bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross-sector co-creation of a community-based physical activity program for breast cancer survivors in Colombia
Authors: Rubio María Alejandra , Mosquera Daniela , Blanco Martha , Montes Felipe , Finck Carolyn , Duval Martin , Trillos Catalina , Jaramillo Ana María , Rosas Lisa G , King Abby C , Sarmiento Olga L
Published: July 2022

Benefits of physical activity (PA) in breast cancer survivors (BCS) are well established. However, programs to promote PA among BCS tailored to real-world contexts within low- to middle-income countries are limited. Cross-sector co-creation can be key to effective and scalable programs for BCS in these countries. This study aimed to evaluate the networking process to engage multisector stakeholders in the co-creation of a PA program for Colombian BCS called My Body. We employed a mixed-methods design including semistructured interviews, workshops and a social network analysis of centrality measures to assess stakeholders’ engagement, resources and skills enabling the collaborative work, challenges, outcomes and lessons learned. The descriptive analysis and the centrality measures of the network revealed that 19 cross-sector stakeholders engaged in the My Body collaborative network. Through ongoing communication and cooperation, My Body built relationships between the academic lead institutions (local and international), and local and national public, private and academic institutions working in public health, sports and recreation, social sciences and engineering fields. The outcomes included the co-creation of the community-based PA program for BCS, its implementation through cross-sector synergies, increased relationships and communications among stakeholders, and successful dissemination of evidence and project results to the collaboration partners and other relevant stakeholders and community members. The mixed-methods assessment enabled understanding of ways to advance cross-sector co-creation of health promotion programs. The findings can help to enable continued development of sustainable cross-sector co-creation processes aimed at advancing PA promotion.
Waterborne disease outbreaks in treated recreational water facilities: a Socio-Ecological Model perspective
Authors: Cullinan Lauren , Dunn Louise , McLean Sarah , Palombo Enzo
Published: July 2022

Treated recreational water facilities, including swimming pools and water play parks, have often been implicated in infectious disease outbreaks. Addressing this problem is complex due to the multiple and interrelated factors contributing to outbreaks in these settings. These factors may relate to inappropriate behaviours of users and operators, lack of and inconsistent regulation of these facilities, insufficient facility maintenance, and problems associated with the design of these facilities. Given the complexity of this issue, we argue that the Socio-Ecological Model (SEM) provides a useful framework to help identify the multi-level influences and factors that have implications for designing interventions to prevent this public health problem, whilst assisting in guiding future research in this area. We apply the SEM to the current literature to help identify the influences and factors contributing to infectious disease outbreaks in treated recreational water facilities to support this argument. We also identify several gaps in the existing research that would benefit from further examination to help prevent infectious disease outbreaks in treated recreational water facilities such as public swimming pools and water play parks.
Polygenic risk score for embryo selection—not ready for prime time
Authors: Polyakov Alex , Amor David J , Savulescu Julian , Gyngell Christopher , Georgiou Ektoras X , Ross Vanessa , Mizrachi Yossi , Rozen Genia
Published: July 2022

Numerous chronic diseases have a substantial hereditary component. Recent advances in human genetics have allowed the extent of this to be quantified via genome-wide association studies, producing polygenic risk scores (PRS), which can then be applied to individuals to estimate their risk of developing a disease in question. This technology has recently been applied to embryo selection in the setting of IVF and preimplantation genetic testing, with limited data to support its utility. Furthermore, there are concerns that the inherent limitations of PRS makes it ill-suited for use as a screening test in this setting. There are also serious ethical and moral questions associated with this technology that are yet to be addressed. We conclude that further research and ethical reflection are required before embryo selection based on PRS is offered to patients outside of the research setting.
HORuS transmission spectroscopy and revised planetary parameters of KELT-7 b
Authors: Tabernero H M , Zapatero Osorio M R , Allende Prieto C , González-Álvarez E , Sanz-Forcada J , López-Gallifa A , Montes D , del Burgo C , González Hernández J I , Rebolo R
Published: July 2022

We report on the high-resolution spectroscopic observations of two planetary transits of the hot Jupiter KELT-7b (Mp = 1.28 ± 0.17MJup, Teq = 2028 K) observed with the High Optical Resolution Spectrograph (HORuS) mounted on the 10.4-m Gran Telescopio Canarias (GTC). A new set of stellar parameters are obtained for the rapidly rotating parent star from the analysis of the spectra. Using the newly derived stellar mass and radius, and the planetary transit data of the Transiting Exoplanet Survey Satellite (TESS) together with the HORuS velocities and the photometric and spectroscopic data available in the literature, we update and improve the ephemeris of KELT-7b. Our results indicate that KELT-7 has an angle λ = −10.55 ± 0.27 deg between the sky projections of the star’s spin axis and the planet’s orbital axis. By combining this angle and our newly derived stellar rotation period of 1.38 ± 0.05 d, we obtained a 3D obliquity ψ = 12.4 ± 11.7 deg (or 167.6 deg), thus reinforcing that KELT-7 is a well-aligned planetary system. We search for the presence of Hα, Li i, Na i, Mg i, and Ca ii features in the transmission spectrum of KELT-7b but we are only able to determine upper limits of 0.08–1.4 per cent on their presence after accounting for the contribution of the stellar variability to the extracted planetary spectrum. We also discuss the impact of stellar variability on the planetary data. Our results reinforce the importance of monitoring the parent star when performing high-resolution transmission spectroscopy of the planetary atmosphere in the presence of stellar activity.
Dust evolution with MUPPI in cosmological volumes
Authors: Parente Massimiliano , Ragone-Figueroa Cinthia , Granato Gian Luigi , Borgani Stefano , Murante Giuseppe , Valentini Milena , Bressan Alessandro , Lapi Andrea
Published: July 2022

We study the evolution of dust in a cosmological volume using a hydrodynamical simulation in which the dust production is coupled with the MUPPI (MUlti Phase Particle Integrator) sub-resolution model of star formation and feedback. As for the latter, we keep as reference the model setup calibrated previously to match the general properties of Milky Way-like galaxies in zoom-in simulations. However, we suggest that an increase of the star formation efficiency with the local dust-to-gas ratio would better reproduce the observed evolution of the cosmic star formation density. Moreover, the paucity of quenched galaxies at low redshift demands a stronger role of active galactic nucleus feedback. We tune the parameters ruling direct dust production from evolved stars and accretion in the interstellar medium to get scaling relations involving dust, stellar mass and metallicity in good agreement with observations. In low-mass galaxies, the accretion process is inefficient. As a consequence, they remain poorer in silicate and small grains than higher mass ones. We reproduce reasonably well the few available data on the radial distribution of dust outside the galactic region, supporting the assumption that the dust and gas dynamics are well coupled at galactic scales.
End-of-Life Nursing Education in US Baccalaureate Degree Nursing Programs
Authors: Jeffers Stephanie , Black Sarah , Alessi Gianna
Published: July 2022

End-of-life (EOL) education in baccalaureate nursing degree programs is critical to prepare nurses to care for patients and families with complex physical and psychosocial needs at the EOL. This quantitative descriptive study examines the current state of EOL education in baccalaureate nursing programs across the United States. Results of this study show that nurse educators continue to use strategies to provide this education; however, the amount and frequency of content delivered require improvement, and support for faculty development is needed.
The General Surgery Residency Experience
Authors: Greenberg Anya L. , Cevallos Jenny R. , Ojute Feyisayo M. , Davis Denise L. , Greene Wendy R. , Lebares Carter C. ,   for the General Surgery Research Collaborative on Resident Wellbeing
Published: July 2022

Objectives:

We explored differences by race/ethnicity in regard to several factors that reflect or impact wellbeing.

Background:

Physician wellbeing has critical ramifications for the US healthcare system, affecting clinical outcomes, patient experience, and healthcare economics. Within surgery, literature examining the association between race/ethnicity and wellbeing has been limited and inconclusive.

Methods:

Residents at 16 academic General Surgery training programs completed an online questionnaire. Racial/ethnic identity, gender identity, post-graduate year (PGY) level, and gap years were self-reported. Differences by race/ethnicity in flourishing (global wellbeing) as well as factors reflecting resilience (mindfulness, personal accomplishment, workplace support, workplace control) and risk (depression, emotional exhaustion, depersonalization, stress, anxiety, workplace demand) were assessed.

Results:

Of 300 respondents (response rate 34%), 179 (60%) were non-male, 123 (41%) were residents of color (ROC), and 53 (18%) were from racial/ethnic groups that are underrepresented in medicine (UIM). Relative to White residents, ROC have significantly lower flourishing and higher anxiety, and these remain significant when adjusting for gender, PGY level, and gap years. Relative to residents overrepresented in medicine (OIM), UIM residents have significantly lower emotional exhaustion and depersonalization after adjusting for gender, PGY level and gap years.

Conclusions:

Disparities in resident wellbeing based on race/ethnicity and UIM/OIM status exist. However, the experience of ROC is not homogeneous. As part of the transformative process to address systemic racism, eliminate disparities in surgical training, and reconceptualize wellbeing as a fundamental asset for optimal surgeon performance, further understanding the specific contributors and detractors of wellbeing among different individuals and groups is critical.
Lessons learned about epithelial sodium channels from transgenic mouse models
Authors: Ehret Elodie , Hummler Edith
Published: July 2022

Purpose of review

This review provides an up-to-date understanding about the regulation of epithelial sodium channel (ENaC) expression and function. In particular, we will focus on its implication in renal Na+ and K+ handling and control of blood pressure using transgenic animal models.

Recent findings

In kidney, the highly amiloride-sensitive ENaC maintains whole body Na+ homeostasis by modulating Na+ transport via epithelia. This classical role is mostly confirmed using genetically engineered animal models. Recently identified key signaling pathways that regulate ENaC expression and function unveiled some nonclassical and unexpected channel regulatory processes. If aberrant, these dysregulated mechanisms may also result in the development of salt-dependent hypertension.

The purpose of this review is to highlight the most recent findings in renal ENaC regulation and function, in considering data obtained from animal models.

Increased ENaC-mediated Na+ transport is a prerequisite for salt-dependent forms of hypertension. To treat salt-sensitive hypertension it is crucial to fully understand the function and regulation of ENaC.
Adjusting non-pharmaceutical interventions based on hospital bed capacity using a multi-operator differential evolution
Authors: Mendoza Victoria May P. , Mendoza Renier , Lee Jongmin , Jung Eunok
Published: July 2022

Without vaccines and medicine, non-pharmaceutical interventions (NPIs) such as social distancing, have been the main strategy in controlling the spread of COVID-19. Strict social distancing policies may lead to heavy economic losses, while relaxed social distancing policies can threaten public health systems. We formulate an optimization problem that minimizes the stringency of NPIs during the prevaccination and vaccination phases and guarantees that cases requiring hospitalization will not exceed the number of available hospital beds. The approach utilizes an SEIQR model that separates mild from severe cases and includes a parameter µ that quantifies NPIs. Payoff constraints ensure that daily cases are decreasing at the end of the prevaccination phase and cases are minimal at the end of the vaccination phase. Using the penalty method, the constrained minimization is transformed into a non-convex, multi-modal unconstrained optimization problem, which is solved using a metaheuristic algorithm called the improved multi-operator differential evolution. We apply the framework to determine optimal social distancing strategies in the Republic of Korea given different amounts and types of antiviral drugs. The model considers variants, booster shots, and waning of immunity. The optimal µ values show that fast administration of vaccines is as important as using highly effective vaccines. The initial number of infections and daily imported cases should be kept minimum especially if the severe bed capacity is low. In Korea, a gradual easing of NPIs without exceeding the severe bed capacity is possible if there are at least seven million antiviral drugs and the effectiveness of the drug in reducing disease severity is at least 86%. Model parameters can be adapted to a specific region or country, or other infectious disease. The framework can also be used as a decision support tool in planning practical and economic policies, especially in countries with limited healthcare resources.

Mathematics Subject Classification

34A55, 34H05, 90C26, 92-10
α-synucleinopathy associated calcium overload and autophagy failure is regulated by gain-of-function of Tousled-like kinase
Authors: Gong Fangyan , Chen Hao , Xiong Ying , Cai Rong , Zhang Jing , Wang Ningli , Liu Lei
Published: July 2022

As a pathological hallmark in Parkinson’s disease (PD), α-synucleinopathy causes multiple cellular damages, including calcium overload, mitochondrial and autophagic dysfunction, and eventually dopamine neuron death. However, the hierarchy of these detrimental events is unclear. InDrosophila, we confirmed that overexpression of α-synuclein could induce all these cytotoxic events. To determine the specific cytotoxic events induced by calcium overload, we established a calcium overload model inDrosophilaand performed genetic screens. We found that calcium overload caused mitochondrial damage and autophagy failure and cell death, and these cytotoxic processes could be strongly rescued by loss of Tousled-like kinase (TLK). Interestingly, loss of TLK also rescued defects induced by α-synuclein overexpression inDrosophila. This suggests that calcium overload acts as the crucial event upstream of mitochondrial and autophagy dysfunction. For TLK regulation of autophagy, our data indicated that a transcriptional factor REPTOR, which regulated the expression of several lysosomal genes, functioned downstream of TLK. In mammalian cells and mice, TLK2 (the homolog ofDrosophilaTLK) was phosphorylated under calcium overload. Upon phosphorylation, TLK2 increased its kinase activity. In addition, TLK2 could phosphorylate CREBRF (the human homolog of REPTOR) to cause its loss of transcription on the lysosomal genes. Moreover, TLK2 knockout mice rescued multi-aspect cytotoxicity induced by calcium overload and α-synuclein overexpression. Our research demonstrates that TLK2 acts as a key regulator to mediate cell death and dysfunctions of mitochondria and autophagy downstream of calcium overload.
An autoregulatory feedback loop converging on H2A ubiquitination drives synovial sarcoma
Authors: Benabdallah Nezha S. , Dalal Vineet , Sotiriou Afroditi , Scott R. Wilder , Kommoss Felix K.F. , Pejkovska Anastasija , Gaspar Ludmila , Wagner Lena , Sánchez-Rivera Francisco J. , Ta Monica , Thornton Shelby , Nielsen Torsten O. , Underhill T. Michael , Banito Ana
Published: July 2022

The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of mSWI/SNF complex, to Polycomb repressive complex 1 (PRC1) target genes. Here we show that the SSX C-terminus, via its SSXRD domain, directs SS18-SSX chromatin binding independently of SS18. SSXRD specific targeting is mediated by interaction with mono ubiquitinated H2A (H2AK119ub1) and histone MacroH2A with which the fusion overlaps genome wide. Variant Polycomb Repressive Complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and is therefore required for SS18-SSX occupancy. Importantly, the SSX C-terminus not only depends on H2AK119ub1 for localization but also further increases it by promoting PRC1.1 complex stability. Consequently, high H2AK119ub1 levels are a feature of murine and human synovial sarcomas. These results reveal an SSX/PRC1 autoregulatory feedback loop that reinforces fusion chromatin binding and therefore its oncogenic activity, and could play a role in a wider range of cancers and physiological settings where SSX proteins are overexpressed.
Discovering host protein interactions specific for SARS-CoV-2 RNA genome
Authors: Giambruno Roberto , Zacco Elsa , Ugolini Camilla , Vandelli Andrea , Mulroney Logan , D’Onghia Manfredi , Giuliani Bianca , Criscuolo Elena , Castelli Matteo , Clementi Nicola , Clementi Massimo , Mancini Nicasio , Bonaldi Tiziana , Gustincich Stefano , Leonardi Tommaso , Tartaglia Gian Gaetano , Nicassio Francesco
Published: July 2022

SARS-CoV-2, a positive single-stranded RNA virus, interacts with host cell proteins throughout its life cycle. These interactions are necessary for the host to recognize and hinder the replication of SARS-CoV-2. For the virus, to translate, transcribe and replicate its genetic material. However, many details of these interactions are still missing. We focused on the proteins binding to the highly structured 5’ and 3’ end regions of SARS-CoV-2 RNA that were predicted by thecatRAPID algorithm to attract numerous proteins, exploiting RNA-Protein Interaction Detection coupled with Mass Spectrometry (RaPID-MS) technology. The validated interactors, which agreed with our predictions, include pseudouridine synthase PUS7 that binds to both ends of the viral RNA. Nanopore direct-RNA sequencing confirmed that the RNA virus is heavily modified, and PUS7 consensus regions were found in both SARS-CoV-2 RNA end regions. Notably, a modified site was detected in the viral Transcription Regulatory Sequence - Leader (TRS-L) and can influence the viral RNA structure and interaction propensity. Overall, our data map host protein interactions within SARS-CoV-2 UTR regions, pinpointing to a potential role of pseudouridine synthases and post-transcriptional modifications in the viral life cycle. These findings contribute to understanding virus-host dynamics and may guide the development of targeted therapies.
Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum
Authors: Paril Jefferson , Pandey Gunjan , Barnett Emma B. , Rane Rahul V. , Court Leon , Walsh Thomas , Fournier-Level Alexandre
Published: July 2022

The genome of the major agricultural weed species, annual ryegrass (Lolium rigidum) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N50=361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.
Unveiling hidden eukaryotes: diversity of Endomyxa (Rhizaria) in coastal marine habitats
Authors: Berney Cédric , Ciaghi Stefan , Romac Sarah , Mahé Frédéric , de Vargas Colomban , Jaillon Olivier , Kirchmair Martin , Bass David , Neuhauser Sigrid
Published: July 2022

Nucleic acid based studies of marine biodiversity often focus on Kingdom-level diversity. Such approaches often largely miss diversity of less studied groups, likely to harbour many unknown lineages which are likely playing significant ecological roles. Among these elusive groups are Endomyxa (Rhizaria), a ubiquitous, but understudied lineage comprising parasites (e.g. Ascetosporea, Phytomyxea), free-living amoebae (e.g. Vampyrellida, Gromia, Filoreta), flagellates (e.g. Tremula, Aquavolon), and unknown environmental lineages. Using Endomyxa-biased primers targeting the hypervariable region V4 of the 18S rRNA gene, we explored the diversity of Endomyxa in marine samples from European coastal sites and compared it to that found in pan-eukaryote V4 libraries of the same samples. In total 458 endomyxan OTUs were identified, of which 38% were only detected by the specific primers. Most are distinct from published sequences, and include novel diversity within known clades, and putative novel lineages. The data revealed variations in endomyxan assemblages related to habitat (benthic vs. pelagic, sampling site), mode of nutrition (parasitic vs. free-living) and nucleic acid type (DNA vs. RNA). Overall, the vast majority of endomyxan diversity occurs in sediments (including Vampyrellida, Reticulosida, and the environmental “Novel Clade 12”) where they form diverse and active communities including many uncharacterised lineages.
An automated workflow for multi-omics screening of microbial model organisms
Authors: Donati Stefano , Mattanovich Matthias , Hjort Pernille , Jacobsen Simo Abdessamad Baallal , Blomquist Sarah Dina , Mangaard Drude , Gurdo Nicolas , Pastor Felix Pacheco , Maury Jérôme , Hanke Rene , Herrgård Markus J. , Wulff Tune , Jakočiūnas Tadas , Nielsen Lars Keld , McCloskey Douglas
Published: July 2022

Multi-omics datasets are becoming of key importance to drive discovery in fundamental research as much as generating knowledge for applied biotechnology. However, the construction of such large datasets is usually time-consuming and expensive. Automation is needed to overcome these issues by streamlining workflows from sample generation to data analysis. Here, we describe the construction of a complex workflow for the generation of high-throughput microbial multi-omics datasets. The workflow comprises a custom-built platform for automated cultivation and sampling of microbes, sample preparation protocols, analytical methods for sample analysis and automated scripts for raw data processing. We demonstrate possibilities and limitations of such workflow in generating data for three biotechnologically relevant model organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida.
Comprehensive analysis of kill switch toxins in plant-beneficial Pseudomonas fluorescens reveals drivers of lethality, stability, and escape
Authors: Halvorsen Tiffany M. , Ricci Dante P. , Park Dan M. , Jiao Yongqin , Yung Mimi C.
Published: July 2022

Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin-antitoxin modules, polymorphic exotoxin-immunity systems, restriction endonuclease-methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, our study reveals that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.
Taxanes act as vascular disrupting agents and increase rate of metastasis when combined with anti-angiogenic therapy
Authors: Nandigama Rajender , Kallius Mathias , Hemmen Katharina , Das Shaoli , Pinnecker Jürgen , Ascheid David , Burkhard Verena , Ali Hla , Rainer Johannes , Scheld Daniela , Herterich Sabine , Zernecke-Madsen Alma , Penack Olaf , Diller Stefan , Camphausen Kevin , Ergün Süleyman , Shankavaram Uma , Heinze Katrin , Escorcia Freddy E. , Henke Erik
Published: July 2022

Taxanes are known to have a profound effect on endothelial cells and the vasculature even at low doses. Here, we show that taxanes, rather than being anti-angiogenic, function more as vascular disrupting agents (VDAs), although they exert a different mechanism of vascular permeabilization when compared to traditional VDAs such as combretastatins. In the tumor context, this VDA-effect leads to a rapid vascular collapse and acute hypoxia. Concomitant treatment with anti-VEGF drugs aggravates hypoxia by blocking vasculogenic rescue mechanisms. While this results in a strong growth-suppressing effect on the tumor, it also increases its invasiveness and metastatic potential. We demonstrate that combination of anti-angiogenic drugs with taxanes blocks tumor reperfusion, intensifies intravasation of circulating tumor cells (CTCs) and strongly increases metastasis. Anti-VEGF drugs are commonly applied in combination with cytotoxic drugs including taxanes. Our findings have significant implications for the clinical use of this drug combination.
The Implicit Assumptions of Classic Functional Responses and Their Multi-Species Extensions
Authors: Palamara Gian Marco , Capitán José A. , Alonso David
Published: July 2022

Functional responses are central to describe consumer-resource interactions. Defined as the per capita average feeding rate of consumers, since Holling’s seminal papers, they have been widely used in ecology. Holling’s central observation was that they often saturate as resource density increases. If the interference between consumers is strong, they also decrease with consumer density. Here we emphasize the stochastic nature of the individual feeding processes and the associated probability distributions of the different behavioral types and show how they control population-averaged feeding rates. We do so by revisiting a classic approach based on the formulation of feeding interactions in terms of individual-based reaction schemes. We highlight the common assumptions underlying the different functional forms and discover a new predator-dependent functional response that should be considered the natural extension of the Holling type II functional response when consumers interference is considered. Our work has clear implications, on the one hand, for both model selection and parameter inference from feeding experiments, and, on the other, for the use of multi-species extensions of these functional responses in population-level food-web dynamic models.
Hidden Markov Modeling of Molecular Orientations and Structures from High-Speed Atomic Force Microscopy Time-Series Images
Authors: Ogane Tomonori , Noshiro Daisuke , Ando Toshio , Yamashita Atsuko , Sugita Yuji , Matsunaga Yasuhiro
Published: July 2022

High-speed atomic force microscopy (HS-AFM) is a powerful technique for capturing the time-resolved behavior of biomolecules. However, structural information in HS-AFM images is limited to the surface geometry of a sample molecule. Inferring latent three-dimensional structures from the surface geometry is thus important for getting more insights into conformational dynamics of a target biomolecule. Existing methods for estimating the structures are based on the rigid-body fitting of candidate structures to each frame of HS-AFM images. Here, we extend the existing frame-by-frame rigid-body fitting analysis to multiple frames to exploit orientational correlations of a sample molecule between adjacent frames in HS-AFM data due to the interaction with the stage. In the method, we treat HS-AFM data as time-series data, and they are analyzed with the hidden Markov modeling. Using simulated HS-AFM images of the taste receptor type 1 as a test case, the proposed method shows a more robust estimation of molecular orientations than the frame-by-frame analysis. The method is widely applicable in integrative modeling of conformational dynamics using real experimental HS-AFM data.

Author summary

Biomolecules dynamically change their structures in cells and perform various functions that are important for life. It is difficult to observe such dynamic structural changes using conventional experimental techniques, such as X-ray crystallography, that mainly observe static atomic structures. Alternative approach is the atomic force microscopy (AFM), a technique to measure the surface geometry of a sample molecule by scanning with an acute tip. Recently, by increasing the imaging rate of the AFM, it has become possible to observe the dynamics of biomolecules at work. However, the information measured with AFM is limited to the surface geometry of a molecule, so it is important to extract three-dimensional structural information from those data. In this study, we develop a method to estimate structural information with higher accuracy.
Haplotype based testing for a better understanding of the selective architecture
Authors: Chen Haoyu , Pelizzola Marta , Futschik Andreas
Published: July 2022

The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies. With this approach, less multiple testing correction is needed, which leads to tests with higher power, especially when the number of candidate haplotypes is small or moderate. Another advantage is that haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing. For a larger number of haplotypes, we investigate methods to combine them to a moderate number of haplotype subsets. The use of haplotypes also permits a better understanding of selective signatures. For this purpose, we propose post hoc tests for the selected haplotypes and differences between their selection coefficients. Using both simulated and real data sets, we illustrate the performance and benefits of our proposed test statistics.
Neuronal selectivity for multiple features in the primary visual cortex
Authors: Wei Wenqing , Merkt Benjamin , Rotter Stefan
Published: July 2022

Neurons in rodent primary visual cortex are simultaneously tuned to several stimulus features, including orientation and spatial frequency of moving gratings used in experiments. Light-induced signals emitted by retinal ganglion cells (RGC) are relayed to the primary visual cortex (V1) via cells in the dorsal lateral geniculate nucleus (dLGN). However, there is currently no agreement on which thalamocortical transformation leads to the neuronal tuning curves observed in experiments. Here, we outline a model that explains the emergence of feature-specific neural responses as the result of a two-step integration process: First, the compound input to cortical neurons comes from a set of retinal sensors randomly placed in the receptive field. Second, the cortical responses to the combined input are shaped by the rectification caused by the spike threshold of the neurons. We performed numerical simulations of a thalamocortical network stimulated by moving gratings and found that simultaneous tuning to orientation and spatial frequency results from this spatio-temporal integration process. We also show how this tuning is related to the complex structure of the receptive fields that reflect the input. We conclude that different types of feature selectivity arise naturally from random thalamocortical projections. Moreover, we describe in detail the underlying neural mechanism.
Enhanced cell viscosity: a new phenotype associated with lamin A/C alterations
Authors: Jebane Cécile , Varlet Alice-Anaïs , Karnat Marc , Hernandez-Cedillo Lucero M. , Lecchi Amélie , Bedu Frédéric , Desgrouas Camille , Vigouroux Corinne , Vantyghem Marie-Christine , Viallat Annie , Rupprecht Jean-François , Helfer Emmanuèle , Badens Catherine
Published: July 2022

Lamin A/C is a well-established key contributor to nuclear stiffness and its role in nucleus mechanical properties has been extensively studied. However, its impact on whole cell mechanics has been poorly addressed, even less so in terms of measurable physical parameters. In the present study, microfluidic experiments combined with theoretical analyses were performed to provide a quantitative estimation of the whole cell mechanical properties. This allowed the characterization of mechanical cell changes induced by lamin A/C alterations resulting from Atazanavir treatment or lipodystrophy-associated LMNA R482W pathogenic variant. Results unveil an increase in the long-time viscosity as a signature of cells affected by lamin A/C alterations. In addition, they show that the whole cell response to mechanical stress is driven not only by the nucleus but also by the nucleo-cytoskeleton links and the microtubule network. This enhanced cell viscosity assessed by our microfluidic device could represent a useful diagnosis marker for lamin-related diseases.
A functional Bayesian model for hydrogen-deuterium exchange mass-spectrometry
Authors: Crook Oliver M. , Chung Chun-wa , Deane Charlotte M.
Published: July 2022

Proteins often undergo structural perturbations upon binding to other proteins or ligands or when they are subject to environmental changes. Hydrogen deuterium exchange mass-spectrometry (HDX-MS) can be used to explore conformational changes in proteins by examining differences in the rate of deuterium incorporation in different contexts. To determine deuterium incorporation rates, HDX-MS measurements are typically made over a time course. Recently introduced methods show that incorporating the temporal dimension into the statistical analysis improves power and interpretation. However, these approaches have technical assumptions which hinder their flexibility. Here, we propose a more flexible methodology by reframing these methods in a Bayesian framework. Our proposed framework has improved algorithmic stability, allows us to perform uncertainty quantification, and can calculate statistical quantities that are inaccessible to other approaches. We demonstrate the general applicability of the method by showing it can perform rigorous model selection on a spike-in HDX-MS experiment and improved interpretation in an epitope mapping experiment. Bayesian analysis of an HDX experiment with an antibody dimer bound to an E3 ubiquitin ligase identifies at least two interaction interfaces where previous methods obtained confounding results due to the complexities of conformation change on binding. Our findings are consistent with the co-crystal structure of these proteins, demonstrating a bayesian approach can identify important binding epitopes from HDX data.
Dynamic live/apoptotic cell assay using phase-contrast imaging and deep learning
Authors: Korczak Zofia , Pineda Jesús , Helgadottir Saga , Midtvedt Benjamin , Goksör Mattias , Volpe Giovanni , Adiels Caroline B.
Published: July 2022

Chemical live/dead assay has a long history of providing information about the viability of cells cultured in vitro. The standard methods rely on imaging chemically-stained cells using fluorescence microscopy and further analysis of the obtained images to retrieve the proportion of living cells in the sample. However, such a technique is not only time-consuming but also invasive. Due to the toxicity of chemical dyes, once a sample is stained, it is discarded, meaning that longitudinal studies are impossible using this approach. Further, information about when cells start programmed cell death (apoptosis) is more relevant for dynamic studies. Here, we present an alternative method where cell images from phase-contrast time-lapse microscopy are virtually-stained using deep learning. In this study, human endothelial cells are stained live or apoptotic and subsequently counted using the self-supervised single-shot deep-learning technique (LodeSTAR). Our approach is less labour-intensive than traditional chemical staining procedures and provides dynamic live/apoptotic cell ratios from a continuous cell population with minimal impact. Further, it can be used to extract data from dense cell samples, where manual counting is unfeasible.
Pyruvate carboxylation identifies Glioblastoma Stem-like Cells opening new metabolic strategy to prevent tumor recurrence
Authors: Renoult Ophélie , Gratas Catherine , Joalland Noémie , Laurent--Blond Mélanie , Awada Hala , Bourgeois Marine , Oliver Lisa , Chiavassa Sophie , Croyal Mikaël , Paris François , Pecqueur Claire
Published: July 2022

Glioblastoma (GBM) are currently associated with a dismal prognosis due to therapeutic resistance. Within the diverse tumor subpopulations, Glioblastoma Stem-like Cells (GSC) have been involved in GBM recurrence. In our study, we demonstrated that these tumor cells can be identified through singular mitochondrial alternative metabolisms. Combining state-of-the-art metabolic studies and the development of a straightforward tumoroid model recapitulating key features of primary GBM cultures, we uncovered a significant use of α-ketoglutarate reductive carboxylation and pyruvate carboxylation in tumoroid GBM cells, catalyzed respectively by isocitrate dehydrogenase and pyruvate carboxylase enzymes. We demonstrated that these singular metabolic features are shared by GBM cells from the mesenchymal subtype and radiation-escaping cells, also involved in recurrence. Finally, we demonstrated that pyruvate carboxylation is required for GBM cell survival in hypoxic niches where glutamine is restricted. Thus, besides providing a new way to identify GSC, our study also opens new therapeutic strategy to limit GBM recurrence.
Core-shell DNA-cholesterol nanoparticles exert lysosomolytic activity in African trypanosomes
Authors: Knieß Robert , Leeder Wolf-Matthias , Reißig Paul , Geyer Felix Klaus , Göringer H. Ulrich
Published: July 2022

Trypanosoma bruceiis the causal infectious agent of African trypanosomiasis in humans and Nagana in livestock. Both diseases are currently treated with a small number of chemotherapeutics, which are hampered by a variety of limitations reaching from efficacy and toxicity complications to drug-resistance problems. Here, we explore the forward design of a new class of synthetic trypanocides based on nanostructured, core-shell DNA-lipid particles. In aqueous solution, the particles self-assemble into micelle-type structures consisting of a solvent-exposed, hydrophilic DNA shell and a hydrophobic lipid core. DNA-lipid nanoparticles have membrane-adhesive qualities and can permeabilize lipid membranes. We report the synthesis of DNA-cholesterol nanoparticles, which specifically subvert the membrane integrity of theT. bruceilysosome, killing the parasite with nanomolar potencies. Furthermore, we provide an example of the programmability of the nanoparticles. By functionalizing the DNA shell with a spliced leader (SL)-RNA-specific DNAzyme, we target a second trypanosome-specific pathway (dual-target approach). The DNAzyme provides a backup to counteract the recovery of compromised parasites, which reduces the risk of developing drug resistance.
Epstein-Barr virus nuclear antigen proteins deploy diverse mechanisms to bind the human genome
Authors: Haque Md. Redwanul , Tushar Abdur Rashid , Park Minjun , Moon Chang In , Rahman M. Sohel , Samee Md. Abul Hassan
Published: July 2022

Viral transcription factors (vTFs) are known to bind the human genome and impact critical biological processes. However, a vTF can infect multiple cell-types, and the extent to which they deploy the same mechanisms for DNA binding across different cell-types is poorly understood. We used the Epstein-Barr virus Nuclear Antigen Proteins 2 and 3 (EBNA2 and EBNA3) to address this gap, the two widely studied vTFs associated with cancers, as case studies. We analyze multiple ChIP-seq datasets of these vTFs from different human cell-lines using a state-of-the-art convolutional neural network model. We show that each vTF uses both cell-type specific and cell-type independent cofactors to bind the human genome. Interestingly, each vTF requires ∼10 cofactors consistently across all binding peaks. Such dependency on a large number of cofactors is in contrast to human TFs since human TFs typically co-bind with 2-3 cofactors. Our de novo motif finding approach also reveals novel sequence motifs at the ChIP peaks of these vTFs. These critical signals were missed by previous studies doing enrichment analysis using known human TFs. Finally, we find that although a vTF impacts similar biological processes across cell-types, it also impacts distinct biological processes in a cell-type specific manner. Our study provides a roadmap for integrative analysis of vTF binding and pinpointing their diverse mechanisms of targeting the human genome across different human cell-types.
Transcriptome responses of the aphid vectorMyzus persicaeare shaped by identities of the host plant and the virus
Authors: Chesnais Quentin , Golyaev Victor , Velt Amandine , Rustenholz Camille , Verdier Maxime , Brault Véronique , Pooggin Mikhail M. , Drucker Martin
Published: July 2022

Background

Numerous studies have documented modifications in vector orientation behavior, settling and feeding behavior, and/or fecundity and survival due to virus infection in host plants. These alterations are often expected to enhance virus transmission, which has led to the hypothesis that such effects are vector manipulations by the virus. However, until now, the gene expression changes correlating with these effects and indicative of modified vector pathways and mechanisms are mostly unknown.

Results

Transcriptome profiling ofMyzus persicaeaphids feeding on turnip yellows virus (TuYV) and cauliflower mosaic virus (CaMV) infectedArabidopsis thalianaandCamelina sativarevealed a substantial proportion of commonly deregulated genes, amongst them many with general functions in plant-virus-aphid interactions. We identified also aphid genes specifically deregulated by CaMV or TuYV infection, which might be related to the viral transmission mode. Furthermore, we observed strong host-specific differences in the gene expression patterns with plant virus infection causing more deregulations of aphid genes onA. thalianathan onC. sativa, likely related to the differences in susceptibility of the plant hosts to these viruses. Finally, stress-related aphid genes were downregulated inM. persicaeon both infected plants, regardless of the virus.

Conclusions

TuYV, relying on the circulative persistent mode of transmission, tended to affect developmental genes. This could increase the proportion of alate aphids, but also affect their locomotion, neuronal activity, and lifespan. CaMV, using the non-circulative non-persistent mode of transmission, had a strong impact on feeding-related genes and in particular those related to salivary proteins. In general, these transcriptome alterations targeted pathways that seem to be particularly adapted to the transmission mode of the corresponding virus and could be evidence of vector manipulation by the virus.
Reduced parasite burden in feral honeybee colonies
Authors: Kohl Patrick L. , D’Alvise Paul , Rutschmann Benjamin , Roth Sebastian , Remter Felix , Steffan-Dewenter Ingolf , Hasselmann Martin
Published: July 2022

Bee parasites are the main threat to apiculture, and since many parasite taxa can spill over from honeybees (Apis mellifera) to other bee species, honeybee disease management is important for pollinator conservation in general. It is unknown whether honeybees that escaped from apiaries (i.e., feral colonies) benefit from natural parasite-reducing mechanisms like swarming or suffer from high parasite pressure due to the lack of medical treatment. In the latter case, they could function as parasite reservoirs and pose a risk to the health of managed honeybees (spillback) and wild bees (spillover). We compared the occurrence of 18 microparasites among managed (N=74) and feral (N=64) honeybee colony samples from four regions in Germany using qPCR. We distinguished five colony types representing differences in colony age and management histories, two variables potentially modulating parasite prevalence. Besides strong regional variation in parasite communities, parasite burden was consistently lower in feral than in managed colonies. The overall number of detected parasite taxa per colony was lower, and Trypanosomatidae, chronic bee paralysis virus, and deformed wing viruses A and B were less prevalent and abundant in feral colonies than in managed colonies. Parasite burden was lowest in newly founded feral colonies, intermediate in overwintered feral colonies and managed nucleus colonies, and highest in overwintered managed colonies and hived swarms. Our study confirms the hypothesis that the natural mode of colony reproduction and dispersal by swarming temporally reduces parasite pressure in honeybees. We conclude that feral colonies are unlikely to contribute significantly to the spread of bee diseases.