We sought to estimate the time burden of anti-cancer drugs approved based on comparisons to best supportive care (BCS), with the assumption that without this drug, a patient could have been treated with observation, home palliative care or hospice services, with minimal time seeking medical care.

Methods

We searched all FDA approvals (2009 - March 2022) for randomized trials that used BCS as a treatment option for an anti-tumor drug in the metastatic setting and abstracted data on treatment related activities. We then estimated time spent on these activities using previously calculated times.

Results

Of the 13 drugs tested against BSC, nine studies demonstrated an improvement in median OS (median 2.1 months). The median monthly time spent for patients in the intervention arm of BSC trials was 15.8 hours.

Conclusion

Time is a valuable resource for people who have cancer, but especially for patients who may have few to no remaining treatment options, and yet, we found that patients can spend up to 16 hours in anti-cancer drug related activities per month.
Receipt of anti-SARS-CoV-2 pharmacotherapies among U.S. Veterans with mild to moderate COVID-19, January-February 2022
Authors: Bajema Kristina L. , Wang Xiao Qing , Hynes Denise M. , Rowneki Mazhgan , Hickok Alex , Cunningham Francesca , Bohnert Amy , Boyko Edward J. , Iwashyna Theodore J. , Maciejewski Matthew L. , Viglianti Elizabeth M. , Streja Elani , Yan Lei , Aslan Mihaela , Huang Grant D. , Ioannou George N.
Published: June 2022

Background

Older adults and persons with medical co-morbidities are at increased risk for severe COVID-19. Several pharmacotherapies demonstrated to reduce the risk of COVID-19-related hospitalization and death have been authorized for use. We describe factors associated with receipt of outpatient COVID-19 pharmacotherapies in the Veterans Health Administration.

Methods

We conducted a retrospective cohort study among Veterans with risk factors for severe COVID-19 who tested positive for SARS-CoV-2 during January and February 2022. We compared receipt of any COVID-19 pharmacotherapy, including sotrovimab, nirmatrelvir plus ritonavir, molnupiravir, or remdesivir versus no antiviral or monoclonal antibody treatment according to demographic characteristics, place of residence, underlying medical conditions, and COVID-19 vaccination using multivariable logistic regression.

Results

During January and February 2022, 16,546 courses of sotrovimab, nirmatrelvir, and molnupiravir were allocated across the Veterans Health Administration. Among 111,717 Veterans testing positive for SARS-CoV-2, 4,233 (3.8%) received any COVID-19 pharmacotherapy, including 2,870 of 92,396 (3.1%) in January and 1,363 of 19,321 (7.1%) in February. Among a subset of 56,206 Veterans with documented COVID-19-related symptoms in the 30 days preceding positive SARS-CoV-2 test, 3,079 of 53,206 (5.5%) received any COVID-19 pharmacotherapy. Untreated Veterans had a median age of 60 years (interquartile range [IQR] 46-71 years) and median 3 underlying medical conditions (IQR 2-5). Veterans receiving any treatment were more likely to be older (adjusted odds ratio [aOR] 1.66, 95% confidence interval [CI] 1.52-1.80, 65-74 versus 50-64 years; aOR 1.67, 95% CI 1.53-1.84 ≥75 versus 50-64 years) and have a higher number of underlying conditions (aOR 1.63, 95% CI 1.48-1.79, 3-4 versus 1-2 conditions; aOR 2.17, 95% CI 1.98-2.39, ≥5 versus 1-2 conditions). Persons of Black versus White race (aOR 0.65, 95% CI 0.60-0.72) and well as persons of Hispanic ethnicity (aOR 0.88, 95% CI 0.77-0.99) were less likely to receive treatment.

Conclusions and Relevance

Although supply of outpatient COVID-19 pharmacotherapies during January and February 2022 was limited, prescription of these pharmacotherapies was underutilized, consistent with early national patterns in dispensing. Racial and ethnic minorities were less likely to receive any pharmacotherapy.
Genomic analysis of a synthetic reversed sequence reveals default chromatin states in yeast and mammalian cells
Authors: Camellato Brendan , Brosh Ran , Maurano Matthew T. , Boeke Jef D.
Published: June 2022

Up to 93% of the human genome may show evidence of transcription, yet annotated transcripts account for less than 5%. It is unclear what makes up this major discrepancy, and to what extent the excess transcription has a definable biological function, or is just a pervasive byproduct of non-specific RNA polymerase binding and transcription initiation. Understanding the default state of the genome would be informative in determining whether the observed pervasive activity has a definable function. The genome of any modern organism has undergone billions of years of evolution, making it unclear whether any observed genomic activity, or lack thereof, has been selected for. We sought to address this question by introducing a completely novel 100-kb locus into the genomes of two eukaryotic organisms, S. cerevisiae and M. musculus, and characterizing its genomic activity based on chromatin accessibility and transcription. The locus was designed by reversing (but not complementing) the sequence of the human HPRT1 locus, including ∼30-kb of both upstream and downstream regulatory regions, allowing retention of sequence features like repeat frequency and GC content but ablating coding information and transcription factor binding sites. We also compared this reversed locus with a synthetic version of the normal human HPRT1 locus in both organismal contexts. Despite neither the synthetic HPRT1 locus nor its reverse version coding for any promoters evolved for gene expression in yeast, we observed widespread transcriptional activity of both loci. This activity was observed both when the loci were present as episomes and when chromosomally integrated, although it did not correspond to any of the known HPRT1 functional regulatory elements. In contrast, when integrated in the mouse genome, the synthetic HPRT1 locus showed transcriptional activity corresponding precisely to the HPRT1 coding sequence, while the reverse locus displayed no activity at all. Together, these results show that genomic sequences with no coding information are active in yeast, but relatively inactive in mouse, indicating a potentially major difference in “default genomic states” between these two divergent eukaryotes.
Co-option of endogenous retroviruses through genetic escape from TRIM28 repression
Authors: Enriquez-Gasca Rocio , Gould Poppy A. , Tunbak Hale , Conde Lucia , Herrero Javier , Chittka Alexandra , Gifford Robert , Rowe Helen M.
Published: June 2022

Endogenous retroviruses (ERVs) have rewired host gene networks through co-option of their enhancers. To explore which ERVs get co-opted and why, we tracked the epigenetic fate of murine IAPEz elements using an in vitro model of embryonic stem cell (ESC) to neural progenitor cell (NPC) differentiation. TRIM28-repression depended on a 190bp sequence, previously shown to confer IAPEzs with retrotransposition activity. A subset of IAPEzs (∼15%) exhibit genetic divergence from this sequence, which we term escapees. While repressed IAPEzs succumb to a previously undocumented epigenetic handover from H3K9me3 in ESCs to H3K27me3 in NPCs, escapee IAPEzs evade repression, resulting in their transcriptional derepression in NPCs. Escapee IAPEzs enhance expression of nearby neural genes and contribute to gene expression differences between mouse strains, which we discern by employing IAPEz insertion polymorphisms. In sum, co-opted ERVs stem from genetic escapees that have lost vital sequences required for both TRIM28 restriction and autonomous retrotransposition.

HIGHLIGHTS

Tracking the epigenetic fate of ERVs through neural differentiation reveals which ERVs are subject to co-option and why.

Most ERVs succumb to H3K9me3 deposition in ESCs with H3K27me3 memory in NPCs.

ERVs that act as enhancers to nearby neural genes have undergone genetic escape from TRIM28 repression.

Epigenetic evasion is an evolutionary trade-off that comes with loss of sequences necessary for retrotransposition.

Abstract Figure

Graphical abstract.
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3
Authors: Peters Christine E. , Schulze-Gahmen Ursula , Eckhardt Manon , Jang Gwendolyn M. , Xu Jiewei , Pulido Ernst H. , Ott Melanie , Gozani Or , Verba Kliment A. , Hüttenhain Ruth , Carette Jan E. , Krogan Nevan J.
Published: June 2022

Enteroviruses cause a number of medically relevant and widespread human diseases with no approved antiviral therapies currently available. Host-directed therapies present an enticing option for this diverse genus of viruses. We have previously identified the actin histidine methyltransferase SETD3 as a critical host factor physically interacting with the viral protease 2A. Here, we report the 3.5 Å cryo-EM structure of SETD3 interacting with coxsackievirus B3 2A at two distinct interfaces, including the substrate-binding surface within the SET domain. Structure-function analysis revealed that mutations of key residues in the SET domain resulted in severely reduced binding to 2A and complete protection from enteroviral infection. Our findings provide insight into the molecular basis of the SETD3-2A interaction and a framework for the rational design of host-directed therapeutics against enteroviruses.
Cytoplasmic membrane thinning observed by interfacial dyes is likely a common effect of bactericidal antibiotics
Authors: Dubey Ashim Kumar , Verma Taru , Sardana Deepika , Khamari Balaram , Alam Parvez , Bulagonda Eswarappa Pradeep , Sen Sobhan , Nandi Dipankar
Published: June 2022

The lipid membrane is a fundamental part of life. However, the effects of different stresses on membranal integrity and physiology are less understood. Using novel 4-aminophthalimide-based membrane-specific dyes (4AP-Cn: n is carbon chain-length), aided with confocal microscopy, fluorescence spectroscopy, molecular dynamics simulations, and flow cytometry, we have studied stress-mediated changes inE. colimembranes. By exploiting the depth-dependent positioning and subsequent environmental sensitivity of the dyes, we have proposed a measure of antibiotic-induced membrane damage: the fluorescence Peak Maxima Difference (PMD) between 4AP-C9 and 4AP-C13. The ROS-influenced PMD quantifies cytoplasmic membrane thickness and measures sensitivity against most bactericidal antibiotics, depending upon the extent of lipid peroxidation. Importantly, we have verified this observation using antibiotic-sensitive and resistant clinical isolates ofE. coliand ESKAPE pathogens likeK. pneumoniaeandEnterobacter spp.This study underscores the role of antibiotic-induced membrane changes; a critical issue given the increasing global antimicrobial resistance.