bluuebunny/crossref_metadata_2025 huggingface dataset:
Aminoflavone upregulates putative tumor suppressor miR-125b-2-3p to inhibit luminal A breast cancer stem cell-like properties
Authors: Mavingire Nicole , Campbell Petreena , Liu Tiantian , Wooten Jonathan , Khan Salma , Chen Xin , Matthews Jason , Wang Charles , Brantley Eileen
Published: March 2022

Metastatic breast cancer is incurable and often due to breast cancer stem cell (CSC)-mediated self-renewal. We previously determined that aryl hydrocarbon receptor (AhR) agonist aminoflavone (AF) inhibits the expression of CSC biomarker α6-integrin (ITGA6) to disrupt the formation of luminal (hormone receptor-positive) mammospheres (3D breast cancer spheroids). In this study, we performed miRNA-sequencing analysis of luminal A MCF-7 mammospheres treated with AF to gain further insight into the mechanism of AF-mediated anti-cancer and anti-breast CSC activity. AF significantly induced the expression of over 70 miRNAs including miR125b-2-3p, a predicted stemness gene regulator. AF-mediated miR125b-2-3p induction was validated in MCF-7 mammospheres and cells. miR125b-2-3p levels were low in breast cancer tissues irrespective of subtype compared to normal breast tissues. While miR125b-2-3p levels were low in MCF-7 cells, they were much lower in AHR100 cells (MCF-7 cells made unresponsive to AhR agonists). The miR125b-2-3p mimic decreased, while the antagomiR125b-2-3p increased the expression of stemness genes ITGA6 and SOX2 in MCF-7 cells. In MCF-7 mammospheres, the miR125b-2-3p mimic decreased only ITGA6 expression though the antagomiR125b-2-3p increased ITGA6, SOX2 and MYC expression. AntagomiR125b-2-3p reversed AF-mediated suppression of ITGA6. The miR125b-2-3p mimic decreased proliferation, migration, and mammosphere formation while the antagomiR125b-2-3p increased proliferation and mammosphere formation in MCF-7 cells. The miR125b-2-3p mimic also inhibited proliferation, mammosphere formation, and migration in AHR100 cells. AF induced AhR- and miR125b2-3p-dependent anti-proliferation, anti-migration, and mammosphere disruption in MCF-7 cells. Our findings suggest miR125b-2-3p is a tumor suppressor and AF upregulates miR125b-2-3p to disrupt mammospheres via mechanisms that rely at least partially on AhR in luminal A breast cancer cells.
Social mobility and biological aging among older adults in the United States
Authors: Graf Gloria Huei-Jong , Zhang Yalu , Domingue Benjamin W , Harris Kathleen Mullan , Kothari Meeraj , Kwon Dayoon , Muennig Peter , Belsky Daniel W
Published: March 2022

Lower socioeconomic status is associated with faster biological aging, the gradual and progressive decline in system integrity that accumulates with advancing age. Efforts to promote upward social mobility may, therefore, extend healthy lifespan. However, recent studies suggest that upward mobility may also have biological costs related to the stresses of crossing social boundaries. We tested associations of life-course social mobility with biological aging using data from participants in the 2016 Health and Retirement Study (HRS) Venous Blood Study who provided blood-chemistry (n = 9,255) and/or DNA methylation (DNAm) data (n = 3,976). We quantified social mobility from childhood to later-life using data on childhood family characteristics, educational attainment, and wealth accumulation. We quantified biological aging using 3 DNAm “clocks” and 3 blood-chemistry algorithms. We observed substantial social mobility among study participants. Those who achieved upward mobility exhibited less-advanced and slower biological aging. Associations of upward mobility with less-advanced and slower aging were consistent for blood-chemistry and DNAm measures of biological aging, and were similar for men and women and for Black and White Americans (Pearson-r effect-sizes ∼0.2 for blood-chemistry measures and the DNAm GrimAge clock and DunedinPoAm pace-of-aging measures; effect-sizes were smaller for the DNAm PhenoAge clock). Analysis restricted to educational mobility suggested differential effects by racial identity; mediating links between educational mobility and healthy aging may be disrupted by structural racism. In contrast, mobility producing accumulation of wealth appeared to benefit White and Black Americans equally, suggesting economic intervention to reduce wealth inequality may have potential to heal disparities in healthy aging.
TBD (OWEN HOLLAND) LTD v SIMONS
Authors:   Court of Appeal
Published: March 2022

H1 Copyright — Designs — Breach of confidence — Ex-employees — Baggage carts — Preservation of evidence — Search orders — Imaging orders — Review of imaged documents — Use of imaged documents — Appropriate safeguards — Interpretation of search orders — Committal proceedings — Applications for permission to commit — Litigation privilege — Common interest privilege — Waiver — Iniquity exception — Security for costs — Appeal to Court of Appeal
The phenomenon of the gender gap among gifted students: the situation in Italy based on analysis of results in mathematics competitions
Authors: Mazza Lorenzo , Gambini Alessandro
Published: March 2022

This paper deals with the gender gap phenomenon as displayed by Italian students participating in mathematical competitions—gifted students. In particular, the results obtained by the entire student population participating in district competitions from 2017 to 2020 were analysed. The combined analysis of the competition results and of the final questionnaire allowed us to highlight and deepen possible causes of the gender gap. It has been observed that girls underestimate themselves, sometimes giving up participating in competitions. Particularly, during the upper secondary school years, increasingly fewer girls choose to attend mathematical competitions. Analysing the results, although the percentage of correct answers between the two genders is fairly similar, the rate of girls who prefer not to answer to avoid mistakes is higher than that of boys.
A Model of Human Small Airway on a Chip for Studies of Subacute Effects of Inhalation Toxicants
Authors: Sakolish Courtney , Georgescu Andrei , Huh Dan Dongeun , Rusyn Ivan
Published: March 2022

Testing for acute inhalation hazards is conducted in animals; however, a number of robust in vitro human cell-based alternatives have been developed and tested. These models range in complexity from cultures of cell lines or primary cells in air-liquid interface on Transwells, to more complex and physiologically relevant flow- and mechanical stimulation-enabled tissue chips. Although the former models are relatively straightforward to establish and can be tested in medium/high throughput, the latter require specialized equipment and lack in throughput. In this study, we developed a device that can be easily manufactured while allowing for the production of a differentiated lung tissue. This multilayered microfluidic device enables coculture of primary human small airway epithelial cells and lung microvascular endothelial cells under physiological conditions for up to 18 days and recreates the parenchymal-vascular interface in the distal lung. To explore the potential of this airway on a chip for applications in inhalation toxicology, we also devised a system that allows for direct gas/aerosol exposures of the engineered airway epithelium to noxious stimuli known to cause adverse respiratory effects, including dry flowing air, lipopolysaccharide, particulate matter, and iodomethane. This study generated quantitative, high-content data that were indicative of aberrant changes in biochemical (lactate dehydrogenase), barrier (dextran permeability), functional (ciliary beating), and molecular (imaging for various markers) phenotypes of the small airway epithelium due to inhalational exposures. This study is significant because it established an in vitro model of human small airway on a chip that can be used in medium/high-throughput studies of subacute effects of inhalation toxicants.
Surgical and Patient-Reported Outcomes of Autologous versus Implant-Based Reconstruction following Infected Breast Device Explantation
Authors: Asaad Malke , Slovacek Cedar , Mitchell David , Liu Jun , Selber Jesse C. , Clemens Mark W. , Chu Carrie K. , Mericli Alexander F. , Butler Charles E.
Published: March 2022

Background:

Implant-based breast reconstruction infections often require implant explantation. Whereas some plastic surgeons pursue autologous reconstruction following the first implant-based breast reconstruction failure caused by infection, others argue that a second attempt is acceptable.

Methods:

The authors conducted a retrospective study of patients who underwent a second reconstruction attempt with implant-based or free flap breast reconstruction following explantation because of infection between 2006 and 2019. Surgical and patient-reported outcomes were compared between the two groups.

Results:

A total of 6093 implant-based breast reconstructions were performed during the study period, of which 130 breasts met our inclusion criteria [implant-based, n = 86 (66 percent); free flap, n = 44 (34 percent)]. No significant differences in rates of overall (25 percent versus 36 percent; p = 0.2) or major (20 percent versus 21 percent; p = 0.95) complications were identified between the free flap and implant-based cohorts, respectively. Implant-based breast reconstruction patients were more likely to experience a second infection (27 percent versus 2 percent; p = 0.0007) and reconstruction failure (21 percent versus 5 percent; p = 0.019). Among irradiated patients, reconstruction failure was reported in 44 percent of the implant-based and 7 percent of the free flap cohorts (p = 0.02). Free flap patients reported significantly higher scores for Satisfaction with Breasts (73.7 ± 20.1 versus 48.5 ± 27.9; p = 0.0046).

Conclusions:

Following implant-based breast reconstruction explantation because of infection, implant-based and free flap breast reconstruction had similar rates of overall and major complications; however, implant-based breast reconstruction had considerably higher rates of infection and reconstructive failures and lower patient-reported scores for Satisfaction with Breasts. Given the high rates of implant-based breast reconstruction failure in patients with prior radiotherapy and infection-based failure, plastic surgeons should strongly consider autologous reconstruction in this patient population.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Rising Trend in Waitlisting for Alcoholic Hepatitis With More Favorable Outcomes Than Other High Model for End-stage Liver Disease in the Current Era
Authors: Bittermann Therese , Mahmud Nadim , Weinberg Ethan M. , Reddy K. Rajender
Published: March 2022

Background.

In the appropriate candidate, liver transplantation (LT) is a viable treatment for alcoholic hepatitis (AH). We compared the waitlisting trends and outcomes of AH patients in the context of others with high Model for End-stage Liver Disease (MELD) score.

Methods.

LT listings for AH between January 1, 2008, and June 12, 2020 were identified in the United Network for Organ Sharing database. Temporal trends in listings for AH were assessed. Covariate adjusted competing risks models evaluated waitlist mortality and LT rates between AH candidates and others with listing native MELD ≥30.

Results.

Between 2008 and 2019, waitlist additions for AH increased 6.5-fold. Waiting time for AH candidates was short (median 10 d). Delisting for clinical improvement was infrequent in AH, albeit higher than MELD ≥30 patients (3.3% versus 0.8%; P < 0.001). Among 99 centers with ≥1 AH listing, AH patients accounted for 0.2%–18.2% of all alcohol-related listings and 0.6%–25.0% of those with native listing MELD ≥30. Overall listing volume was larger at these 99 centers than the 40 with no AH listings (P < 0.001). AH candidates in 2014–2020 experienced improved waitlist survival (adjusted subhazard ratio, 0.67; 95% confidence interval, 0.52-0.86; P = 0.002) and higher transplant rates (adjusted subhazard ratio, 1.14; 95% confidence interval, 1.04-1.25; P = 0.006) versus other MELD ≥30 candidates.

Conclusions.

There has been a rising trend in waitlisting patients with AH and high MELD score. Liver disease causes influence waitlist outcomes and those of AH candidates are more favorable. Further research and allocation adjustments may be needed to ensure equitable organ allocation, based on liver disease cause, for those on the LT waitlist.
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Authors: Won Miyoung , Hong Seung-Beom , Han Byeong-Hak , Kwon Soon-Wo
Published: March 2022

A Gram-negative, non-motile, strictly aerobic and rod- or filamentous-shaped strain, CJU-R4T, was isolated from a flower of royal azalea (Rhododendron schlippenbachii) collected in the Republic of Korea. Strain CJU-R4T was catalase-positive and oxidase-negative, and grew at 15–33 °C (optimum, 28–20 °C), at pH 5.0–8.0 (optimum, pH 7.0–8.0), and in the presence of 0–1 % NaCl (w/v; optimum, 0 %). Strain CJU-R4T had the highest 16S rRNA gene sequence similarity to

Spirosoma oryzae

RHs22T (96.6 %), revealing less than 93 % sequence similarity to other type strains. Phylogenetic and phylogenomic analysis also revealed strain CJU-R4T formed a robust cluster with

S. oryzae

RHs22T. The major fatty acids were summed feature 3 (comprising C16 : 1
 ω7c and/or C16 : 1
 ω6c; 33.0 %), C16 : 1
 ω5c (22.1 %), iso-C15 : 0 (12.6 %) and C16 : 0 (10.7 %). The polar lipids were composed of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. Menaquinone-7 was detected as the sole respiratory quinone. The genomic DNA G+C content was 55.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain CJU-R4T and

Spirosoma oryzae

DSM 28354T were 81.5 and 23.9 %, respectively. Based on the results of the phenotypic and genotypic analyses, strain CJU-R4T is considered to represent a novel species of the genus

Spirosoma

, for which the name Spirosoma rhododendri sp. nov. is proposed. The type strain is CJU-R4T (=KACC 21264T=NBRC 114513T).
A Rapid, High Throughput, Viral Infectivity Assay using Automated Brightfield Microscopy with Machine Learning
Authors: Dodkins Rupert , Delaney John R. , Overton Tess , Scholle Frank , Frias Alba , Crisci Elisa , Huq Nafisa , Jordan Ingo , Kimata Jason T. , Goldberg Ilya G.
Published: March 2022

Infectivity assays are essential for the development of viral vaccines, antiviral therapies and the manufacture of biologicals. Traditionally, these assays take 2–7 days and require several manual processing steps after infection. We describe an automated assay (AVIA™), using machine learning (ML) and high-throughput brightfield microscopy on 96 well plates that can quantify infection phenotypes within hours, before they are manually visible, and without sample preparation. ML models were trained on HIV, influenza A virus, coronavirus 229E, vaccinia viruses, poliovirus, and adenoviruses, which together span the four major categories of virus (DNA, RNA, enveloped, and non-enveloped). A sigmoidal function, fit to virus dilution curves, yielded an R2 higher than 0.98 and a linear dynamic range comparable to or better than conventional plaque or TCID50 assays. Because this technology is based on sensitizing AIs to specific phenotypes of infection, it may have potential as a rapid, broad-spectrum tool for virus identification.
Nucleic Acid Adductomics – the Next Generation of Adductomics for Assessing Environmental Health Risk
Authors: Cooke Marcus S. , Chang Yuan-Jhe , Chen Yet-Ran , Hu Chiung-Wen , Chao Mu-Rong
Published: March 2022

The exposome describes the totality of internal and external environmental exposures, across the life course. Components of the exposome have been linked to an increased risk of various, major diseases. To identify the precise nature, and size, of risk, in this complex mixture of exposures, powerful tools are needed to link exposure, cellular consequences, and health/disease. The most biologically informative biomarkers of the exposome should, to varying extents, reflect the dose of the exposure on the body or target organ(s), a subsequent effect on the biological system and, ideally, possess a role in disease. Modification of nucleic acids (NA) is a key consequence of environmental exposures, and while cellular DNA adductomics aims to evaluate the totality to DNA modifications in the genome, an approach which encompasses modifications of all nucleic acids, would be far more comprehensive, and therefore informative. To address this, we propose a cellular and urinary NA adductomics approach for the assessment of both DNA and RNA modifications, including modified (2’-deoxy)ribonucleosides (2’dN/rN), modified nucleobases (nB), plus: DNA-DNA, RNA-RNA, DNA-RNA, DNA-protein, and RNA-protein crosslinks (DDCL, RRCL, DRCL, DPCL, and RPCL, respectively). Supporting the feasibility of this approach, we presented preliminary, proof-of-principle results, which revealed the presence of over 1,000 modified NA moieties, and at least six types of NA modifications, in a representative, pooled urine from healthy subjects, including modified 2’-dN, modified rN, modified nB, DRCL, RRCL and RPCL, many of which were novel/unexpected. We suggest that NA adductomics will provide a more comprehensive approach to the study of nucleic acid modifications, which will facilitate a range of advances, including the identification of novel, unexpected modifications e.g., RNA-RNA, and DNA-RNA crosslinks; key modifications associated with mutagenesis; agent-specific mechanisms; and adductome signatures of key environmental agents, leading to the dissection of the exposome, and its role in human health/disease, across the life course.
Price and Tax Elasticity of Alcohol Consumption: Evidence from Seven Indian States
Authors: Gupta Samarth , Chowdhury Soumi Roy , Pohit Sanjib , Tullu Fikru Tesfaye , Joshi Pradeep
Published: March 2022

In this paper, we develop a novel methodology for constructing price indices of India Made Foreign Liquor (IMFL), which account for incompatible state-level taxation structure and policies across seven states in India. We use this price index to compute price and tax elasticity of IMFL in the seven states. We find that a 1% increase in price leads to only a 0.057% decline in consumption while a 1% increase in tax reduces alcohol consumption by 0.14%. We extend our estimates to show that a 10% increase in taxes will lead to an 8.4% increase in tax revenue. Our results are the most updated estimates of alcohol consumption elasticities, which overcomes several challenges such as varying manufacturing costs across states and varying tax across types of products within states, which other papers do not.
A complete MAPK cascade, a calmodulin, and a protein phosphatase act downstream of CRK receptor kinases and regulate Arabidopsis innate immunity
Authors: Bai Fangwen , Stratmann Johannes W. , Matton Daniel P.
Published: March 2022

Mitogen-activated protein kinase (MAPK) cascades are critical signal transduction modules in stress responses, but how their composition and mode of activation induces a stress response is poorly understood. We showed in Arabidopsis that CRK21, a cysteine-rich receptor-like protein kinase (CRK), phosphorylates MAPK kinase kinase 20 (MKKK20) and thus directly activates a novel MAPK cascade, consisting of MKKK20, the MAPK kinase MKK3, and the MAPK MPK6. Furthermore, the protein phosphatase PP2C76 and the calmodulin CaM7 were identified as negative and positive modulators of the cascade, respectively. Loss-of-function in components of the MAPK cascade or in CaM7 led to susceptibility to the bacterial pathogen Pseudomonas syringae and the fungal pathogen Botrytis cinerea. In contrast, loss-of-function of PP2C76 as well as transient overexpression of the genes in the MAPK cascade and CaM7 conferred resistance to the pathogens. Moreover, seven additional CRKs interacted with MKKK20 in vivo, and four of these were highly expressed after inoculation with P. syringae. In summary, our findings demonstrate that the novel CRK21-MKKK20-MKK3-MPK6 signaling pathway functions in immunity to fungal and bacterial pathogens and that CRKs may function in directly activating MKKKs.
Individual differences in late positive potential amplitude and theta power predict cue-induced eating
Authors: Gibney Kyla , Kypriotakis George , Versace Francesco
Published: March 2022

Both the brain's reward and cognitive control systems are known to regulate cue-induced eating. Although it is established that individual differences in affective processing of food-related cues predict cue-induced eating, we have yet to investigate how both affective and cognitive mechanisms act in tandem to regulate cue-induced eating. In the present study, our goal was to characterize the mechanisms that make some individuals vulnerable to cue-induced eating while leaving others resilient. We recorded electroencephalogram (EEG) from 59 adults while they viewed emotional & food-related images that preceded the delivery of food rewards (candies) or nonfood objects (beads [control]). We measured the amplitude of the late positive potential (LPP; a measure of motivational salience) in response to the images and power in the theta (4-8 Hz) frequency band (a measure of cognitive control) after the candy or bead was dispensed to the participant. We found that individuals with larger LPP responses to food cues than to pleasant images (C>P group) ate significantly more during the experiment than did those with larger LPP responses to pleasant images than to food cues (P>C group, p < 0.001). Furthermore, we found that individuals with higher theta power after dispensation of the candy than of the bead (CA>BE) ate significantly more than did those with higher theta power after dispensation of the bead than of the candy (BE>CA, p < 0.001). Finally, we found that the crossed P>C and BE>CA group ate less (p < 0.001) than did the other three groups formed by crossing the LPP and theta group assignments, who exhibited similar eating behavior on average (p = 0.662). These findings demonstrate that motivational salience and cognitive control converge to independently confer vulnerability or resilience to cue-induced behaviors, underscoring the need for individualized treatments to mitigate maladaptive behaviors.
vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework
Authors: Nagraj V. P. , Scholz Matthew , Jessa Shakeel , Ge Jianye , Woerner August E. , Budowle Bruce , Huang Meng , Turner Stephen D.
Published: March 2022

Motivation

Genotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes.

Results

We have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in VCF files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of kind and type of error.

Software Availability

vcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).
Molecular characterization of cell types in the squid Loligo vulgaris
Authors: Duruz Jules , Sprecher Marta , Kaldun Jenifer C. , Alsoudy Alsayed , Tschanz-Lischer Heidi , van Geest Geert , Nicholson Pamela , Bruggmann Rémy , Sprecher Simon G.
Published: March 2022

Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.
Identification of a novel chalcone reductase gene for isoliquiritigenin biosynthesis in dahlia (Dahlia variabilis)
Authors: Ohno Sho , Yamada Haruka , Maruyama Kei , Deguchi Ayumi , Kato Yasunari , Yokota Mizuki , Tatsuzawa Fumi , Hosokawa Munetaka , Doi Motoaki
Published: March 2022

Butein is one of flavonoids conferring bright yellow flower color and is a precursor of aurone in some species. Butein is synthesized by two steps, 3-malonyl CoA and 4-coumaloyl CoA are converted to isoliquiritigenin in the first step, and then isoliquiritigenin is converted to butein in the second step. In the first step, chalcone synthase (CHS) and chalcone reductase (CHR) catalyze this reaction, however, CHR has been reported for the isoflavone biosynthesis pathway in legumes, and CHR for butein biosynthesis has not yet been isolated. In this study, we report CHR that is evolutionally different gene from legume species is involved in isoliquiritigenin biosynthesis in dahlia. To isolate CHR gene, we conducted comparative RNA-seq analysis between ‘Shukuhai’ and its butein-loss lateral mutant ‘Rinka’. We found DvCHR showed significant difference in expression levels that encodes an aldo-keto reductase (AKR) 13 family protein, which was phylogenetically different from legume CHRs belonging to AKR4A family. Gene expression levels and genotype of DvCHR were correlated with butein accumulation among various dahlia cultivars. Though single over expression of DvCHR was not able to accumulate isoliquiritigenin in tobacco, co-overexpression of DvCHR with a chalcone glucosyltransferase Am4′CGT and a MYB transcription factor CaMYBA successfully induced isoliquiritigenin accumulation. In addition, DvCHR homologous gene expression was detected from butein or aurone accumulating Coreopsideae species but not from non-butein or non-aurone accumulating Asteraceae species. These results indicated DvCHR functions as chalcone reductase for butein biosynthesis in dahlia, and isoliquiritigenin biosynthesis in Coreopsideae species has been developed independently from legume species.
High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD phenotypes in human lung fibroblasts
Authors: Schwartz Uwe , Prada Maria Llamazares , Pohl Stephanie T. , Richter Mandy , Tamas Raluca , Schuler Michael , Keller Corinna , Mijosek Vedrana , Muley Thomas , Schneider Marc A. , Quast Karsten , Hey Joschka , Heußel Claus P. , Warth Arne , Winter Hauke , Serçin Özdemirhan , Karmouty-Quintana Harry , Herth Felix , Koch Ina , Petrosino Giuseppe , Mardin Balca R. , Weichenhan Dieter , Jurkowski Tomasz P. , Imbusch Charles D. , Brors Benedikt , Benes Vladimir , Jung Brigit , Wyatt David , Stahl Heiko , Plass Christoph , Jurkowska Renata Z.
Published: March 2022

Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired differentiation, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. The epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD patients, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes, including epigenetic factors. Using phenotypic screens, we verified the regulator capacity of multiple candidates and linked them to repair processes in the human lung.

Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across stages of COPD. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic respiratory diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.
A widely applicable and cost-effective method for general and specific RNA-protein complex isolation
Authors: Balzarini Sam , Van Ende Roosje , Voet Arnout , Geuten Koen
Published: March 2022

Despite important methodological advances made in the past few years, a widely applicable, cost-effective and easily scalable procedure that can be routinely used to isolate ribonucleoprotein complexes (RNPs) remains elusive. We describe a versatile method that connects aspects of existing methods in a workflow optimized to reach the above goals and called it “Silica-based Acidic Phase Separation (SAPS)-capture”. To validate the method, the 18S rRNP of S. cerevisiae was captured. To illustrate its applicability, we isolated a repertoire of RNPs in A. thaliana. This procedure can provide the community with a powerful tool to advance the study of ribonomes and RNPs in any organism or tissue type.
Analytic representation of inhomogeneous-resolution maps of three-dimensional scalar fields
Authors: Urzhumtsev Alexandre G. , Lunin Vladimir Y.
Published: March 2022

Refinement of macromolecular atomic models versus experimental maps in cryo-electron microscopy and crystallography is a critical step in structure solution. For an appropriate comparison, model maps should mimic imperfections of the experimental ones, mainly atomic disorder and its limited resolution, often inhomogeneous over the molecule. We construct these model maps as a sum of atomic contributions expressed through a specially designed function describing a solitary spherical wave. Thanks to this function, atomic contributions analytically depend on both an atomic disorder and the local resolution, a value associated now with each atom. Such fully analytic dependence of inhomogeneous-resolution map values on model parameters permits an efficient refinement of all these parameters together and, beyond structural biology, opens a way to solve similar problems in other research domains.

One-Sentence Summary

An analytic decomposition of 3D-oscillating functions results in efficient tools to calculate maps and refine atomic models.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
Authors: Gustavsson Emil K. , Zhang David , Reynolds Regina H. , Garcia-Ruiz Sonia , Ryten Mina
Published: March 2022

Motivation

The advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.

Availability and implementation

ggtranscript is available at https://github.com/dzhang32/ggtranscript, DOI: https://doi.org/10.5281/zenodo.6374061
NDR1/2 kinases regulate membrane trafficking, enable efficient autophagy and prevent neurodegeneration
Authors: Roșianu Flavia , Mihaylov Simeon R , Eder Noreen , Martiniuc Antonie , Claxton Suzanne , Flynn Helen R , Jalal Shamsinar , Domart Marie-Charlotte , Collinson Lucy , Skehel Mark , Snijders Ambrosius P , Krause Matthias , Tooze Sharon A , Ultanir Sila K
Published: March 2022

Autophagy is essential for neuronal development and its deregulation contributes to neurodegenerative diseases. NDR1 and NDR2 are highly conserved kinases implicated in neuronal development, mitochondrial health and autophagy, but how they affect mammalian brain developmentin vivois not known. Using single and doubleNdr1/2knockout mouse models we show that, dual, but not individual loss ofNdr1/2in neurons causes neurodegeneration during brain development, but also in adult mice. Proteomic and phosphoproteomic comparisons betweenNdr1/2knockout and control brains revealed novel kinase substrates and indicated that endocytosis is significantly affected in the absence of NDR1/2. We validated the endocytic protein, Raph1/Lpd1 as a novel NDR1/2 substrate and showed that both NDR1/2 and Raph1 are critical for endocytosis and membrane recycling. In NDR1/2 knockout brains, we observed prominent accumulation of transferrin receptor, p62 and ubiquitinated proteins, indicative of a major impairment of protein homeostasis. Furthermore, the levels of LC3-positive autophagosomes were reduced in knockout neurons, implying that reduced autophagy efficiency mediates p62 accumulation and neurotoxicity. Mechanistically, pronounced mislocalisation of the transmembrane autophagy protein ATG9A at the neuronal periphery, impaired axonal ATG9A trafficking and increased ATG9A surface levels further confirm defects in membrane trafficking and could underlie the impairment in autophagy. We provide novel insight into the roles of NDR1/2 kinases in maintaining neuronal health.

Highlights

Dual neuronalNdr1andNdr2knockout during development or in adult mice causes neurodegeneration.

Phosphoproteomics comparison ofNdr1/2knockouts with control littermates shows endocytosis and membrane trafficking to be affected and reveals novel substrates.

Raph1/Lamellipodin is a novel NDR1/2 substrate that is required for TfR endocytosis.

Ndr1/2knockout brains exhibit a severe defect in ubiquitinated protein clearance and reduced autophagy.

NDR1/2 and Raph1 are required for the trafficking of the only transmembrane autophagy protein, ATG9A.
Context-independent expression of spatial code in hippocampus
Authors: Kapl S. , Tichanek F. , Zitricky F. , Jezek K.
Published: March 2022

Hippocampus plays a crucial role in formation and retrieval of spatial memory across mammals and episodic memory in humans. Episodic as well as spatial memories can be retrieved irrespectively of subject’s awake behavioral state and independently of its actual spatial context. The nature of hippocampal network activity during such out-context retrieval has not been described so far, though. Theoretically, context-independent spatial memory retrieval suggests a shift from the hippocampal spatial representations coding the actual- to the remembered context. In this study we show in rats that CA3 neuronal population can switch spontaneously across representations and transiently activate another stored familiar spatial pattern without a direct external sensory cuing. This phenomenon qualitatively differs from the well described sharp wave-related pattern reactivations during immobility. Here it occurred under theta oscillatory state during an active exploration and reflected the preceding experience of sudden environment change. The respective out-context coding spikes appeared later in the theta cycle than the in-context ones. Finally, the experience induced as well an emergence of population vectors with a co-expression of both codes segregated into different phases of the theta cycle.
Deciphering the fibre-orientation independent component of R2* (R2,iso*) in the human brain with a single multi-echo gradient-recalled-echo measurement under varying microstructural conditions
Authors: Fritz Francisco J. , Mordhorst Laurin , Ashtarayeh Mohammad , Periquito Joao , Pohlmann Andreas , Morawski Markus , Jaeger Carsten , Niendorf Thoralf , Pine Kerrin J. , Callaghan Martina F. , Weiskopf Nikolaus , Mohammadi Siawoosh
Published: March 2022

The effective transverse relaxation rate (R2*) is sensitive to the microstructure of the human brain, e.g. the g-ratio characterising the relative myelination of axons. However, R2* depends on the orientation of the fibres relative to the main magnetic field degrading its reproducibility and that of any microstructural derivative measure. To decipher its orientation-independent part (R2,iso*), a second-order polynomial in time (M2) can be applied to single multi-echo gradient-recalled-echo (meGRE) measurements at arbitrary orientation. The linear-time dependent parameter,β1, of M2 can be biophysically related to R2,iso* when neglecting the signal from the myelin water (MW) in the hollow cylinder fibre model (HCFM). Here, we examined the effectiveness of M2 using experimental and simulated data with variable g-ratio and fibre dispersion. We showed that the fittedβ1effectively estimates R2,iso*when using meGRE with long maximum echo time (TEmax≈ 54 ms) but its microscopic dependence on the g-ratio was not accurately captured. This error was reduced to less than 12% when accounting for the MW contribution in a newly introduced biophysical expression forβ1. We further used this new expression to estimate the MW fraction (0.14) and g-ratio (0.79) in a human optic chiasm. However, the proposed method failed to estimate R2,iso* for a typicalin-vivomeGRE protocol (TEmax≈ 18 ms). At this TEmaxand around the magic angle, the HCFM-based simulations failed to explain the R2*-orientation-dependence. In conclusion, estimation of R2,iso* with M2in vivorequires meGRE protocols with very long TEmax≈ 54 ms.
Genotype by microbiome interactions have large effects on growth in Lotus japonicus
Authors: Bamba Masaru , Akyol Turgut Yigit , Azuma Yusuke , Quilbe Johan , Andersen Stig Uggerhøj , Sato Shusei
Published: March 2022

Biological interactions between plants and their root microbiomes are pivotal for plant growth. Even though the plant genotype [G], soil microbiome [C], and growth conditions (environment) [E] are core factors shaping the root microbiome, their relationships remain unclear. We disentangled the effects of G, C, E, and their interactions on the Lotus root microbiome and plant growth using a cross-inoculation approach that reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. We found that a large proportion of the root microbiome composition was determined by C and E and that G-related (G, G × C, and G × E) effects were significant but small. In contrast, the interactions between G and C had a more pronounced effect on plant shoot growth than C alone. Our findings indicate that most microbiome variations controlled by C have little effect on the plant phenotype, whereas G × C interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention in efforts to optimize crop yield and resilience.
Resistance of mitochondrial DNA to chemical-induced germline mutations is independent of mitophagy in C. elegans
Authors: Leuthner Tess C , Benzing Laura , Kohrn Brendan F , Bergemann Christina M , Hipp Michael J , Hershberger Kathleen A , Mello Danielle F , Sokolskyi Tymofii , Merutka Ilaria R , Seay Sarah A , Kennedy Scott R , Meyer Joel N
Published: March 2022

Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. After 1,750 generations, we detected 2,270 single nucleotide mutations. Heteroplasmy is pervasive in C. elegans and mtDNA mutagenesis is dominated by C:G → A:T mutations generally attributed to oxidative damage, yet there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature. Mitophagy may play a role in eliminating mtDNA damage or deleterious mutations, and mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in overall mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3,050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.
High Quality Phasing Using Linked-Read Whole Genome Sequencing of Patient Cohorts Informs Genetic Understanding of Complex Traits
Authors: Mastromatteo Scott , Chen Angela , Gong Jiafen , Lin Fan , Thiruvahindrapuram Bhooma , Sung Wilson WL , Whitney Joe , Wang Zhuozhi , Patel Rohan V , Keenan Katherine , Halevy Anat , Panjwani Naim , Avolio Julie , Wang Cheng , Côté-Maurais Guillaume , Bégin Stéphanie , Adam Damien , Brochiero Emmanuelle , Bjornson Candice , Chilvers Mark , Price April , Parkins Michael , van Wylick Richard , Mateos-Corral Dimas , Hughes Daniel , Smith Mary Jane , Morrison Nancy , Tullis Elizabeth , Stephenson Anne L , Wilcox Pearce , Quon Bradley S , Leung Winnie M , Solomon Melinda , Sun Lei , Ratjen Felix , Strug Lisa J
Published: March 2022

Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. For population studies, phase is often inferred from external data but read-based phasing approaches that span long genomic distances would be more accurate because they enable both genotype and phase to be obtained from a single dataset. To demonstrate how read-based phasing can provide functional insights, we sequenced 477 individuals with Cystic Fibrosis (CF) using linked-read sequencing. We benchmark read-based phasing with different short- and long-read sequencing technologies, prioritize linked-read technology as the most informative and produce a benchmark phase call set from reference sample HG002 for the community. The 477 samples display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, which facilitates understanding of complex CF alleles. Fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus demonstrates a 20 kb deletion and a PRSS2 missense variant p.Thr8Ile (rs62473563) independently contribute to meconium ileus risk (p=0.0028, p=0.011, respectively) and are PRSS2 pancreas eQTLs (p=9.5e-7 and p=1.4e-4, respectively), explaining the mechanism by which these polymorphisms contribute to CF. Phase enables access to haplotypes that can be used for genome graph or reference panel construction, identification of cis-effects, and for understanding disease associated loci. The phase information from linked-reads provides a causal explanation for variation at a CF-relevant locus which also has implications for the genetic basis of non-CF pancreatitis to which this locus has been reported to contribute.
Primate dopamine neurons activated in rewarding environment by tonic disinhibition from amygdala
Authors: Maeda Kazutaka , Inoue Ken-ichi , Takada Masahiko , Hikosaka Okihide
Published: March 2022

Seeking out good and avoiding bad objects is critical for survival. In practice, objects are rarely good every time or everywhere, but only at the right time or place. Whereas the basal ganglia (BG) are known to mediate goal-directed behavior, for example, saccades to rewarding objects, it remains unclear how such simple behaviors are rendered contingent on higher-order factors, including environmental context. Here we show that amygdala neurons are sensitive to environments and regulate dopamine (DA) neurons via an inhibitory projection to substantia nigra pars reticulata (SNr) neurons. We combined optogenetics and multi-channel recording to demonstrate that rewarding environments induce tonic firing changes in DA neurons. These tonic responses are mediated by disinhibition via GABAergic projection onto DA neurons from SNr, which in turn are suppressed by inhibitory projection from the amygdala. Thus, the amygdala provides an additional source of learning to BG circuits, namely contingencies imposed by the environment.
Multimodal microscale mechanical mapping of cancer cells in complex microenvironments
Authors: Nikolić Miloš , Scarcelli Giuliano , Tanner Kandice
Published: March 2022

The mechanical phenotype of the cell is critical for survival following deformations due to confinement and fluid flow. One idea is that cancer cells are plastic and adopt different mechanical phenotypes under different geometries that aid in their survival. Thus, an attractive goal, is to disrupt the cancer cells’ ability to adopt multiple mechanical states. To begin to address this question, we aimed to quantify the diversity of these mechanical states usingin vitrobiomimetics to mimicin vivo2D and 3D extracellular matrix environments. Here, we used two modalities Brillouin microscopy (∼GHz) and broadband frequency (3-15kHz) optical tweezer microrheology to measure microscale cell mechanics. We measured the response of intracellular mechanics of cancer cells cultured in 2D and 3D environments where we modified substrate stiffness, dimensionality (2D versus 3D), and presence of fibrillar topography. We determined that there was good agreement between two modalities despite the difference in timescale of the two measurements. These findings on cell mechanical phenotype in different environments confirm a correlation between modalities that employ different mechanisms at different temporal scales (Hz-kHz vs. GHz). We also determined that observed heterogeneity in cell shape that is more closely linked to the cells’ mechanical state. We also determined that individual cells in multicellular spheroids exhibit a lower degree of mechanical heterogeneity when compared to single cells cultured in monodisperse 3D cultures. Moreover, the observed decreased heterogeneity among cells in spheroids suggested that there is mechanical cooperativity between cells that make up a single spheroid.