bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-term variability of proton density fat fraction in pancreas and liver assessed by multi-echo chemical-shift encoding-based MRI at 3 T
Authors: Machann Jürgen , Hasenbalg Maytee , Dienes Julia , Wagner Robert , Köhn Arvid , Birkenfeld Andreas L. , Nikolaou Konstantin , Kullmann Stephanie , Schick Fritz , Heni Martin
Published: June 2021

BACKGROUND

Quantification of pancreatic fat (PF) and intrahepatic lipids (IHL) is of increasing interest in cross-sectional epidemiological and interventional studies in subjects at risk for metabolic diseases. Up to now, short- and medium-term variations as well as their dependence on actual nutritional status are almost unknown.

PURPOSE or HYPOTHESIS

To assess short-term intraday variations of PF/IHL after a high-fat meal as well as medium-term changes after 5 days of high-caloric diet with a 1500 kcal surplus on individual daily energy requirement.

STUDY TYPE

(retrospective/prospective/longitudinal/case control/cohort etc.) Prospective cohort study.

SUBJECTS

Twelve healthy subjects (6m/6f) for intraday variations, 15 healthy male subjects for medium-term high-caloric diet and 11 age- and BMI-matched controls.

FIELDSTRENGTH/SEQUENCE

3 T whole-body imager (Magnetom Vida, Siemens Healthineers, Erlangen, Germany), assessment of proton density fat fraction by chemical-shift encoded MRI (multi-echo gradient echo sequence, qDixon).

ASSESSMENT

Manually drawn regions of interest in head, body and tail of pancreas as well as in liver by an experienced medical physicist carefully avoiding inclusion of surrounding visceral fat (pancreas) or blood-vessels (liver).

STATISTICAL TESTS (please list the significance level)

Repeated measurements Anova for variabilities of PF and IHL, linear correlation analyses for relation of PF, IHL and BMI. Significance level p < 0.05 for all.

RESULTS (must have numerical data and statistical testing for each phrase)

Non-significant changes in PF in both studies (2.5±0.9 vs. 2.5±1.0% after high-fat meal, 1.4±0.8 vs. 1.6±0.6% after high-caloric diet and 1.6±0.7 vs. 1.8±1.0% in the isocaloric control group), unchanged IHL after high-fat meal (2.5±0.9 vs. 2.4±1.0 %) and in the control group (1.1±0.6 vs. 1.2±1.1%), but significantly increased IHL after 5-day high-caloric diet (1.6±2.2% vs. 2.6±3.6%, p < 0.05).

DATA CONCLUSION

Daytime and nutritional status have no significant influence on ectopic fat depots in pancreas and liver and will therefore represent no major confounders in epidemiologic or clinical studies.
A novel strategy for the detection of SARS-CoV-2 variants based on multiplex PCR-MALDI-TOF MS
Authors: Zhao Fei , Zhang Jianzhong , Wang Xuemei , Hou Xuexin , Qin Tian , Meng Fanliang , Xu Xiaona , Li Tianyi , Zhou Haijian , Kan Biao , Lu Jinxing , Xiao Di
Published: June 2021

Background

The second wave of coronavirus disease 2019 (COVID-19) has been incessantly causing catastrophe worldwide, and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants causes further uncertainty regarding epidemic risk. Here, a novel strategy for the detection of SARS-CoV-2 variants using multiplex PCR coupled with MALDI-TOF MS was developed.

Methods

Plasmids carrying gene sequences containing 9 mutation types in 7 mutated sites (HV6970del, N501Y, K417N, P681H, D614G, E484K, L452R, E484Q and P681R) in the receptor-binding domain of the spike protein of SARS-CoV-2 variants were synthesized. Using the nucleic acid sequence of SARS-CoV-2 nonvariant and a synthetic SARS-CoV-2-variant-carrying plasmid, a MALDI-TOF MS method based on the single-base mass probe extension of multiplex PCR amplification products was established to detect the above nine mutation types. The detection limit of this method was determined via the concentration gradient method. Twenty-one respiratory tract pathogens (9 bacteria, 11 respiratory viruses) and pharyngeal swab nucleic acid samples from healthy people were selected for specific validation. Sixteen samples from COVID-19 patients were used to verify the accuracy of this method.

Results

The 9 mutation types could be detected simultaneously by triple PCR amplification coupled with MALDI-TOF MS. SARS-CoV-2 and all six variants (B.1.1.7, B.1.351, B.1.429, B.1.526, P.1 and B.1.617) could be identified. The detection limit for all 9 sites was 1.5×103 copies. The specificity of this method was 100%, and the accuracy of real-time PCR CT values less than 30 among positive samples was 100%. This method is open and extensible, and can be used in a high-throughput manner, easily allowing the addition of new mutation sites as needed to identify and track new SARS-CoV-2 variants as they emerge.

Conclusions

Multiplex PCR-MALDI-TOF MS provides a new detection option with practical application value for SARS-CoV-2 and its variant infection.

Key point

An all-in-one SARS-CoV-2 variant identification method based on a multiplex PCR-MALDI-TOF MS system was developed. All of the SARS-CoV-2 variants can be identified based on 9 types of 7 mutated sites of RBD of spike protein using this method.
A clinical observational analysis of aerosol emissions from dental procedures
Authors: Dudding T. , Sheikh S. , Gregson F. , Haworth J. , Haworth S. , Main B.G. , Shrimpton A.J. , Hamilton F.W. ,   AERATOR group, Ireland A.J. , Maskell N.A. , Reid J.P. , Bzdek B.R. , Gormley M.
Published: June 2021

Aerosol generating procedures (AGPs) are defined as any procedure releasing airborne particles <5 μm in size from the respiratory tract. There remains uncertainty about which dental procedures constitute AGPs. We quantified the aerosol number concentration generated during a range of periodontal, oral surgery and orthodontic procedures using an aerodynamic particle sizer, which measures aerosol number concentrations and size distribution across the 0.5–20 μm diameter size range. Measurements were conducted in an environment with a sufficiently low background to detect a patient’s cough, enabling confident identification of aerosol. Phantom head control experiments for each procedure were performed under the same conditions as a comparison. Where aerosol was detected during a patient procedure, we assessed whether the size distribution could be explained by the non-salivary contaminated instrument source in the respective phantom head control procedure using a two-sided unpaired t-test (comparing the mode widths (log(σ)) and peak positions (DP,C)). The aerosol size distribution provided a robust fingerprint of aerosol emission from a source. 41 patients underwent fifteen different dental procedures. For nine procedures, no aerosol was detected above background. Where aerosol was detected, the percentage of procedure time that aerosol was observed above background ranged from 12.7% for ultrasonic scaling, to 42.9% for 3-in-1 air + water syringe. For ultrasonic scaling, 3-in-1 syringe use and surgical drilling, the aerosol size distribution matched the non-salivary contaminated instrument source, with no unexplained aerosol. High and slow speed drilling produced aerosol from patient procedures with different size distributions to those measured from the phantom head controls (mode widths log(σ)) and peaks (DP,C), p< 0.002) and, therefore, may pose a greater risk of salivary contamination. This study provides evidence for sources of aerosol generation during common dental procedures, enabling more informed evaluation of risk and appropriate mitigation strategies.
Using real-time data to guide decision-making during an influenza pandemic: a modelling analysis
Authors: Haw David J. , Biggerstaff Matthew , Prasad Pragati , Walker Joseph , Grenfell Bryan , Arinaminpathy Nimalan
Published: June 2021

Influenza pandemics typically occur in multiple waves of infection, often associated with initial emergence of a novel virus, followed (in temperate regions) by a later resurgence accompanying the onset of the annual influenza season. Here, we examined whether data collected from an initial pandemic wave could be informative, for the need to implement non-pharmaceutical measures in any resurgent wave. Drawing from the 2009 H1N1 pandemic in 10 states in the USA, we calibrated simple mathematical models of influenza transmission dynamics to data for virologically confirmed hospitalisations during the initial ‘spring’ wave. We then projected pandemic outcomes (cumulative hospitalisations) during the fall wave, and compared these projections with data. Model results show reasonable agreement for all states that reported a substantial number of cases in the spring wave. Using this model we propose a probabilistic decision framework that can be used to determine the need for pre-emptive measures such as postponing school openings, in advance of a fall wave. This work illustrates how model-based evidence synthesis, in real-time during an early pandemic wave, could be used to inform timely decisions for pandemic response.
Paraoxonase and acylated homoserine lactones in urine from patients with urinary tract infections-- relationship to microbial diversity by 16S rRNA gene sequencing
Authors: Lafleur John , Meisel Jacquelyn S. , Commichaux Seth , Amdur Richard L. , Pop Mihai , Silby Mark W.
Published: June 2021

Paraoxonase (PON) comprises a trio of mammalian enzymes that have been reported to have a number of roles including the inhibition of bacterial virulence and biofilm formation by microorganisms that quorum sense with acylated homoserine lactones (AHLs). PON have previously been reported to inhibit P. aeruginosa biofilm formation in mammalian airways and skin. An innate immune role for PON in urinary tract infection has not previously been reported. We performed western blots for PON1 in urine from patients with urinary tract infection (UTI), and also tested UTI urine for the presence of AHLs using a cellular reporter system. Urine sample microbiota was assessed through sequencing of the 16S rRNA marker gene. We report here that PON1 was not found in the urine of control subjects, however, in patients with UTI, PON1 was associated with the presence of E. coli in urine. AHLs, but not PON, were found in the bulk urine of those with P. aeruginosa UTI. Microbial consortia of PON positive UTI urine was found to be distinct from PON negative UTI urine; differentially over-represented bacteria in PON positive samples included a number of environmental opportunists. We hypothesize that PON may inhibit the quorum sensing activity of AHLs in UTI, as has previously described in skin and airways.
High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells
Authors: Chen Jennifer S. , Chow Ryan D. , Song Eric , Mao Tianyang , Israelow Benjamin , Kamath Kathy , Bozekowski Joel , Haynes Winston A. , Filler Renata B. , Menasche Bridget L. , Wei Jin , Alfajaro Mia Madel , Song Wenzhi , Peng Lei , Carter Lauren , Weinstein Jason S. , Gowthaman Uthaman , Chen Sidi , Craft Joe , Shon John C. , Iwasaki Akiko , Wilen Craig B. , Eisenbarth Stephanie C.
Published: June 2021

T follicular helper (Tfh) cells are the conventional drivers of protective, germinal center (GC)-based antiviral antibody responses. However, loss of Tfh cells and GCs has been observed in patients with severe COVID-19. As T cell-B cell interactions and immunoglobulin class switching still occur in these patients, non-canonical pathways of antibody production may be operative during SARS-CoV-2 infection. We found that both Tfh-dependent and -independent antibodies were induced against SARS-CoV-2 as well as influenza A virus. Tfh-independent responses were mediated by a population we call lymph node (LN)-Th1 cells, which remain in the LN and interact with B cells outside of GCs to promote high-affinity but broad-spectrum antibodies. Strikingly, antibodies generated in the presence and absence of Tfh cells displayed similar neutralization potency against homologous SARS-CoV-2 as well as the B.1.351 variant of concern. These data support a new paradigm for the induction of B cell responses during viral infection that enables effective, neutralizing antibody production to complement traditional GCs and even compensate for GCs damaged by viral inflammation.

One-Sentence Summary

Complementary pathways of antibody production mediate neutralizing responses to SARS-CoV-2.
A combination of RBD and NTD neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants
Authors: Haslwanter Denise , Dieterle M. Eugenia , Wec Anna Z. , O’Brien Cecilia M. , Sakharkar Mrunal , Florez Catalina , Tong Karen , Rappazzo C. Garrett , Lasso Gorka , Vergnolle Olivia , Wirchnianski Ariel S. , Bortz Robert H. , Laudermilch Ethan , Fels J. Maximilian , Mengotto Amanda , Malonis Ryan J. , Georgiev George I. , Quiroz Jose A. , Wrapp Daniel , Wang Nianshuang , Dye Kathryn E. , Barnhill Jason , Dye John M. , McLellan Jason S. , Daily Johanna P. , Lai Jonathan R. , Herbert Andrew S. , Walker Laura M. , Chandran Kartik , Jangra Rohit K.
Published: June 2021

Most known SARS-CoV-2 neutralizing antibodies (nAbs), including those approved by the FDA for emergency use, inhibit viral infection by targeting the receptor-binding domain (RBD) of the spike (S) protein. Variants of concern (VOC) carrying mutations in the RBD or other regions of S reduce the effectiveness of many nAbs and vaccines by evading neutralization. Therefore, therapies that are less susceptible to resistance are urgently needed. Here, we characterized the memory B-cell repertoire of COVID-19 convalescent donors and analyzed their RBD and non-RBD nAbs. We found that many of the non-RBD-targeting nAbs were specific to the N-terminal domain (NTD). Using neutralization assays with authentic SARS-CoV-2 and a recombinant vesicular stomatitis virus carrying SARS-CoV-2 S protein (rVSV-SARS2), we defined a panel of potent RBD and NTD nAbs. Next, we used a combination of neutralization-escape rVSV-SARS2 mutants and a yeast display library of RBD mutants to map their epitopes. The most potent RBD nAb competed with hACE2 binding and targeted an epitope that includes residue F490. The most potent NTD nAb epitope included Y145, K150 and W152. As seen with some of the natural VOC, the neutralization potencies of COVID-19 convalescent sera were reduced by 4-16-fold against rVSV-SARS2 bearing Y145D, K150E or W152R spike mutations. Moreover, we found that combining RBD and NTD nAbs modestly enhanced their neutralization potential. Notably, the same combination of RBD and NTD nAbs limited the development of neutralization-escape mutantsin vitro, suggesting such a strategy may have higher efficacy and utility for mitigating the emergence of VOC.

Importance

The US FDA has issued emergency use authorizations (EUAs) for multiple investigational monoclonal antibody (mAb) therapies for the treatment of mild to moderate COVID-19. These mAb therapeutics are solely targeting the receptor binding domain of the SARS-CoV-2 spike protein. However, the N-terminal domain of the spike protein also carries crucial neutralizing epitopes. Here, we show that key mutations in the N-terminal domain can reduce the neutralizing capacity of convalescent COVID-19 sera. We report that a combination of two neutralizing antibodies targeting the receptor binding and N-terminal domains may have higher efficacy and is beneficial to combat the emergence of virus variants.
Deep integrative models for large-scale human genomics
Authors: Sigurdsson Arnór I. , Westergaard David , Winther Ole , Lund Ole , Brunak Søren , Vilhjálmsson Bjarni J. , Rasmussen Simon
Published: June 2021

Polygenic risk scores (PRSs) are expected to play a critical role in achieving precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predictors mainly capture additive relationships and are limited in data modalities they can use. Here, we developed a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), specifically designed for large scale genomics data. The framework supports multi-task (MT) learning, automatic integration of other clinical and biochemical data, and model explainability. When applied to individual level data in the UK Biobank, we found that GLN outperformed LASSO for a wide range of diseases and in particularly autoimmune diseases. Furthermore, we show that this was likely due to modelling epistasis, and we showcase this by identifying widespread epistasis for Type 1 Diabetes. Furthermore, we trained PRS by integrating genotype, blood, urine and anthropometrics and found that this improved performance for 93% of 290 diseases and disorders considered. Finally, we found that including genotype data provided better calibrated PRS models compared to using measurements alone. EIR is available athttps://github.com/arnor-sigurdsson/EIR.
An efficient GUI-based clustering software for simulation and Bayesian cluster analysis of single-molecule localization microscopy data
Authors: Kutz Saskia , Zehrer Ando C. , Svetlitckii Roman , Balta Gülce S. Gülcüler , Galli Lucrezia , Kleber Susanne , Martin-Villalba Ana , Ewers Helge
Published: June 2021

Ligand binding of membrane proteins triggers many important cellular signaling events by the lateral aggregation of ligand-bound and other membrane proteins in the plane of the plasma membrane. This local clustering can lead to the co-enrichment of molecules that create an intracellular signal or bring sufficient amounts of activity together to shift an existing equilibrium towards the execution of a signaling event. In this way, clustering can serve as a cellular switch. The underlying uneven distribution and local enrichment of the signaling cluster's constituting membrane proteins can be used as a functional readout. This information is obtained by combining single-molecule fluorescence microscopy with cluster algorithms that can reliably and reproducibly distinguish clusters from fluctuations in the background noise to generate quantitative data on this complex process.

Cluster analysis of single-molecule fluorescence microscopy data has emerged as a proliferative field, and several algorithms and software solutions have been put forward. However, in most cases, such cluster algorithms require multiple analysis parameters to be defined by the user, which may lead to biased results. Furthermore, most cluster algorithms neglect the individual localization precision connected to every localized molecule, leading to imprecise results. Bayesian cluster analysis has been put forward to overcome these problems, but so far, it has entailed high computational cost, increasing runtime drastically. Finally, most software is challenging to use as they require advanced technical knowledge to operate.

Here we combined three advanced cluster algorithms with the Bayesian approach and parallelization in a user-friendly GUI and achieved up to an order of magnitude faster processing than for previous approaches. Our work will simplify access to a well-controlled analysis of clustering data generated by SMLM and significantly accelerate data processing. The inclusion of a simulation mode aids in the design of well-controlled experimental assays.
Rostral Anterior Cingulate Activations inversely relate to Reward Payoff Maximation & predict Depressed Mood
Authors: Balasubramani Pragathi Priyadharsini , Diaz-Delgado Juan , Grennan Gillian , Alim Fahad , Zafar-Khan Mariam , Maric Vojislav , Ramanathan Dhakshin , Mishra Jyoti
Published: June 2021

Choice selection strategies and decision making are typically investigated using multiple-choice gambling paradigms that require participants to maximize reward payoff. However, research shows that performance in such paradigms suffers from individual biases towards the frequency of gains to choose smaller local gains over larger longer term gain, also referred to as melioration. Here, we developed a simple two-choice reward task, implemented in 186 healthy human adult subjects across the adult lifespan to understand the behavioral, computational, and neural bases of payoff maximization versus melioration. The observed reward choice behavior on this task was best explained by a reinforcement learning model of differential future reward prediction. Simultaneously recorded and source-localized electroencephalography (EEG) showed that diminished theta-band activations in the right rostral anterior cingulate cortex (rACC) correspond to greater reward payoff maximization, specifically during the presentation of cumulative reward information at the end of each task trial. Notably, these activations (greater rACC theta) predicted depressed mood symptoms, thereby showcasing a reward processing marker of potential clinical utility.

Significance Statement

This study presents cognitive, computational and neural (EEG-based) analyses of a rapid reward-based decision-making task. The research has the following three highlights. 1) It teases apart two core aspects of reward processing, i.e. long term expected value maximization versus immediate gain frequency melioration based choice behavior. 2) It models reinforcement learning based behavioral differences between individuals showing that observed performance is best explained by differential extents of reward prediction. 3) It investigates neural correlates in 186 healthy human subjects across the adult lifespan, revealing specific theta band cortical source activations in right rostral anterior cingulate as correlates for maximization that further predict depressed mood across subjects.
Integrative transcriptomics reveals ectopic lipid homeostasis mechanisms in non-endocrine cells of the teleost pituitary
Authors: Ager-Wick Eirill , Maugars Gersende , Krogh Kristine von , Nourizadeh-Lillabadi Rasoul , Siddique Khadeeja , Fontaine Romain , Weltzien Finn-Arne , Henkel Christiaan
Published: June 2021

Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. It communicates the needs of the organism to different organs by secreting hormones into the bloodstream. Here, we have used the model fish medaka to investigate the developmental dynamics in the pituitary using a comprehensive RNA-seq time series. By linking developmental expression trends to single-cell RNA-seq profiles, we show how the transcriptional activities of cell types change during sexual maturation. One of the most prominent changes is the decline of the non-endocrine folliculo-stellate cell populations, and especially of rare cells expressing genes encoding secreted lipid transport proteins. As these genes are typically associated with the liver, this reveals the existence of unexpected connections between endocrine communication, lipid homeostasis, and sexual maturation.
SARS-CoV-2 Alpha, Beta and Delta variants display enhanced Spike-mediated Syncytia Formation
Authors: Rajah Maaran Michael , Hubert Mathieu , Bishop Elodie , Saunders Nell , Robinot Remy , Grzelak Ludivine , Planas Delphine , Dufloo Jérémy , Gellenoncourt Stacy , Bongers Alice , Zivaljic Marija , Planchais Cyril , Guivel-Benhassine Florence , Porrot Françoise , Mouquet Hugo , Chakrabarti Lisa , Buchrieser Julian , Schwartz Olivier
Published: June 2021

Severe COVID-19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS-CoV-2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighbouring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha and Beta spread and fusion in cell cultures. Alpha and Beta replicated similarly to D614G reference strain in Vero, Caco-2, Calu-3 and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Alpha, Beta and D614G fusion was similarly inhibited by interferon induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes differentially modified fusogenicity, binding to ACE2 and recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS-CoV-2 emerging variants display enhanced syncytia formation.

Synopsis

The Spike protein of the novel SARS-CoV-2 variants are comparative more fusogenic than the earlier strains. The mutations in the variant spike protein differential modulate syncytia formation, ACE2 binding, and antibody escape.

The spike protein of Alpha, Beta and Delta, in the absence of other viral proteins, induce more syncytia than D614G

The ACE2 affinity of the variant spike proteins correlates to their fusogenicity

Variant associated mutations P681H, D1118H, and D215G augment cell-cell fusion, while antibody escape mutation E484K, K417N and Δ242-244 hamper it.

Variant spike-mediated syncytia formation is effectively restricted by IFITMs
Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells
Authors: Bakoulis Stylianos , Krautz Robert , Alcaraz Nicolas , Salvatore Marco , Andersson Robin
Published: June 2021

Transposable elements are an abundant source of transcription factor binding sites and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable elements, in particular endogenous retroviral elements, carry open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding sites, shedding light on the formation of regulatory programs and the origins of regulatory elements.
INDEHISCENT regulates explosive seed dispersal
Authors: Galstyan Anahit , Sarchet Penny , Campos-Martin Rafael , Adibi Milad , Nikolov Lachezar A. , Antón Miguel Pérez , Rambaud-Lavigne Léa , Gan Xiangchao , Hay Angela
Published: June 2021

How traits evolve to produce novelty or stasis is an open question in biology. We investigate this question in Cardamine hirsuta, a relative of Arabidopsis thaliana that employs explosive fracture to disperse its seeds. This trait evolved through key morphomechanical innovations that distinguish the otherwise very similar, dehiscent fruit of these two species. Using CRISPR/Cas9, we show that dehiscence zone formation is absolutely required for explosive fracture in C. hirsuta, and is controlled by the bHLH transcription factor INDEHISCENT (IND). Using mutant screens, we identified the MADS-box transcription factor FRUITFULL (FUL) as a negative regulator of IND in C. hirsuta. Although FUL function is conserved in C. hirsuta, the consequences of IND mis-expression differ in ful mutants of C. hirsuta versus A. thaliana. In ful mutants of both species, valve tissue is replaced by dehiscence zone tissue, which comprises two distinct cell types: lignified layer and separation layer cells. While A. thaliana ful mutants develop stunted fruit with ectopic lignified layer cells, C. hirsuta ful mutants have elongated fruit with ectopic separation layer cells. We show that IND dose determines the proportion of these two cell types in ectopic dehiscence zones. We also show that the extent of ectopic lignification caused by IND mis-expression determines fruit length. Our findings indicate developmental system drift in the conserved gene network patterning dehiscent fruit in two related Brassicaceae species.
Litter characteristics and helping context during early life shape the responsiveness of the stress axis in a wild cooperative breeder
Authors: Cohas Aurélie , Bichet Coraline , Garcia Rébecca , Pardonnet Sylvia , Lardy Sophie , Rey Benjamin
Published: June 2021

Stress responses have evolved to quickly and appropriately deal with environmental stressors in order to secure or restore homeostasis. Since the regulation of stress hormones plays a key adaptive role, the regulatory processes controlling stress hormones levels may be under high selective pressure. The social environment during early life (parents and litter characteristics) strongly affects ontogeny of the hypothalamic-pituitary-adrenal (HPA) axis. In cooperative breeders, offspring are also confronted with helpers but whether and how variation in the helping context can affect HPA axis responsiveness of offspring remains unanswered. Combining dexamethasone suppression and adrenocorticotropic hormone stimulation tests, we investigated the link between the social environment and the characteristics of the HPA axis at the early stages of life in wild Alpine marmots. We show that when raised in the presence of helpers, marmot pups exhibit a greater capacity not only to mount, but also to turn off a stress response. The capacity to mount a stress response was also higher as the pups were raised in large litters. Determining impacts of such social modulation of the HPA axis functioning on individual fitness would make an important contribution to our understanding of the evolution of cooperative breeding.
Prediction and Characterization of Disorder-Order Transition Regions in Proteins by Deep Learning
Authors: Yan Ziang , Omori Satoshi , Yamada Kazunori D , Nishi Hafumi , Kinoshita Kengo
Published: June 2021

The biological functions of proteins are traditionally thought to depend on well-defined three-dimensional structures, but many experimental studies have shown that disordered regions lacking fixed three-dimensional structures also have crucial biological roles. In some of these regions, disorder–order transitions are also involved in various biological processes, such as protein-protein interaction and ligand binding. Therefore, it is crucial to study disordered regions and structural transitions for further understanding of protein functions and folding. Owing to the costs and time requirements of experimental identification of natively disordered or transitional regions, the development of effective computational methods is a key research goal. In this study, we used overall residue dependencies and deep representation learning for prediction and reused the obtained disordered regions for the prediction of disorder–order transitions. Two similar and related prediction tasks were combined. Firstly, we developed a novel deep learning method, Res-BiLstm, for residue-wise disordered region prediction. Our method outperformed other predictors with respect to almost all criteria, as evaluated using an independent test set. For disorder-order transition prediction, we proposed a transfer learning method, Res-BiLstm-NN, with an acceptable but unbalanced performance, yielding reasonable results. To grasp underlining biophysical principles of disorder-order transitions, we performed qualitative analyses on the obtained results and discovered that most transitions have strong disordered or ordered preferences, and more transitions are consistent with the ordered state than the disordered state, different from conventional wisdom. To the best of our knowledge, this is the first sizable-scale study of transition prediction.

Availability

https://github.com/Yanzziang/Transition_Disorder_Prediction

Contact

kengo@ecei.tohoku.ac.jp
Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions
Authors: Didier Gilles , Laurin Michel
Published: June 2021

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model.

Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences.

We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals.

This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.
Control of SARS-CoV-2 infection after Spike DNA or Spike DNA+Protein co-immunization in rhesus macaques
Authors: Rosati Margherita , Agarwal Mahesh , Hu Xintao , Devasundaram Santhi , Stellas Dimitris , Chowdhury Bhabadeb , Bear Jenifer , Burns Robert , Donohue Duncan , Pessaint Laurent , Andersen Hanne , Lewis Mark G. , Terpos Evangelos , Dimopoulos Meletios Athanasios , Wlodawer Alexander , Mullins James I. , Venzon David. J. , Pavlakis George N. , Felber Barbara K
Published: June 2021

The speed of development, versatility and efficacy of mRNA-based vaccines have been amply demonstrated in the case of SARS-CoV-2. DNA vaccines represent an important alternative since they induce both humoral and cellular immune responses in animal models and in human trials. We tested the immunogenicity and protective efficacy of DNA-based vaccine regimens expressing different prefusion-stabilized SARS-CoV-2 Spike antigens upon intramuscular injection followed by electroporation in rhesus macaques. Different Spike DNA vaccine regimens induced antibodies that potently neutralized SARS-CoV-2 in vitro and elicited robust T cell responses. The DNA-only vaccine regimens were compared to a regimen that included co- immunization of Spike DNA and protein in the same anatomical site, the latter of which showed significant higher antibody responses. All vaccine regimens led to control of SARS-CoV-2 intranasal/intratracheal challenge and absence of virus dissemination to the lower respiratory tract. Vaccine-induced binding and neutralizing antibody titers and antibody-dependent cellular phagocytosis inversely correlated with transient virus levels in the nasal mucosa. Importantly, the Spike DNA+Protein co-immunization regimen induced the highest binding and neutralizing antibodies and showed the strongest control against SARS-CoV-2 challenge in rhesus macaques.

Author summary

Anti-Spike neutralizing antibodies provide strong protection against SARS-CoV-2 infection in animal models, and correlate with protection in humans, supporting the notion that induction of strong humoral immunity is key to protection. We show induction of robust antibody and T cell responses by different Spike DNA-based vaccine regimens able to effectively mediate protection and to control SARS-CoV-2 infection in the rhesus macaque model. This study provides the opportunity to compare vaccines able to induce different humoral and cellular immune responses in an effort to develop durable immunity against the SARS-CoV-2. A vaccine regimen comprising simultaneous co-immunization of DNA and Protein at the same anatomical site showed best neutralizing abilities and was more effective than DNA alone in inducing protective immune responses and controlling SARS-CoV-2 infection. Thus, an expansion of the DNA vaccine regimen to include co-immunization with Spike protein may be of advantage also for SARS-CoV-2.
Target Dependent Coordinated Biogenesis Ensures Cascaded Expression of miRNAs in Activated Murine Macrophage
Authors: Chatterjee Susanta , Mukherjee Ishita , Bose Mainak , Bhattacharjee Shreya , Chakrabarti Saikat , Bhattacharyya Suvendra N.
Published: June 2021

MicroRNAs (miRNAs) repress protein expression by binding to the 3’ UTR of the target mRNAs. By exploring the effect of target mRNA on biogenesis of cognate miRNAs, we have noted miRNA with higher number of binding sites (primary miRNA) coordinates the biogenesis and activity of another miRNA (secondary miRNA) having binding sites on the 3’ UTR of a common target mRNA. From the quantitative data obtained from macrophage cells, we detected miR-146a-5p as a “primary” miRNA that coordinates biogenesis of “secondary” miR-125b, miR-21 or miR-142-3p to target new sets of mRNAs to balance the immune response in activated macrophage cells. Interestingly, target dependent coordinated biogenesis of miRNAs, happening on the rough endoplasmic reticulum attached membrane, ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs where a cascaded effect of primary miRNA on its secondary targets has been detected. Extensive computational analysis for the presence of coordinated biogenesis pairs of miRNAs in mammalian cells has also allowed us to construct a coordinate biogenesis repository to determine context specific coordinated biogenesis relationships exists for specific pairs of miRNAs in mammalian cells.

Graphical Abstract

miRNA with higher number of binding sites (primary miRNA) can coordinates the biogenesis and activity of another miRNA (secondary miRNA)

Target dependent coordinated biogenesis of miRNAs ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs on rER attached polysomes

miR-146a-5p acts as a “primary” miRNA to coordinate biogenesis of “secondary” miR-125b, miR-21 or miR-142-3p in activated macrophage cells

Coordinate biogenesis balance the immune response in activated macrophage cells by ensuring propagation of primary miRNAs effect to diverse target mRNAs through secondary miRNAs.
Evolutionary analysis of gene ages across TADs associates chromatin topology with whole genome duplications
Authors: James Caelinn , Trevisan-Herraz Marco , Juan David , Rico Daniel
Published: June 2021

Topologically associated domains (TADs) are interaction sub-networks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localise by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localisation patterns between the genes born during vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggests that TADs could play a role in organising ancestral functions and evolutionary novelty.

Highlights

TADs coincide with clusters of genes that are close in their evolutionary age.

Whole genome duplications mark a transition in gene age co-localisation clusters.

Gene age co-localisation patterns are associated with TAD insulation.

Young essential genes share TADs and interact with old genes.
Cas9-targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants
Authors: Merkulov Pavel , Gvaramiya Sofya , Komakhin Roman , Omarov Murad , Dudnikov Maxim , Kocheshkova Alina , Konstantinov Zakhar , Soloviev Alexander , Karlov Gennady , Divashuk Mikhail , Kirov Ilya
Published: June 2021

Transposable element insertions (TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large, complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that reflect mobilome dynamics are difficult to track using short reads. To address these challenges, we combined Cas9-targeted Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of theEVADÉ(EVD) retrotransposon in wild-typeArabidopsis thalianaand rapidly obtained up to 40x sequence coverage. Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of theEVDtransposon in theddm1genome uncovered the crucial role of DNA methylation in shapingEVDinsertion preference. We also investigated somatic transposition events of theONSENtransposon family, finding that genes that are downregulated during heat stress are preferentially targeted byONSENs. Finally, we detected hypomethylation of novel somatic insertions for twoONSENs. CANS and NanoCasTE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.
Genetically engineered insects with sex-selection and genetic incompatibility enable population suppression
Authors: Upadhyay Ambuj , Feltman Nathan R , Sychla Adam , Das Siba R , Maselko Maciej , Smanski Michael J
Published: June 2021

Engineered Genetic Incompatibility (EGI) is a method to create species-like barriers to sexual reproduction. It has applications in pest control that mimic Sterile Insect Technique when only EGI males are released. This can be facilitated by introducing conditional female-lethality to EGI strains to generate a sex-sorting incompatible male system (SSIMS). Here we demonstrate a proof of concept by combining tetracycline-controlled female lethality constructs with apyramus-targeting EGI line in the model insectDrosophila melanogaster. We show that both functions (incompatibility and sex-sorting) are robustly maintained in the SSIMS line and that this approach is effective for population suppression in cage experiments. Further we show that SSIMS males remain competitive with wild-type males for reproduction with wild-type females, including at the level of sperm competition.
The incentive circuit: memory dynamics in the mushroom body of Drosophila melanogaster
Authors: Gkanias Evripidis , McCurdy Li Yan , Nitabach Michael N , Webb Barbara
Published: June 2021

Insects adapt their response to stimuli, such as odours, according to their pairing with positive or negative reinforcements, such as sugar or shock. Recent electrophysiological and imaging findings in Drosophila melanogaster allow detailed examination of the neural mechanisms supporting the acquisition, forgetting and assimilation of memories. We propose that this data can be explained by the combination of a dopaminergic plasticity rule that supports a variety of synaptic strength change phenomena, and a circuit structure (derived from neuroanatomy) between dopaminergic and output neurons that creates different roles for specific neurons. Computational modelling shows that this circuit allows for rapid memory acquisition, transfer from short-term to long-term, and exploration/exploitation trade-off. The model can reproduce the observed changes in the activity of each of the identified neurons in conditioning paradigms and can be used for flexible behavioural control.
Provenance Attestation of Human Cells Using Physical Unclonable Functions
Authors: Li Yi , Bidmeshki Mohammad Mahdi , Kang Taek , Nowak Chance M. , Makris Yiorgos , Bleris Leonidas
Published: June 2021

We introduce a novel methodology, namely CRISPR-Engineered Attestation of Mammalian Cells using Physical Unclonable Functions (CREAM-PUFs), which can serve as the cornerstone for formally verifying transactions in human cell line distribution networks. A PUF is a physical entity which provides a measurable output that can be used as a unique and irreproducible identifier for the artifact wherein it is embedded. Popularized by the electronics industry, silicon PUFs leverage the inherent physical variations of semiconductor manufacturing to establish intrinsic security primitives for attesting integrated circuits. Owing to the stochastic nature of these variations and the multitude of steps involved, photo-lithographically manufactured silicon PUFs are impossible to reproduce (thus unclonable). Inspired by the success of silicon PUFs, we sought to exploit a combination of sequence-restricted barcodes and the inherent stochasticity of CRISPR-induced non-homologous end joining DNA error repair to create the first generation of genetic physical unclonable functions in three distinct human cells (HEK293, HCT116, and HeLa). We demonstrate that these CREAM-PUFs are robust (i.e., they repeatedly produce the same output), unique (i.e., they do not coincide with any other identically produced PUF), and unclonable (i.e., they are virtually impossible to replicate). Accordingly, CREAM-PUFs can serve as a foundational principle for establishing provenance attestation protocols for protecting intellectual property and confirming authenticity of engineered cell lines.
Disruption of folate metabolism causes poor alignment and spacing of mouse conceptuses for multiple generations
Authors: Wilkinson Amy L. , Menelaou Katerina , Rakoczy Joanna , Tan Xiu S. , Watson Erica D.
Published: June 2021

Abnormal uptake or metabolism of folate increases risk of human pregnancy complications, though the mechanism is unclear. Here, we explore how defective folate metabolism influences early development by analysing mice with anMtrrgthypomorphic mutation. MTRR is necessary for methyl group utilisation from the folate cycle, and theMtrrgtallele disrupts this process. We show that the spectrum of phenotypes previously observed inMtrrgt/gtconceptuses at embryonic day (E) 10.5 is apparent from E8.5 including developmental delay, congenital malformations, and placental phenotypes (e.g., eccentric chorioallantoic attachment). Notably, we report misalignment of someMtrrgtconceptuses within their implantation sites from E6.5. The degree of skewed growth occurs across a continuum, with eccentric chorioallantoic attachment now re-characterised as a severe form of conceptus misalignment. Additionally, someMtrrgt/gtconceptuses display twinning. Therefore, we implicate folate metabolism in blastocyst orientation and spacing at implantation. Embryo development is influenced by skewed growth since developmental delay and heart malformations (but not neural tube defects) associate with severe misalignment ofMtrrgt/gtconceptuses. Patterning of trophoblast lineage markers is largely unaffected in skewedMtrrgt/gtconceptuses at E8.5 indicating trophoblast differentiation was normal when misaligned. Typically, the uterus guides conceptus orientation. Accordingly, we manipulate the maternalMtrrgenotype and assess conceptus alignment.Mtrr+/gt, andMtrrgt/gtmothers, plusMtrr+/+mothers, exhibit misaligned conceptuses at E6.5. While progesterone and/or BMP2 signalling required for decidualisation might be disrupted, normal gross decidual morphology, patterning, and blood perfusion is evident regardless of conceptus alignment, arguing against a uterine defect. Given the important finding thatMtrr+/+mothers also display conceptus misalignment, a grandparental effect is explored. Multigenerational phenotype inheritance is characteristic of theMtrrgtmodel, though the mechanism remains unclear. Genetic pedigree analysis reveals that severe skewing associates with theMtrrgenotype of either maternal grandparent. Moreover, misalignment is independent of the uterus and instead is attributed to an embryonic mechanism based on blastocyst transfer experiments. Overall, our data indicates that abnormal folate metabolism influences conceptus orientation over multiple generations with implications for subsequent development. Our study casts light on the complex role of folate metabolism during development beyond a direct maternal effect.