bluuebunny/crossref_metadata_2025 huggingface dataset:
A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes
Authors: Wilder Catera L. , Lefaudeux Diane , Mathenge Raisa , Kishimoto Kensei , Munoz Alma Zuniga , Nguyen Minh A. , Meyer Aaron S. , Cheng Quen J. , Hoffmann Alexander
Published: August 2022

Type I interferons (IFN) induce powerful anti-viral and innate immune responses via the transcription factor, IFN-stimulated gene factor (ISGF3). However, in some pathological contexts type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN-β also activates an inflammatory gene expression program in contrast to IFN-λ3, a type III IFN, which elicits only the common anti-viral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus-specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK-STAT/IRF signaling network that may produce distinct biological responses, and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it.

HIGHLIGHTS

High dose IFN-β activates a pro-inflammatory gene program in epithelial cells.

IFN-β, but not IFN-λ3, induces a second, potentiated phase in ISGF3 activity.

ISGF3 induces its subunits to form a stimulus-contingent positive feedback loop.

The positive feedback motif is required for the pro-inflammatory gene program.
DUnet: A deep learning guided protein-ligand binding pocket prediction
Authors: Wang Xinglong , Zhao Beichen , Yang Penghui , Tan Yameng , Ma Ruyi , Rao Shengqi , Du Jianhui , Chen Jian , Zhou Jingwen , Liu Song
Published: August 2022

Investigating protein-ligand binding sites is the key step in engineering protein/enzyme activity and selectivity. In this study, we developed a 3D convolutional neural network DUnet that derived from DenseNet and UNet for predicting the protein-ligand binding sites. To train DUnet, the features of protein 3D structure were extracted by describing the atomic physical characters, and the ligand binding sites were used as training labels. DUnet was trained using three dataset, the scPDB dataset (collecting of protein-ligand complexes from Protein Data Bank), scPDB and SC6K (collecting of protein-ligand complexes deposited after January 1st, 2018 from Protein Data Bank) datasets, and scPDB and its derived dataset by rotating the samples in the dataset. DUnet displayed better performance than the current state-of-art methods during the benchmark test using independent validation sets, and enlarging the training set contributed to better accuracy. We developed a small dataset contains commonly used industrial enzymes for testing DUnet and found that it was also accurate in predicting the substrate binding sites. We experimentally characterized the substrate binding sites of microbial transglutaminase according to the prediction and showed the significance of these sites. Finally, DUnet was used to predict the ligand binding sites of Swiss-Prot annotated proteins.
Proof of Concept: detection of cell free RNA from EDTA plasma in patients with lung cancer and non-cancer patients
Authors: Mullins Kristin E. , Seneviratne Chamindi , Shetty Amol C. , Jiang Feng , Christenson Robert , Stass Sanford
Published: August 2022

Nucleic acid sequencing technologies have advanced significantly in recent years, allowing the development of liquid biopsies as new means to detect cancer biomarkers and cancer heterogenicity. Most of the assays available clinically focus on cell free DNA, however, cell free RNA (cfRNA) is also present and has the potential to complement and improve cancer detection especially in cancers like lung cancer, which are usually only diagnosed at late stages and therefore have poor long-term survival outcomes. Remnant EDTA plasma was collected from lung cancer patients and non-cancer individuals at the University of Maryland Medical Center. RNA was extracted and processed for next generation sequencing with a tagmentation-based library preparation approach. cfRNA was successfully extracted and sequenced from 52 EDTA-treated plasma samples with volumes as low as 1.5 mL. This quantity was sufficient to prepare libraries with the length of libraries averaging from 264bp to 381bp and resulted in over 2.2 to 3.6 million total sequence reads respectively. Sequential dilution of cfRNA samples from healthy individuals indicated that the starting cfRNA concentration influenced the detection of differentially expressed genes. This proof-of-concept study provides a framework for screening cfRNA for identifying biomarkers for early detection of lung cancer (and other cancers), using minimal amounts of samples (1.5 ml) from standard EDTA 3-mL collection tubes routinely used for patient care. Further studies in large populations are required to establish limit of detection and other parameters including precision, accuracy, sensitivity, and specificity, to standardize this method.
Unravelling habituation for COVID-19-related information: A panel data study in Japan
Authors: Fukui Shinya
Published: August 2022

This study examines people’s habituation to COVID-19-related information over almost three years. Using publicly available data from 47 Japanese prefectures, we analyse how human mobility responded to COVID-19-related information, such as the number of COVID-19-infected cases and the declaration of a state of emergency (DSE), using an interactive effects model, which is a type of panel data regression. The results show that Japanese citizens were generally fearful and cautious in the first wave of an unknown infection; however, they gradually became habituated to similar infection information during subsequent waves. Nevertheless, the level of habituation decreased in response to different types of infections, such as new variants. By contrast, regarding the DSE, it is more plausible to consider that human mobility responds to varying requests rather than habituate them. We also find spatial spillovers of infection information on human mobility using a spatial weight matrix included in the regression model. The implementation of flexible human mobility control policies by closely monitoring human mobility can prevent excessive or insufficient mobility control requests. Such a flexible policy can efficiently suppress infection spread and prevent economic activity reduction more than necessary. These implications are useful for evidence-based policymaking during future pandemics.
Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for Hepatitis C: a single arm mechanistic pilot study
Authors: Flower Barnaby , Hung Le Manh , McCabe Leanne , Ansari M. Azim , Le Ngoc Chau , Vo Thi Thu , Vu Thi Kim Hang , Nguyen Thi Ngoc Phuong , Phuong Le Thanh , Quang Vo Minh , Trong Thuan Dang , Le Thi Thao , Bao Tran Nguyen , Kingsley Cherry , Smith David , Hoglund Richard M. , Tarning Joel , Kestelyn Evelyne , Pett Sarah L , van Doorn Rogier , van Nuil Jennifer Ilo , Turner Hugo , Thwaites Guy , Barnes Eleanor , Rahman Motiur , Walker Ann Sarah , Day Jeremy , Van Vinh Chau Nguyen , Cooke Graham S
Published: August 2022

Background

WHO has called for research into predictive factors for selecting persons who could be successfully treated with shorter durations of direct acting antiviral (DAA) therapy for Hepatitis C. We evaluated early virological response as a means of shortening treatment and explored host, viral and pharmacokinetic contributors to treatment outcome.

Methods

Duration of sofosbuvir and daclatasvir (SOF/DCV) was determined according to day 2 (D2) virologic response for HCV genotype (gt) 1- or 6-infected adults in Vietnam with mild liver disease. Participants received 4 or 8 weeks treatment according to whether D2 HCV RNA was above or below 500 IU/ml (standard duration is 12 weeks). Primary endpoint was sustained virological response (SVR12). Those failing therapy were retreated with 12 weeks SOF/DCV. Host IFNL4 genotype and viral sequencing was performed at baseline, with repeat viral sequencing if virological rebound was observed. Levels of SOF, its inactive metabolite GS-331007 and DCV were measured on day 0 and 28.

Results

Of 52 adults enrolled, 34 received 4 weeks SOF/DCV, 17 got 8 weeks and one withdrew. SVR12 was achieved in 21/34 (62%) treated for 4 weeks, and 17/17 (100%) treated for 8 weeks. Overall 38/51 (75%) were cured with first-line treatment (mean duration 37 days). Despite a high prevalence of putative NS5A-inhibitor resistance associated substitutions (RAS), all first-line treatment failures cured after retreatment (13/13). We found no evidence treatment failure was associated with host IFNL4 genotype, viral subtype, baseline RAS or DCV levels. SOF metabolite levels were higher in those failing 4-week therapy.

Conclusions

Shortened SOF/DCV therapy, with retreatment if needed, reduces DAA use while maintaining high cure rates. D2 virologic response alone does not adequately predict SVR12 with 4 weeks treatment.

Funding

Funded by the Medical Research Council (grant MR/P025064/1) and The Global Challenges Research Fund (Wellcome Trust Grant 206/296/Z/17/Z).)

Clinical trial number

ISRCTN17100273
The role of vaccination and public awareness in medium-term forecasts of monkeypox incidence in the United Kingdom
Authors: Brand SPC , Cavallaro M , Hilton J , Guzman-Rincon LM , House T , Keeling MJ , Nokes DJ
Published: August 2022

Monkeypox virus (MPXV) is spreading rapidly through close human-to-human contact primarily amongst communities of men-who-have-sex-with-men (MSM). Behavioural change arising from increased knowledge and health warnings may decelerate the rate of transmission and Vaccinia-based vaccination is likely to be an effective longer-term intervention. Here we investigate the current epidemic within the UK population and simulate control options over a 12 week projection using a stochastic discrete-population transmission model which includes MSM status, rate of formation of new sexual partners, and an underlying random sized metapopulation structure. We find that the virus may have already infected a significant proportion of the MSM group with the highest sexual activity (32.5%; 15.9% - 44.9% prediction IQR); the associated immunity, albeit among groups that form a small but sexually active part of the MSM community in the UK, coupled to behavioural driven decrease in the transmission rate of individuals infected with monkeypox, leads to case incidence flattening and then declining over the projection period (12 weeks). Vaccination is most beneficial when targeted to MSM with highest activity if delivered in the near term to further interrupt transmission amongst those driving the epidemic.
Cannabis, identity, and attitudes: a qualitative study in adolescents who do and do not use cannabis
Authors: Karashiali Christiana , Lawn Will , Petrilli Kat , Mokrysz Claire , Black Georgia
Published: August 2022

Background and objective

Cannabis use during adolescence is common. Cannabis use and identity are thought to influence one another. This study aimed to examine what London-based adolescents (aged 16-17 years) think about cannabis use, its relationships with identity, and its benefits and harms.

Method

Three semi-structured focus groups interviews were conducted, two with adolescents who use cannabis (n=3 and n=5) and one with adolescents who do not use cannabis (n=6). Participants also completed a drug-use questionnaire.

Results

Thematic analysis (TA) revealed four identities. Two identities emerged from both groups: ‘The person who uses cannabis is chilled’ and ‘The person who uses cannabis is sometimes ostracised’. Two identities emerged from the group of adolescents who used cannabis: ‘The person who uses cannabis is an expert in risky things’ and ‘The person who uses cannabis is not addicted’. Skunk was identified as potentially more harmful than hash, but more powerful and pleasurable.

Conclusion

The findings provide insight into how cannabis use shape personal and social identity amongst teenagers in London in the late 2010s. Those who use cannabis described the benefits of cannabis, including socialising and for relaxation, and emphasised they are not addicted. Stigmatising and devaluing attitudes were held by some non-users about adolescents who use cannabis. Stereotypes seem to still exist, despite cannabis normalisation. Implications for research and policy are outlined.
Comparison of Structural Diagnosis and Management (SDM) approach and Myofascial Release (MFR) for improving planter heel pain, ankle range of motion and disability: A Randomized Clinical Trial
Authors: Akter Sapia , Hossain Mohammad Shahadat , Hossain K M Amran , Uddin Zakir , Hossain Mohammad Anwar , Alom Foisal , Kabir Md. Feroz , Walton Lori Maria , Raigangar Veena
Published: August 2022

Purpose

This study compared the effect of Structural Diagnosis and Management (SDM) approach over Myofascial Release (MFR) on gastrocnemii, soleus and plantar fascia in patients with plantar heel pain.

Subjects

Sixty-four (n=64) subjects, aged 30-60 years, with a diagnosis of plantar heel pain, plantar fasciitis or calcaneal spur by a physician and according to ICD-10. Participants were equally allocated to MFR (n=32) and SDM (n=32) group by hospital randomization and concealed allocation.

Methods

In this assessor blinded randomized clinical trial, the control group performed MFR (three tissue specific stretching techniques) and the experimental group performed 2 tissue-specific interventions utilizing the Structural Diagnosis and Management (SDM) concept for 12 sessions over a 4-week period. In addition, both groups received strengthening exercises and other conventional treatments. Pain, activity limitations and disability were assessed as primary outcomes utilizing the foot function index (FFI) and range of motion (ROM) of the ankle dorsiflexors and plantar flexors were measured with a universal goniometer. Secondary outcomes were measured using the Foot Ankle Disability Index (FADI) and 10-point manual muscle testing process for the ankle dorsiflexors and plantar flexors.

Result

Both MFR and SDM groups exhibited significant improvements from baseline in all outcome variables, including: pain, activity level, disability, range of motion and function after the 12-week intervention period (p<.05), The SDM group showed more significant improvements than MFR for FFI pain (p=.001), FFI activity (p=.009), FFI (p= .001) and FADI (p=.002).

Conclusion

MFR and SDM approaches are both effective to reduce pain, improving function, ankle range of motion, and reduce disability in plantar heel pain. However, the SDM approach is significantly superior (for reducing pain, improving function and reducing disability (p<.05).
Revealing geographic transmission pattern of COVID-19 using neighborhood-level simulation with human mobility data and SEIR model: A Case Study of South Carolina
Authors: Ning Huan , Li Zhenlong , Qiao Shan , Zeng Chengbo , Zhang Jiajia , Olatosi Bankole , Li Xiaoming
Published: August 2022

Direct human physical contact accelerates COVID-19 transmission. Smartphone mobility data has been an emerging data source to reveal fine-grained human mobility, which can be used to estimate the intensity of physical contact surrounding different locations. Our study applied smartphone mobility data to simulate the second wave spreading of COVID-19 in January 2021 in three major metropolitan statistical areas (Columbia, Greenville, and Charleston) in South Carolina, United States. Based on the simulation, the number of historical county-level COVID-19 cases was allocated to neighborhoods (Census blockgroups) and points of interest (POIs), and the transmission rate of each allocated place was estimated. The result reveals that the COVID-19 infections during the study period mainly occurred in neighborhoods (86%), and the number is approximately proportional to the neighborhood’s population. Restaurants and elementary and secondary schools contributed more COVID-19 infections than other POI categories. The simulation results for the coastal tourism Charleston area show high transmission rates in POIs related to travel and leisure activities. The results suggest that the neighborhood-level infectious controlling measures are critical in reducing COVID-19 infections. We also found that the households of lower socioeconomic status may be an umbrella against infection due to fewer visits to places such as malls and restaurants associated with their low financial status. Control measures should be tailored to different geographic locations since transmission rates and infection counts of POI categories vary among metropolitan areas.
BaySyn: Bayesian Evidence Synthesis for Multi-system Multiomic Integration
Authors: Bhattacharyya Rupam , Henderson Nicholas , Baladandayuthapani Veerabhadran
Published: August 2022

The discovery of cancer drivers and drug targets are often limited to the biological systems - from cancer model systems to patients. While multiomic patient databases have sparse drug response data, cancer model systems databases, despite covering a broad range of pharmacogenomic platforms, provide lower lineage-specific sample sizes, resulting in reduced statistical power to detect both functional driver genes and their associations with drug sensitivity profiles. Hence, integrating evidence across model systems, taking into account the pros and cons of each system, in addition to multiomic integration, can more efficiently deconvolve cellular mechanisms of cancer as well as learn therapeutic associations. To this end, we proposeBaySyn- a hierarchicalBayesian evidencesynthesis framework for multi-system multiomic integration. BaySyn detects functionally relevant driver genes based on their associations with upstream regulators using additive Gaussian process models and uses this evidence to calibrate Bayesian variable selection models in the (drug) outcome layer. We apply BaySyn to multiomic cancer cell line and patient datasets from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas, respectively, across pan-gynecological cancers. Our mechanistic models implicate several relevant functional genes across cancers such as PTPN6 and ERBB2 in the KEGG adherens junction gene set. Furthermore, our outcome model is able to make higher number of discoveries in drug response models than its uncalibrated counterparts under the same thresholds of Type I error control, including detection of known lineage-specific biomarker associations such as BCL11A in breast and FGFRL1 in ovarian cancers. All our results and implementation codes are freely available via aninteractive R Shiny dashboard.
Epidemiology of leprosy identified through active case detection in six districts of Nepal
Authors: Mahato Ram Kumar , Ghimire Uttam , Lamsal Madhav , Bajracharya Bijay , Poudel Mukesh , Naapit Prashanna , Lama Krishna , Dahal Gokarna , Hayman David TS , Karna Ajit Kumar , Pandey Basudev , Das Chuman Lal , Paudel Krishna Prasad
Published: August 2022

Background

Nepal has achieved and sustained elimination of leprosy as a public health problem since 2009, but 17 districts and 3 provinces have yet to eliminate the disease. Pediatric cases and grade-2 disabilities (G2D) indicate recent transmission and late diagnosis respectively, which necessitate active and early case detection. This operational research was performed to identify approaches best suited for early case detection, determine community-based leprosy epidemiology, and identify hidden leprosy cases early and respond with prompt treatment.

Methods

Active case detection was performed by: house-to-house visits among vulnerable populations (n=26,469), contact examination and tracing (n=7,608) and screening prison populations (n=4,428) in Siraha, Bardiya, Rautahat, Banke, Lalitpur and Kathmandu districts of Nepal.

Results

New case detection rates were highest for contact tracing (250), followed by house-to-house visits (102) and prison screening (45) per 100,000 population screened. However, cost per case identified was cheapest for house-to-house visits (Nepalese rupee (NPR) 76,500/case), then contact tracing (NPR90,286/case) and prison screening (NPR298,300/case). House-to-house and contact tracing case paucibacillary/multibacillary (PB:MB) ratios were 59:41 and 68:32; female/male ratios 63:37 and 57:43; pediatric cases 11% in both approaches; and G2D 11% and 5% respectively. Developing leprosy was similar among household and neighbor contacts (Odds ratios (OR)=1.4, 95% confidence interval (CI), 0.24-5.85) and for contacts of MB versus PB cases (OR=0.7, 0.26-2.0). Attack rates were similar among household contacts of MB cases (0.32%, 0.07-0.94%) and PB cases (0.13%, 0.03-0.73) and neighbor contacts of MB cases (0.23%, 0.1-0.46) and PB cases (0.48%, 0.19-0.98). BCG vaccination with scar presence had a significant protective effect against leprosy (OR=0.42, 0.22-0.81).

Conclusions

The most effective case identification approach here is contact tracing, followed by house-to-house visits in vulnerable populations and screening in prisons, though house-to-house visits were cheaper. The findings suggest hidden cases, recent transmission, and late diagnosis in the community exist and highlight the importance of early case detection.
Antigen Specific T Cells in People with Obesity at Five Months Following ChAdOx1 COVID-19 Vaccination
Authors: Wrigley Kelly Neil E. , De Barra Conor , Shaamile Ferrah , Holland Aisling , Shaw Liam , Mallon Patrick W.G. , O’Connell Jean , Hogan Andrew E. , O’Shea Donal
Published: August 2022

Background/Objectives

People with obesity (PWO) face an increased risk of severe outcomes from COVID-19, including hospitalisation, ICU admission and death. Obesity has been seen to impair immune memory following vaccination against influenza, hepatitis B, tetanus, and rabies. Little is known regarding immune memory in PWO following COVID-19 adenovirus vector vaccination.

Subjects/Methods

We investigated SARS-CoV-2 specific T cell responses in 50 subjects, five months following a two-dose primary course of ChAdOx1 nCoV-19 (AZD1222) vaccination. We further divided our cohort into PWO (n=30) and matched controls (n=20). T cell (CD4+, CD8+) cytokine responses (IFNγ, TNFα) to SARS-CoV-2 spike peptide pools were determined using multicolour flow cytometry.

Results

Circulating T cells specific for SARS-CoV-2 were readily detected across our cohort, with robust responses to spike peptide stimulation across both T cell lines. PWO and controls had comparable levels of both CD4+and CD8+SARS-CoV-2 spike specific T cells. Polyfunctional T cells – associated with enhanced protection against viral infection – were detected at similar frequencies in both PWO and controls.

Conclusions

These data indicate that PWO who have completed a primary course of ChAdOx1 COVID-19 vaccination have robust, durable, and functional antigen specific T cell immunity that is comparable to that seen in people without obesity.
Significant increase of emergency department visits for heat-related emergency conditions in the United States from 2008 – 2019: a comprehensive nationwide study
Authors: Dring Penelope , Armstrong Megan , Alexander Robin , Xiang Henry
Published: August 2022

Introduction

Exposure to high temperatures is detrimental to human health. As climate change is expected to increase the frequency of extreme heat events, as well as raise ambient temperatures, an investigation into the burden of heat-related emergency department visits is necessary to assess the human health impact of this growing public health crisis.

Methods

Emergency department visits were sourced from the Healthcare Cost and Utilization Project Nationwide Emergency Department Sample. This dataset collects emergency department visit information from 989 facilities that represent a 20-percent stratified sample of United States hospital-owned emergency departments. Visits were included in this study if the medical diagnosis contained an ICD-9-CM or ICD-10-CM code specific to heat-related emergency conditions. Weighted heat-related emergency department visit counts were generated to estimate the total counts for heat-related emergency department visits across the United States. Visit year and month, hospital geographic region, patient age, and sex were recorded. Incidence rates per 100,000 US population, visit counts, and visit count percent change were analyzed on both a national scale and stratified by month, region, age, and sex.

Results

A total of 1,007,134 weighted heat-related emergency department visits between 2008 - 2019 were included in this study. The annual incidence rate per 100,000 US population increased by an average of 5.73% (95% CI: 8.64% – 20.1%) per year across the study period, rising from 20.56 in 2008 to 30.41 in 2019. For the twelve-year period, the burden of heat-related emergency department visits was greatest in the South (51.41%). Most cases occurred in July (29.56%), with visits increasing to the greatest degree in July (19.25%, 95% CI: 20.75% – 59.26%) and March (14.36%, 95% CI: 19.53% – 48.25%).

Conclusions

This study found a significant increase in emergency department visits for heat-related emergency conditions across the United States from the years 2008 to 2019.
Mitochondria morphology governs ATP production rate
Authors: Garcia Guadalupe C. , Gupta Kavya , Bartol Thomas M. , Sejnowski Terrence J. , Rangamani Padmini
Published: August 2022

Abstract

Life is based on energy conversion. In particular, in the nervous system significant amounts of energy are needed to maintain synaptic transmission and homeostasis. To a large extent, neurons depend on oxidative phosphorylation in mitochondria to meet their high energy demand (Pekkurnaz and Wang, 2022). For a comprehensive understanding of the metabolic demands in neuronal signaling, accurate models of ATP production in mitochondria are required. Here, we present a thermodynamically consistent model of ATP production in mitochondria based on previous work (Pietrobon and Caplan, 1985; Magnus and Keizer, 1997; Metelkin et al., 2006; Garcia et al., 2019). The significant improvement of the model is that the reaction rate constants are set such that detailed balance is satisfied. Moreover, using thermodynamic considerations, the dependence of the reaction rate constants on membrane potential, pH, and substrate concentrations are explicitly provided. These constraints assure the model is physically plausible. Furthermore, we explore different parameter regimes to understand in which conditions ATP production or its export are the limiting steps in making ATP available in the cytosol. The outcomes reveal that, under the conditions used in our simulations, ATP production is the limiting step and not its export. Finally, we performed spatial simulations with nine 3D realistic mitochondrial reconstructions and linked the ATP production rate in the cytosol with morphological features of the organelles.

1.

Summary

In this work, Garcia et al present a thermodynamically consistent model for ATP production in mitochondria, in which reaction rate constants are set such that detailed balance is satisfied. Simulations revealed that ATP production, but not its export, is the limiting step, and simulations with 3D mitochondrial reconstructions linked the ATP production rate in the cytosol with the morphological features of the organelles.
Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain
Authors: Tanaka Ryokei , Wu Di , Li Xiaowei , Tibbs-Cortes Laura E. , Wood Joshua C. , Magallanes-Lundback Maria , Bornowski Nolan , Hamilton John P. , Vaillancourt Brieanne , Li Xianran , Deason Nicholas T. , Schoenbaum Gregory R. , Buell C. Robin , DellaPenna Dean , Yu Jianming , Gore Michael A.
Published: August 2022

With an essential role in human health, tocochromanols are mostly obtained by consuming seed oils; however, the vitamin E content of the most abundant tocochromanols in maize grain is low. Several large-effect genes withcis-acting variants affecting mRNA expression are mostly responsible for tocochromanol variation in maize grain, with other relevant associated quantitative trait loci (QTL) yet to be fully resolved. Leveraging existing genomic and transcriptomic information for maize inbreds could improve prediction when selecting for higher vitamin E content. Here, we first evaluated a multikernel genomic best linear unbiased prediction (MK-GBLUP) approach for modeling known QTL in the prediction of nine tocochromanol grain phenotypes (12–21 QTL per trait) within and between two panels of 1,462 and 242 maize inbred lines. On average, MK-GBLUP models improved predictive abilities by 7.0 to 13.6% when compared to GBLUP. In a second approach with a subset of 545 lines from the larger panel, the highest average improvement in predictive ability relative to GBLUP was achieved with a multi-trait GBLUP model (15.4%) that had a tocochromanol phenotype and transcript abundances in developing grain for a few large-effect candidate causal genes (1–3 genes per trait) as multiple response variables. Taken together, our study illustrates the enhancement of prediction models when informed by existing biological knowledge pertaining to QTL and candidate causal genes.

Core Ideas

With varying levels of vitamin E activity, tocochromanols found in maize grain are essential for human health

Selecting for higher vitamin E content in maize grain can be enhanced with genomic prediction

Prediction models leveraging existing biological knowledge were evaluated in two panels of maize inbred lines

Multikernel prediction models based on previously identified QTL improved predictive ability

A multi-trait prediction model that had transcript abundances of a few large-effect causal genes performed the best
Cryo-electron tomography and deep learning denoising reveal native chromatin landscapes of interphase nuclei
Authors: Fatmaoui Fadwa , Carrivain Pascal , Grewe Diana , Jakob Burkhard , Victor Jean-Marc , Leforestier Amélie , Eltsov Mikhail
Published: August 2022

The folding of nucleosome chains influences DNA availability for functional interactions necessary to the regulation of transcription, DNA replication and repair. Despite models based on in vitro studies, the nucleosome chain geometry within the crowded cell nucleus remains elusive. Using cryo-electron tomography and deep learning-based denoising, we directly observed the path of nucleosomal and linker DNA in situ in unstained flash-frozen Drosophila embryos. We quantified linker length and curvature characterizing a disordered zig-zag chromatin folding motif, with a low degree of linker bending. Additionally, nucleosome conformational variability with non-canonical structures and sub-nucleosomal particles were seen as individual objects, without structure averaging, highlighting the high structural heterogeneity of native chromatin.

One-Sentence Summary

Cryo-ET reveals local zig-zag motifs in interphase chromatin, a range of nucleosome conformations, and sub-nucleosomal particles.
The RSK-RPS6 Axis Controls the Preconditioning Effect and Induces Spinal Cord Regeneration
Authors: Decourt Charlotte , Schaeffer Julia , Blot Beatrice , Paccard Antoine , Excoffier Blandine , Pende Mario , Nawabi Homaira , Belin Stephane
Published: August 2022

Unlike immature neurons and neurons from the peripheral nervous system (PNS), mature neurons from the central nervous system (CNS) cannot regenerate after injury. In the past 15 years, huge progress has been made to identify molecules and pathways necessary for neuroprotection and/or regeneration after CNS injury. In most regenerative models, phosphorylated ribosomal protein S6 (p-RPS6) is upregulated in neurons, which is often associated with an activation of the mTOR pathway. However, the exact contribution of post-translational modifications of this ribosomal protein in CNS regeneration remains elusive. In this study, we demonstrate that RPS6 phosphorylation is essential for PNS and CNS regeneration. We show that this phosphorylation is induced during the preconditioning effect in dorsal root ganglion (DRG) neurons, and that it is controlled by the p90S6 kinase RSK2. Our results reveal that RSK2 controls the preconditioning effect and that the RSK2-RPS6 axis is key for this process, as well as for PNS regeneration. Finally, we demonstrate that RSK2 promotes CNS regeneration in the dorsal column and allows functional recovery. Our data establish the critical role of RPS6 phosphorylation controlled by RSK2 in CNS regeneration and give new insights into the mechanism related to axon growth and circuit formation after traumatic lesion.
Reduced wound healing and angiogenesis in aged zebrafish and turquoise killifish
Authors: Örling Johanna , Kosonen Katri , Villman Jenna , Reichard Martin , Paatero Ilkka
Published: August 2022

Impaired wound healing is associated with aging and has significant effects on human health on an individual level, but also the whole health care sector. Deficient angiogenesis appears to be involved in the process, but the underlying biology is still poorly understood. This is at least partially being explained by complexity and costs in using mammalian aging models.

To understand aging-related vascular biology of impaired wound healing, we have utilized zebrafish and turquoise killifish fin regeneration models. The regeneration of caudal fin after resection was significantly reduced in old individuals in both species. Age-related changes in angiogenesis, vascular density and expression levels of angiogenesis biomarker VEGF-A were observed. Furthermore, anti-angiogenic drug, vascular endothelial growth factor receptor blocking inhibitor SU5416 reduced regeneration indicating a key role for angiogenesis in the regeneration of aging caudal fin despite aging-related changes in vasculature.

Taken together, our data indicates that these fish models are suitable for studying aging-related decline in wound healing and associated alterations in aging vasculature.
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress
Authors: Do Brian T. , Hsu Peggy P. , Vermeulen Sidney Y. , Wang Zhishan , Hirz Taghreed , Abbott Keene L. , Aziz Najihah , Replogle Joseph M. , Bjelosevic Stefan , Paolino Jonathan , Nelson Samantha , Block Samuel , Darnell Alicia M. , Ferreira Raphael , Zhang Hanyu , Milosevic Jelena , Schmidt Daniel R. , Chidley Christopher , Harris Isaac S. , Weissman Jonathan S. , Pikman Yana , Stegmaier Kimberly , Cheloufi Sihem , Su Xiaofeng A. , Sykes David B. , Vander Heiden Matthew G.
Published: August 2022

Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that modulating aspects of metabolism could alter cell state along differentiation trajectories. Here we find that nucleotide depletion and DNA replication stress are common drivers of cell state progression across a variety of normal and transformed hematopoietic systems. DNA replication stress-induced cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress leads to increased activity at primed regulatory loci and expression of lineage-appropriate maturation genes while progenitor TF activity is still present. Altering the baseline cell state by manipulating the cohort of transcription factors expressed redirects the effect of replication stress towards induction of a different set of lineage-specific genes. The ability of replication stress to selectively activate primed maturation programs across different cellular contexts suggests a general mechanism by which metabolism can promote lineage-appropriate and potentially therapeutically relevant cell state transitions.
Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma
Authors: Gopal Raj K. , Vantaku Venkata R. , Panda Apekshya , Reimer Bryn , Rath Sneha , To Tsz-Leung , Fisch Adam S. , Cetinbas Murat , Livneh Maia , Calcaterra Michael J. , Gigliotti Benjamin J. , Pierce Kerry , Clish Clary B. , Dias-Santagata Dora , Sadow Peter M. , Wirth Lori J. , Daniels Gilbert H. , Sadreyev Ruslan I. , Calvo Sarah E. , Parangi Sareh , Mootha Vamsi K.
Published: August 2022

Oncocytic (Hürthle cell) carcinoma of the thyroid (HCC) is genetically characterized by complex I mitochondrial DNA mutations and widespread chromosomal losses. Here, we utilize RNA-seq and metabolomics to identify candidate molecular effectors activated by these genetic drivers. We find glutathione biosynthesis, amino acid metabolism, mitochondrial unfolded protein response, and lipid peroxide scavenging, a safeguard against ferroptosis, to be increased in HCC. A CRISPR-Cas9 knockout screen in a new HCC model reveals which pathways are key for fitness, and highlights loss of GPX4, a defense against ferroptosis, as a strong liability. Rescuing complex I redox activity with the yeast NADH dehydrogenase (NDI1) in HCC cells diminishes ferroptosis sensitivity, while inhibiting complex I in normal thyroid cells augments ferroptosis induction. Our work demonstrates unmitigated lipid peroxide stress to be an HCC vulnerability that is mechanistically coupled to the genetic loss of mitochondrial complex I activity.

Significance

Oncocytic (Hürthle cell) carcinoma of the thyroid (HCC) is a unique tumor with a remarkable accumulation of mitochondria. HCC harbors unique genetic alterations, including mitochondrial DNA (mtDNA) mutations in complex I genes and widespread loss-of-heterozygosity in the nuclear DNA. With less favorable clinical outcomes, new therapies for HCC are needed, especially since these tumors show intrinsic resistance to radioactive iodine, which is one of the main treatments for metastatic well-differentiated thyroid cancer. An absence of authentic HCC cell lines and animal models has hindered the mechanistic understanding of this disease and slowed therapeutic progress. In this study, we describe the transcriptomic and metabolomic landscape of HCC and present new HCC models that recapitulate key mtDNA and nuclear DNA alterations. A targeted CRISPR-Cas9 knockout screen in an HCC cell line highlights the molecular programs nominated by our -omics profiling that are required for cell fitness. This screen suggests that lipid peroxide scavenging, a defense system against an iron-dependent form of cell death known as ferroptosis, is a vulnerability in HCC that is coupled to complex I loss, and that targeting this pathway may help patients with HCC.
MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data
Authors: Wang Zichen , Natekar Parth , Tea Challana , Tamir Sharon , Hakozaki Hiroyuki , Schöneberg Johannes
Published: August 2022

Mitochondria form a network in the cell that rapidly changes through fission, fusion, and motility. This four-dimensional (4D, x,y,z,time) temporal network has only recently been made accessible through advanced imaging methods such as lattice light-sheet microscopy. Quantitative analysis tools for the resulting datasets however have been lacking. Here we present MitoTNT, the first-in-class software forMitochondrialTemporalNetworkTracking in 4D live-cell fluorescence microscopy data. MitoTNT uses spatial proximity and network topology to compute an optimal tracking. Tracking is >90% accurate in dynamic spatial mitochondria simulations and are in agreement with published motility results in vitro. Using MitoTNT, we reveal correlated mitochondrial movement patterns, local fission and fusion fingerprints, asymmetric fission and fusion dynamics, cross-network transport patterns, and network-level responses to pharmacological manipulations. MitoTNT is implemented in python with a JupyterLab interface. The extendable and user-friendly design aims at making temporal network tracking accessible to the wider mitochondria community.
Genome size variation and evolution during invasive range expansion in an introduced plant
Authors: Cang F. Alice , Welles Shana R. , Wong Jenny , Ziaee Maia , Dlugosch Katrina M.
Published: August 2022

Plants demonstrate some of the greatest variation in genome size among eukaryotes, and their genome sizes can vary dramatically across individuals and populations within species. This genetic variation can have consequences for traits and fitness, but few studies have been able to attribute genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle,Centaurea solstitialis, in California, USA. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for ‘colonizer’ traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations.
A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer
Authors: Bar Dror , Fishman Lior , Zheng Yueyuan , Unterman Irene , Schlesinger Devorah , Eden Amir , Lin De-Chen , Berman Benjamin P.
Published: August 2022

Global loss of DNA methylation in mammalian genomes occurs during aging and cancer, primarily in heterochromatin-associated Partially Methylated Domains (PMDs). It has previously been shown that local sequence context (100bp) has a strong influence on the rate of demethylation of individual CpG dinucleotides within PMDs. Here, we train a deep learning model to capture this sequence dependence, finding that methylation loss in healthy tissues and cancer can be predicted with high accuracy based on the 150bp surrounding a CpG. We use a published whole-genome map of the re-methylation rate of newly synthesized DNA during mitosis to show that CpGs with a “slow-loss” sequence context are efficiently re-methylated, while CpGs with a “fast-loss” sequence context are inefficiently re-methylated. Intriguingly, we find that the 10% most slow-loss CpGs lose almost no DNA methylation in healthy cell types, but lose significant DNA methylation in many cancer types. This finding suggests that loss of DNA methylation at slow-loss CpGs could underlie some cancer-specific transcriptional deregulation that has been linked to DNA hypomethylation, including the derepression of cancer antigens and transposable elements.
Posteromedial cortical networks encode visuomotor prediction errors.
Authors: Takeuchi Ryosuke F. , Sato Akinori Y. , Ito Kei N. , Yokoyama Hiroshi , Miyata Reiji , Ueda Rumina , Kitajima Konosuke , Kamaguchi Riki , Suzuki Toshiaki , Isobe Keisuke , Honda Naoki , Osakada Fumitaka
Published: August 2022

Predicting future events based on internal models is essential for animal survival. Predictive coding postulates that errors between prediction and observation in lower-order areas update predictions in higher-order areas through the hierarchy. However, it is unclear how predictive coding is implemented in the hierarchy of the brain. Herein, we report the neural mechanism of the hierarchical processing and transmission of bottom-up prediction error signals in the mouse cortex. Ca2+ imaging and electrophysiological recording in virtual reality revealed responses to visuomotor mismatches in the retrosplenial, dorsal visual, and anterior cingulate cortex. These mismatch responses were attenuated when mismatches became predictable through experience. Optogenetic inhibition of bottom-up signals reduced a behavioral indicator for prediction errors. Moreover, cellular-level mismatch responses were modeled by Bayesian inference using a state-space model. This study demonstrates hierarchical circuit organization underlying prediction error propagation, advancing the understanding of predictive coding in sensory perception and learning in the brain.
Stimulation of platelet P2Y1 receptors by different endogenous nucleotides leads to functional selectivity via biased signalling
Authors: Arkless Kate L , Pan Dingxin , Shankar-Hari Manu , Amison Richard T. , Page Clive P. , Rahman Khondaker Miraz , Pitchford Simon C.
Published: August 2022

Background and Purpose

Platelet function during inflammation is dependent on activation by endogenous nucleotides. Non-canonical signalling via the P2Y1 receptor is important for these non-thrombotic functions of platelets. However, apart from ADP, the role of other endogenous nucleotides acting as agonists at P2Y1 receptors is unknown. This study compared the effects of ADP, Ap3A, NAD+, ADP-ribose, and Up4A on platelet functions contributing to inflammation or haemostasis.

Experimental Approach

Platelets obtained from healthy human volunteers were incubated with ADP, Ap3A, NAD+, ADP-ribose or Up4A, with aggregation and fibrinogen binding measured (examples of function during haemostasis) or before exposure to fMLP to measure platelet chemotaxis (an inflammatory function). In silico molecular docking of these nucleotides to the binding pocket of P2Y1 receptors was then assessed.

Key Results

Platelet aggregation and binding to fibrinogen induced by ADP was not mimicked by NAD+, ADP-ribose, and Up4A. However, these endogenous nucleotides induced P2Y1-dependent platelet chemotaxis, an effect that required RhoA and Rac-1 activity, but not canonical PLC activity. Analysis of molecular docking of the P2Y1 receptor revealed distinct differences of amino acid interactions and depth of fit within the binding pocket by Ap3A, NAD+, ADP-ribose or Up4A compared to ADP.

Conclusion and Implications

Platelet function (aggregation vs motility) can be differentially modulated by biased-agonist activation of P2Y1 receptors. This may be due to the character of the ligand-binding pocket interaction. This has implications for future therapeutic strategies aimed to suppress platelet activation during inflammation without affecting haemostasis as is the requirement of current ant-platelet drugs.