bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary Data in Nursing Research
Authors: Keeler Courtney , Curtis Alexa Colgrove
Published: March 2022

Editor's note: This is the ninth article in a series on clinical research by nurses. The series is designed to give nurses the knowledge and skills they need to participate in research, step by step. Each column will present the concepts that underpin evidence-based practice—from research design to data interpretation. The articles will be accompanied by a podcast offering more insight and context from the authors. To see all the articles in the series, go to https://links.lww.com/AJN/A204.
The Suffering of Simone
Authors: Glover Eileen J.
Published: March 2022

Contemplating the intractable misery of certain psychiatric conditions.
Does An Osteotomy Performed in Congenital Pseudarthrosis of the Tibia Heal?
Authors: Nahm Nickolas J. , Makarewich Christopher A. , Rosenwasser Katherine A. , Herzenberg John E. , McClure Philip K.
Published: March 2022

Background:

Shortening and deformity of the tibia commonly occur during the treatment of congenital pseudarthrosis of the tibia (CPT). The role of osteotomies in lengthening and deformity correction remains controversial in CPT. This study evaluates the approach to and outcome after osteotomy performed in CPT.

Methods:

We performed an IRB approved retrospective review of consecutive patients with CPT treated at our institution from 2010 through 2019. Patients who underwent osteotomies were included in this study.

Results:

Nine patients (10 osteotomies—5 proximal metaphyseal and 5 diaphyseal) with a median age at osteotomy of 8.9 years (range: 4 to 21 y) were included. Six patients had neurofibromatosis-1, 1 had cleidocranial dysplasia, and 2 patients had idiopathic CPT. Four osteotomies were performed for deformity correction, 3 osteotomies to allow intramedullary instrumentation, and 3 osteotomies for lengthening. Five osteotomies were preceded by zolendronate treatment before surgery. Nine were fixed with a rod supplemented with external fixation (7) or locking plates (2). One osteotomy was stabilized with locked intramedullary nailing alone. Four osteotomies were supplemented with autologous bone graft, and bone morphogenic protein-2 was utilized in 3 osteotomies. Median time to healing was 222.5 days (range: 124 to 323 d). One osteotomy (locked intramedullary nailing) required grafting at 5.5 months and then healed uneventfully. Median healing index for patients undergoing lengthening was 57.9 days/cm (range: 35 to 81 d/cm). All 3 osteotomies performed for lengthening required a second osteotomy for preconsolidation at a mean of 34 days. Other complications included compartment syndrome requiring fasciotomy (n=2), tibial osteomyelitis (n=1), and fracture distal to cross-union (n=1).

Conclusions:

Contrary to much of the established practice, osteotomies may be safely performed in CPT for various indications. All osteotomies healed with only 1 osteotomy requiring secondary bone grafting. Although time to healing of the osteotomy was generally prolonged, this study suggests, somewhat surprisingly, that preconsolidation can occur frequently in lengthening procedures.

Level of Evidence:

Level IV—case series.
Corneal Epithelial Thickness Mapping in the Diagnosis of Ocular Surface Disorders Involving the Corneal Epithelium: A Comparative Study
Authors: Levy Arielle , Georgeon Cristina , Knoeri Juliette , Tourabaly Moïse , Leveziel Loïc , Bouheraoua Nacim , Borderie Vincent M.
Published: March 2022

Purpose:

The purpose of this study was to analyze the role of corneal epithelial thickness (ET) mapping provided by spectral domain optical coherence tomography in the diagnosis of ocular surface disorders (OSDs) involving the corneal epithelium.

Design:

This was a retrospective comparative study.

Methods:

Institutional settings are as follows. Study population includes 303 eyes with an OSD and 55 normal eyes (controls). Observation procedures include spectral domain optical coherence tomography with epithelial mapping in the central 6 mm. Main outcome measures include ET map classification (normal, doughnut, spoke-wheel, localized/diffuse, and thinning/thickening patterns) and ET data and statistics (minimum, maximum, and SD). A quantitative threshold was determined with receiver operating curves to distinguish pathological from normal corneas. Sensitivity and specificity of classification and quantitative data were calculated using all eyes to assess the ability to distinguish corneas with a given corneal disorder from other conditions.

Results:

Classification of full agreement between 3 readers was obtained in 75.4% to 99.4% of cases. Main OSD features were keratoconus (135 eyes), doughnut pattern (sensitivity/specificity = 56/94%), and max–min ET ≥ 13 μm (84/43%); limbal deficiency (56 eyes), spoke-wheel pattern (66/98%), and max–min ET ≥ 14 μm (91/59%); epithelial basement membrane dystrophy (55 eyes), inferior thickening pattern (55/92%), and central ET > 56 μm (53/81%); dry eye (21 eyes), superior thinning pattern (67/88%), and minimal ET ≤ 44 μm (86/48%); pterygium (10 eyes), nasal thickening pattern (100/86%), and nasal ET > 56 μm (80/71%); and in situ carcinoma (11 eyes), max ET > 60 μm (91/60%), and ET SD >5 μm (100/58%).

Conclusions:

The epithelial map pattern recognition combined with quantitative analysis of ET is relevant for the diagnosis of OSDs and for distinguishing various OSDs from each other. Deep learning analysis of big data could lead to the fully automated diagnosis of these disorders.
Concussion-Associated Gene Variant COMT rs4680 Is Associated With Elite Rugby Athlete Status
Authors: Antrobus Mark R. , Brazier Jon , Callus Peter , Herbert Adam J. , Stebbings Georgina K. , Day Stephen H. , Kilduff Liam P. , Bennett Mark A. , Erskine Robert M. , Raleigh Stuart M. , Collins Malcolm , Pitsiladis Yannis P. , Heffernan Shane M. , Williams Alun G.
Published: March 2022

Objective:

Concussions are common match injuries in elite rugby, and reports exist of reduced cognitive function and long-term health consequences that can interrupt or end a playing career and produce continued ill health. The aim of this study was to investigate the association between elite rugby status and 8 concussion-associated risk polymorphisms. We hypothesized that concussion-associated risk genotypes and alleles would be underrepresented in elite rugby athletes compared with nonathletes.

Design:

A case–control genetic association study.

Setting:

Institutional (university).

Participants:

Elite White male rugby athletes [n = 668, mean (SD) height 1.85 (0.07) m, mass 102 (12) kg, and age 29 (7) years] and 1015 nonathlete White men and women (48% men).

Interventions:

Genotype was the independent variable, obtained by PCR of genomic DNA using TaqMan probes.

Main Outcome Measure:

Elite athlete status with groups compared using χ2 and odds ratio (OR).

Results:

The COMT rs4680 Met/Met (AA) genotype, Met allele possession, and Met allele frequency were lower in rugby athletes (24.8%, 74.6%, and 49.7%, respectively) than nonathletes (30.2%, 77.6%, and 54.0%; P < 0.05). The Val/Val (GG) genotype was more common in elite rugby athletes than nonathletes (OR 1.39, 95% confidence interval 1.04-1.86). No other polymorphism was associated with elite athlete status.

Conclusions:

Elite rugby athlete status is associated with COMT rs4680 genotype that, acting pleiotropically, could affect stress resilience and behavioral traits during competition, concussion risk, and/or recovery from concussion. Consequently, assessing COMT rs4680 genotype might aid future individualized management of concussion risk among athletes.
Defining the Concept and Clinical Features of Epistemic Trust
Authors: Knapen Saskia , van Diemen Roos , Hutsebaut Joost , Fonagy Peter , Beekman Aartjan
Published: March 2022

Early identification of “patients at risk” for not completing regular treatment or not benefitting (sufficiently) from treatment might be among the most cost-effective strategies in mental health care. The recently introduced concept of epistemic trust (ET) may have the potential value to predict patients at risk and therefore act as a marker of treatment outcome. We argue that ET may be the final common pathway through which aversive relational experiences in the past result in interpersonal dysfunctioning, which in turn result in dysfunctional therapeutic relationships, rendering it difficult for patients to trust whatever is offered to learn in therapy. Hence, the concept of ET can play an essential role in personalized medicine, allowing for a more tailored treatment assignment to specific patients' characteristics, which may improve treatment outcomes. In this brief report, we define the clinical features of ET by describing its core domains based on consensus of expert opinion on the concept. The response rate was high, and there was a high level of agreement across experts, demonstrating a strong consensus between experts on the definition and clinical features of ET and mistrust and its significance to the understanding of personality disorders.

By means of having a clear definition of the clinical features of ET, we hope to make it accessible for assessment.
Building Nurse Manager Well-being by Reducing Healthcare System Demands
Authors: Warshawsky Nora E.
Published: March 2022

The National Academies of Medicine consensus study committee reported that US healthcare workers experience high levels of burnout resulting from external pressures on the healthcare system and the organization of work. Nurse managers are especially susceptible to burnout. This column provides evidence-based strategies to improve the work environment, reduce the burden of job demands, and promote well-being among nurse managers.
Professional Governance in a Time of Crisis
Authors: Porter-O'Grady Tim , Pappas Sharon
Published: March 2022

The global COVID-19 health crisis has significantly altered the structures and processes of healthcare in innumerable unanticipated ways. No profession has been more impacted or challenged than nursing. In many settings, nursing professional governance has been abandoned or neglected. The impact of this trend is outlined in this article. The authors suggest to nurse leaders that nursing professional governance can be an invaluable mechanism for nursing engagement in the midst of managing a crisis.
Ethical Dilemmas in Global Plastic Surgery: Divergent Perspectives of Local and Visiting Surgeons
Authors: Schoenbrunner Anna R. , McIntyre Joyce K. , Nthumba Peter , Muchemwa Faith Chengetavyi , Sigler Alicia , Gosman Amanda A.
Published: March 2022

Background:

As more of the world’s resources are directed toward improving patient access to safe surgical and anesthesia care, there is a growing concern that volunteer surgeons’ “desire to help” has numerous unintended consequences. The purpose of this study was to ask in-country, local surgeons and visiting volunteer plastic surgeons about the frequency of ethical dilemmas for different types of global surgery collaborations and to assess their perception of compliance with the concepts of autonomy, beneficence, nonmaleficence, and justice.

Methods:

A cross-sectional email survey tool was sent to a representative sample of domestic American Society of Plastic Surgeons members, all international members of the American Society of Plastic Surgeons, and international partners of the Volunteers in Plastic Surgery committee of the Plastic Surgery Foundation. The survey response rate was 7.7 percent, with 356 respondents from 65 countries.

Results:

This survey data showed a statistically significant divergence of perspectives between local and visiting surgeons in regard to scope of practice, quality of patient care, impact on local health care systems, perception of the quality of care by local providers, the integrity of the informed consent process, and photography in global plastic surgery collaborations. Though the short-term mission trip model was particularly polarizing when comparing the responses of local and visiting surgeons, educational and research exchanges may also significantly interrupt local health care and incite ethical lapses.

Conclusion:

This survey provides quantitative insight into the impact of current global plastic surgery collaborations and highlights ethical areas of disagreement between local and visiting surgeons.
The RNA-dependent RNA polymerase of the infectious pancreatic necrosis virus is linked to viral mRNA acting as a cap substitute
Authors: González-Catrilelbún Sebastián , Cartagena Julio , Vargas Deborah , Breguel-Serrano Pamela , Sandino Ana María , Rivas-Aravena Andrea
Published: March 2022

The infectious pancreatic necrosis virus (IPNV) is responsible for significant economic losses in the aquaculture industry. It is an unenveloped virus with an icosahedral capsid. Its viral genome comprises two dsRNA segments, A and B. Segment A contains a small ORF, which encodes VP5, and a large ORF, which encodes a polyprotein that generates the structural proteins and the viral protease. Segment B encodes the RNA-dependent RNA polymerase (RdRp), called VP1 in this free form, or Vpg when it covalently attaches to the viral RNA. The viral genome does not have cap or poly(A). Instead, each 5′ end is linked to the Vpg. Recently, we demonstrated that mRNA-A contains an internal ribosome entry site (IRES) to command polyprotein synthesis. However, the presence of Vpg on IPNV mRNAs and its impact on cellular translation has not been investigated. This research demonstrates that IPNV mRNAs are linked to Vpg and that this protein inhibits cap-dependent translation on infected cells. Also, it is demonstrated that Vpg interacts with eIF4E and that rapamycin treatment partially diminishes the viral protein synthesis. In addition, we determined that an IRES does not command translation of IPNV mRNA-B. We show that VPg serves as a cap substitute during the initiation of IPNV translation, contributing to understanding the replicative cycle of Birnaviruses. Our results indicate that the viral protein VP1/Vpg is multifunctional, having a significant role during IPNV RNA synthesis as the RdRp and the primer for IPNV RNA synthesis and translation as the viral protein genome, acting as a cap substitute.
Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine
Authors: Kurhade Chaitanya , Zou Jing , Xia Hongjie , Cai Hui , Yang Qi , Cutler Mark , Cooper David , Muik Alexander , Jansen Kathrin U. , Xie Xuping , Swanson Kena A. , Shi Pei-Yong
Published: March 2022

The newly emerged Omicron SARS-CoV-2 has 3 distinct sublineages: BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected at 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralized USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of >20; the neutralization geometric mean titers (GMTs) against the four viruses were 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s were 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.
Unique molecular signatures sustained in circulating monocytes and regulatory T cells in Convalescent COVID-19 patients
Authors: Hoffmann Andrew D. , Weinberg Sam E. , Swaminathan Suchitra , Chaudhuri Shuvam , Mubarak Hannah Faisal , Schipma Matthew J. , Mao Chengsheng , Wang Xinkun , El-Shennawy Lamiaa , Dashzeveg Nurmaa K. , Wei Juncheng , Mehl Paul J. , Shihadah Laura J. , Wai Ching Man , Ostiguin Carolina , Jia Yuzhi , D’Amico Paolo , Wang Neale R. , Luo Yuan , Demonbreun Alexis R. , Ison Michael G. , Liu Huiping , Fang Deyu
Published: March 2022

Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized multi-omic single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including covenlesent COVID-19 and sero-negative controls. The reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells are significantly associated with the patients recovered from severe COVID-19. Consistently, sc-RNA seq analysis reveals seven heterogeneous clusters of monocytes (M0-M6) and ten Treg clusters (T0-T9) featuring distinct molecular signatures and associated with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocyte and Treg expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters with S100 family genes: S100A8 & A9 with high HLA-I whereas S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, and a unique TGF-β high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-ived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (>= 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.
Localized and Distributed Representations of Person Knowledge for Faces
Authors: Shehzad Zarrar , Taylor JohnMark , McCarthy Gregory
Published: March 2022

Modular neural models of face processing posit that face-associated person-knowledge is localized in, or accessed through, the ventral anterior temporal lobe (vATL). However, some studies have suggested that person-knowledge is more widely distributed within a larger face-processing network that includes the mid-fusiform gyrus (‘fusiform face area’). Here, we conducted an fMRI study to distinguish whether person-knowledge is localized or distributed by comparing brain responses evoked by synthetic faces, for which participants had learned person-knowledge (biographical facts) and faces for which the subjects had learned only physical facts. After extensive training, participants were cued to recall a particular biographical or physical fact about the upcoming face. In an alternate passive-viewing task, participants were shown the same faces but were not cued to recall biographical or physical facts. Classification analyses (MVPA) were performed on several a priori chosen face-selective regions (ROIs) in the ventral temporal cortex. Within each ROI tested in isolation, MVPA discriminated faces associated with person-knowledge from faces only associated with physical facts. This result is consistent with a distributed model for person-knowledge. However, when tested in a single model to separate shared and unique information, unique information was limited to the left mid-fusiform and vATL posterior (vATL-p) ROIs. Moreover, the feature weights from these two areas showed that only left vATL-p was specialized for processing biographical facts. This latter result was obtained only when these biographical facts were explicitly retrieved in the cueing task. Thus, our results indicate that the left vATL-p represents explicit recall of face-associated person-knowledge.

New & Noteworthy

Whether person knowledge for faces is localized in a domain-specific region, vATL, or distributed in many domain-general brain regions, including the mid-fusiform gyrus, is hotly contested. We resolve this debate by using multivariate analyses to partial fMRI signal from different brain regions into unique and shared variance. Our findings show that unique information for person knowledge is found in both the vATL and mid-fusiform but only the vATL represents explicit recall of face-associated person knowledge.
Planting graphene quantum dots in PEGylated nanoparticles for enhanced and multimodal in vivo imaging of tumor
Authors: Yan Hao , Wang Qian , Wang Jingyun , Shang Wenting , Xiong Zhiyuan , Zhao Lingyun , Sun Xiaodan , Tian Jie , Feng Si-Shen , Kang Feiyu
Published: March 2022

Photoluminescent graphene quantum dots (GQDs) have recently attracted considerable attention for biomedical applications owing to the interesting physicochemical and photophysical properties, and prominent biocompatibility and biosafety. However, although much progress has been achieved in therapy and in vitro bioimaging, broad and crucial in vivo fluorescence bioimaging and synergistically working with other nanomedicine are very challenging and limited. Herein, we in situ implanted GQDs in the PEGylated layer of nanoparticles (NPs) via a bottom-up approach to obtain the NPs (core)-GQDs-PEG multifunctional nanoprobe (NPC-GQDs-PEG), which prolonged the blood circulation of GQDs more than four times and increased the tumor accumulation 7~8 times than GQDs used alone. Under assisted by the flexible microscope, the GQDs were successfully used for in vivo real-time monitoring of local NPs pharmacokinetics, in vivo multimodality imaging, and fluorescence imaging-guided tumor surgery. The approach of implanting GQDs in PEGylated nanomedicine and synergistic working provide a new strategy for in vivo biomedical applications of GQDs.
High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection
Authors: Colles Frances M. , Karasova Daniela , Crhanova Magdalena , Preston Stephen G. , Smith Adrian L. , Dawkins Marian S. , Rychlik Ivan , Gebhardt-Henrich Sabine G.
Published: March 2022

Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 weeks of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh faecal samples collected from broiler flocks aged 23-28 days. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant amongst flocks that would be determined to be Campylobacter ‘positive’ by conventional means, but a diverse pattern was seen amongst flocks that were Campylobacter ‘negative’. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.
Maximizing the Anti-tumor Potential of Immune Checkpoint Blockade through Modulation of Myeloid-specific CXCL16 and STAT1 Signaling
Authors: Palakurthi Bhavana , Guldner Ian H. , Liu Xiyu , Martino Anna K. , Wang Qingfei , Fross Shaneann , Neff Ryan A. , Golomb Samantha M. , Howe Erin N. , Zhang Siyuan
Published: March 2022

Sensitivity to immune checkpoint blockades (ICB) depends on the overall balance of immunogenic and immunosuppressive signals in the tumor immune microenvironment (TIME). Chemotherapy as an immunostimulatory strategy showed potential in improving ICB’s clinical efficacy. Yet, evolution of highly plastic tumor-associated myeloid cells hinders ICB’s potential to reach its full therapeutic potential. In this study, we leveraged single-cell transcriptomic and trajectory analyses to delineate TIME dynamics after chemotherapy priming. We found that metronomic chemotherapy (MCT) treatment led to an accelerated T cell exhaustion through CXCL16-mediated recruitment of peripheral immature myeloid cells and expansion of STAT1-driven PD-L1 expressing myeloid cells. Inhibiting STAT1 signaling in MCT-primed breast cancer relieved T cell exhaustion and significantly enhanced the efficacy of anti-PD-1 ICB treatment. Our study leveraged single-cell analyses to dissect the dynamics of breast cancer TIME and provides a pre-clinical rationale to translate the anti-STAT1 plus anti-PD-1 combinatorial immunotherapy regimen to maximize ICB’s efficacy.

Manuscript Summary

Single-cell analyses on low dose chemotherapy primed breast tumor-associated immune cells demonstrates a parallel coexistence of immunogenic and immunosuppressive myeloid cell subsets. Modulating STAT1 signaling in the tumor microenvironment fine-tunes immunogenic and immunosuppressive balance and maximizes the anti-PD-1 immunotherapy efficacy in chemotherapy-primed breast cancer.
Transient Water Wires Mediate Selective Proton Transport in Designed Channel Proteins
Authors: Kratochvil Huong T. , Watkins Laura C. , Mravic Marco , Somberg Noah H. , Thomaston Jessica L. , Nicoludis John M. , Liu Lijun , Hong Mei , Voth Gregory A. , DeGrado William F.
Published: March 2022

Summary paragraph

Selective proton transport through proteins is essential for forming and utilizing proton gradients in cells. Protons are conducted along hydrogen-bonded “wires” of water molecules and polar sidechains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways inferred from static protein structures. We hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess proton itself in the water wire. To test this hypothesis, we used molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+over Na+. These studies inform mechanisms of biological proton conduction and principles for engineering proton-conductive materials.
A unifiedin vitrotoin vivofluorescence lifetime screening platform yields amyloid β aggregation inhibitors
Authors: Collins Súil , van Vliet Liisa , Gielen Fabrice , Janeček Matej , Valladolid Sara Wagner , Poudel Chetan , Fusco Giuliana , De Simone Alfonso , Michel Claire , Kaminski Clemens F. , Spring David R , Hollfelder Florian , Kaminski Schierle Gabriele S
Published: March 2022

Inhibiting the aggregation of amyloid β (1-42) is a promising strategy for the development of disease-modifying Alzheimer’s disease therapeutics. To date, however, no sufficiently efficacious inhibitors have been identified, despite the best efforts of >200 advanced drug development campaigns. This failure can be attributed to limitations in current compound screening andin vivovalidation assays. Here, we report anin vitrotoin vivoscreening platform based on the use of a fluorescence lifetime aggregation sensor. The microfluidic “nanoFLIM” assay developed circumvents issues that plague conventional assays, such as lack of reproducibility, high cost and artefactual false read-outs. The fluorescence lifetime sensor can also dynamically monitor peptide aggregation in cellular andCaenorhabditis elegansdisease models, providing directly comparable aggregation kinetics, which is not achievable by any other method. The power of this unified system for accelerating hit-to-lead strategies, lowering attrition rates and expeditingin vivoscreening, was demonstrated with a pilot screening campaign of 445 compounds, revealing a new inhibitor that can inhibit amyloid β self-assemblyin vitroas well as in cellular and whole organism disease models.
Deciphering TP53 mutant Cancer Evolution with Single-Cell Multi-Omics
Authors: Rodriguez-Meira Alba , Norfo Ruggiero , Wen Wei Xiong , Chédeville Agathe L. , Rahman Haseeb , O’Sullivan Jennifer , Wang Guanlin , Louka Eleni , Kretzschmar Warren W. , Paterson Aimee , Brierley Charlotte , Martin Jean-Edouard , Demeule Caroline , Bashton Matthew , Sousos Nikolaos , Hamblin Angela , Guermouche Helene , Pasquier Florence , Marzac Christophe , Girodon François , Drummond Mark , Harrison Claire , Plo Isabelle , Jacobsen Sten Eirik W. , Psaila Bethan , Thongjuea Supat , Antony-Debré Iléana , Mead Adam J
Published: March 2022

TP53 is the most commonly mutated gene in human cancer, typically occurring in association with complex cytogenetics and dismal outcomes. Understanding the genetic and non-genetic determinants of TP53-mutation driven clonal evolution and subsequent transformation is a crucial step towards the design of rational therapeutic strategies. Here, we carry out allelic resolution single-cell multi-omic analysis of haematopoietic stem/progenitor cells (HSPC) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukaemia (AML), a tractable model of TP53-mutant cancer evolution. All patients showed dominant TP53 ‘multi-hit’ HSPC clones at transformation, with a leukaemia stem cell transcriptional signature strongly predictive of adverse outcome in independent cohorts, across both TP53-mutant and wild-type AML. Through analysis of serial samples and antecedent TP53-heterozygous clones, we demonstrate a hitherto unrecognised effect of chronic inflammation, which supressed TP53 wild-type HSPC whilst enhancing the fitness advantage of TP53 mutant cells. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukaemia, and are of broader relevance to other cancer types.
The hidden intricacies of aquaporins: Remarkable details in a common structural scaffold
Authors: Gössweiner-Mohr Nikolaus , Siligan Christine , Pluhackova Kristyna , Umlandt Linnea , Köfler Sabina , Trajkovska Natasha , Horner Andreas
Published: March 2022

Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of 4 representatives, we identify key aspects of AQP stability, gating, selectivity, pore geometry and oligomerization, with a potential impact on channel functionality. We challenge the general view of AQPs possessing a continuous open water pore and depict that AQPs selectivity is not exclusively shaped by pore lining residues but also by the relative arrangement of transmembrane helices. Moreover, our analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, we establish a novel numbering scheme of the conserved AQP scaffold facilitating direct comparison and prediction of potential structural effects of e.g. disease-causing mutations. Additionally, our results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.
LTD-inducing low frequency stimulation enhances p-Tau181 and p-Tau217 in an age-dependent manner in live rats
Authors: Zhang Yangyang , Yang Yin , Hu Zhengtao , Zhu Manyi , Qin Shuangying , Yu Pengpeng , Li Bo , Xu Jitian , Rowan Michael J. , Hu Neng-Wei
Published: March 2022

The progressive cognitive decline in Alzheimer’s disease (AD) patients correlates with the extent of tau pathology, in particular tau hyperphosphorylation, which is strongly age-associated. Although elevation of phosphorylated tau (p-Tau) on residues Thr181 (p-Tau181), Thr217 (p-Tau217), and Thr231 (p-Tau231) in cerebrospinal fluid or blood are recently proposed to be particularly sensitive markers of early AD, the generation of p-Tau during brain activity is poorly understood. A major form of synaptic plasticity, long-term depression (LTD), has recently been linked to the enhancement of tau phosphorylation. Here we show that low frequency stimulation (LFS), used to induce LTD, enhances p-Tau181 and p-Tau217 in an age-dependent manner in the hippocampus of live rats. In contrast, phosphorylation at residues Thr231, Ser202/Thr205, and Ser396 is less sensitive to LFS. Pharmacological antagonism of either NMDA or metabotropic glutamate 5 (mGluR5) receptors inhibits the elevation of both p-Tau181 and p-Tau217. Targeting ageing with a small molecule cognitive enhancer ISRIB (trans-isomer) prevents the enhancement of p-Tau by LFS in aged rats. Together, our data provide anin vivomeans to uncover brain plasticity-related cellular and molecular processes of tau phosphorylation in health and ageing conditions.
Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria
Authors: Uzun Maria , Koziaeva Veronika , Dziuba Marina , Leão Pedro , Krutkina Maria , Grouzdev Denis
Published: March 2022

Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. MTB belonging to one of such phyla,Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g.,mam, mms) andmangenes, which were considered to be specific for this group. However, the recent discovery ofmangenes in MTB from theThermodesulfobacteriotaphylum has raised several questions about the inheritance of these genes in MTB. In this work, three newmangenes containing MTB genomes affiliated withNitrospirotaandThermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of allNitrospirotawas most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylumNitrospirotaby horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from theMagnetobacteriaceaeto theDissulfurispiraceaefamily withinNitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.
Serotonin Modulates an Inhibitory Input to the Central Amygdala from the Ventral Periaqueductal Gray
Authors: Hon Olivia J. , DiBerto Jeffrey F. , Mazzone Christopher M. , Sugam Jonathan , Bloodgood Daniel W. , Hardaway J. Andrew , Husain Mariya , Kendra Alexis , McCall Nora M. , Lopez Alberto J. , Kash Thomas L. , Lowery-Gionta Emily G.
Published: March 2022

Fear is an adaptive state that drives defensive behavioral responses to specific and imminent threats. The central nucleus of the amygdala (CeA) is a critical site of adaptations that are required for the acquisition and expression of fear, in part due to alterations in the activity of inputs to the CeA. Here, we characterize a novel GABAergic input to the CeA from the ventral periaqueductal gray area (vPAG) using fiber photometry and ex vivo whole-cell slice electrophysiology combined with optogenetics and pharmacology. GABA transmission from this ascending vPAG-CeA input was enhanced by bath application of serotonin via activation of serotonin type 2C (5HT2C) receptors. Results indicate that these receptors are presynaptic. Interestingly, we found that GABA release from the vPAG-CeA input is enhanced following fear learning via activation of 5HT2C receptors and that this pathway is dynamically engaged during fear learning. Additionally, we characterized serotonin release in the CeA during fear learning and recall for the first time using fiber photometry coupled to a serotonin biosensor. Together, these findings describe a mechanism by which serotonin modulates GABA release from ascending vPAG GABA inputs to the CeA and characterize a role for this pathway in fear learning.
Excitatory-Inhibitory Recurrent Dynamics Produce Robust Visual Grids and Stable Attractors
Authors: Zhang Xiaohan , Long Xiaoyang , Zhang Sheng-Jia , Chen Zhe Sage
Published: March 2022

Spatially modulated grid cells has been recently found in the rat secondary visual cortex (V2) during activation navigation. However, the computational mechanism and functional significance of V2 grid cells remain unknown, and a theory-driven conceptual model for experimentally observed visual grids is missing. To address the knowledge gap and make experimentally testable predictions, here we trained a biologically-inspired excitatory-inhibitory recurrent neural network (E/I-RNN) to perform a two-dimensional spatial navigation task with multisensory (e.g., velocity, acceleration, and visual) input. We found grid-like responses in both excitatory and inhibitory RNN units, and these grid responses were robust with respect to the choices of spatial cues, dimensionality of visual input, activation function, and network connectivity. Dimensionality reduction analysis of population responses revealed a low-dimensional torus-like manifold and attractor, showing the stability of grid patterns with respect to new visual input, new trajectory and relative speed. We found that functionally similar receptive fields with strong excitatory-to-excitatory connection appeared within fully connected as well as structurally connected networks, suggesting a link between functional grid clusters and structural network. Additionally, multistable torus-like attractors emerged with increasing sparsity in inter- and intra-subnetwork connectivity. Finally, irregular grid patterns were found in a convolutional neural network (CNN)-RNN architecture while performing a visual sequence recognition task. Together, our results suggest new computational mechanisms of V2 grid cells in both spatial and non-spatial tasks.

Highlights

Grid patterns emerge in trained RNNs with multisensory inputs

Grid patterns are robust to the RNN input and network connectivity

Population responses show emergent ring-like manifolds and attractors

Grid-like patterns persist in RNNs while performing a non-spatial task.
Improving the Safety of Cultured Meat Using Basal Medium Prepared using Food Ingredients
Authors: Kanayama Takanori , Tanaka Keita , Shimada Haruna , Ichiyama Koji , Higuchi Sadaharu , Kawashima Ikko
Published: March 2022

Currently, meat production involves environmental issues and high costs; one solution to address this may be to produce meat via cell culture. Therefore, there is an urgent demand for the development of cell culture methods that replace raw materials with food materials to produce cultured meat as food. In this study, we designed food-grade-Dulbecco’s Modified Eagle’s Medium (FG-DMEM); when the cells cultured in FG-DMEM and regular DMEM were compared, there was no significant difference in cell growth or differentiation. Therefore, FG-DMEM can be used for research and safe production of cultured meat.
Telomere-to-telomere human DNA replication timing profiles
Authors: Massey Dashiell J. , Koren Amnon
Published: March 2022

The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
An engineered ACE2 decoy receptor can be administered by inhalation and potently targets the BA.1 and BA.2 omicron variants of SARS-CoV-2
Authors: Zhang Lianghui , Narayanan Krishna K. , Cooper Laura , Chan Kui K. , Devlin Christine A. , Aguhob Aaron , Shirley Kristie , Rong Lijun , Rehman Jalees , Malik Asrar B. , Procko Erik
Published: March 2022

Monoclonal antibodies targeting the SARS-CoV-2 spike (S) glycoprotein neutralize infection and are efficacious for the treatment of mild-to-moderate COVID-19. However, SARS-CoV-2 variants have emerged that partially or fully escape monoclonal antibodies in clinical use. Notably, the BA.2 sublineage of B.1.1.529/omicron escapes nearly all monoclonal antibodies currently authorized for therapeutic treatment of COVID-19. Decoy receptors, which are based on soluble forms of the host entry receptor ACE2, are an alternative strategy that broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22.v2.4-IgG1 was previously shown to be effective in vivo against SARS-CoV-2 variants when administered intravenously. Here, the inhalation of sACE22.v2.4-IgG1 is found to increase survival and ameliorate lung injury in K18-hACE2 transgenic mice inoculated with a lethal dose of the virulent P.1/gamma virus. Loss of catalytic activity reduced the decoy’s therapeutic efficacy supporting dual mechanisms of action: direct blocking of viral S and turnover of ACE2 substrates associated with lung injury and inflammation. Binding of sACE22.v2.4-IgG1 remained tight to S of BA.1 omicron, despite BA.1 omicron having extensive mutations, and binding exceeded that of four monoclonal antibodies approved for clinical use. BA.1 pseudovirus and authentic virus were neutralized at picomolar concentrations. Finally, tight binding was maintained against S from the BA.2 omicron sublineage, which differs from S of BA.1 by 26 mutations. Overall, the therapeutic potential of sACE22.v2.4-IgG1 is further confirmed by inhalation route and broad neutralization potency persists against increasingly divergent SARS-CoV-2 variants.
Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance
Authors: Naito Ken , Wakatake Takanori , Shibata Tomoko F. , Iseki Kohtaro , Shigenobu Shuji , Takahashi Yu , Ogiso-Tanaka Eri , Muto Chiaki , Teruya Kuniko , Shiroma Akino , Shimoji Makiko , Satou Kazuhito , Hirano Takashi , Nagano Atsushi J. , Tomooka Norihiko , Hasebe Mitsuyasu , Fukushima Kenji , Sakai Hiroaki
Published: March 2022

Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.
Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity
Authors: Broz Amanda K , Keene Alexandra , Gyorfy Matheus Fernandes , Hodous Mychaela , Johnston Iain G , Sloan Daniel B
Published: March 2022

The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted across generations or eliminated through genetic bottlenecks is not well understood in plants, in part because their low mutation rates make these variants so infrequent. Disruption of MutS Homolog 1 (MSH1), a gene involved in plant organellar DNA repair, results in numerous de novo point mutations, which we used to quantitatively track the inheritance of single nucleotide variants in mitochondrial and plastid genomes in Arabidopsis. We found that heteroplasmic sorting (the fixation or loss of a variant) was rapid for both organelles, greatly exceeding rates observed in animals. In msh1 mutants, plastid variants sorted faster than those in mitochondria and were typically fixed or lost within a single generation. Effective transmission bottleneck sizes for plastids and mitochondria were N ≈ 1 and 4, respectively. Restoring MSH1 function further increased the rate of heteroplasmic sorting in mitochondria (N ≈ 1.3), potentially due to its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. Heteroplasmic sorting also favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes can potentially accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.

Significance statement

Mitochondria and plastids play essential roles in eukaryotic life; thus, mutations in these organellar genomes can have severe consequences. In animals, early germline sequestration creates genetic “bottlenecks” providing cell-to-cell variance in mitochondrial mutations upon which selection can act. However, the dynamics of organellar mutations in plants and other organisms that lack early germline segregation remain unclear. Here, we show that sorting of mutations in plant organellar genomes proceeds very rapidly – much faster than in animals. In mitochondria, this process is accelerated by MSH1, a gene involved in recombination and repair of organellar genomes. This suggests that in plants, recombinational repair creates cell-to-cell variance in the frequency of organellar mutations, facilitating selection in the absence of a classical germline bottleneck.