bluuebunny/crossref_metadata_2025 huggingface dataset:
Shielding individuals at high risk of COVID-19: a micro-simulation study
Authors: van Zandvoort Kevin , Favas Caroline , Checchi Francesco
Published: January 2022

Background

One of the proposed interventions for mitigating COVID-19 epidemics, particularly in low-income and crisis-affected settings, is to physically isolate individuals known to be at high risk of severe disease and death due to age or co-morbidities. This intervention, known as ‘shielding’, could be implemented in various ways. If shielded people are grouped together in residences and isolation is imperfect, any introduction of infections within the shielding group could cause substantial mortality and thus negate the intervention’s benefits. We explored the effectiveness of shielding under various modalities of implementation and considered mitigation measures to reduce its possible harms.

Methods

We used an individual-based mathematical model to simulate the evolution of a COVID-19 epidemic in a population of which a fraction above a given age cut-off are relocated to shielding residences, in which they have variable levels of contacts with their original household, the outside world and fellow shielding residents. We set our simulation with the context of an internally displaced persons’ camp in Somaliland, for which we had recently collected data on household demographics and social mixing patterns. We compared an unmitigated epidemic with a shielding intervention accompanied by various measures to reduce the risk of virus introduction and spread within the shielding residences. We did sensitivity analyses to explore parameters such as residence size, reduction in contacts, basic reproduction number, and prior immunity in the population.

Results

Shielded residences are likely to be breached with infection during the outbreak. Nonetheless, shielding can be effective in preventing COVID-19 infections in the shielded population. The effectiveness of shielding is mostly affected by the size of the shielded residence, and by the degree by which contacts between shielded and unshielded individuals are reduced. Reductions in contacts between shielded individuals could further increase the effectiveness of shielding, but is only effective in larger shielded residences. Large shielded residences increase the risk of infection, unless very large reductions in contacts can be achieved. In epidemics with a lower reproduction number, the effectiveness of shielding could be negative effectiveness.

Discussion

Shielding could be an effective method to protect the most at-risk individuals. It should be considered where other measures cannot easily be implemented, but with attention to the epidemiological situation. Shielding should only be implemented through small to medium-sized shielding residences, with appropriate mitigation measures such as reduced contact intensity between shielded individuals and self-isolation of cases to prevent subsequent spread.
Magnetic torque-driven living microrobots for enhanced tumor infiltration
Authors: Gwisai T. , Mirkhani N. , Christiansen M. G. , Nguyen T.T. , Ling V. , Schuerle S.
Published: January 2022

Bacterial microrobots combining self-propulsion and magnetic guidance are increasingly recognized as promising drug delivery vehicles for targeted cancer therapy. Thus far, control strategies have either relied on poorly scalable magnetic field gradients or employed directing magnetic fields with propulsive forces limited by the bacterial motor. Here, we present a magnetic torque-driven actuation scheme based on rotating magnetic fields to wirelessly control Magnetospirillum magneticum AMB-1 bearing versatile liposomal cargo. We observed a 4-fold increase in conjugate translocation across a model of the vascular endothelium and found that the primary mechanism driving this increased transport is torque-driven surface exploration at the cell interface. Using spheroids as a 3D tumor model, fluorescently labeled bacteria colonized their core regions with up to 21-fold higher signal in samples exposed to rotating magnetic fields. In addition to enhanced transport, we demonstrated the suitability of this magnetic stimulus for simultaneous actuation and inductive detection of AMB-1. Finally, we demonstrated that RMF significantly enhances AMB-1 tumor accumulation in vivo following systemic intravenous administration in mice. Our findings suggest that scalable magnetic torque-driven control strategies can be leveraged advantageously with biohybrid microrobots.

One-Sentence Summary

Magnetic torque-driven motion enhances infiltration of living microrobots across physiological barriers both in vitro and in vivo.
Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes
Authors: Meister Michael T. , Groot Koerkamp Marian J. A. , de Souza Terezinha , Breunis Willemijn B. , Frazer-Mendelewska Ewa , Brok Mariël , DeMartino Jeff , Manders Freek , Calandrini Camilla , Kerstens Hinri H. D. , Janse Alex , Dolman M. Emmy M. , Eising Selma , Langenberg Karin P. S. , van Tuil Marc , Knops Rutger R. G. , van Scheltinga Sheila Terwisscha , Hiemcke-Jiwa Laura S. , Flucke Uta , Merks Johannes H. M. , van Noesel Max M. , Tops Bastiaan B. J. , Hehir-Kwa Jayne Y. , Kemmeren Patrick , Molenaar Jan J. , van de Wetering Marc , van Boxtel Ruben , Drost Jarno , Holstege Frank C. P.
Published: January 2022

Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here we describe the generation of a collection of pediatric RMS tumor organoid (tumoroid) models comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within four to eight weeks, indicating the feasibility of personalized drug screening. Molecular, genetic and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to six months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 withTP53knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions.
Tree House Explorer: A Novel Genome Browser for Phylogenomics
Authors: Harris Andrew J. , Foley Nicole M. , Williams Tiffani L. , Murphy William J.
Published: January 2022

Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
Integrated genomic analysis of AgRP neurons reveals that IRF3 regulates leptin’s hunger-suppressing effects
Authors: Heyward Frankie D. , Liu Nan , Jacobs Christopher , Ivison Rachael , Machado Natalia , Uner Aykut , Srinivasan Harini , Patel Suraj J. , Gulko Anton , Sermersheim Tyler , Orkin Stuart H. , Tsai Linus , Rosen Evan D.
Published: January 2022

AgRP neurons in the arcuate nucleus of the hypothalamus (ARC) coordinate homeostatic changes in appetite associated with fluctuations in food availability and leptin signaling. Identifying the relevant transcriptional regulatory pathways in these neurons has been a priority, yet such attempts have been stymied due to their low abundance and the rich cellular diversity of the ARC. Here we generated AgRP neuron-specific transcriptomic and chromatin accessibility profiles during opposing states of fasting-induced hunger and leptin-induced hunger suppression. Cis-regulatory analysis of these integrated datasets enabled the identification of 28 putative hunger-promoting and 29 putative hunger-suppressing transcriptional regulators in AgRP neurons, 16 of which were predicted to be transcriptional effectors of leptin. Within our dataset, Interferon regulatory factor 3 (IRF3) emerged as a leading candidate mediator of leptin-induced hunger-suppression. Gain- and loss-of-function experiments in vivo confirm the role of IRF3 in mediating the acute satiety-evoking effects of leptin in AgRP neurons, while live-cell imaging in vitro indicate that leptin can activate neuronal IRF3 in a cell autonomous manner. Finally, we employ CUT&RUN to uncover direct transcriptional targets of IRF3 in AgRP neurons in vivo. Thus, our findings identify AgRP neuron-expressed IRF3 as a key transcriptional effector of the hunger-suppressing effects of leptin.
Hippocampal Volume, Neurite Density and Trace Eye-Blink Conditioning in Young Children
Authors: Vieites Vanessa , Ralph Yvonne , Reeb-Sutherland Bethany , Dick Anthony Steven , Mattfeld Aaron T. , Pruden Shannon M.
Published: January 2022

The current study examined the relations between hippocampal structure (e.g., volume and neurite density) and performance on a trace eye blink conditioning (EBC) task in young children. Our first aim assessed whether individual differences in hippocampal volume were associated with trace EBC performance, using both percent Conditioned Responses (% CR) and CR onset latency or the average latency (ms) at which the child started their blink, as measures of hippocampal-dependent associative learning. Our second aim evaluated whether individual differences in hippocampal neurite density were associated with EBC performance using the same outcome measures. Typically developing 4- to 6-year-olds (N = 31; 14 girls; Mage = 5.67; SDage = 0.89) completed T1 and diffusion-weighted MRI scans and a 15-minute trace eyeblink conditioning task outside of the scanner. % CR and CR onset latency were computed across all tone-puff and tone-alone trials. While hippocampal volume was not associated with any of our EBC measures, greater hippocampal neurite density bilaterally, was associated with later CR onset. In other words, children with greater left and right hippocampal neurite density blinked closer to the US (i.e., air puff) than children with less hippocampal neurite density, indicating that structural changes in the hippocampus assisted in the accurate timing of conditioned responses.
Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses
Authors: Moreno Nicolas , Moreno-Chaparro Daniela , Usabiaga Florencio Balboa , Ellero Marco
Published: January 2022

Many viruses, such as SARS-CoV-2 or Influenza, possess spike-decorated envelopes. Depending on the virus type, a large variability is present in spikes number, morphology and reactivity, which remains generally unexplained. Since viruses’ transmissibility depend on features beyond their genetic sequence, new tools are required to discern the effects of spikes functionality, interaction, and morphology. Here, we postulate the relevance of hydrodynamic interactions in the viral infectivity of enveloped viruses and propose micro-rheological characterization as a platform for viruses differentiation. To understand how the spikes affect virion mobility and infectivity, we investigate the diffusivity of spike-decorate structures using mesoscopic-hydrodynamic simulations. Furthermore, we explored the interplay between affinity and passive viral transport. Our results revealed that the diffusional mechanism of SARS-CoV-2 is strongly influenced by the size and distribution of its spikes. We propose and validate a universal mechanism to explain the link between optimal virion structure and maximal infectivity for many virus families.
Characterizing RNA-binding Ligands on Structures, Chemical Information, Binding Affinity and Drug-likeness
Authors: Fan Cong , Wang Xin , Ling Tianze , Zhao Huiying
Published: January 2022

Recent studies suggest RNAs playing essential roles in many cell activities and act as promising drug targets. However, limited development has been achieved in detecting RNA-ligand interactions. To guide the discovery of RNA-binding ligands, it is necessary to characterize them comprehensively. We established a database, RNALID that collects RNA-ligand interactions validated by low-throughput experiment. RNALID contains 358 RNA-ligand interactions. Comparing to other databases, 94.5% of ligands in RNALID are completely or partially novel collections, and 51.78% have novel two-dimensional (2D) structures. The ligand structure analysis indicated that multivalent ligands (MV), ligands binding with cellular mRNA (mRNA), ligands binding with RNA from virus (vRNA) and ligands binding with RNA containing repetitive sequence (rep RNA) are more structurally conserved in both 2D and 3D structures than other ligand types. Binding affinity analysis revealed that interactions between ligands and rep RNA were significantly stronger (two-tailed MW-U test P-value = 0.012) than the interactions between ligands and non-rep RNAs; the interactions between ligands and vRNA were significantly stronger (two-tailed MW-U test P-value = 0.012) than those between ligands and mRNA. Drug-likeness analysis indicated that small molecule (SM) ligands binding with non-rep RNA or vRNA may have higher probability to be drugs than other types of ligands. Comparing ligands in RNALID to FDA-approved drugs and ligands without bioactivity indicated that RNA-binding ligands are different from them in chemical properties, structural properties and drug-likeness. Thus, characterizing the RNA-ligand interactions in RNALID in multiple respects provides new insights into discovering and designing druggable ligands binding with RNA.

KEY POINTS

We established a database, RNALID, by collecting RNA-ligand interactions validated by low-throughput experiments, which contains 358 RNA-ligand interactions, and 94.5% of them are completely or partially novel collections.

Ligands in RNALID were divided into fourteen types, and were analyzed on chemical properties, spatial properties, binding affinity and drug-likeness. Small molecule (SM) ligands binding with non-repeat RNA or virus RNA were indicated having higher probability to be drugs than other types of ligands.

Ligands in RNALID were different from protein-binding ligands and ligands without bioactivity in chemical properties, structural properties and drug-likeness.
Resonant fluctuations of selection pressure exponentially accelerate fitness valley crossing
Authors: Salvo Mario E. Di , Reynolds Kimberly A. , Lin Milo M.
Published: January 2022

Two functional protein sequences can sometimes be separated by a fitness valley - a series of low or non-functional intermediate mutations that must be traversed to reach a more optimal or refined function. Time-varying selection pressure modulates evolutionary sampling of such valleys. Yet, how the amplitude and frequency of fluctuating selection influence the rate of protein evolution is poorly understood. Here, we derive a simple equation for the time-dependent probability of crossing a fitness valley as a function of evolutionary parameters: valley width, protein size, mutation rate, and selection pressure. The equation predicts that, under low selection pressure, the valley crossing rate is magnified by a factor that depends exponentially on valley width. However, after a characteristic time set by the evolutionary parameters, the rate rapidly decays. Thus, there is an optimal frequency of selection-pressure fluctuations that maximizes the rate of protein optimization. This result is reminiscent of the resonance frequency in mechanical systems. The equation unites empirical and theoretical results that were previously disconnected, and is consistent with time-dependent in vitro and clinical data. More generally, these results suggest that seasonal and climate oscillations could synchronously drive protein evolution at the resonant frequency across a range of organism hosts and timescales. This theory could also be applied to optimize de novo protein evolution in laboratory directed evolution using time-varying protocols.
Interpreting tree ensemble machine learning models with endoR
Authors: Ruaud Albane , Pfister Niklas , Ley Ruth E , Youngblut Nicholas D
Published: January 2022

Background

Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa or genomic content may be associated. Results: We developed endoR, a method to interpret a fitted tree ensemble model. First, endoR simplifies the fitted model into a decision ensemble from which it then extracts information on the importance of individual features and their pairwise interactions and also visualizes these data as an interpretable network. Both the network and importance scores derived from endoR provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed the performance of endoR on both simulated and real metagenomic data. We found endoR to infer true associations with more or comparable accuracy than other commonly used approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to gain insights into components of the microbiome that predict the presence of human gut methanogens, as these hydrogen-consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association betweenMethanobacteriaceaeandChristensenellales. Additionally, we observed thatMethanobacteriaceaeare associated with a network of hydrogen-producing bacteria. Conclusion: Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems. An implementation of endoR is available as an open-source R-package on GitHub (https://github.com/leylabmpi/endoR).
Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis
Authors: Menardo Fabrizio
Published: January 2022

Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether difference in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, and molecular clock), and found that all these factors, except the length of the infectious period and R0, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: 1) clustering results and TBL depend on many factors that have nothing to do with transmission, 2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success.
The rosy future paradox: Positive future thinking without task relevance enhances negative biases and anxiety for aversive events
Authors: Montijn Nicole D. , Gerritsen Lotte , van Son Dana , Engelhard Iris. M.
Published: January 2022

Expectations have an important role in guiding behavior and the interpretation of novel information, but can contain negative biases such as is the case in anxiety disorders. Positive future thinking may provide an accessible way to attenuate these negatively biases. However, much is still unclear about the optimal form of such positive interventions, and it is unknown if the effects go beyond subjective experience. Here, we used a positive future thinking intervention to adapt the way a stressful event is experienced. Participants imagined either task-relevant (N = 21) or irrelevant (N = 21) positive future events before being subjected to the Trier Social Stress Task, or did not receive the intervention (N= 20). We recorded resting state EEG during the anticipation and recovery phases of the TSST to assess intervention and trait anxiety related differences in the level of frontal delta-beta coupling, which is considered a neurobiological substrate of emotion regulation. Results show that the intervention reduces event-related stress and anxiety, and increases social fixation behavior and task performance, but only if future thinking is task relevant. Paradoxically, task-irrelevant positive future thoughts enhance negative perceptual biases and stress reactivity. This increase in stress reactivity in the task-irrelevant group was corroborated by the elevated levels frontal delta-beta coupling during event anticipation, especially for those with high trait anxiety. This suggests an increased demand for emotion regulation following the task-irrelevant intervention, possibly due to the contextual incongruence between positive imagery and the stressor. Together, these results show that positive future thinking can mitigate the negative emotional, behavioral and neurobiological consequences of a stressful event, but that it should not be applied indiscriminately. Task-relevant positive future thinking can be an accessible way to boost efficacy of exposure therapy for pathological anxiety, and can help people deal with negative anticipation in daily life.
Reduced interferon antagonism but similar drug sensitivity in Omicron variant compared to Delta variant SARS-CoV-2 isolates
Authors: Bojkova Denisa , Widera Marek , Ciesek Sandra , Wass Mark N. , Michaelis Martin , Cinatl Jindrich
Published: January 2022

The SARS-CoV-2 Omicron variant is currently causing a large number of infections in many countries. A number of antiviral agents are approved or in clinical testing for the treatment of COVID-19. Despite the high number of mutations in the Omicron variant, we here show that Omicron isolates display similar sensitivity to eight of the most important anti-SARS-CoV-2 drugs and drug candidates (including remdesivir, molnupiravir, and PF-07321332, the active compound in paxlovid), which is of timely relevance for the treatment of the increasing number of Omicron patients. Most importantly, we also found that the Omicron variant displays a reduced capability of antagonising the host cell interferon response. This provides a potential mechanistic explanation for the clinically observed reduced pathogenicity of Omicron variant viruses compared to Delta variant viruses.
In planta transcriptomics reveals conflicts between pattern-triggered immunity and the AlgU sigma factor regulon
Authors: Wang Haibi , Lovelace Amelia , Smith Amy , Kvitko Brian H.
Published: January 2022

In previous work, we determined the transcriptomic impacts of flg22 pre-induced Pattern Triggered Immunity (PTI) in Arabidopsis thaliana on the pathogen Pseudomonas syringae pv. tomato DC3000 (Pto). During PTI exposure we observed expression patterns in Pto reminiscent of those previously observed in a Pto algU mutant. AlgU is a conserved extracytoplasmic function sigma factor which has been observed to regulate over 950 genes in Pto in vitro. We sought to identify the AlgU regulon in planta.and which PTI-regulated genes overlapped with AlgU-regulated genes. In this study, we analyzed transcriptomic data from RNA-sequencing to identify the AlgU in planta regulon and its relationship with PTI. Our results showed that approximately 224 genes are induced by AlgU, while another 154 genes are downregulated by AlgU in Arabidopsis during early infection. Both stress response and virulence-associated genes were induced by AlgU, while the flagellar motility genes are downregulated by AlgU. Under the pre-induced PTI condition, more than half of these AlgU-regulated genes have lost induction/suppression in contrast to naïve plants, and almost all function groups regulated by AlgU were affected by PTI.
The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements
Authors: Botelho João , Cazares Adrian , Schulenburg Hinrich
Published: January 2022

Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), in the ESKAPE pathogens. We characterized over 1700 complete ESKAPE genomes and found that different MGE types are asymmetrically distributed across these pathogens. While some MGEs are capable of exchanging DNA beyond the genus (and phylum) barrier, most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and antimicrobial resistance (AMR) genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we found that CRISPR targets vary according to MGE type: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IME CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.
Visual search training benefits from the integrative effect of enhanced covert attention and optimized overt eye movements
Authors: Zhang Qi , Huang Zhibang , Li Liang , Li Sheng
Published: January 2022

Training serves as an effective approach to improve visual search performance when the target does not automatically pop out from the distractors. In the present study, we trained participants on a conjunction visual search task and examined the training effects in behavior and eye movement. The results of Experiments 1 to 4 showed that training improved behavioral performance and reduced the number of saccades and overall scanning time. Training also increased the search initiation time before the first saccade and the proportion of trials in which the participants correctly identified the target without any saccade, but these effects were modulated by stimulus’ parameters. In Experiment 5, we simultaneously recorded eye movements and EEG signals and the results revealed significant N2pc components after the stimulus onset (i.e., stimulus-locked) and before the first saccade (i.e., saccade-locked) when the search target was the trained one. These N2pc components can be considered as the neural signatures for the enhanced covert attention to the trained target. Together with the training-induced increase in functional visual field, these mechanisms could support the beneficial effects of increased search initiation time and reduced number of saccades. These findings suggest that visual search training enhanced covert attention to target and optimized overt eye movements to facilitate search performance.
Seed-competent tau monomer initiates pathology in PS19 tauopathy mice
Authors: Mirbaha Hilda , Chen Dailu , Mullapudi Vishruth , Terpack Sandi Jo , White Charles L. , Joachimiak Lukasz A. , Diamond Marc I.
Published: January 2022

Tau aggregation into ordered assemblies causes myriad neurodegenerative tauopathies. We previously reported that tau monomer exists in either inert (Mi) or seed-competent (Ms) conformational ensembles, and that Ms encodes strains, which are biologically active, self-propagating assemblies. We have previously isolated Ms from tauopathy brains, but it is unknown if disease begins with Ms formation followed by fibril assembly, or if Ms derives from fibrils and is an epiphenomenon. Consequently, we studied a tauopathy mouse model (PS19) that expresses full-length human (1N4R) tau containing a disease-associated mutation (P301S). Using tau repeat domain biosensor cells, we detected insoluble tau seeding activity at 2 months. We found insoluble tau protein assemblies by immunoblot at 3 months. We next immunopurified monomer from mice aged 1-6 weeks using size exclusion chromatography. We detected soluble seeding activity at 4 weeks, before insoluble material or larger assemblies, with assemblies ranging from n=1-3 tau units. By 5 and 6 weeks, large soluble assemblies had formed. This indicated the first detectable pathological forms of tau were Ms. We next tested for post-translational modifications of tau monomer from 1-6 weeks. We detected no phosphorylation unique to Ms in PS19 or Alzheimer’s disease brain. We conclude that tauopathy begins with formation of Ms monomer, whose activity is phosphorylation-independent. Ms self-assembles to form oligomers before it forms insoluble fibrils. The conversion of tau monomer from Mi to Ms thus constitutes the first detectable step in the initiation of tauopathy in this mouse model, with obvious implications for origins of disease in humans.
Wetland loss in the Ñeembucú Wetlands Complex, Paraguay, using remote sensing
Authors: O’Leary Frances
Published: January 2022

South American wetlands are of global importance, yet limited delineation and monitoring restricts informed decision-making around the drivers of wetland loss. A growing human population and increasing demand for agricultural products has driven wetland loss and degradation in the Neotropics. Understanding of wetland dynamics and land use change can be gained through wetland monitoring. The Ñeembucú Wetlands Complex is the largest wetland in Paraguay, lying within the Paraguay-Paraná-La Plata River system. This study aims to use remotely sensed data to map land cover between 2006 and 2021, quantify wetland change over the 15-year study period and thus identify land cover types vulnerable to change in the Ñeembucú Wetlands Complex. Forest, dryland vegetation, vegetated wetland and open water were identified using Random Forest supervised classifications trained on visual inspection data and field data. Annual change of −0.34, 4.95, −1.65, 0.40 was observed for forest, dryland, vegetated wetland and open water, respectively. Wetland and forest conversion is attributed to agricultural and urban expansion. With ongoing pressures on wetlands, monitoring will be a key tool for addressing change and advising decision-making around development and conservation of valuable ecosystem goods and services in the Ñeembucú Wetlands Complex.
Testing a theoretical framework for the environment-species abundance paradigm: a new approach to the Abundant Centre Hypothesis
Authors: Maitra Alakananda , Pandit Rohan , Mungee Mansi , Athreya Ramana
Published: January 2022

The linkage between environment, a species’ fitness and its abundance is central to the theory of evolution. So far, all studies of this linkage have been heuristic and empirical due to an inability to determine fitness either experimentally (independent of abundance) or theoretically (from species-environment interaction). One category of such studies involves the Abundant Centre Hypothesis which posits that a species’ abundance rises to a maximum at the centre of its range. We argue that the confusing mix of results from ACH studies arises from ignoring the central premise that the abundance distribution cannot be independent of the environment. First, we employed a theoretical framework to identify an environmental context (an elevational transect; 200-2800 m in the eastern Himalayas) likely to favour ACH. We then improved upon some previously identified conceptual and methodological shortcomings of ACH studies. Using systematically collected bird data (245 species; 15867 records) from that transect we found that the community average abundance profile is symmetric, as expected by ACH. Notwithstanding which, the abundance profiles of individual species showed a small degree of asymmetry which was correlated with elevation. This elevational dependence may be due to the hard elevational limits at the lower and upper ends of the mountain, as expected from theoretical considerations. We also showed that the average abundance profile shape is close to gaussian, while ruling out uniform and inverted-quadratic shapes. This work demonstrates that selecting a particular category of environmental contexts can help in integrating theoretical tools into a field dominated by empirical studies. Such a union should spur the development of more detailed and testable theoretical models for better insights in an important field.
Engineering Protein Activity into Off-the-Shelf DNA Devices
Authors: Sekhon Harsimranjit , Loh Stewart N.
Published: January 2022

DNA-based devices are relatively straightforward to design by virtue of their predictable folding, but they lack biological activity. Conversely, protein-based devices offer a myriad of biological functions but are much more difficult to design due to their complex folding. This study bridges the fields of DNA engineering and protein engineering to generate a protein switch that is activated by a specific DNA sequence. A single protein switch, engineered from nanoluciferase using the alternate frame folding mechanism and herein called nLuc-AFF, is paired with different DNA technologies to create a biosensor for a DNA or RNA sequence of choice, sensors for serotonin and ATP, and a computational device that processes two DNA inputs. nLuc-AFF is a genetically-encoded, ratiometric, blue/green-luminescent biosensor whose output can be quantified by cell phone camera. nLuc-AFF is not falsely activated by decoy DNA and it retains full ratiometric readout in 100 % serum. The design approach can be applied to other proteins and enzymes to convert them into DNA-activated switches.
Cell type specific IL-27p28 (IL-30) deletion uncovers an unexpected regulatory function of IL-30 in autoimmune inflammation
Authors: Kim Dongkyun , Kim Sohee , Kang Myung-su , Yin Zhinan , Min Booki
Published: January 2022

IL-27 is an IL-12 family cytokine with immune regulatory properties, capable of modulating inflammatory responses, including autoimmunity. While extensive studies investigated the major target cells of IL-27 mediating its functions, the source of IL-27 especially during tissue specific autoimmune inflammation has not formally been examined. IL-27p28 subunit, also known as IL-30, was initially discovered as an IL-27-specific subunit, and it has thus been deemed as a surrogate marker to denote IL-27 expression. However, IL-30 can be secreted independently of Ebi3, a subunit that forms bioactive IL-27 with IL-30. Moreover, IL-30 itself may act as a negative regulator antagonizing IL-27. In this study, we exploited various cell type specific IL-30-deficient mouse models and examined the source of IL-30 in T cell mediated autoimmune neuroinflammation. We found that IL-30 expressed by infiltrating and CNS resident APC subsets, infiltrating myeloid cells, microglia, and astrocytes, is key limiting the inflammation. However, dendritic cell-derived IL-30 was dispensable for the disease development. Unexpectedly, in cell type specific IL-30 deficient mice that develop severe EAE, IL-30 expression in the remaining wild-type APC subsets is disproportionately increased, suggesting that increased endogenous IL-30 production may be involved in the severe pathogenesis. In support, systemic recombinant IL-30 administration induced severe EAE. Our results demonstrate that dysregulated endogenous IL-30 expression may interfere with immune regulatory functions of IL-27, promoting encephalitogenic inflammation in vivo.
The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome
Authors: Yim Won Cheol , Swain Mia L. , Ma Dongna , An Hong , Bird Kevin A. , Curdie David D. , Wang Samuel , Don Ham Hyun , Luzuriaga-Neira Agusto , Kirkwood Jay S. , Hur Manhoi , Solomon Juan K. Q. , Harper Jeffrey F. , Kosma Dylan K. , Alvarez-Ponce David , Cushman John C. , Edger Patrick P. , Mason Annaliese S. , Pires J. Chris , Tang Haibao , Zhang Xingtan
Published: January 2022

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinata’s superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.
High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets
Authors: MacMillan Hannah J. , Kong Yahui , Calvo-Roitberg Ezequiel , Alonso Laura C. , Pai Athma A.
Published: January 2022

The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with beta cell proliferation. Recent studies have found that expression of circular species of ANRIL is linked to the regulation of cardiovascular phenotypes. Less is known about how the abundance of circular ANRIL may influence T2D phenotypes. Herein, we sequence circular RNA in pancreatic islets to characterize circular isoforms of ANRIL. We identify highly expressed circular ANRIL isoforms whose expression is correlated across dozens of individuals and characterize ANRIL splice sites that are commonly involved in back-splicing. We find that samples with the T2D risk allele in ANRIL exon 2 had higher ratios of circular to linear ANRIL compared to protective-allele carriers, and that higher circular:linear ANRIL was associated with decreased beta cell proliferation. Our study points to a combined involvement of both linear and circular ANRIL species in T2D phenotypes and opens the door for future studies of the molecular mechanisms by which ANRIL impacts cellular function in pancreatic islets.
Got Milk? Maternal immune activation during the mid-lactational period affects nutritional milk quality and adolescent offspring sensory processing in male and female rats
Authors: DeRosa Holly , Caradonna Salvatore G. , Tran Hieu , Marrocco Jordan , Kentner Amanda C.
Published: January 2022

Previous studies have underscored the importance of breastfeeding and parental care on offspring development and behavior. However, their contribution as dynamic variables in animal models of early life stress are often overlooked. In the present study, we investigated how lipopolysaccharide (LPS)-induced maternal immune activation (MIA) on postnatal day (P)10 affects maternal care, milk, and offspring development. MIA was associated with elevated milk corticosterone concentrations on P10, which recovered by P11. In contrast, both milk triglyceride and percent creamatocrit values demonstrated a prolonged decrease following inflammatory challenge. Adolescent MIA offspring were heavier, which is often suggestive of poor early life nutrition. While MIA did not decrease maternal care quality, there was a significant compensatory increase in maternal licking and grooming the day following inflammatory challenge. However, this did not protect against disrupted neonatal huddling or later-life alterations in sensorimotor gating, conditioned fear, mechanical allodynia, or reductions in hippocampal parvalbumin expression in MIA offspring. MIA-associated changes in brain and behavior were likely driven by differences in milk nutritional values and not by direct exposure to LPS or inflammatory molecules as neither LPS binding protein nor interleukin-6 milk levels differed between groups. These findings reflected comparable microbiome and transcriptomic patterns at the genome-wide level. Animal models of early life stress can impact both parents and their offspring. One mechanism that can mediate the effects of such stressors is changes to maternal lactation quality which our data show can confer multifaceted and compounding effects on offspring physiology and behavior.
Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers
Authors: Bayer Barbara , McBeain Kelsey , Carlson Craig A , Santoro Alyson E
Published: January 2022

Nitrifying microorganisms, including ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrite-oxidizing bacteria, are the most abundant chemoautotrophs in the ocean and play an important role in the global carbon cycle by fixing dissolved inorganic carbon (DIC) into biomass. The release of organic compounds by these microbes is less well known but may represent an as-yet unaccounted source of dissolved organic carbon (DOC) available to heterotrophic marine food webs. Here, we provide measurements of cellular carbon and nitrogen quotas, DIC fixation yields and DOC release of ten phylogenetically diverse marine nitrifiers grown in multiple culture conditions. All investigated strains released DOC during growth, making up on average 5-15% of the fixed DIC. Neither substrate concentration nor temperature affected the proportion of fixed DIC released as DOC, but release rates varied between closely related species. Our results also indicate previous studies may have underestimated DIC fixation yields of marine nitrite oxidizers due to partial decoupling of nitrite oxidation from CO2 fixation, and due to lower observed yields in artificial compared to natural seawater medium. The results of this study provide values for biogeochemical models of the global carbon cycle, and help to further constrain the implications of nitrification-fueled chemoautotrophy for marine food-web functioning and the biological sequestration of carbon in the ocean.
The Mitochondrial RNA Granule Modulates Manganese-Dependent Cell Toxicity
Authors: Werner E. , Gokhale A. , Ackert M. , Xu C. , Wen Z. , Roberts A. M. , Roberts B. R. , Vrailas-Mortimer A. , Crocker A. , Faundez V.
Published: January 2022

Prolonged manganese exposure causes manganism, a neurodegenerative movement disorder. The identity of adaptive and non-adaptive cellular processes targeted by manganese remains mostly unexplored. Here we study mechanisms engaged by manganese in genetic cellular models known to increase susceptibility to manganese exposure, the plasma membrane manganese efflux transporter SLC30A10 and the mitochondrial Parkinson’s gene PARK2. We found that SLC30A10 and PARK2 mutations as well as manganese exposure compromised the mitochondrial RNA granule as well as mitochondrial transcript processing. These RNA granule defects led to impaired assembly and function of the mitochondrial respiratory chain. Notably, cells that survived a cytotoxic manganese challenge had impaired RNA granule function, thus suggesting that this granule phenotype was adaptive. CRISPR gene editing of subunits of the mitochondrial RNA granule, FASTKD2 or DHX30, as well as pharmacological inhibition of mitochondrial transcription-translation, were protective rather than deleterious for survival of cells acutely exposed to manganese. Similarly, adultDrosophilamutants with defects in the mitochondrial RNA granule componentscullywere safeguarded from manganese-induced mortality. We conclude that the downregulation of the mitochondrial RNA granule function is a protective mechanism for acute metal toxicity.

Significance Statement

Mutations in the manganese efflux transporter SLC30A10 and the mitochondrial Parkinson’s gene PARK2, cause neurodegeneration and increased susceptibility to toxic manganese exposure. Thus, molecular processes affected in both mutants could offer insight into fundamental mechanisms conferring susceptibility or resilience to environmental and genetic factors associated with neurodegeneration. Here we report that SLC30A10 and PARK2 mutations compromise an understudied structure, the mitochondrial RNA granule, which is required for processing polycistronic mitochondrial RNAs. Cells andDrosophilalacking mitochondrial RNA granule components were resistant to manganese exposure. We conclude that the downregulation of the mitochondrial RNA granule function is an adaptive mechanism for cells exposed to manganese.
Purification of Labeled Oligonucleotides by Precipitation with Ethanol
Authors: Green Michael R. , Sambrook Joseph
Published: January 2022

If labeled oligonucleotides are to be used only as probes in hybridization experiments, complete removal of unincorporated label is generally not necessary. However, to reduce background to a minimum, the bulk of the unincorporated label should be separated from the labeled oligonucleotide. Most of the residual unincorporated precursors can be removed from the preparation by differential precipitation with ethanol, as described in this protocol, if the oligonucleotide is >18 nt in length.