bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional Pathway and Process Enrichment Analysis of Genes Associated With Morphological Abnormalities of the Outer Ear
Authors: Meng Xiaolu , Pan Bo , Zhang Zeya , Guo Peipei , Wang Changchen , Huang Xin , Si Nuo , Jiang Haiyue
Published: August 2022

Congenital anomalies of the outer ear are common birth defects, including a variety of congenital deformities or malformations ranging from mild structural anomalies to total absence of the ear. Despite its high incidence and detrimental impact on patients, the etiology of outer ear abnormalities remains poorly understood. The goal of this study was to summarize the related genes and improve our understanding of the genetic etiology of morphological abnormalities of the outer ear. Human Phenotype Ontology (HPO) database, Mouse Genome Informatics (MGI) database, and PubMed search engine were used to acquire the genes associated with abnormal human or mouse outer ear. Metascape was employed on the genes above to conduct functional annotation, pathway and process enrichment analysis, protein-protein interaction network analysis, and MCODE component analysis. After a comprehensive review of the databases and literature, we identified 394 human genes and 148 mouse genes that have been associated with abnormal phenotypes of the outer ear, and we identified several biological pathways for human and mouse respectively. Especially, the analysis of common genes shared by human and mouse emphasized the importance of certain genes (PAX6, PBX1, HOXA1, HOXA2, TBX1, TBX15, PRRX1, and HMX1) in the embryonic development of the external ear. Through our analysis of genes associated with morphological abnormalities of the outer ear, the authors have shown that embryonic development pathways take important roles in the morphogenesis of abnormal external ear and highlighted some potential genetic drivers.
Developing a National Trauma Research Action Plan (NTRAP): Results from the Long-term Outcomes Research Gap Delphi Survey
Authors: Herrera-Escobar Juan P. , Reidy Emma , Phuong Jimmy , Brasel Karen J. , Cuschieri Joseph , Fallat Mary , Potter Benjamin K. , Price Michelle A. , Bulger Eileen M. , Haider Adil H. ,   the NTRAP Long-term Outcomes Panel
Published: August 2022

Background

In the National Academies of Sciences, Engineering, and Medicine 2016 report on trauma care, the establishment of a National Trauma Research Action Plan (NTRAP) to strengthen and guide future trauma research was recommended. To address this recommendation, the Department of Defense funded the Coalition for National Trauma Research to generate a comprehensive research agenda spanning the continuum of trauma and burn care. We describe the gap analysis and high-priority research questions generated from the NTRAP panel on long-term outcomes.

Methods

Experts in long-term outcomes were recruited to identify current gaps in long-term trauma outcomes research, generate research questions, and establish the priority for these questions using a consensus-driven, Delphi survey approach from February 2021 through August 2021. Panelists were identified using established Delphi recruitment guidelines to ensure heterogeneity and generalizability including both military and civilian representation. Panelists were encouraged to use a PICO format to generate research questions: Patient/Population; Intervention; Compare/Control; Outcome model. On subsequent surveys, panelists were asked to prioritize each research question on a 9-point Likert scale, categorized to represent low-, medium-, and high-priority items. Consensus was defined as ≥60% of panelists agreeing on the priority category.

Results

Thirty-two subject matter experts generated 482 questions in 17 long-term outcome topic areas. By Round 3 of the Delphi, 359 (75%) questions reached consensus, of which 107 (30%) were determined to be high priority, 252 (70%) medium priority, and 0 (0%) low priority. Substance abuse & pain was the topic area with the highest number of questions. Health services (not including mental health or rehabilitation) (64%), mental health (46%), and geriatric population (43%) were the topic areas with the highest proportion of high-priority questions.

Conclusions

This Delphi gap analysis of long-term trauma outcomes research identified 107 high-priority research questions that will help guide investigators in future long-term outcomes research.

Level of evidence

Level IV
The effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective multicenter cohort study
Authors: Piekos Samantha N. , Hwang Yeon Mi , Roper Ryan T. , Sorensen Tanya , Price Nathan D. , Hood Leroy , Hadlock Jennifer J.
Published: August 2022

Background

COVID-19 infection in pregnant people has previously been shown to increase the risk for poor maternal-fetal outcomes. Despite this, there has been a lag in COVID-19 vaccination in pregnant people due to concerns over the potential effects of the vaccine on maternal-fetal outcomes. Here we examine the impact of COVID-19 vaccination and booster on maternal COVID-19 breakthrough infections and birth outcomes.

Methods

This was a retrospective multicenter cohort study on the impact of COVID-19 vaccination on maternal-fetal outcomes for people that delivered (n=86,833) at Providence St. Joseph Health across Alaska, California, Montana, Oregon, New Mexico, Texas, and Washington from January 26, 2021 through July 11, 2022. Cohorts were defined by vaccination status at time of delivery: unvaccinated (n=48,492), unvaccinated propensity score matched (n=26,790), vaccinated (n=26,792; two doses of mRNA-1273 Moderna or BNT162b2 Pfizer-BioNTech), and/or boosted (n=7,616). The primary outcome was maternal COVID-19 infection. COVID-19 vaccination status at delivery, COVID-19 infection-related health care, preterm birth (PTB), stillbirth, very low birth weight (VLBW), and small for gestational age (SGA) were evaluated as secondary outcomes.

Findings

Vaccinated pregnant people were significantly less likely to have a maternal COVID-19 infection than unvaccinated matched (p<0.0001) pregnant people. During a maternal COVID-19 infection, vaccinated pregnant people had similar rates of hospitalization (p=0.23), but lower rates of supplemental oxygen (p<0.05) or vasopressor (p<0.05) use than those in an unvaccinated matched cohort. Compared to an unvaccinated matched cohort, vaccinated people had significantly lower stillbirth rate (p<0.01) as well as no difference in rate of PTB (p=0.35), SGA (p=0.79), or rate of VLBW (>1,500 g; 0.31). Vaccinated people who were boosted had significantly lower rates of maternal COVID-19 infections (p<0.0001), COVID-19 related hospitalization (p<0.05), PTB (p<0.05), stillbirth (p<0.01), SGA (p<0.05), and VLBW (p<0.01), compared to vaccinated people that did not receive a third booster dose five months after completing the initial vaccination series.

Interpretation

COVID-19 vaccination protects against adverse maternal-fetal outcomes with booster doses conferring additional protection against COVID-19 infection. It is therefore important for pregnant people to have high priority status for vaccination, and for them to stay current with their COVID-19 vaccination schedule.

Funding

This study was funded by the National Institute for Child Health & Human Development and the William O. and K. Carole Ellison Foundation.
The association between cardiovascular health and peripheral and central auditory functions in adults: a protocol for a systematic review
Authors: Daly Rosie C. , O’Donnell Emma , Barrett Laura , Füllgrabe Christian
Published: August 2022

Introduction

The ability to process sounds decreases with advancing age and the already high prevalence of people with hearing loss (HL) is estimated to increase further over time. Hearing loss reduces speech identification which is important for day-to-day communication. In addition, it can lead to social isolation, depression, and lower quality of life. Current hearing rehabilitation strategies (eg, hearing aids) provide some benefits, but are not always accepted by hearing-impaired listeners and are less successful in real-life listening situations. Consequently, alternative rehabilitation strategies, such as the manipulation of cardiovascular (CV) health for the prevention and rehabilitation of HL, should be explored. Some research suggests that CV health and auditory functions are related, but the existence of such a link has not been systematically evaluated. This manuscript outlines the protocol for a systematic review of published research on the association between CV health and peripheral and central auditory functions across the adult lifespan and for all levels of hearing abilities.

Method and analysis

The Preferred Reporting Items for Systematic reviews and Meta-Analyses Protocols (PRISMA-P) checklist will be followed. Studies included for analysis will be original peer-reviewed articles, measuring cardiovascular health and hearing abilities to explore their relationship. Participants will be aged ≥18 years and will have various levels of hearing sensitivity and of CV health. Databases will be searched, using key words, to obtain evidence that meets the defined set of inclusion criteria. Data will be extracted and examined by two reviewers. Quality checks will occur, and, if appropriate, a meta-analysis will be performed. Data analysis will be completed and reported in a full systematic review, following the PRISMA guidelines.

Ethics and dissemination

No ethical approval is needed for the systematic review as only published data will be analysed. Findings will be disseminated at conferences and in peer-reviewed journals.

Systematic review registration

PROSPERO CRD42022353002

STRENGTHS AND LIMITATIONS OF THIS STUDY

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The protocol follows the guidelines set out in the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P).

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The systematic review will consider both direct and indirect measures of CV health.

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The relationship of CV health with peripheral and with central auditory functioning will be examined.

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Results will indicate whether the manipulation of CV health could be used as an alternative rehabilitation strategy for HL.

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The systematic review will only include studies in the English language.
Psychological resilience mediates the relationship between perceived neuropsychological impairment and quality of life in a sample of patients with multiple sclerosis
Authors: Broche-Pérez Yunier , Jiménez-Morales Rodneys M. , Monasterio-Ramos Laura Ortiz , Bauer Johana
Published: August 2022

The impact of subjective cognitive concerns (SCCs) on the quality of life (QoL) of patients with multiple sclerosis (PwMS) has practically not been studied. In this study the relationship between subjective cognitive concerns and quality of life in PwMS was explored. Furthermore, to explore whether psychological resilience acts as a mediator in the relationship between SCCs and QoL. A total of 214 PwMS were surveyed using the Multiple Sclerosis Quality of Life Inventory, the Multiple Sclerosis Neuropsychological Questionnaire (MSNQ) and the Connor-Davidson Resilience Scale. Our results showed that, SCCs is a predictor of levels of perceived QoL in PwMS. Patients who report higher scores on the MSNQ also showed a worse quality of life in global terms. The results also showed that resilience mediates the relationship between SCCs and QoL, both for the physical dimension of quality of life (physical health composite) and for the mental health dimension (mental health composite). In our patients, as resilience levels increase, the negative impact of SCCs on QoL decreases. Considering that resilience is a modifiable protective factor, the implementation of interventions aimed at enhancing resilience can have a favorable impact on the psychological well-being and quality of life of patients with multiple sclerosis.
Correlation Analysis of Demographic Characteristics of Internal Medicine Residents on the Training Effect of Flipped Teaching Based on Video Conference
Authors: Zhang Xiao-Yu
Published: August 2022

Objective

I aimed to clarify whether the demographic characteristics of internal medicine residents are related to the training effect of Flipped Teaching based on Video Conference, so as to further improve the teaching management and quality control.

Methods

A total of 43 residents who participated in the Flipped Teaching based on Video Conference in April and June were included as the research objects. Online examination was conducted for these residents, and the demographic characteristics of these residents and their examination score were quantitatively analyzed, so as to clarify the correlation between the demographic characteristics of these residents and their examination score.

Results

The average score of 43 residents in the online examination was 72.0(64.0-79.0). 40 residents passed the exam, accounting for 93.0%. The bivariate correlations analysis showed that the age, gender, educational background, training batch and training phase of residents were not correlated with the examination score; all P > 0.05. The age, gender, educational background, training batch and training phase of these residents were not correlated with the examination score by single linear regression and multiple linear regression analysis; all P > 0.05.

Conclusion

Age, gender, educational background, training batches and training phases of internal medicine residents are not related to the examination score after Flipped Teaching based on Video Conference. Demographic characteristics may not be related to the training effect of residents through preliminary study.
Antisense oligonucleotide to SARS-Cov-2 trs gene: antiviral activity on an in vitro model and possibilities of vital and postmortem diagnosis of COVID-19
Authors: Goryachev A.N. , Shtro A.A. , Galochkina A.V. , Goryacheva A.S.
Published: August 2022

The data on the relevance of the 5 ‘-AGC CGA GTG ACA GCC ACA CAG antisense oligonucleotide for binding to the trs-gene of the SARS-CoV-2 virus, which causes the new coronavirus infection COVID-19, are presented. The high stability and conservatism of this section of the SARS-CoV-2 genome is shown, which allows it to be used as an application point for antisense oligonucleotides. By evaluating plaque inhibition, the ability of this antisense oligonucleotide with phosphorothioate and 2’-oxymethyl modification to suppress viral replication was found. The effective dosage reducing the virus titer by 50% is 3.84 mcg/ml. No toxicity was shown up to a dosage of 100 μg/mL, which is more than 28.8 chemotherapeutic index. The ability of this oligonucleotide conjugated to the fluorescent dye TAMRA to detect the SARS-CoV-2 virus in the fluorescent hybridization reaction in situ in cytological preparations of nasopharyngeal smears and blood smears, as well as in histological preparations of internal tissues is shown.
Real-world evidence with a retrospective cohort of 15,968 Andalusian COVID-19 hospitalized patients suggests 21 new effective treatments and one drug that increases death risk
Authors: Loucera Carlos , Carmona Rosario , Esteban-Medina Marina , Bostelmann Gerrit , Muñoyerro-Muñiz Dolores , Villegas Román , Peña-Chilet María , Dopazo Joaquin
Published: August 2022

Despite the extensive vaccination campaigns in many countries, COVID-19 is still a major worldwide health problem because of its associated morbidity and mortality. Therefore, finding efficient treatments as fast as possible is a pressing need. Drug repurposing constitutes a convenient alternative when the need for new drugs in an unexpected medical scenario is urgent, as is the case with COVID-19. Using data from a central registry of electronic health records (the Andalusian Population Health Database, BPS), the effect of prior consumption of drugs for other indications previous to the hospitalization with respect to patient survival was studied on a retrospective cohort of 15,968 individuals, comprising all COVID-19 patients hospitalized in Andalusia between January and November 2020. Covariate-adjusted hazard ratios and analysis of lymphocyte progression curves support a significant association between consumption of 21 different drugs and better patient survival. Contrarily, one drug, furosemide, displayed a significant increase in patient mortality.
Artificial Intelligence-Based Clustering and Characterization of Parkinson’s Disease Trajectories
Authors: Birkenbihl Colin , Ahmad Ashar , Massat Nathalie J , Raschka Tamara , Avbersek Andreja , Downey Patrick , Armstrong Martin , Fröhlich Holger
Published: August 2022

Parkinson’s disease (PD) is a highly heterogeneous disease both with respect to arising symptoms and its progression over time. This hampers the design of disease modifying trials for PD as treatments which would potentially show efficacy in specific patient subgroups could be considered ineffective in a heterogeneous trial cohort. Establishing clusters of PD patients based on their progression patterns could help to entangle the exhibited heterogeneity, illuminate clinical differences among patient subgroups, and identify the biological pathways and molecular players which underlie the evident differences. Further, stratification of patients into clusters with distinct progression patterns could help to recruit more homogeneous trial cohorts. In the present work, we applied an artificial intelligence-based algorithm to model and cluster longitudinal PD progression trajectories from the Parkinson’s Progression Markers Initiative. Using a combination of six clinical outcome scores covering both motor and non-motor symptoms, we were able to identify specific clusters of PD that showed significantly different patterns of PD progression. The inclusion of genetic variants and biomarker data allowed us to associate the established progression clusters with distinct biological mechanisms, such as perturbations in vesicle transport or neuroprotection. Furthermore, we found that patients of identified progression clusters showed significant differences in their responsiveness to symptomatic treatment. Taken together, our work contributes to a better understanding of the heterogeneity encountered when examining and treating patients with PD, and points towards potential biological pathways and genes that could underlie those differences.
Applying a Socio-Ecological Model to Understand Factors Impacting Demand for Childhood Vaccinations in Nigeria, Uganda, and Guinea
Authors: Bell James , Lartey Belinda , Spickernell Gemma , Darrell Natasha , Salt Frances , Gardner Cassie , Richards Emily , Fasakin Lanre , Egbeniyi Shadrach , Odongo Emmanuel , Ssenkungu James , Kouadio Rigobert Kotchi , Cissé Mamadi , Rérambyah Axel Bruno Ayiya Igowa , Adou Maikol , West Rebecca , Sharma Sunny
Published: August 2022

Vaccines have reduced child mortality across the world, but low levels of demand for vaccination threatens to undermine progress. Existing frameworks to understand demand tend to prioritise caregivers’ decision-making processes. We aimed to build a wider understanding of vaccine demand by applying an adapted socio-ecological model to analyse 158 interviews with caregivers and fathers of young children, and community influencers in Nigeria, Uganda, and Guinea. We found that several factors come together to inform a caregiver’s demand for vaccination, including their familial and social relationships, their interactions with government and healthcare institutions, and the wider social and cultural norms in their communities. The study suggests that interventions targeted at families and communities instead of individuals could be effective. The results could be used to ensure that vaccine demand frameworks used by researchers and intervention designers are comprehensive and consider a wider range of influences on the caregiver.
From Prediction to Action: Dissociable Roles of Ventral Tegmental Area and Substantia Nigra Dopamine Neurons in Instrumental Reinforcement
Authors: Fraser Kurt M. , Pribut Heather J. , Janak Patricia H. , Keiflin Ronald
Published: August 2022

Reward-seeking requires the coordination of motor programs to achieve goals. Midbrain dopamine neurons are critical for reinforcement and their activation is sufficient for learning about cues, actions, and outcomes. Here we examine in detail the mechanisms underlying the ability of ventral tegmental area (VTA) and substantia nigra (SNc) dopamine neurons to support instrumental learning. By exploiting numerous behavioral tasks in combination with time-limited optogenetic manipulations, we reveal that VTA and SNc dopamine neurons generate reinforcement through separable psychological processes. VTA dopamine neurons imbue actions and their associated cues with motivational value that allows flexible and persistent pursuit whereas SNc dopamine neurons support time-limited, precise, action-specific learning that is non-scalable and inflexible. This architecture is reminiscent of actor-critic reinforcement learning models with VTA and SNc instructing the critic and actor, respectively. Our findings indicate that heterogeneous dopamine systems support unique forms of instrumental learning that ultimately result in disparate reward-seeking strategies.
Collateral impacts of pandemic COVID-19 drive the nosocomial spread of antibiotic resistance
Authors: Smith David R. M. , Shirreff George , Temime Laura , Opatowski Lulla
Published: August 2022

Circulation of multidrug-resistant bacteria (MRB) in healthcare facilities is a major public health problem. These settings have been greatly impacted by the COVID-19 pandemic, notably due to surges in COVID-19 caseloads and the implementation of infection control measures. Yet collateral impacts of pandemic COVID-19 on MRB epidemiology remain poorly understood. Here, we present a dynamic transmission model in which SARS-CoV-2 and MRB co-circulate among patients and staff in a hospital population in an early pandemic context. Responses to SARS-CoV-2 outbreaks are captured mechanistically, reflecting impacts on factors relevant for MRB transmission, including contact behaviour, hand hygiene compliance, antibiotic prescribing and population structure. In a first set of simulations, broad parameter ranges are accounted for, representative of diverse bacterial species and hospital settings. On average, COVID-19 control measures coincide with MRB prevention, including fewer incident cases and fewer cumulative person-days of patient MRB colonization. However, surges in COVID-19 caseloads favour MRB transmission and lead to increased rates of antibiotic resistance, especially in the absence of concomitant control measures. In a second set of simulations, methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Escherichia coli are simulated in specific hospital wards and pandemic response scenarios. Antibiotic resistance dynamics are highly context-specific in these cases, and SARS-CoV-2 outbreaks significantly impact bacterial epidemiology only in facilities with high underlying risk of bacterial transmission. Crucially, antibiotic resistance burden is reduced in facilities with timelier, more effective implementation of COVID-19 control measures. This highlights the control of antibiotic resistance as an important collateral benefit of robust pandemic preparedness.

Significance Statement

Impacts of COVID-19 on the spread of antibiotic resistance are poorly understood. Here, an epidemiological model accounting for the simultaneous spread of SARS-CoV-2 and antibiotic-resistant bacteria is presented. The model is tailored to healthcare settings during the first wave of the COVID-19 pandemic, and accounts for hand hygiene, inter-individual contact behaviour, and other factors relevant for pathogen spread. Simulations demonstrate that public health policies enacted to slow the spread of COVID-19 also tend to limit bacterial transmission. However, surges in COVID-19 cases simultaneously select for higher rates of antibiotic resistance. Selection for resistance is thus mitigated by prompt implementation of effective COVID-19 prevention policies. This highlights the control of antibiotic resistance as an important collateral benefit of pandemic preparedness.
Backscattering Mueller Matrix polarimetry on whole brain specimens shows promise for minimally invasive mapping of microstructural orientation features
Authors: Bonaventura Justina , Morara Kellys , Carlson Rhea , Comrie Courtney , Daigle Noelle , Hutchinson Elizabeth , Sawyer Travis W.
Published: August 2022

Understanding microscale physiology and microstructural cellular features of the brain is key to understanding the mechanisms of neurodegenerative diseases and injury, as well as the prominent changes that neurons and glia in the brain undergo in development and aging which reflect functional state. Non-invasive imaging modalities sensitive to the microscale - especially diffusion magnetic resonance imaging (dMRI) - are extremely promising for three-dimensional mapping of cellular microstructure of brain tissues and brain connectivity via tractography; however, there is a need for robust validation techniques to verify and improve the biological accuracy of fiber orientation information derived from these techniques. Recent advances in dMRI acquisition and modeling have moved toward probing of the more complex grey matter architecture, challenging current validation techniques, which are largely based on ex vivo staining and microscopy focusing on white matter. Polarized light imaging (PLI) has been shown to be a successful technique for high resolution, direct, microstructural imaging and has been applied to dMRI validation with clear advantages over conventional staining and microscopy techniques. Conventionally, PLI is applied to thin, sectioned samples in transmission mode, but unlike histologic staining, PLI can be extended to operate with high sensitivity in reflectance mode and even extended to 3D imaging to bridge the gap toward in vivo validation of dMRI measurements of orientation features in both gray and white matter of the brain. In this report we investigate the use of backscattering Mueller Matrix polarimetry to characterize the microstructural content of intact Ferret brain specimens. The experimental results show that backscattering polarimetry can probe white matter fiber coherence and fiber orientation in whole brain specimens, and show promise for probing grey matter microstructure. Ultimately, these preliminary results motivate further study to fully understand how backscattering polarimetry can best be used for validation of in vivo microstructural imaging of the brain.
Enhancement of vestibular motion discrimination by small stochastic whole-body perturbations in young healthy humans
Authors: Scaleia Barbara La , Lacquaniti Francesco , Zago Myrka
Published: August 2022

Noisy galvanic vestibular stimulation has been shown to improve vestibular perception in healthy subjects. Here, we sought to obtain similar results using more natural stimuli consisting of small-amplitude motion perturbations of the whole body. Thirty participants were asked to report the perceived direction of antero-posterior sinusoidal motion on a MOOG platform. We compared the baseline perceptual thresholds with those obtained by applying small, stochastic perturbations at different power levels along the antero-posterior axis, symmetrically distributed around a zero-mean. At the population level, we found that the thresholds for all but the highest level of noise were significantly lower than the baseline threshold. At the individual level, the threshold was lower with at least one noise level than the threshold without noise in 87% of participants. Thus, small, stochastic oscillations of the whole body can increase the probability of detecting subthreshold vestibular signals, possibly due to stochastic resonance mechanisms. We suggest that, just as the external noise of the present experiments, also the spontaneous random oscillations of the body associated with standing posture are beneficial by enhancing vestibular thresholds with a mechanism similar to stochastic resonance. The results are also relevant from a clinical perspective, since they raise the possibility of improving motion perception in people with elevated thresholds due to aging or vestibulopathy by means of small-amplitude motion perturbations.

HIGHLIGHTS

Small-amplitude motion perturbations of the whole body improve vestibular perceptual thresholds of motion discrimination in young healthy people

Improvements occur at optimal levels of noise amplitude, idiosyncratic to each subject

The findings are consistent with the phenomenon of stochastic resonance

The new method can applied to people with elevated thresholds due to aging or vestibulopathy
A Deep Redox Proteome Profiling Workflow and Its Application to Skeletal Muscle of a Duchene Muscular Dystrophy Model
Authors: Day Nicholas J. , Zhang Tong , Gaffrey Matthew J. , Zhao Rui , Fillmore Thomas L. , Moore Ronald J. , Rodney George G. , Qian Wei-Jun
Published: August 2022

Perturbation to the redox state accompanies many diseases and its effects are viewed through oxidation of biomolecules, including proteins, lipids, and nucleic acids. The thiol groups of protein cysteine residues undergo an array of redox post-translational modifications (PTMs) that are important for regulation of protein and pathway function. To better understand what proteins are redox regulated following a perturbation, it is important to be able to comprehensively profile protein thiol oxidation at the proteome level. Herein, we report a deep redox proteome profiling workflow and demonstrate its application in measuring the changes in thiol oxidation along with global protein expression in skeletal muscle from mdx mice, a model of Duchenne Muscular Dystrophy (DMD). In depth coverage of the thiol proteome was achieved with >18,000 Cys sites from 5608 proteins in muscle being quantified. Compared to the control group, mdx mice exhibit markedly increased thiol oxidation, where ~2% shift in the median oxidation occupancy was observed. Pathway analysis for the redox data revealed that coagulation system and immune-related pathways were among the most susceptible to increased thiol oxidation in mdx mice, whereas protein abundance changes were more enriched in pathways associated with bioenergetics. This study illustrates the importance of deep redox profiling in gaining a greater insight into oxidative stress regulation and pathways/processes being perturbed in an oxidizing environment.

Graphical Abstract

Highlights

Deep redox profiling workflow results in stoichiometric quantification of thiol oxidation for > 18,000 Cys sites in muscle

Thiol redox changes were much more pronounced than protein abundance changes for the overlapping set of proteins

Redox changes are most significant in coagulation and immune response pathways while abundance changes on bioenergetics pathways
FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer
Authors: Wilde Blake R. , Chakraborty Nishma , Matulionis Nedas , Hernandez Stephanie , Ueno Daiki , Gee Michayla E. , Esplin Edward D. , Ouyang Karen , Nykamp Keith , Shuch Brian , Christofk Heather R.
Published: August 2022

The tricarboxylic citric acid cycle enzyme fumarate hydratase (FH) is a tumor suppressor. When lost in cells, its substrate fumarate accumulates to mM levels and drives oncogenic signaling and transformation. Germline alterations lead to an autosomal dominant condition known as hereditary leiomyomatosis and renal cell cancer (HLRCC) where patients are predisposed to various benign tumors and an aggressive form of kidney cancer.FHalterations of unclear significance are frequently observed with germline testing; thus, there is an unmet need to classifyFHvariants by their cancer-associated risk, allowing for screening, early diagnosis and treatment. Here we quantify catalytic efficiency of 74 FH variants of uncertain significance. Over half were enzymatically inactive which is strong evidence of pathogenicity. We generated a panel of HLRCC cell lines expressing FH variants with a range of catalytic activities, then correlated fumarate levels with metabolic features. We found that fumarate accumulation blocks purine biosynthesis, rendering FH-deficient cells reliant on purine salvage to maintain purine nucleotide pools. Genetic or pharmacologic inhibition of the purine salvage pathway reduced HLRCC tumor growthin vivo. Together, these findings suggest pathogenicity of many patient-associatedFHvariants and reveal purine salvage as a targetable vulnerability in FH-deficient tumors.

Statement of Significance

This study functionally characterizes patient-associated FH variants with unknown significance for pathogenicity. This study also reveals nucleotide salvage pathways as a targetable feature of FH-deficient cancers, which are shown to be sensitive to the purine salvage pathway inhibitor 6-mercaptopurine. This presents a new rapidly translatable treatment strategy for FH-deficient cancers.
Architectural Groups of a Subtelomeric Gene Family Evolve Along Distinct Paths in Candida albicans
Authors: Dunn Matthew J. , Simonton Emily , Slot Jason C. , Anderson Matthew Z.
Published: August 2022

Subtelomeres are dynamic genomic regions shaped by elevated rates of recombination, mutation, and gene birth/death. These processes contribute to formation of lineage-specific gene family expansions that commonly occupy subtelomeres across eukaryotes. Investigating the evolution of subtelomeric gene families is complicated by the presence of repetitive DNA and high sequence similarity among gene family members that prevents accurate assembly from whole genome sequences. Here we investigated the evolution of the telomere-associated (TLO) gene family in Candida albicans using 189 complete coding sequences retrieved from 23 genetically diverse strains across the species. TLO genes conformed to the three major structural groups (α /β /γ) previously defined in the genome reference strain but significantly differed in the degree of within-group diversity and positional conservation. One group, TLOβ, was always found at the same chromosome arm with strong sequence similarity among all strains. In contrast, diverse Tloα sequences have proliferated among chromosome arms. Tloγ genes formed seven primary clades that included each of the previously identified Tloγ genes from the genome reference strain with limited mobility among chromosome arms. Structural groups displayed regions of high conservation that resolved newly identified functional motifs, providing insight into potential regulatory mechanisms that distinguish groups. Thus, by resolving intra-species subtelomeric gene variation, it is possible to identify previously unknown gene family complexity that may underpin adaptive functional variation.
Genetic silencing of AKT induces melanoma cell death
Authors: Parkman Gennie L. , Turapov Tursun , Kircher David A. , Burnett William J. , Stehn Christopher M. , O’Toole Kayla , Flaherty Ryan , Elmer Riley C. , Culver Katie M. , Foth Mona , Andtbacka Robert H. I. , Lum David H. , Judson-Torres Robert , VanBrocklin Matthew W. , Holmen Sheri L. , McMahon Martin
Published: August 2022

Aberrant activation of the PI3K-AKT pathway is common in melanoma but efforts to drug this pathway have proven largely ineffective in patients. In this study, we observed that pharmacological inhibition of AKT was ineffective whereas genetic silencing of all three AKT paralogs significantly abrogated melanoma cell growth through effects on mTORC signaling. This phenotype could be rescued by overexpression of AKT but was dependent on kinase activity. Interestingly, expression of the serine/threonine kinase SGK1 was increased following genetic suppression of AKT but only expression of activated SGK1 could rescue the lethal effect of AKT knockdown. SGK1 also increases tumor growth and decreases survival in a BRAFV600E-driven mouse model of melanoma. Pharmacological inhibition of SGK and AKT reduced cell proliferation. These results demonstrate that SGK1 can compensate for AKT loss in this context and suggest that dual targeting of SGK1 and AKT may represent a novel therapeutic strategy in this disease.

SIGNIFICANCE

Although the AKT1, 2 & 3 genes encode: Bona fide oncoprotein kinases; well-validated downstream effectors of PI3’-lipids and: pleiotropic regulators of numerous aberrant properties of cancer cells, their role in melanoma progression and/or maintenance is poorly understood. Here we explore the effects of genetic or pharmacological inhibitors of AKT1-3 and conclude that combined inhibition of AKT plus the related SGK protein kinases may be required to inhibit melanomagenesis.
A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds
Authors: Li Leiting , Song Jingjing , Zhang Meiling , Iqbal Shahid , Li Yuanyuan , Zhang Heng , Zhang Hui
Published: August 2022

Chia is an annual crop whose seeds have the highest content of α-linolenic acid (ALA) of any plant species. We generated a high-quality assembly of the chia genome using circular consensus sequencing of PacBio. The assembled six chromosomes are composed of 21 contigs and have a total length of 361.7 Mb. Genome annotation revealed a 53.5% repeat content and 35,850 protein-coding genes. Chia shared a common ancestor withSalvia splendens~6.1 million years ago. Utilizing the reference genome and two transcriptome datasets, we identified candidate fatty acid desaturases responsible for ALA biosynthesis during chia seed development. Because the seed ofS. splendenscontains significantly lower proportion of ALA but similar total contents of unsaturated fatty acids, we suggest that strong expression of twoShFAD3genes are critical for the high ALA content of chia seeds. This genome assembly will serve as a valuable resource for breeding, comparative genomics, and functional genomics studies of chia.
Cell Senescence-Independent Ageing of Human Skin
Authors: Wordsworth J. , Fullard N. , Welsh C. , Maltman V. , Bascom C. , Tasseff R. , Isfort R. , Costello L. , Scanlan R. , Przyborski S. , Shanley D.
Published: August 2022

Skin ageing is defined in part by collagen depletion and fragmentation that leads to a loss of mechanical tension. This is currently believed to reflect, in part, the accumulation of senescent cells. We compared the expression of genes and proteins for components of the extracellular matrix (ECM) as well as their regulators and found that senescent cells produced more matrix metalloproteinases (MMPs) than proliferating cells from adult and neonatal donors. This was consistent with senescent cells contributing to increased matrix degradation with age; however, cells from adult donors proved significantly less capable of producing new collagen than neonatal or senescent cells, and they showed significantly lower myofibroblast activation as determined by the marker α-SMA. Functionally, adult cells also showed slower migration than neonatal cells. We concluded that while increased collagen degradation with age might reflect senescent cell accumulation, the reduced collagen production that prevents the skin from maintaining homeostasis must reflect senescence-independent processes.
A tissue dissociation method optimized for ATAC-seq and CUT&RUN inDrosophilapupal tissues
Authors: Buchert Elli M. , Fogarty Elizabeth A. , Uyehara Christopher M. , McKay Daniel J. , Buttitta Laura A.
Published: August 2022

Chromatin accessibility, histone modifications and transcription factor binding are highly dynamic duringDrosophilametamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on manyDrosophilatissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymaticin situmethods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is optimized for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10thof the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymaticin situapproaches to interrogate gene regulatory networks duringDrosophilametamorphosis.
CRISPR-Cas9 editing induces Loss of Heterozygosity in the pathogenic yeast Candida parapsilosis
Authors: Lombardi Lisa , Bergin Sean A. , Ryan Adam , Butler Geraldine
Published: August 2022

Genetic manipulation is often used to study gene function. However, unplanned genome changes (including Single Nucleotide Polymorphisms (SNPs), aneuploidy and Loss of Heterozygosity (LOH)) can affect the phenotypic traits of the engineered strains. Here, we show that CRISPR-Cas9 editing can induce LOH in the diploid human pathogenic yeast Candida parapsilosis. We sequenced the genomes of ten isolates that were edited with CRISPR-Cas9 and found that the designed changes were present in nine. However, we also observed LOH in all isolates, and aneuploidy in two isolates. LOH occurred most commonly downstream of the Cas9 cut site and extended to the telomere in three isolates. In two isolates we observed LOH on chromosomes that were not targeted by CRISPR-Cas9. Two different isolates exhibited cysteine and methionine auxotrophy caused by LOH at a heterozygous site in MET10, approximately 11 and 157 kb downstream from the Cas9 target site, respectively. C. parapsilosis isolates have relatively low levels of heterozygosity. However, our results show that mutation complementation to confirm observed phenotypes is important even when using CRISPR-Cas9, which is now the gold standard of genetic engineering.

IMPORTANCE

CRISPR-Cas9 has greatly streamlined gene editing, and is now the gold standard and first choice for genetic engineering. However, we show that in diploid species extra care should be taken in confirming the cause of any phenotypic changes observed. We show that the Cas9-induced double strand break is often associated with loss of heterozygosity in the asexual diploid human fungal pathogen Candida parapsilosis. This can result in deleterious heterozygous variants (e.g. stop gain in one allele) becoming homozygous resulting in unplanned phenotypic changes. Our results stress the importance of mutation complementation even when using CRISPR-Cas9.
Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem
Authors: Andronis Christina E. , Jacques Silke , Lopez-Ruiz Francisco J. , Lipscombe Richard , Tan Kar-Chun
Published: August 2022

BACKGROUND

Phytopathogenic oomycetes constitute some of the most devastating plant pathogens that cause significant crop and horticultural loss. Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and a variety of crops. This pathogen can survive through harsh environmental conditions which gives it an advantage over its susceptible hosts. The only implemented chemical used to control P. cinnamomi is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it works directly on the pathogen or through the host. Additionally, resistance to phosphite is emerging in P. cinnamomi isolates and other oomycete phytopathogens.

RESULTS

The mode of action of phosphite on the pathogen and through a model host was investigated using label-free quantitative proteomics. In vitro treatment of P. cinnamomi with phosphite hinders growth by interfering with metabolism, signalling and gene expression, traits that are not observed in the tolerant isolate. When the model host L. angustifolius was treated with phosphite, enrichment of proteins that are associated with photosynthesis, carbon fixation and lipid metabolism in the host was observed. An increase in the production of a range of defence-related proteins was observed.

CONCLUSION

We hypothesise direct and indirect models of the multi-modal action of phosphite that directly targets the pathogen as well as alters plant metabolism and immune response.
Hierarchical processing underpins competition in tactile perceptual bistability
Authors: Darki Farzaneh , Ferrario Andrea , Rankin James
Published: August 2022

Ambiguous sensory information can lead to spontaneous alternations between perceptual states, recently shown to extend to tactile perception. The authors recently proposed a simplified form of tactile rivalry which evokes two competing percepts for a fixed difference in input amplitudes across antiphase, pulsatile stimulation of the left and right fingers. This study addresses the need for a tactile rivalry model that captures the dynamics of perceptual alternations and that incorporates the structure of the somatosensory system. The model features hierarchical processing with two stages; a first stage resolves perceptual competition, leading to perceptual alternations; and a second stage encodes perceptual interpretations. The first stage could be located downstream of brainstem nuclei and the second stage could be located within the primary somatosensory cortex (area 3b). The model captures dynamical features specific to the tactile rivalry percepts and produces general characteristics of perceptual rivalry: input strength dependence of dominance times (Levelt’s proposition II), short-tailed skewness of dominance time distributions and the ratio of distribution moments. The presented modelling work leads to experimentally testable predictions. The same hierarchical model could generalise to account for percept formation, competition and alternations for bistable stimuli that involve pulsatile inputs from the visual and auditory domains.

Author summary

Perceptual ambiguity involving the touch sensation has seen increased recent interest. It provides interesting opportunity to explore how our perceptual experience is resolved by dynamic computations in the brain. We recently proposed a simple form of tactile rivalry where stimuli consisted of antiphase sequences of high and low intensity pulses delivered to the right and left index fingers. The stimulus can be perceived as either one simultaneous pattern of vibration on both hands, or as a pattern of vibrations that jumps from one hand to the other, giving a sensation of apparent movement. During long presentation of the stimuli, one’s perception switches every 5–20 seconds between these two interpretations, a phenomenon called tactile perceptual bistability. This study presents the first computational model for tactile bistability and is based on the structure of sensory brain areas. The model captures important characteristics of perceptual interpretations for tactile rivalry. We offer predictions in terms of how left-right tactile intensity differences are encoded and propose a location for the encoding of perceptual interpretations in sensory brain areas. The model provides a generalisable framework that can make useful predictions for future behavioural experiments with tactile and other types of stimuli.