bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of left ventricle myocardial deformation in a hemorrhagic shock swine model by two-dimensional speckle tracking echocardiography
Authors: Doria de Vasconcellos Henrique , Saad Karen Ruggeri , Saad Paulo Fernandes , Otsuki Denise Aya , Ciuffo Luisa A. , Lester Laeben , Koike Marcia Kiyomi , Armstrong Anderson da Costa , Lima Joao A. C. , Montero Edna Frasson de Souza
Published: April 2022

BACKGROUND

Trauma-induced secondary cardiac injury has been associated with significant adverse cardiovascular events. Speckle tracking echocardiography is a novel technology that allows an accurate and reproducible cardiac structure and function assessment. We evaluated the left ventricle (LV) myocardial deformation by speckle tracking echocardiography in a hemorrhagic shock (HS) swine model.

METHODS

Seven healthy male Landrace pigs were included in this study. Severe HS was reached through three sequentially blood withdraws of 20% of estimated blood volume, and it was maintained for 60 minutes. Volume resuscitation was performed using all precollected blood volume. A 1.8- to 4.2-MHz phased-array transducer was used to acquire the two-dimensional echocardiography images. Strain measurements were obtained semiautomatically by wall motion tracking software. Results are presented as medians and interquartile ranges and compared using Wilcoxon rank-sum test. A p value of <0.05 was considered statistically significant.

RESULTS

The median weight was 32 (26.1–33) kg, and the median total blood volume withdrawn was 1,100 (1,080–1,190) mL. During the severe HS period, the median arterial systemic pressure was 39 (36–46) mm Hg, and the cardiac index was 1.7 (1.6–2.0) L/min/m2. There was statistically significant absolute decrease in the global longitudinal strain 2 hours postresuscitation comparing with the basal measurements (−9.6% [−10.7 to −8.0%] vs. −7.9% [−8.1 to −7.4%], p = 0.03). There were no statistically significant differences between the basal and 2 hours postresuscitation assessments in the invasive/noninvasive hemodynamic, other two-dimensional echocardiogram (LV ejection fraction, 49.2% [44–54.3%] vs. 53.2% [51.5–55%]; p = 0.09), and circumferential strain (−10.6% [−14.4 to −9.0%] vs. −8.5% [−8.6 to −5.2%], p = 0.06) parameters.

CONCLUSION

In this experimental swine model of controlled HS, LV global longitudinal strain analysis accurately characterizes the timing and magnitude of subclinical cardiac dysfunction associated with trauma-induced secondary cardiac injury.
Public Understandings of the Definition and Determination of Death: A Scoping Review
Authors: Zheng Katina , Sutherland Stephanie , Hornby Laura , Shemie Sam D. , Wilson Lindsay , Sarti Aimee J.
Published: April 2022

Background.

Advances in medicine and technology that have made it possible to support, repair, or replace failing organs challenge commonly held notions of life and death. The objective of this review is to develop a comprehensive description of the current understandings of the public regarding the meaning/definition and determination of death.

Methods.

This scoping review was conducted in compliance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews checklist. Online databases were used to identify articles published from 2003 to 2021. Two reviewers (S.S. and K.Z.) screened the articles using predefined inclusion and exclusion criteria, extracted data for specific content variables, and performed descriptive examination. Complementary searches of reference lists complemented the final study selection. A search strategy using vocabulary of the respective databases was created, and criteria for the inclusion and exclusion of the articles were established.

Results.

Seven thousand four hundred twenty-eight references were identified. Sixty were retained for analysis, with 4 additional references added from complementary searches. A data extraction instrument was developed to iteratively chart the results. A qualitative approach was conducted to thematically analyze the data. Themes included public understanding/attitudes toward death and determination of death (neurological determination and cardiocirculatory determination of death), death and organ donation, public trust and legal variability, and media impacts.

Conclusions.

This review provides a current and comprehensive overview of the literature related to the general public’s understanding and attitudes toward death and death determination and serves to highlight the gaps in this topic.
Epileptic Seizure Induced by Head-Up Tilt: A Case Series Study
Authors: Toprani Sheela , Jaradeh Safwan , Falco-Walter Jessica J.
Published: April 2022

Purpose:

Epilepsy and syncope can be difficult to distinguish, with misdiagnosis resulting in unnecessary or incorrect treatment and disability. Combined tilt-table and video EEG (vEEG) testing (tilt-vEEG) is infrequently used to parse these entities even at large centers. Because of the discovery of a rare case of epileptic seizure induced by head-up tilt (HUT) (no prior cases have been published), the authors sought to verify the rarity of this phenomenon.

Methods:

An observational, retrospective case series study of all combined tilt-vEEG studies performed at Stanford Health Care over a 2-year period was performed. Studies were grouped into categories: (1) abnormal tilt and normal vEEG; (2) abnormal vEEG and normal tilt; (3) abnormal vEEG and abnormal tilt; (4) normal tilt and normal vEEG, with neurologic symptoms; and (5) normal tilt and normal vEEG without neurologic symptoms.

Results:

Sixty-eight percent of patients had an abnormal study (categories A–C), with only 3% having both an abnormal tilt and an abnormal EEG (category C). Of these, one patient had a focal epileptic seizure induced by HUT. With HUT positioning, the patient stopped answering questions and vEEG showed a left temporal seizure; systolic blood pressure abruptly dropped to 89 mm Hg (64 mm Hg below baseline); heart rate did not change, but pacemaker showed increased firing (threshold: <60 bpm).

Conclusions:

Combined tilt-table and vEEG evaluation was able to identify a previously unreported scenario—head-up tilt provocation of an epileptic seizure—and improve treatment. Combined tilt and vEEG testing should be considered for episodes that persist despite treatment to confirm proper diagnosis.
Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21
Authors: Allué-Guardia Anna , Koenig Sara S. K. , Martinez Ricardo A. , Rodriguez Armando L. , Bosilevac Joseph M. , Feng† Peter , Eppinger Mark
Published: April 2022

Infections with globally disseminated Shiga toxin-producing

Escherichia coli

(STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains’ featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.
Multiplexed biosensor for point-of-care COVID-19 monitoring: CRISPR-powered unamplified RNA diagnostics and protein-based therapeutic drug management
Authors: Johnston Midori , Ates H. Ceren , Glatz Regina , Mohsenin Hasti , Schmachtenberg Rosanne , Göppert Nathalie , Huzly Daniela , Urban Gerald A. , Weber Wilfried , Dincer Can
Published: April 2022

In late 2019 SARS-CoV-2 rapidly spread to become a global pandemic, therefore, measures to attenuate chains of infection, such as high-throughput screenings and isolation of carriers were taken. Prerequisite for a reasonable and democratic implementation of such measures, however, is the availability of sufficient testing opportunities (beyond reverse transcription PCR, the current gold standard). We, therefore, propose an electrochemical, microfluidic multiplexed biosensor in combination with CRISPR/Cas-powered assays for point-of-care nucleic acid testing. In this study, we simultaneously screen for and identify SARS-CoV-2 infections (Omicron-variant) in clinical specimens (Sample-to-result time: ∼30 min), employing LbuCas13a, whilst bypassing reverse transcription as well as target amplification of the viral RNA, both of which are necessary for detection via PCR and multiple other methods. In addition, we demonstrate the feasibility of combining assays based on different classes of biomolecules, in this case protein-based antibiotic detection, on the same device. The programmability of the effector and multiplexing capacity (up to six analytes) of our platform, in combination with a miniaturized measurement setup, including a credit card sized near field communication (NFC) potentiostat and a microperistaltic pump, provide a promising on-site tool for identifying individuals infected with variants of concern and monitoring their disease progression alongside other potential biomarkers or medication clearance.
Delta/ Omicron and BA.1/BA.2 co-infections occurring in Immunocompromised hosts
Authors: Leuking Richard , Narasimhan Madhusudhanan , Mahimainathan Lenin , Muthukumar Alagar R , Liu Yan , Xing Chao , Larsen Christian P. , Clark Andrew , SoRelle Jeffrey A.
Published: April 2022

Concomitant infection of multiple SARS-CoV-2 variants has become an increasing concern, as this scenario increases the likelihood of recombinant variants. Detecting co-infection of SARS-CoV-2 variants is difficult to detect by whole genome sequencing approaches, but genotyping methods facilitate detection. We describe 2 cases of Delta/Omicron and 2 cases of Omicron sublineage BA.1/ BA.2 co-infection as detected by a multiplex genotyping fragment analysis method. Findings were confirmed by whole genome sequencing. Review of the patient characteristics revealed co-morbidities and conditions which weaken the immune system and may make them more susceptible to harboring SARS-CoV-2 variant co-infections.
Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy and periventricular calcifications
Authors: Rosenhahn Erik , O’Brien Thomas J. , Zaki Maha S. , Sorge Ina , Wieczorek Dagmar , Rostasy Kevin , Vitobello Antonio , Nambot Sophie , Alkuraya Fowzan S. , Hashem Mais O. , Alhashem Amal , Tabarki Brahim , Alamri Abdullah S. , Al Safar Ayat H. , Bubshait Dalal K. , Alahmady Nada F. , Gleeson Joseph G. , Abdel-Hamid Mohamed S. , Lesko Nicole , Ygberg Sofia , Correia Sandrina P. , Wredenberg Anna , Alavi Shahryar , Seyedhassani Seyed M. , Nasab Mahya Ebrahimi , Hussien Haytham , Omar Tarek , Harzallah Ines , Touraine Renaud , Tajsharghi Homa , Morsy Heba , Houlden Henry , Shahrooei Mohammad , Ghavideldarestani Maryam , Lemke Johannes R. , Sticht Heinrich , Jamra Rami Abou , Brown Andre E. X. , Maroofian Reza , Platzer Konrad
Published: April 2022

PPFIBP1 encodes for the liprin-β1 protein which has been shown to play a role in neuronal outgrowth and synapse formation in Drosophila melanogaster. By exome sequencing, we detected nine ultra-rare homozygous loss-of-function variants in 14 individuals from 10 unrelated families. The individuals presented with moderate to profound developmental delay, often refractory early-onset epilepsy and progressive microcephaly. Further common clinical findings included muscular hypertonia, spasticity, failure to thrive and short stature, feeding difficulties, impaired hearing and vision, and congenital heart defects. Neuroimaging revealed abnormalities of brain morphology with leukoencephalopathy, cortical abnormalities, and intracranial periventricular calcifications as major features. In a fetus with intracranial calcifications, we identified a rare homozygous missense variant that by structural analysis was predicted to disturb the topology of the SAM-domain region that is essential for protein-protein interaction. For further insight in the effects of PPFIBP1 loss-of-function, we performed automated behavioural phenotyping of a Caenorhabditis elegans PPFIBP1/hlb-1 knockout model which revealed defects in spontaneous and light-induced behaviour and confirmed resistance to the acetylcholinesterase inhibitor aldicarb suggesting a defect in the neuronal presynaptic zone. In conclusion, we present bi-allelic loss-of-function variants in PPFIBP1 as a novel cause of an autosomal recessive neurodevelopmental disorder.
Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC
Authors: Wurtzer Sebastien , Levert Morgane , Dhenain Eloïse , Accrombessi Heberte , Manco Sandra , Fagour Nathalie , Goulet Marion , Boudaud Nicolas , Gaillard Lucie , Bertrand Isabelle , Challant Julie , Masnada Sophie , Azimi Sam , Guillon-Ritz Miguel , Robin Alban , Mouchel Jean-Marie ,   OBEPINE SIG, Moulin Laurent
Published: April 2022

Throughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the majority populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and proportions of VOCs identified by sequencing of isolated patient strains. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation in human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.
Interleukin-6 as a predictor of early weaning from invasive mechanical ventilation in patients with acute respiratory distress syndrome
Authors: Sakai Kazuya , Nishii Mototsugu , Saji Ryo , Matsumura Reo , Ogawa Fumihiro , Takeuchi Ichiro
Published: April 2022

Background

Therapeutic effects of steroids on acute respiratory distress syndrome (ARDS) requiring mechanical ventilation (MV) have been reported. However, predictive indicators of early weaning from MV post-treatment have not yet been defined, making treating established ARDS challenging. Interleukin (IL)-6 has been associated with the pathogenesis of ARDS.

Objective

Our aim was to clarify clinical utility of IL-6 level in ventilated patients with established ARDS.

Methods

Clinical, treatment, and outcome data were evaluated in 119 invasively ventilated patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-mediated ARDS. Plasma levels of IL-6 and C-reactive protein (CRP) were measured on days 1, 4, and 7 after intubation.

Results

Fifty-two patients were treated with dexamethasone (steroid group), while the remaining 67 patients were not (non-steroid group). Duration of MV use was significantly shorter in the steroid group compared to non-steroid group (11.5±0.6 vs. 16.1±1.0 days, P = 0.0005, respectively) along with significantly decreased levels of IL-6 and CRP. Even when restricted to the steroid group, among variables post-MV, IL-6 level on day 7 was most closely correlated with duration of MV use (Spearman’s rank correlation coefficient [ρ] = 0.73, P < 0.0001), followed by CRP level on day 7 and the percentage change in IL-6 or CRP levels between day 1 and day 7. Moreover, among these variables, IL-6 levels on day 7 showed the highest accuracy for withdrawal from MV within 11 days (AUC: 0.88), with optimal cutoff value of 20.6 pg/mL. Consistently, the rate of MV weaning increased significantly earlier in patients with low IL-6 (≤ 20.6 pg/mL) than in those with high IL-6 (> 20.6 pg/mL) (log-rank test P < 0.0001).

Conclusions

In invasively ventilated patients with established ARDS due to SARS-CoV-2, plasma IL-6 levels served as a predictor of early withdrawal from MV after dexamethasone administration.
Overlapping and distinct cis-acting requirements for oskar mRNA localization pathways
Authors: Eichler Catherine E. , Grunberg Michelle E. , Gavis Elizabeth R.
Published: April 2022

Localization of oskar mRNA to the posterior of the Drosophila oocyte is essential for abdominal patterning and germline development. oskar localization is a multi-step process involving temporally and mechanistically distinct transport modes. Numerous cis-acting elements and trans-acting factors have been identified that mediate earlier motor-dependent transport steps leading to accumulation of oskar at the posterior. Little is known, however, about what features of oskar are required for the later localization phase, that occurs by diffusion with local entrapment and results in the accumulation of large oskar ribonucleoprotein granules by the end of oogenesis. Here we test whether cis- and trans-acting requirements for kinesin-dependent oskar transport, the structured oskar spliced localization element (SOLE) and the exon junction complex (EJC), are also required for late-phase localization. In contrast to kinesin-dependent motility, late-phase localization is independent of the EJC and depends not only on the structure but also the sequence of the SOLE. Late-phase localization also requires the oskar 3’ UTR and we show that the 3’ UTR is sufficient for ribonucleoprotein granule selectivity.
Prepandemic prevalence estimates of fatty liver disease and fibrosis defined by liver elastography in the United States
Authors: Unalp-Arida Aynur , Ruhl Constance E.
Published: April 2022

Background & Aims

Fatty liver disease is a growing public health burden with serious consequences. We estimated prepandemic prevalence of fatty liver disease determined by transient elastography assessed hepatic steatosis and fibrosis, and examined associations with lifestyle and other factors in a United States population sample.

Methods

Liver stiffness and controlled attenuation parameter (CAP) were assessed on 7,923 non-Hispanic white, non-Hispanic black, non-Hispanic Asian, and Hispanic men and women aged 20 years and over in the National Health and Nutrition Examination Survey (NHANES) 2017-March 2020 prepandemic data.

Results

The prevalence of fatty liver disease estimated by CAP >300 dB/m was 28.8% and of fibrosis (liver stiffness >8 kPa) was 10.4%. Only 7.2% of participants with fatty liver disease and 10.9% with fibrosis reported being told by a health care provider that they had liver disease. In addition to known risk factors such as metabolic factors and ALT, persons with fatty liver disease were less likely to meet physical activity guidelines, more likely to be sedentary for 12 or more hours a day, and reported a less healthy diet. Persons with fibrosis were less likely to have a college degree and reported a less healthy diet.

Conclusion

In the U.S. population, most persons with fatty liver disease are unaware of their condition. Although physical activity and dietary modifications might reduce the fatty liver disease burden, the COVID pandemic has been less favorable for lifestyle changes. There is an urgent need for fatty liver disease management in high-risk individuals using transient elastography or other noninvasive methods to intervene in disease progression.
Immunogenicity of BNT162b2 COVID-19 vaccine in New Zealand adults
Authors: Priddy Frances H. , Williams Michael , Carson Simon , Lavender Brittany , Mathieson Julia , Frampton Chris , Moreland Nicole J. , McGregor Reuben , Williams Georgia , Brewerton Maia , Gell Katie , Ussher James , Gros Graham Le
Published: April 2022

Background

There is very little known about SARS-CoV-2 vaccine immune responses in New Zealand populations at greatest risk for serious COVID-19 disease.

Methods

This prospective cohort study assessed immunogenicity in BNT162b2 mRNA vaccine recipients in New Zealand without previous COVID-19, with enrichment for Māori, Pacific peoples, older adults ≥ 65 years of age, and those with co-morbidities. Serum samples were analysed at baseline and 28 days after second dose for presence of quantitative anti-S IgG by chemiluminescent microparticle immunoassay and for neutralizing capacity against Wuhan, Beta, Delta, and Omicron BA.1 strains using a surrogate viral neutralisation assay.

Results

285 adults with median age of 52 years were included. 55% were female, 30% were Māori, 28% were Pacific peoples, and 26% were ≥65 years of age. Obesity, cardiac and pulmonary disease and diabetes were more common than in the general population. All participants received 2 doses of BNT162b2 vaccine. At 28 days after second vaccination, 99.6% seroconverted to the vaccine, and anti-S IgG and neutralising antibody levels were high across gender and ethnic groups. IgG and neutralising responses declined with age. Lower responses were associated with age ≥75 and diabetes, but not BMI. The ability to neutralise the Omicron BA.1 variant in vitro was severely diminished but maintained against other variants of concern.

Conclusions

Vaccine antibody responses to BNT162b2 were generally robust and consistent with international data in this COVID-19 naïve cohort with representation of key populations at risk for COVID-19 morbidity. Subsequent data on response to boosters, durability of responses and cellular immune responses should be assessed with attention to elderly adults and diabetics.
PEP7 is a ligand for receptor kinase SIRK1 to regulate aquaporins and root growth
Authors: Wang Jiahui , Xi Lin , Wu Xu Na , König Stefanie , Rohr Leander , Neumann Theresia , Harter Klaus , Schulze Waltraud X.
Published: April 2022

Plant receptor kinases constitute a large protein family that regulate various aspects of development and responses to external biotic and abiotic cues. Functional characterization of this protein family and particularly the identification of their ligands remains a major challenge in plant biology. Previously, we identified plasma membrane-intrinsic SUCROSE INDUCED RECEPTOR KINASE 1 (SIRK1) and QIAN SHOU KINASE 1 (QSK1) as a receptor / co-receptor pair involved in regulation of aquaporins in response to osmotic conditions induced by sucrose. Here, we identified a member of the Elicitor Peptide (PEP) family, namely PEP7, as the specific ligand of receptor kinase SIRK1. PEP7 binds to the extracellular domain of SIRK1 with a binding constant of 1.44±0.79 µM and is secreted to the apoplasm specifically in response to sucrose treatment. Stabilization of a signaling complex involving SIRK1, QSK1 and aquaporins as substrates is mediated by alterations in the external sucrose concentration or by PEP7 application. Moreover, the presence of PEP7 induces the phosphorylation of aquaporins in vivo and enhance water influx into protoplasts. The loss-of-function mutant of SIRK1 is not responsive to external PEP7 treatment regarding kinase activity, aquaporin phosphorylation and water influx activity. Our data indicate that the PEP7/SIRK1/QSK1 complex represents a crucial perception and response module mediating sucrose-controlled water flux in plants.
Screening of the optimal CpG-oligodeoxynucleotide for anti-inflammatory responses in avian macrophage cell line HD11
Authors: Ichikawa Kennosuke , Matsuzaki Mei , Ezaki Ryo , Horiuchi Hiroyuki , Yamamoto Yoshinari
Published: April 2022

CpG-oligodeoxynucleotides (CpG-ODN) has been shown to possess immunostimulatory features in both mammals and birds. However, compared to its pro-inflammatory effects, little is known about the anti-inflammatory responses triggered by CpG-ODN in avian cells. Hence, in this study, we aimed to characterize the anti-inflammatory response in the chick macrophage cell line HD11 under the stimulation of five kinds of CpG-ODN: CpG-A1585, CpG-AD35, CpG-B1555, CpG-BK3, and CpG-C2395. Single-stimulus CpG-B1555, CpG-BK3, and CpG-C2395 induced the interleukin (IL)-10 expression without causing cellular injury. The effects of pretreatment with each CpG-ODN before subsequent lipopolysaccharide stimulation were also evaluated. Interestingly, only CpG-C2395 maintained a high expression level in this situation. Finally, expression analysis of inflammation-related genes, such as the tumor necrosis factor-α, IL-1β, IL-6, and Toll-like receptor 4, was conducted, and pretreatment with CpG-C2395 significantly reduced their expression. Overall, our results shed light on the anti-inflammatory responses triggered by CpG-C2395 stimulation using a comparative analysis of three major classes of CpG-ODN in chick macrophages.
Cryo-EM reveals an entangled kinetic trap in the folding pathway of a catalytic RNA
Authors: Bonilla Steve L. , Vicens Quentin , Kieft Jeffrey S.
Published: April 2022

Functional RNAs fold through complex pathways that can contain misfolded “kinetic traps.” A complete model of RNA folding requires understanding the formation of such misfolded states, but they are difficult to characterize due to their transient and potentially conformationally dynamic nature. We used cryo-electron microscopy (cryo-EM) to visualize a long-lived misfolded state in the folding pathway of the Tetrahymena thermophila group I intron, a paradigmatic RNA structure-function model system. The structure revealed how this state forms native-like secondary structure and tertiary contacts but contains two incorrectly crossed strands, consistent with a previous model. This incorrect topology mispositions a critical catalytic domain and cannot be resolved locally, as extensive refolding is required. This work provides a structural framework for interpreting decades of biochemical and functional studies and demonstrates the power of cryo-EM for the exploration of RNA folding pathways.
Unaltered T cell responses to common antigens in individuals with Parkinson’s disease
Authors: Williams Gregory P. , Muskat Kaylin , Frazier April , Xu Yaqian , Mateus José , Grifoni Alba , da Silva Antunes Ricardo , Weiskopf Daniela , Amara Amy W. , Standaert David G. , Goldman Jennifer G. , Litvan Irene , Alcalay Roy N. , Sulzer David , Lindestam Arlehamn Cecilia S. , Sette Alessandro
Published: April 2022

Background and Objectives

Parkinson’s disease (PD) is associated with a heightened inflammatory state, including activated T cells. However, it is unclear whether these PD T cell responses are antigen specific or more indicative of generalized hyperresponsiveness. Our objective was to measure and compare antigen-specific T cell responses directed towards antigens derived from commonly encountered human pathogens/vaccines in patients with PD and age-matched healthy controls (HC).

Methods

Peripheral blood mononuclear cells (PBMCs) from 20 PD patients and 19 age-matched HCs were screened. Antigen specific T cell responses were measured by flow cytometry using a combination of the activation induced marker (AIM) assay and intracellular cytokine staining.

Results

Here we show that both PD patients and HCs show similar T cell activation levels to several antigens derived from commonly encountered human pathogens/vaccines in the general population. Similarly, we also observed no difference between HC and PD in the levels of CD4 and CD8 T cell derived cytokines produced in response to any of the common antigens tested. These antigens encompassed both viral (coronavirus, rhinovirus, respiratory syncytial virus, influenza, cytomegalovirus) and bacterial (pertussis, tetanus) targets.

Conclusions

These results suggest the T cell dysfunction observed in PD may not extend itself to abnormal responses to commonly encountered or vaccine-target antigens. Our study supports the notion that the targets of inflammatory T cell responses in PD may be more directed towards autoantigens like α-synuclein (α-syn) rather than common foreign antigens.
β-cell responses to high fat feeding: A role and mechanism for redox sensing by SENP1
Authors: Lin Haopeng , Suzuki Kunimasa , Smith Nancy , Li Xi , Nalbach Lisa , Fuentes Sonia , Spigelman Aliya F , Dai Xiaoqing , Bautista Austin , Ferdaoussi Mourad , Aggarwal Saloni , Pepper Andrew R , Roma Leticia P , Ampofo Emmanuel , Li Wen-hong , MacDonald Patrick E
Published: April 2022

Pancreatic β-cells respond to metabolic stress by upregulating insulin secretion, however the underlying mechanisms remain unclear. In β-cells from overweight humans without diabetes, and mice fed a high-fat diet for 2 days, insulin exocytosis and secretion are enhanced without increased Ca2+influx. β-cell RNA-seq suggests altered metabolic pathways early following HFD, where we find increased basal oxygen consumption, proton leak, but a more reduced cytosolic redox state. Increased β-cell exocytosis after 2-day HFD is dependent on this reduced intracellular redox and requires thesentrin-specific SUMO-protease-1(SENP1). Mice with either pancreas- or β-cell-specific SENP1 deletion fail to up-regulate exocytosis and become rapidly glucose intolerant after 2-day HFD. Mechanistically, redox-sensing by SENP1 requires a thiol group at C535 which together with Zn+-binding suppresses basal protease activity and unrestrained β-cell exocytosis and increases SENP1 sensitivity to regulation by redox signals.
Oncogenic mutations ofPIK3CAlead to increased membrane recruitment driven by reorientation of the ABD, p85 and C-terminus
Authors: Jenkins Meredith L , Ranga-Prasad Harish , Parson Matthew AH , Harris Noah J , Rathinaswamy Manoj K , Burke John E
Published: April 2022

PIK3CAencoding the phosphoinositide 3-kinase (PI3K) p110α catalytic subunit is frequently mutated in cancer, with mutations occurring widely throughout the primary sequence. The full set of mechanisms underlying how PI3Ks are activated by all oncogenic mutations on membranes are unclear. Using a synergy of biochemical assays and hydrogen deuterium exchange mass spectrometry (HDX-MS), we reveal unique regulatory mechanisms underlying PI3K activation. Engagement of p110α on membranes leads to disengagement of the ABD of p110α from the catalytic core, and the C2 domain from the iSH2 domain of the p85 regulatory subunit. PI3K activation also requires reorientation of the p110α C-terminus, with mutations that alter the inhibited conformation of the C-terminus increasing membrane binding. Mutations at the C-terminus (M1043I/L, H1047R, G1049R, and N1068KLKR) activate p110α through distinct mechanisms, with this having important implications for mutant selective inhibitor development. This work reveals unique mechanisms underlying how PI3K is activated by oncogenic mutations, and explains how double mutants can synergistically increase PI3K activity.
Organizing laboratory information to analyze the reproducibility of experimental workflows
Authors: Peccoud Jean , Johnson Derek , Peccoud Samuel , Setchell Julia , Zhou Wen
Published: April 2022

Reproducibility is the cornerstone of scientific experiments. Assessing the reproducibility of an experiment requires analyzing the contribution of different factors to the variation of the observed data. Suitable data structures need to be defined prior to the data collection effort so that data associated with these factors can be recorded and associated with observations of the variable of interest. The resulting datasets can be analyzed statistically to estimate the effect of experimental factors on the observed data using ANOVA models. Custom data structures to document the execution of experimental workflows are defined in a research data management system. The data produced by multiple repetitions of a plasmid purification process and a cell culture process are analyzed using the Kruskal–Wallis H-test to identify factors contributing to their variation. Repetitions of the plasmid purification process do not lead to significant differences in extraction yields. Statistically significant differences in plasmid solution purity are identified but the differences are small enough that are not biologically relevant. The maintenance of two cell lines over many generations leads to similar datasets. However, different media preparations appear to influence the variation of cell viability and harvested cell counts in unexpected ways that may be the indirect expression of hidden effects not captured in the data structure.
Enhancing Prime Editing Efficiency and Flexibility with Tethered and Split pegRNAs
Authors: Feng Ying , Liu Siyuan , Mo Qiqin , Xiao Xiao , Liu Pengpeng , Ma Hanhui
Published: April 2022

Prime editing (PE) has advantages for small insertion, deletion or point mutations without double-stranded DNA breaks. The 3’-extension of pegRNAs could negatively affect its stability or folding and comprise the PE activity. Here we generated stem-loop PEs (sPEs) by adding stem-loop aptamers at the 3’-terminal of pegRNA, which can be tethered to Cas9 nickase resulting in tethered PEs (tPEs). sPEs and tPEs increased the small insertion, deletion or point mutations efficiency by 2-4-fold on average in HEK293, U2OS and HeLa cells. We split the modified pegRNAs into sgRNA and prime RNA. The resulting split pegRNA prime editors (SnPEs) maintain the PE activity and increase flexibility.
Disentangling leaf-microbiome interactions inArabidopsis thalianaby network mapping
Authors: Li Kaihang , Cheng Kexin , Wang Haochen , Zhang Qi , Yang Yan , Jin Yi , He Xiaoqing , Wu Rongling
Published: April 2022

The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions – mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140-728 SNPs responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22-43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.

IMPORTANCE

It is found that plant genes act as microbiome gatekeepers to select which microbes get to live inside the leaves for health. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact. This work illustrates a more comprehensive picture of the genetic architecture underlying the leaf microbiome by network mapping. This study also dissects how genetic variants affect its fecundity by direct path and indirect path through microbial network, revealing the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes. Future studies could benefit from this work to improve understanding the underlying genetic mechanisms that govern the relationships between plants and their microbiomes, and to manipulate plant genetic system to reconfigure microbiome. Plants could become more efficient at selecting their microbial partners to improve their health, resilience, and productivity.
High incidence of sotrovimab resistance and viral persistence after treatment of immunocompromised patients infected with the SARS-CoV-2 Omicron variant
Authors: Huygens Sammy , Munnink Bas Oude , Gharbharan Arvind , Koopmans Marion , Rijnders Bart
Published: April 2022

Background

Sotrovimab is a monoclonal antibody that neutralizes SARS-CoV-2 by binding to a highly conserved epitope in the receptor binding domain. It retains activity against the Omicron BA.1 variant and is used to treat immunocompromised patients as they are at increased risk for a severe outcome of COVID-19.

Methods

We studied viral evolution in 47 immunocompromised patients infected with Omicron BA.1 or 2 and treated with sotrovimab. SARS-CoV-2 PCR was performed at baseline and weekly thereafter until Ct-value was ≥ 30. All RNA samples were sequenced to determine the variant and occurrence of mutations, in particular in the Spike protein, after treatment.

Results

Twenty-four (51%) of the 47 patients were male and their median age was 63 years. Thirty-one (66%) had undergone a solid organ transplantation and 13 (28%) had received prior B-cell depleting therapy. Despite a history of vaccination, 24 of 30 patients with available data on anti-SARS-CoV-2 IgG Spike antibodies prior to treatment with sotrovimab had very low or no antibodies. Median time to viral clearance (Ct-value ≥ 30) after treatment was 15 days (IQR 7-22). However, viral RNA with low Ct-values was continuously detected for at least 28 days after treatment in four patients infected with BA.1. Mutations in the Spike protein at position 337 or 340 were observed in all four patients. Similar mutations were also found after treatment of two patients with a BA.2 infection but both cleared the virus within two weeks. Thus following treatment with sotrovimab, spike mutations associated with reduced in vitro susceptibility were detected in 6 of 47 (13%) patients.

Conclusion

Viral evolution towards resistance against sotrovimab can explain treatment failure in most immunocompromised patients and these patients can remain infectious after treatment. Therefore, documenting viral clearance after treatment is recommended to avoid that these patients unintentionally become a source of new, sotrovimab resistant, variants. Research on direct acting antivirals and possibly combination therapy for the treatment of COVID-19 in immunocompromised patients is needed.
STIMULATE-ICP-Delphi (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways Delphi): Study protocol
Authors: van der Feltz-Cornelis Christina M. , Sweetman Jennifer , Allsopp Gail , Attree Emily , Crooks Michael G. , Cuthbertson Daniel J , Forshaw Denise , Gabbay Mark , Green Angela , Heightman Melissa , Hillman Toby , Hishmeh Lyth , Khunti Kamlesh , Lip Gregory Y.H. , Lorgelly Paula , Montgomery Hugh , Strain W. David , Wall Emma , Watkins Caroline , Williams Nefyn , Wootton Dan G. , Banerjee Amitava ,   the STIMULATE-ICP Consortium
Published: April 2022

Introduction

As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic, integrated care. The evolution of integrated care systems (ICSs) in the UK presents an important opportunity to explore areas of mutual benefit to LTC, multi-morbidity and Long COVID care. There may be benefits in comparing and contrasting ICPs for Long COVID with ICPs for other LTCs.

Methods and analysis

This study aims to evaluate health services requirements for ICPs for Long COVID and their applicability to other LTCs including multi-morbidity and the overlap with medically not yet explained symptoms (MNYES). The study will follow a Delphi design and involve an expert panel of stakeholders including people with lived experience, as well as clinicians with expertise in Long COVID and other LTCs. Study processes will include expert panel and moderator panel meetings, surveys, and interviews. The Delphi process is part of the overall STIMULATE-ICP programme, aimed at improving integrated care for people with Long COVID.

Ethics and dissemination

Ethical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.

Registration

Researchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.
A genetic variant of the Wnt receptor LRP6 accelerates synapse degeneration during ageing and in Alzheimer’s disease
Authors: Jones Megan E. , Büchler Johanna , Dufor Tom , Boroviak Katharina , Metzakopian Emmanouil , Gibb Alasdair , Salinas Patricia C.
Published: April 2022

Synapse loss strongly correlates with cognitive decline in Alzheimer’s Disease (AD), but the underlying mechanisms are poorly understood. Studies suggest that deficient Wnt signalling, a pathway required for neuronal connectivity, contributes to synapse dysfunction and loss in AD. Consistent with this idea, a variant ofLrp6, (Lrp6-val), which confers reduced Wnt signalling, has been linked to late onset AD. However, the impact ofLrp6-valon synapses in the healthy and AD brain has not been examined. Using CRISPR/Cas9 genome editing, we generated a novel knock-in mouse model carrying thisLrp6variant to study its role in synaptic integrity.Lrp6-valmice develop normally and do not exhibit morphological brain abnormalities. Hippocampal neurons fromLrp6-valmice do not respond to Wnt7a, a Wnt ligand that promotes synaptic assembly through the Frizzled-5 (Fz5) receptor. Activation of the Wnt pathway by Wnt ligands leads to the formation of a complex between LRP6 and Fz5. In contrast, LRP6-Val impairs the formation of the LRP6-Fz5 complex elicited by Wnt7a, as detected by proximity ligation assay (PLA). We demonstrate thatLrp6-valmice exhibit structural and functional synaptic defects that become more pronounced with age, consistent with decreased canonical Wnt signalling during ageing. To investigate the contribution of this variant to AD,Lrp6-valmice were crossed tohAPPNL-G-F/NL-G-F(NL-G-F), a knock-in AD mouse model. The presence of theLrp6-valvariant significantly exacerbates synapse loss around amyloid-β plaques inNL-G-Fmice. Our findings uncover a novel role for theLrp6-valvariant in synapse vulnerability during ageing and its contribution to synapse degeneration in AD.
Host range expansion of Shigella phage Sf6 evolves through the dual roles of its tailspike
Authors: Subramanian Sundharraman , Dover John A. , Parent Kristin N. , Doore Sarah M.
Published: April 2022

The first critical step in a virus’s infection cycle is attachment to its host. This interaction is precise enough to ensure the virus will be able to productively infect the cell, but some flexibility can be beneficial to enable co-evolution and host range switching or expansion. Like many bacterial viruses, bacteriophage Sf6 utilizes a two-step process to recognize and attach to its host, Shigella flexneri. Sf6 first recognizes the lipopolysaccharide (LPS) structure of S. flexneri, then binds to either outer membrane protein (Omp) A or OmpC. This phage typically infects serotype Y strains but can also form small, turbid plaques on serotype 2a2 with greatly reduced plating efficiency, suggesting inefficient infection. To examine the interactions between Sf6 and this sub-optimal host, phage were experimentally evolved using mixed populations of S. flexneri serotypes Y and 2a2. The recovered mutants could infect serotype 2a2 with greater efficiency than the ancestral Sf6, forming clear plaques on both serotypes. All mutations mapped to two distinct regions of the tailspike protein: 1) adjacent to, but not part of, the LPS binding site near the N-terminus; and 2) at the distal, C-terminal tip of the protein. Rather than weak interactions between the Sf6 tailspike and 2a2 O-antigen, LPS of this serotype appears to inhibit infection by binding the wild-type particles more strongly, effectively removing them from the environment. These mutations reduce the inhibitory effect by either reducing electrostatic interactions with the O-antigen or increasing reliance on the Omp secondary receptors.