bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrated care systems model approach for speech and language therapy head and neck cancer services in England: service development and re-design in Cheshire and Merseyside
Authors: Sheldrick Heulwen , Houghton Lisa , Fleming Catriona , Crane Julie
Published: May 2022

Purpose of review

The incidence of head and neck cancer (HNC) is increasing globally and changes in treatment mean that patients are living longer with the condition. It is recognised that while there have been improvements at the diagnostic phase of the pathway, follow-up and on-going care can be fragmented and inequitable. Integrated care models (ICMs) are acknowledged as beneficial. The National Health Service in England is moving to a model whereby services are being re-organised to integrated care systems. This paper reviews the literature and discusses potential models of care to enhance speech and language therapy (SLT) provision for patients with HNC in line with the emerging ICS.

Recent findings

The COVID-19 pandemic has provided an opportunity to review service provision and SLT teams quickly adapted to offering remote support. Discussions are currently on-going to explore the potential for patient initiated follow-up via the PETNECK 2 trial and the Buurtzorg ‘neighbourhood model’ holds promise.

ICMs put the patient at the centre of care and have reported benefits for experience of care and clinical outcomes. Navigating organisational structures is complex. The Buurtzorg model provides a practical and theoretical framework to support organisational change.
Testing for fitness epistasis in a transplant experiment identifies a candidate adaptive locus inTimemastick insects
Authors: Villoutreix Romain , de Carvalho Clarissa F. , Gompert Zachariah , Parchman Thomas L. , Feder Jeffrey L. , Nosil Patrik
Published: May 2022

Identifying the genetic basis of adaptation is a central goal of evolutionary biology. However, identifying genes and mutations affecting fitness remains challenging because a large number of traits and variants can influence fitness. Selected phenotypes can also be difficult to knowa priori, complicating top–down genetic approaches for trait mapping that involve crosses or genome-wide association studies. In such cases, experimental genetic approaches, where one maps fitness directly and attempts to infer the traits involved afterwards, can be valuable. Here, we re-analyse data from a transplant experiment involvingTimemastick insects, where five physically clustered single-nucleotide polymorphisms associated with cryptic body coloration were shown to interact to affect survival. Our analysis covers a larger genomic region than past work and revealed a locus previously not identified as associated with survival. This locus resides near a gene,Punch(Pu),involved in pteridine pigments production, implying that it could be associated with an unmeasured coloration trait. However, by combining previous and newly obtained phenotypic data, we show that this trait is not eye or body coloration. We discuss the implications of our results for the discovery of traits, genes and mutations associated with fitness in other systems, as well as for supergene evolution.

This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386
Authors: McHugh Rebecca E. , Munnoch John T. , Roe Andrew J. , Hoskisson Paul A.
Published: May 2022

We report the genome sequence of Streptomyces goldiniensis ATCC 21386, a strain which produces the anti-bacterial and anti-virulence polyketide, aurodox. The genome of S. goldiniensis ATCC 21386 was sequenced using a multiplatform hybrid approach, revealing a linear genome of ~10 Mbp with a G+C content of 71%. The genome sequence revealed 36 putative biosynthetic gene clusters (BGCs), including a large region of 271 Kbp that was rich in biosynthetic capability. The genome sequence is deposited in DDBJ/EMBL/GenBank with the accession number PRJNA602141.
Diabetic retinopathy screening using a portable retinal camera in Vanuatu
Authors: Caceres Juan , Zhang Yibing , Boe Lawrence , Zhou Yunshu , Besirli Cagri , Paulus Yannis M , Rosenthal Julie M.
Published: May 2022

ABTRACT

Background and Objective

Proof-of-concept study to test the feasibility of using an all-in-one portable retinal camera for the screening of diabetic retinopathy in the Pacific island of Vanuatu.

Study Design/Materials and Methods

From February 10, 2020, through February 28, 2020, 49 patients with diabetes mellitus from three islands in Vanuatu were recruited to participate in the study. Demographics, basic health data and retinal photography were obtained. A non-mydriatic, handheld camera was used (Volk Pictor Plus).

Results

Eleven participants (24%) had referral-warranted diabetic retinopathy. There was moderately high inter-rater reliability for our dependent variables: referral status (κ = 0.62, 95% CI 0.42-0.83), retinopathy severity (κ = 0.76, 95% CI 0.55-0.96), and clinically significant macular edema (κ = 0.50, 95% CI 0.25-0.74)

Conclusions

Our study confirms that portable handheld cameras can be used to obtain retinal images of sufficient quality for diabetic retinopathy screening even in resource limited environments like Vanuatu. Among this cohort, a relatively high (24%) prevalence of referral-warranted diabetic retinopathy was found in Vanuatu.
Analyzing open-ended questions in research: A commonly used category selection methodology
Authors: Agosto Arroyo Luis D. , Fitzmaurice Angerica , Feric Zlatan , Kaeli David , Meeker John , Vega Carmen Velez , Alshawabkeh Akram , Cordero José F. , Cardona-Cordero Nancy R.
Published: May 2022

A closer examination of consumer product brands and how they are associated with levels of potential endocrine disrupting chemicals should be explored. The large number of brands available and changes in consumer preferences for certain brands makes it difficult to develop questionnaires that include all brands. Open-ended brand reporting questions are an option, but they bring challenges in identifying each brand given the multiple possibilities of variations in brand name reporting. We report a method for transforming product brand data reported as text to brand codes that allows quantitative analysis of brand use and its association with endocrine disrupting chemicals. We selected 14 consumer products to be included in our analyses. To evaluate commonly used brand selection, we used Cohen’s power calculations for two-sample t-tests in R (version 1.3.0). Considering a moderate effect size (Cohen’s d) of 0.5, each test will include the most used brand and the least used brand among the commonly used brands per product and visit. We compared how the commonly used brand selection differ per product in terms of the number of brands it selected, the total sample size and the power calculated by creating a correlation matrix and analyzing the relationship between power, commonly used brands, and brand usage. The correlation coefficient between the commonly used brand frequency of each visit approximated 0.99. From all products, fabric softener, conditioner, and lotion where the products that attained the highest power. The differences in brand use distributions per product provided an optimal environment for evaluating the performance of the commonly used brand selection methodology. It provides enough flexibility when selecting exposure groups that it could be applied to any open-ended questions, and it proves significantly useful when accounting for repeated measures.
Reversible thiol oxidation increases mitochondrial electron transport complex enzyme activity but not respiration in cardiomyocytes from patients with end-stage heart failure
Authors: Kumar Ravi A. , Thome Trace , Sharaf Omar , Ryan Terence E. , Arnaoutakis George J. , Jeng Eric I. , Ferreira Leonardo F.
Published: May 2022

Cardiomyocyte dysfunction in patients with end-stage heart failure with reduced ejection fraction (HFrEF) stems from mitochondrial dysfunction that contributes to an energetic crisis. Mitochondrial dysfunction reportedly relates to increased markers of oxidative stress, but the impact of reversible thiol oxidation on myocardial mitochondrial function in patients with HFrEF has not been investigated. In the present study, we assessed mitochondrial function in ventricular biopsies from patients with end-stage HFrEF in the presence and absence of the thiol reducing agent dithiothreitol (DTT). Isolated mitochondria exposed to DTT had increased enzyme activity of complexes I (p = 0.009) and III (p = 0.018) of the electron transport system, while complexes II (p = 0.630) or IV (p = 0.926) showed no changes. However, increased enzyme activity did not carry over to measurements of mitochondrial respiration in permeabilized bundles. Oxidative phosphorylation conductance (p = 0.439), maximal respiration (p = 0.312), and ADP sensitivity (p = 0.514) were unchanged by 5 mM DTT treatment. These results indicate that mitochondrial function can be modulated through reversible thiol oxidation, but other components of mitochondrial energy transfer are rate limiting in end-stage HFrEF. Optimal therapies to normalize cardiac mitochondrial respiration in patients with end-stage HFrEF may benefit from interventions to reverse thiol oxidation that limits complex I and III activities.
The mating system of the common house spider Parasteatoda tepidariorum
Authors: Angelakakis Apostolos , Turetzek Natascha , Tuni Cristina
Published: May 2022

Mating systems, with varying female mating rates occurring with the same partner (monogamy) or with multiple mates (polyandry), can have far reaching consequences for population viability and the rate of gene flow. Here, we investigate the mating system of the common house spider Parasteatoda tepidariorum (Theridiidae), an emerging model for genetic studies, with yet undescribed reproductive behavior. It is hypothesized that spiders belonging to this family have low re-mating rates. We paired females twice with the same male (monogamy) or with different males (polyandry), scored behaviors and mating success and fitness resulting from single- and double-matings, either monogamous or polyandrous. Despite the study being explorative in nature, we predict successful matings to be more frequent during first encounters, to reduce the risk of remaining unmated. For re-mating to be adaptive, we expect higher fitness of double-mated females, and polyandrous females to experience highest mating success and fitness if reproductive gains are achieved by mating with multiple partners. We show that the majority of the females mated once, not necessarily on their first encounter, and the likelihood of re-mating did not differ between monogamous and polyandrous encounters. The number of matings did not affect fitness, indicated by similar offspring production in females. Female twanging of the web, a behavior that likely advertises female receptivity, lead successful matings, suggesting female control. We discuss how the species ecology, with high mating costs for males and potentially limited female receptivity, may shape a mating system with low mating rates.
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro
Authors: Yadav Ruchi , Courouble Valentine V. , Dey Sanjay K. , Harrison Jerry Joe E.K. , Timm Jennifer , Hopkins Jesse B. , Slack Ryan L. , Sarafianos Stefan G. , Ruiz Francesc X. , Griffin Patrick R. , Arnold Eddy
Published: May 2022

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its ∼30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages as: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein. Our data suggest that the nsp7- 10/11 structure in complex with Mpro strongly resembles the unbound polyprotein, and that both polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we used limited proteolysis assays to characterize the effect of a series of inhibitors/binders on Mpro processing of nsp7-11 and Mpro inhibition using a polyprotein substrate.

Teaser

We elucidated the structural basis of order of cleavage of SARS-CoV-2 nsp7-11 polyprotein, with implications for Mpro inhibition.
Monitoring for SARS-CoV-2 drug resistance mutations in broad viral populations
Authors: Sedova Mayya , Jaroszewski Lukasz , Iyer Mallika , Godzik Adam
Published: May 2022

The search for drugs against COVID-19 and other diseases caused by coronaviruses focuses on the most conserved and essential proteins, mainly the main (Mpro) and the papain-like (PLpro) proteases and the RNA-dependent RNA polymerase (RdRp). Nirmatrelvir, an inhibitor for Mpro, was recently approved by FDA as a part of a two-drug combination, Paxlovid, and many more drugs are in various stages of development. Multiple candidates for the PLpro inhibitors are being studied, but none have yet progressed to clinical trials. Several repurposed inhibitors of RdRp are already in use. We can expect that once anti-COVID-19 drugs become widely used, resistant variants of SARS-CoV-2 will emerge, and we already see that for the drugs targeting SARS-CoV-2 RdRp. We hypothesize that emergence of such variants can be anticipated by identifying possible escape mutations already present in the existing populations of viruses. Our group previously developed the coronavirus3D server (https://coronavirus3d.org), tracking the evolution of SARS-CoV-2 in the context of the three-dimensional structures of its proteins. Here we introduce dedicated pages tracking the emergence of potential drug resistant mutations to Mpro and PLpro, showing that such mutations are already circulating in the SARS-CoV-2 viral population. With regular updates, the drug resistance tracker provides an easy way to monitor and potentially predict the emergence of drug resistance-conferring mutations in the SARS-CoV-2 virus.
M-Risk: A framework for assessing global fisheries management efficacy of sharks, rays, and chimaeras
Authors: Sherman C. Samantha , Sant Glenn , Simpfendorfer Colin A. , Digel Eric D. , Zubick Patrick , Johnson Grant , Usher Michael , Dulvy Nicholas K.
Published: May 2022

Fisheries management is essential to guarantee sustainable capture of target species and avoid undesirable declines of incidentally captured species. A key challenge is halting and reversing declines of shark and ray species, and specifically assessing the degree to which management is sufficient to avoid declines in relatively data-poor fisheries. While ecological risk analyses focus on intrinsic ‘productivity’ and extrinsic ‘susceptibility’, one would ideally consider the influence of ‘fisheries management’. Currently, there is no single management evaluation that can be applied to a combination of fishery types at the scale of individual country or Regional Fisheries Management Organisations (RFMOs). Here, we outline a management risk (M-Risk) framework for sharks, rays, and chimaeras used to evaluate species’ risk to overfishing resulting from ineffective management. We illustrate our approach with application to one country (Ecuador) and RFMO (Inter-American Tropical Tuna Commission) and illustrate the variation in scores among species. We found that while both management units assessed had similar overall scores, the scores for individual attributes varied. Ecuador scored higher in reporting-related attributes, while the IATTC scored higher in attributes related to data collection and use. We evaluated whether management of individual species was sufficient for their relative sensitivity by combining the management risk score for each species with their intrinsic sensitivity to determine a final M-Risk score. This framework can be applied to determine which species face the greatest risk of overfishing and be used by fisheries managers to identify effective management policies by replicating regulations from countries with lower risk scores.
Iron regulates contrasting toxicity of uropathogenic Eschericia coli in macrophages and epithelial cells
Authors: Dabral Deepti , Ghosh Hiren , Niwa Masato , Hirayama Tasuku , Boer Rinse de , Vos Marjon de , van den Bogaart Geert
Published: May 2022

By far most urinary tract infections are caused by genetically diverse uropathogenic Escherichia coli (UPEC). Knowledge of the virulence mechanisms of UPEC is critical for drug development, but most studies focus on only a single strain of UPEC. In this study, we compared the virulence mechanisms of four antibiotic-resistant and highly pathogenic UPEC isolates in human blood monocyte-derived macrophages and a bladder epithelial cell (BEC) line: ST999, ST131, ST1981 and ST95. We found that while non-pathogenic E. coli strains are efficiently killed by macrophages in bactericidal single membrane vacuoles, the UPEC strains survive within double-membrane vacuoles. On side-by-side comparison, we found that whereas ST999 only carries Fe3+ importers, ST95 carries both Fe2+ and Fe3+ importers and the toxins haemolysin and colibactin. Moreover, we found that ST999 grows in the Fe3+ rich vacuoles of BECs and macrophages with concomitant increased expression of haem receptor chuA and the hydrogen peroxide sensor oxyR. In contrast, ST95 produces toxins in iron-depleted conditions similar to that of the urinary tract. Whereas ST95 also persist in the iron rich vacuoles of BECs, it produces colibactin in response to low Fe3+ contributing to macrophage death. Thus, iron regulates the contrasting toxicities of UPEC strains in macrophages and bladder epithelial cells due to low and high labile iron concentrations, respectively.

Key findings

Antibiotics resistant uropathogenic E. coli strains ST999, ST131, ST1981, and ST95 survive within spacious double membrane vacuoles. Non-pathogenic E. coli strains XL1 blue and MG1655 are cleared in single membrane vacuoles in macrophages.

ST999 lacks Fe2+ importer and toxins, and grows in iron rich vacuoles of macrophages and bladder epithelial cells.

ST95 carries both Fe2+ and Fe3+ importers and grows in iron low conditions.

ST95 expresses toxins and induces cell death of infected macrophages, but not of bladder epithelial cells.

Bladder epithelial cells have a higher pool of labile iron than macrophages. Differential expression of virulence factors by ST999 and ST95 in bladder epithelial cells and macrophages is dependent on iron concentration.
Inferring light responses of primate retinal ganglion cells using intrinsic electrical signatures
Authors: Zaidi Moosa , Aggarwal Gorish , Shah Nishal P. , Karniol-Tambour Orren , Goetz Georges , Madugula Sasi , Gogliettino Alex R. , Wu Eric G. , Kling Alexandra , Brackbill Nora , Sher Alexander , Litke Alan M. , Chichilnisky E.J.
Published: May 2022

Reproducing high-acuity vision with an epiretinal implant will likely require inferring the natural light responses of diverse RGC types in the implanted retina, without measuring them directly. Here we demonstrate an approach that exploits intrinsic electrical features of primate RGCs. First, ON-parasol and OFF-parasol RGCs were identified with 95% accuracy using electrical features. Then, the somatic electrical footprint, predicted cell type, and average linear-nonlinear-Poisson model parameters of each cell type were used to infer a light response model for each cell. Across five retinas, these models achieved an average correlation with measured firing rates of 0.49 for white noise visual stimuli and 0.50 for natural scenes stimuli, compared to 0.65 and 0.58 respectively for models fitted to recorded light responses, an upper bound. This finding, and linear decoding of images from predicted RGC activity, suggested that the inference approach may be useful for high-fidelity sight restoration.
A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains
Authors: Breda Jeremie , Banerjee Arka , Jayachandran Rajesh , Pieters Jean , Zavolan Mihaela
Published: May 2022

Macrophages are cells of the innate immune system that provide the first line of defense against pathogens. Their functional and morphological heterogeneity is well known, though the origin of this heterogeneity is still debated. Furthermore, while mouse strains differ in the type of immune responses that they mount to individual pathogens, the range of gene expression variation among their macrophages in the absence of a specific stimulus is not known. By applying single cell RNA sequencing we here reveal the gene expression variation in pre-stimulation macrophage populations from specific pathogen-free BALB/c and C57BL/6 mice, two mouse strains that give prototypical Th2 and Th1-biased immune responses, directed towards extracellular or intracellular pathogens, respectively. We show that intrinsic differences between the macrophages of these two strains are detectable before any specific stimulation and we place the gene expression profile of these cells within the range of variation that is measured uponin vitrostimulation with pro-inflammatory lipopolysaccharide (LPS) and interferon γ (IFN), or anti-inflammatory IL-4. We find that C57BL/6 mice show stronger evidence of macrophage polarization than BALB/c mice, which could explain their resistance to pathogens such asLeishmania. Our computational methods for analyzing single cell RNA sequencing data, controlling for common sources of stochastic variation, can be more generally adopted to uncover biological variation between cell populations.
Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy
Authors: Brotzakis Z. Faidon , Löhr Thomas , Truong Steven , Hoff Samuel E. , Bonomi Massimiliano , Vendruscolo Michele
Published: May 2022

In recent years, major advances in cryo-electron microscopy (cryo-EM) have enabled the routine determination of complex biomolecular structures at atomic resolution. An open challenge for this approach, however, concerns large systems that exhibit continuous dynamics. To address this problem, we developed the metadynamic electron-microscopy metainference (MEMMI) method, which incorporates metadynamics, an enhanced conformational sampling approach, into the metainference method of integrative structural biology. MEMMI enables the simultaneous determination of the structure and dynamics of large heterogeneous systems by combining cryo-EM density maps with prior information through molecular dynamics, while at the same time modelling the different sources of error. To illustrate the method, we apply it to elucidate the dynamics of an amyloid fibril of the islet amyloid polypeptide (IAPP). The resulting conformational ensemble provides an accurate description of the structural variability of the disordered region of the amyloid fibril, known as fuzzy coat. The conformational ensemble also reveals that in nearly half of the structural core of this amyloid fibril the side-chains exhibit liquid-like dynamics despite the presence of the highly ordered network backbone of hydrogen bonds characteristic of the cross-β structure of amyloid fibrils.
HMMerge: an Ensemble Method for Improving Multiple Sequence Alignment
Authors: Park Minhyuk , Warnow Tandy
Published: May 2022

Despite advances in method development for multiple sequence alignment over the last several decades, the alignment of datasets exhibiting substantial sequence length heterogeneity, especially when the input sequences include very short sequences (either as a result of sequencing technologies or of large deletions during evolution) remains an inadequately solved problem. We present HMMerge, a method to compute an alignment of datasets exhibiting high sequence length heterogeneity, or to add short sequences into a given “backbone” alignment. HMMerge builds on the technique from its predecessor alignment methods, UPP and WITCH, which build an ensemble of HMMs for the backbone alignment and add the remaining sequences into the backbone alignment using the ensemble. HMMerge differs from UPP and WITCH by building a new HMM for each query sequence: it uses a novel ensemble approach to combine the HMMs, each weighted by the probability of generating the query sequence, into a single HMM. Then it applies the Viterbi algorithm to add the query sequence into the backbone alignment. We show that using this “merged” HMM provides better accuracy than the current approach in UPP and matches or improves on WITCH for adding short sequences into backbone alignments. HMMerge is freely available at https://github.com/MinhyukPark/HMMerge.
Huddling nest use are the optimal strategies for heat conservation in a social marsupial: lessons from biophysical models
Authors: Nespolo Roberto F. , Peña Isabella , Mejías Carlos , Ñunque Abel , Altamirano Tomás , Bozinovic Francisco
Published: May 2022

Endothermy, understood as the maintenance of continuous and high body temperatures (TB) due to the combination of metabolic heat production and an insulative cover, is severely challenged in small endotherms of cold environments. As a response, social clustering, and nest use (collectively, “communal nesting”) are common strategies for heat conservation in small mammals and birds. To quantify the actual amount of energy that is saved by communal nesting, we studied the social marsupialDromiciops gliroides(monito del monte), a relict marsupial species from the cold forests of southern South America. It is hypothesized that sociability in this marsupial was driven by the cold, for which we calculated the energetic benefits that communal nesting confers. Using biophysical models and experimental coolings, we simulated heat exchanges experienced by grouped or solitary individuals, and also individuals within nests, collected from the field. Assuming a model of passive cooling, we calculated the net energy cost of euthermic maintenance (Ecost: the total energy needed to maintain euthermia). We adjusted 50 cooling curves, to exponential decay models, and found in all cases that the strategy minimizing heat loss is to be clustered within a nest, for which the Ecostwas the minimum. This was significantly lower than the clustered condition, outside the nest, a reduction that represents almost half of energy consumption per day in a resting, thermoneutral condition for this marsupial. Overall, our results suggest that the strategy that significantly maximized heat conservation, compared with alternative strategies, was communal nesting. These findings support the idea that, in this social mammal, sociality is driven by bioenergetic benefits.
Ablation of SYK kinase from primary human Natural Killer cells via CRISPR/Cas9 enhances cytotoxicity and cytokine production
Authors: Dahlvang James D. , Dick Jenna K. , Sangala Jules A. , Pomeroy Emily J. , Snyder Kristin M. , Moushon Juliette M. , Thefaine Claire E. , Wu Jianming , Hamilton Sara E. , Felices Martin , Miller Jeffrey S. , Walcheck Bruce , Webber Beau R. , Moriarity Branden S. , Hart Geoffrey T.
Published: May 2022

Cytomegalovirus (CMV) infection alters natural killer (NK) cell phenotype and function toward a more memory-like immune state. These cells, termed adaptive NK cells, typically express CD57 and NKG2C but lack expression of the Fc receptor γ chain (Gene:FCER1G, FcRγ), PLZF, and SYK. Functionally, adaptive NK cells display enhanced antibody-dependent cellular cytotoxicity (ADCC) and cytokine production. However, the mechanism behind this enhanced function is unknown. To understand what drives cytotoxicity and cytokine production in adaptive NK cells, we optimized a CRISPR/Cas9 system to ablate genes from primary human NK cells. ADCC by human NK cells is exclusively mediated by the CD16A (FcγRIIIA) signaling apparatus, which includes FcRγ, CD3ζ, SYK, SHP-1, ZAP-70, and the transcription factor PLZF. We ablated the genes encoding these molecules and tested subsequent ADCC and cytokine production. We found that ablating the FcRγ chain caused a modest increase in TNFα production. Ablation of PLZF did not enhance ADCC or cytokine production. Importantly, SYK kinase ablation significantly enhanced both cytotoxicity and cytokine production, while ZAP-70 kinase ablation diminished function. Ablation of the phosphatase SHP-1 resulted in mixed effects on function, with NK cells demonstrating enhanced cytotoxicity but reduced cytokine production. These results indicate that the enhanced cytotoxicity and cytokine production of CMV-induced adaptive NK cells is more likely due to the loss of SYK than the lack of FcRγ or PLZF. The lack of SYK expression may limit SHP-1-mediated inhibition of CD16A signaling, leading to enhanced cytotoxicity and cytokine production. In addition to providing mechanistic answers about CMV-induced adaptive NK cell functionality, our results indicate that NK chimeric antigen receptor (CAR) therapeutics that invoke ADCC signaling molecules (e.g., CD3ζ chain) may benefit from ablating SYK, while maintaining ZAP-70, to increase functionality.
Correlations across timing cues in natural vocalizations predict biases in judging synthetic sound burst durations
Authors: Jané Matthew , Pisupati Sashank , Smith Kasey E. , Castro-Tonelli Luan , Melo-Thomas Liana , Schwarting Rainer K.W. , Wohr Markus , Chrobak James J. , Read Heather L.
Published: May 2022

It is well known that animals rely on multiple sources of information in order to successfully identify sounds in natural environments, to make decisions that are optimal for their survival. For example, rats use duration and pitch cues to respond appropriately to prosocial and distress vocalizations (Saito et al., 2019). Vocalization duration cues are known to co-vary with other temporal cues (Khatami et al., 2018), yet little is known about whether animals rely upon such co-variations to successfully discriminate sounds. In the current study, we find natural alarm vocalizations in rats have onset and offset slopes that are correlated with their duration. Accordingly, vocalizations with faster onset slopes are more likely to have shorter durations. Given that vocalization slopes begin and end within milliseconds, they could provide rapid perceptual cues for predicting and discriminating vocalization duration. To examine this possibility, we train rodents to discriminate duration differences in sequences of synthetic vocalizations and examine how artificially changing the slope impacts duration judgments. We find animals are biased to misjudge a range of synthetic vocalizations as being shorter in duration when the onset and offset slopes are artificially fast. Moreover, this bias is reduced when rats are exposed to multiple synthetic vocalization bursts. The observed perceptual bias is accurately captured by a Bayesian decision-theoretic model that utilizes the empirical joint distribution of duration and onset slopes in natural vocalizations as a prior during duration judgements of synthetic vocalizations. This model also explains why the bias is reduced when more evidence is accumulated across multiple bursts, reducing the prior’s influence. These results support the theory that animals are sensitive to fine-grained statistical co-variations in auditory timing cues and integrate this information optimally with incoming sensory evidence to guide their decisions.
Developmental transitions coordinate assembly of the Coxiella burnetii Dot/Icm type IV secretion system
Authors: Park Donghyun , Steiner Samuel , Shao Meng , Roy Craig R. , Liu Jun
Published: May 2022

Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique bi-phasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV) that transitions to a metabolically active large cell variant (LCV) that replicates inside the lysosome-derived host vacuole. A Dot/Icm type IV secretion system (T4SS), which can deliver over 100 effector proteins to host cells, is essential for the biogenesis of the vacuole and for intracellular replication. How the distinct C. burnetii life cycle impacts the assembly and function of the Dot/Icm T4SS has remained unknown. Here, we combine advanced cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) imaging to visualize all developmental transitions and assembly of the Dot/Icm T4SS. Importantly, assembled Dot/Icm T4SSs were not present in the infectious SCV. The appearance of an assembled Dot/Icm machine correlated with the transition of the SCV to the LCV intracellularly. Furthermore, temporal characterization of C. burnetii morphological changes revealed regions of the inner membrane that invaginated to form tightly packed stacks during the LCV to SCV transition at late stages of infection, which could enable the SCV to LCV transition that occurs upon infection of a new host cell. Overall, these data establish how C. burnetii developmental transitions control critical bacterial processes to promote intracellular replication and transmission.
Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking
Authors: Wong V. C. , Houlihan P.R. , Liu H. , Walpita D. , DeSantis M.C. , Liu Z. , O’Shea E. K.
Published: May 2022

AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing long-term potentiation (LTP) to increase synaptic transmission, but how AMPAR-containing vesicles are selectively trafficked to these synapses during LTP is not known. Here we developed a strategy to label AMPAR GluA1 subunits expressed from the endogenous loci of rat hippocampal neurons such that the motion of GluA1-containing vesicles in time-lapse sequences can be characterized using single-particle tracking and mathematical modeling. We find that GluA1- containing vesicles are confined and concentrated near sites of stimulation-induced plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F- actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of neuronal activity.
Ligand-induced shifts in conformational ensembles that predict transcriptional activation
Authors: Khan Sabab Hasan , Braet Sean M , Koehler Stephen John , Elacqua Elizabeth , Anand Ganesh S , Okafor C. Denise
Published: May 2022

Nuclear receptors function as ligand-regulated transcription factors whose ability to regulate diverse physiological processes is closely linked with conformational changes induced upon ligand binding. Understanding how conformational populations of nuclear receptors are shifted by various ligands could illuminate strategies for the design of synthetic modulators to regulate specific transcriptional programs. Here, we investigate ligand-induced conformational changes using a reconstructed, ancestral nuclear receptor. By making substitutions at a key position, we engineer receptor variants with altered ligand specificities. We use atomistic molecular dynamics (MD) simulations with enhanced sampling to generate ensembles of wildtype and engineered receptors in combination with multiple ligands, followed by conformational analysis and prediction of ligand activity. We combine cellular and biophysical experiments to allow correlation of MD-based predictions with functional ligand profiles, as well as elucidation of mechanisms underlying altered transcription in receptor variants. We determine that conformational ensembles accurately predict ligand responses based on observed population shifts, even within engineered receptors that were constitutively active or transcriptionally unresponsive in experiments. These studies provide a platform which will allow structural characterization of physiologically-relevant conformational ensembles, as well as provide the ability to design and predict transcriptional responses in novel ligands.
Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co-stimulation in a mice acute-on-chronic liver failure model
Authors: Chen Feng , Che Zhaodi , Liu Yingxia , Luo Pingping , Xiao Lu , Song Yali , Wang Cunchuan , Dong Zhiyong , Li Mianhuan , Tipoe George L. , Wu Dongqing , Yang Min , Lv Yi , Wang Fei , Wang Hua , Xiao Jia
Published: May 2022

Boosting stem cell resilience against an extrinsically harsh recipient environment is critical to therapeutic efficiency of stem cell-based transplantation innovations in liver disease contexts. We aimed to establish the efficacy of a transient plasmid-based preconditioning strategy to boost mesenchymal stromal cells (MSCs) capacity for anti-inflammation/antioxidant defense and paracrine actions on recipient hepatocytes. In MSCs, the master antioxidant regulator Nrf2 was found to bind directly to the antioxidant response element in the DKK1 promoter region. Activation of Nrf2 and DKK1 enhanced the anti-stress capacities of MSCs in vitro. In an acute-on-chronic liver failure (ACLF) murine model, transient co-overexpression of Nrf2 and DKK1 via plasmid transfection markedly improved MSC resilience against inflammatory and oxidative assaults, boosted MSC transplantation efficacy and promoted recipient liver regeneration because of a shift from the activation of the anti-regenerative IFN-γ/STAT1 pathway to the pro-regenerative IL-6/STAT3 pathway in the liver. Moreover, specific ablation of DKK1 receptor CKAP4 but not LRP6 in recipient hepatocytes nullified therapeutic benefits from MSC transplantation. In long-term observations, tumorigenicity was undetected in mice following transplantation of such transiently preconditioned MCSs. In conclusion, co-stimulation of Nrf2/DKK1 signaling decisively and safely improves the efficacy of human MSC-based therapies in mouse ACLF models through apparently CKAP4-dependent paracrine mechanisms.
Partial Destabilization of Amyloid-β Protofibril by Methionine Photo-oxidation: A Molecular Dynamic Simulation Study
Authors: Maghsoodi Fahimeh , Martin Tye D. , Chi Eva Y.
Published: May 2022

Selective photosensitized oxidation of amyloid protein aggregates is being investigated as a possible therapeutic strategy for treating Alzheimer’s disease (AD). Photo-oxidation has been shown to lead to the degradation of amyloid-β (Aβ) aggregates, ameliorate aggregate toxicity and reduce aggregate levels in the brains of AD animal models. To shed light on the mechanism by which photo-oxidation induces fibril destabilization, we carried out an all-atom molecular dynamics (MD) simulation to examine the effect of methionine (Met35) oxidation on the conformation and stability of a highly β-sheet-rich Aβ9-40protofibril composed of 12 monomers. Analyses of up to 1 μs MD simulations showed that the oxidation of the Met35 residues reduced the overall conformational stability of the protofibril. Specifically, Met35 oxidation that resulted in the addition of hydrophilic oxygens disrupted the hydrophobic interface that stabilizes the stacking of the two hexamers that composed the protofibril. The oxidized protofibril is more solvent exposed, less compact, and exhibits more backbone flexibility. However, it retained the underlying U-shaped architecture of each peptide. Although some loss of β-sheets occurred, a significant portion (~76%) remained. twisting of the peptides along the protofibril axis was observed, and the hexamers remained. Our simulation results are thus consistent with our experimental observation that photo-oxidation of Aβ40 fibrils results in the dis-agglomeration and fragmentation of Aβ fibrils, but did not cause complete disruption of the fibrillar morphology or β-sheet structures. The partial destabilization of Aβ aggregates supports the further development of photosensitized platforms for the selective targeting and clearance of Aβ aggregates as a therapeutic strategy for treating AD.
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
Authors: Yan Guanao , Song Dongyuan , Li Jingyi Jessica
Published: May 2022

Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in FASTQ and BAM formats) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that cell-ranger is a preferred scRNA-seq UMI deduplication tool, and HMMRATAC and MACS3 achieve top performance in scATAC-seq peak calling.
Pattern of frustration formation in the functional brain network
Authors: Saberi Majid , Khosrowabadi Reza , Khatibi Ali , Misic Bratislav , Jafari Gholamreza
Published: May 2022

The brain is a frustrated system that contains conflictual link arrangements named frustration. The frustration as a source of disorder prevents the system from settling into low energy states and provides flexibility for brain network organization. In this research, we tried to identify the pattern of frustration formation in the brain at the levels of region, connection, canonical network, and hemisphere. We found that frustration formation has not a uniform pattern. Some subcortical elements have an active role in frustration formation, despite many low contributed cortical elements. Frustrating connections are mostly between-network types and triadic frustrations are mainly formed between three regions from three distinct canonical networks. Although there were no significant differences between brain hemispheres. We also did not find any robust differences between the frustration formation patterns of various lifespan stages. Our results may be interesting for those who study the organization of brain links and promising for those who want to manipulate brain networks.
PhyGraFT: a network-based method for phylogenetic trait analysis
Authors: Matsumoto Hirotaka , Matsui Motomu
Published: May 2022

With the determination of numerous viral and bacterial genome sequences, phylogeny-trait associations are now being studied. In these studies, phylogenetic trees were first reconstructed, and trait data were analyzed based on the reconstructed tree. However, in some cases, such as fast evolution sequences and gene-sharing network data, reconstructing the phylogenetic tree is challenging. In such cases, network-thinking, instead of tree-thinking, is gaining attention. Here, we propose a novel network-thinking approach, PhyGraFT, to analyze trait data from the network. We validated that PhyGraFT can find phylogenetic signals and associations of traits with the simulation dataset. We applied PhyGraFT for influenza type A and virome gene-sharing datasets. As a result, we identified several evolutionary structures and their associated traits. Our approach is expected to provide novel insights into network-thinking not only for typical phylogenetics but also for various biological data, such as antibody evolution.
Suction feeding of West African lungfish (Protopterus annectens): An XROMM analysis of jaw mechanics, cranial kinesis, and hyoid mobility
Authors: Gartner Samantha M. , Whitlow Katrina R. , Laurence-Chasen J.D. , Kaczmarek Elska B. , Granatosky Michael C. , Ross Callum F. , Westneat Mark W.
Published: May 2022

Suction feeding in fishes is characterized by rapid cranial movements, but extant lungfishes (Sarcopterygii: Dipnoi) exhibit a reduced number and mobility of cranial bones relative to actinopterygian fishes. Despite fusion of cranial elements, lungfishes are proficient at suction feeding, though the impacts of novel cranial morphology and reduced cranial kinesis on feeding remain poorly understood. We used X-ray Reconstruction of Moving Morphology (XROMM) to study the kinematics of seven mobile skeletal elements (neurocranium, upper jaw, lower jaw, tongue, ceratohyal, clavicle, and cranial rib) and two muscles (costoclavicular portion of the hypaxialis and rectus cervicis) during the feeding strikes of West African lungfish (Protopterus annectens). We found that feeding byP. annectenson non-evasive prey is relatively slow, with a mean time to peak gape of 273 ms. Lower jaw depression and clavicular rotation were hingelike, with one degree of freedom, but the ceratohyals rotated in a complex motion involving depression and long-axis rotation. We quantified the relative contributions to oral cavity volume change (RCVC) and found that oral cavity expansion is created primarily by ceratohyal and clavicle motion.P. annectenssuction feeds relatively slowly but successfully through muscle shortening of hypaxial and rectus cervicis muscles contributing to hyoid mobility.

Summary Statement

Three-dimensional hyoid movements and clavicle retraction generate suction during the relatively slow, but successful, feeding strikes of the West African lungfish (Protopterus annectens).
Multi-synaptic boutons are a feature of CA1 hippocampal connections that may underlie network synchrony
Authors: Rigby Mark , Grillo Federico , Compans Benjamin , Neves Guilherme , Gallinaro Julia , Nashashibi Sophie , Vizcay-Barrena Gema , Levet Florian , Sibarita Jean-Baptiste , Kirkland Angus , Fleck Roland A. , Clopath Claudia , Burrone Juan
Published: May 2022

Excitatory synapses are typically described as single synaptic boutons (SSBs), where one presynaptic bouton contacts a single postsynaptic spine. Using serial section block face scanning electron microscopy, we found that this textbook definition of the synapse does not fully apply to the CA1 region of the hippocampus. Roughly half of all excitatory synapses in the stratum oriens involved multi-synaptic boutons (MSBs), where a single presynaptic bouton containing multiple active zones contacted many postsynaptic spines (from 2 to 7) on the basal dendrites of different cells. The fraction of MSBs increased during development (from P21 to P100) and decreased with distance from the soma. Curiously, synaptic properties such as active zone (AZ) or postsynaptic density (PSD) size exhibited less within-MSB variation when compared to neighbouring SSBs, features that were confirmed by super-resolution light microscopy. Computer simulations suggest that these properties favour synchronous activity in CA1 networks.