bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning
Authors: Riba Andrea , Oravecz Attila , Durik Matej , Jiménez Sara , Alunni Violaine , Cerciat Marie , Jung Matthieu , Keime Céline , Keyes William M. , Molina Nacho
Published: March 2021

The cell cycle is a fundamental process of life, however, a quantitative understanding of gene regulation dynamics in the context of the cell cycle is still far from complete. Single-cell RNA-sequencing (scRNA-seq) technology gives access to its dynamics without externally perturbing the cell. Here, we build a high-resolution map of the cell cycle transcriptome based on scRNA-seq and deep-learning. By generating scRNA-seq libraries with high depth, in mouse embryonic stem cells and human fibroblasts, we are able to observe cycling patterns in the unspliced-spliced RNA space for single genes. Since existing methods in scRNA-seq are not efficient to measure cycling gene dynamics, we propose a deep learning approach to fit these cycling patterns sorting single cells across the cell cycle. We characterize the cell cycle in asynchronous pluripotent and differentiated cells identifying major waves of transcription during the G1 phase and systematically study the G1-G0 transition where the cells exit the cycle. Our work presents to the scientific community a broader understanding of RNA velocity and cell cycle maps, that we applied to pluripotency and differentiation. Our approach will facilitate the study of the cell cycle in multiple cellular models and different biological contexts, such as cancer and development.
Style Transfer Using Generative Adversarial Networks for Multi-Site MRI Harmonization
Authors: Liu Mengting , Maiti Piyush , Thomopoulos Sophia , Zhu Alyssa , Chai Yaqiong , Kim Hosung , Jahanshad Neda
Published: March 2021

Large data initiatives and high-powered brain imaging analyses require the pooling of MR images acquired across multiple scanners, often using different protocols. Prospective cross-site harmonization often involves the use of a phantom or traveling subjects. However, as more datasets are becoming publicly available, there is a growing need for retrospective harmonization, pooling data from sites not originally coordinated together. Several retrospective harmonization techniques have shown promise in removing cross-site image variation. However, most unsupervised methods cannot distinguish between image-acquisition based variability and cross-site population variability, so they require that datasets contain subjects or patient groups with similar clinical or demographic information. To overcome this limitation, we consider cross-site MRI image harmonization as a style transfer problem rather than a domain transfer problem. Using a fully unsupervised deep-learning framework based on a generative adversarial network (GAN), we show that MR images can be harmonized by inserting the style information encoded from a reference image directly, without knowing their site/scanner labelsa priori. We trained our model using data from five large-scale multi-site datasets with varied demographics. Results demonstrated that our styleencoding model can harmonize MR images, and match intensity profiles, successfully, without relying on traveling subjects. This model also avoids the need to control for clinical, diagnostic, or demographic information. Moreover, we further demonstrated that if we included diverse enough images into the training set, our method successfully harmonized MR images collected from unseen scanners and protocols, suggesting a promising novel tool for ongoing collaborative studies.
Efficiency of the synthetic self-splicing RiboJ ribozyme is robust tocis- andtrans-changes in genetic background
Authors: Vlková Markéta , Morampalli Bhargava Reddy , Silander Olin K.
Published: March 2021

The expanding knowledge of the variety of synthetic genetic elements has enabled the construction of new and more efficient genetic circuits and yielded novel insights into molecular mechanisms. However, context dependence, in which interactions between proximal (cis) or distal (trans) elements affect the behaviour of these elements, can reduce their general applicability or predictability. Genetic insulators, which mitigate unintended context-dependentcis-interactions, have been used to address this issue. One of the most commonly used genetic insulators is a self-splicing ribozyme called RiboJ, which can be used to decouple upstream 5’ UTR in mRNA from downstream sequences (e.g., open reading frames). Despite its general use as an insulator, there has been no systematic study quantifying the efficiency of RiboJ splicing or whether this autocatalytic activity is robust totrans- andcis-genetic context. Here, we determine the robustness of RiboJ splicing in the genetic context of six widely divergentE. colistrains. We also check for possiblecis-effects by assessing two SNP versions close to the catalytic site of RiboJ. We show that mRNA molecules containing RiboJ are rapidly spliced even during rapid exponential growth and high levels of gene expression, with a mean efficiency of 98%. We also show that neither thecis- nortrans-genetic context has a significant impact on RiboJ activity, suggesting this element is robust to bothcis- andtrans-genetic changes.
High throughput genome-wide single cell protein:DNA binding site mapping by targeted insertion of promoters (TIP-seq)
Authors: Bartlett Daniel A. , Dileep Vishnu , Henikoff Steve , Gilbert David M.
Published: March 2021

Assessing cell to cell, and importantly, chromosome to chromosome, heterogeneity in cellular phenotypes is a central goal of modern cell biology. However, chromatin profiling in single cells has been extremely challenging, and single chromosome profiling has not been achieved. In cases where single cell methods have shown promise, success has been mainly limited to histone proteins and/or require highly specialized equipment or cell type specific protocols and are relatively low throughput. Here, we have combined the advantages of tagmentation, linear amplification and combinatorial indexing to produce a high throughput single cell DNA binding site mapping method that does not require specialized equipment and is capable of multiplexing several samples/ target proteins in one experiment. Targeted Insertion of Promoters (TIP-seq) uses Tn5 fused to protein A (as with CUT&Tag) to insert a T7 RNA polymerase promoter into sites adjacent to an antibody bound to a chromatin protein of interest, followed by linear amplification of flanking DNA with T7 polymerase, cDNA preparation and PCR indexing. Tip-seq provides ∼10-fold higher unique reads and thus higher coverage per single cell compared to state-of-the-art methods. We apply TIP-seq to map histone modifications, RNA PolII and CTCF binding sites in single human and mouse cells. TIP-seq will also be adaptable for other platforms, such as 10X genomics and ICELL8. In summary, TIP-seq provides a high-throughput, low-cost method for single cell protein mapping, that yields substantially higher coverage per cell and signal to noise than existing methods.
Decreased synthesis and variable gene transcripts of oxytocin in a domesticated avian species
Authors: Tobari Yasuko , Theofanopoulou Constantina , Mori Chihiro , Sato Yoshimi , Marutani Momoka , Fujioka Sayaka , Konno Norifumi , Suzuki Kenta , Furutani Akari , Hakataya Shiomi , Yao Cheng-Te , Yang En-Yun , Tsai Chia-Ren , Tang Pin-Chi , Chen Chih-Feng , Boeckx Cedric , Jarvis Erich D. , Okanoya Kazuo
Published: March 2021

The Bengalese finch was domesticated more than 250 years ago from the wild white-rumped munia. Similar to other domesticated species, Bengalese finches show a reduced fear response and have lower corticosterone levels, compared to white-rumped munias. Bengalese finches and munias also have different song types. Since oxytocin (OT) has been found to be involved in stress coping and auditory processing, we tested whether theOTsequence and brain expression pattern and content differ in wild munias and domesticated Bengalese finches. We identified intra-strain variability in the untranslated regions of theOTsequence in Bengalese finches in comparison to the muniaOT. Several of these changes fall in specific transcription factor binding sites, which show either a conserved or a relaxed evolutionary trend in the avian lineage, and in vertebrates in general. Althoughin situhybridization in several hypothalamic nuclei did not reveal significant differences in the number of cells expressingOTbetween the two strains, real-time quantitative PCR showed significantly lowerOTmRNA expression in the diencephalon of the Bengalese finches relative to munias. Our study thus points to a decreasedOTsynthesis in the domestic strain compared with the wild strain in birds. This is an opposite pattern from that found in some domesticated mammals, suggesting that different processes ofOTfunction might have occurred in mammals and birds under domestication.
Micro-region transcriptomics of fixed human tissue using Pick-Seq
Authors: Maliga Zoltan , Nirmal Ajit J. , Ericson Nolan G. , Boswell Sarah A. , U’Ren Lance , Podyminogin Rebecca , Chow Jennifer , Chen Yu-An , Chen Alyce A. , Weinstock David M. , Lian Christine G. , Murphy George F. , Kaldjian Eric P. , Santagata Sandro , Sorger Peter K.
Published: March 2021

Spatial transcriptomics and multiplexed imaging are complementary methods for studying tissue biology and disease. Recently developed spatial transcriptomic methods use fresh-frozen specimens but most diagnostic specimens, clinical trials, and tissue archives rely on formaldehyde-fixed tissue. Here we describe the Pick-Seq method for deep spatial transcriptional profiling of fixed tissue. Pick-Seq is a form of micro-region sequencing in which small regions of tissue, containing 5-20 cells, are mechanically isolated on a microscope and then sequenced. We demonstrate the use of Pick-Seq with several different fixed and frozen human specimens. Application of Pick-Seq to a human melanoma with complex histology reveals significant differences in transcriptional programs associated with tumor invasion, proliferation, and immuno-editing. Parallel imaging confirms changes in immuno-phenotypes and cancer cell states. This work demonstrates the ability of Pick-Seq to generate deep spatial transcriptomic data from fixed and archival tissue with multiplexed imaging in parallel.
Targetingde novolipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer
Authors: Bartolacci Caterina , Andreani Cristina , Vias Do Vale Gonçalo , Berto Stefano , Melegari Margherita , Crouch Anna C. , Baluya Dodge L. , Kemble George , Hodges Kurt , Starrett Jacqueline , Politi Katerina , Starnes Sandra L. , Lorenzini Daniele , Raso Maria Gabriela , Soto Luisa Solis , Behrens Carmen , Kadara Humam , Gao Boning , Gerber David , Wistuba Ignacio I. , Minna John D. , McDonald Jeffrey , Scaglioni Pier Paolo
Published: March 2021

MutantKRAS(KM) is the most common oncogene in lung cancer (LC). KM regulates several metabolic networks, but their role in tumorigenesis is still not sufficiently characterized to be exploited in cancer therapy. To identify metabolic networks specifically deregulated in KMLC, we characterized the lipidome of genetically engineered LC mice, cell lines, patient derived xenografts and primary human samples. We also determined that KMLC, but not EGFR-mutant (EGFR-MUT) LC, is enriched in triacylglycerides (TAG) and phosphatidylcholines (PC). We also found that KM upregulates fatty acid synthase (FASN), a rate-limiting enzyme in fatty acid (FA) synthesis promoting the synthesis of palmitate and PC. We determined that FASN is specifically required for the viability of KMLC, but not of LC harboring EGFR-MUT or wild type KRAS. Functional experiments revealed that FASN inhibition leads to ferroptosis, a reactive oxygen species (ROS)-and iron-dependent cell death. Consistently, lipidomic analysis demonstrated that FASN inhibition in KMLC leads to accumulation of PC with polyunsaturated FA (PUFA) chains, which are the substrate of ferroptosis. Integrating lipidomic, transcriptome and functional analyses, we demonstrated that FASN provides saturated (SFA) and monounsaturated FA (MUFA) that feed the Lands cycle, the main process remodeling oxidized phospholipids (PL), such as PC. Accordingly, either inhibition of FASN or suppression of the Lands cycle enzymes PLA2 and LPCAT3, promotes the intracellular accumulation of lipid peroxides and ferroptosis in KMLC bothin vitroandin vivo. Our work supports a model whereby the high oxidative stress caused by KM dictates a dependency on newly synthesized FA to repair oxidated phospholipids, establishing a targetable vulnerability. These results connect KM oncogenic signaling, FASN induction and ferroptosis, indicating that FASN inhibitors already in clinical trial in KMLC patients (NCT03808558) may be rapidly deployed as therapy for KMLC.
The potential of dynamic physiological traits in young tomato plants to predict field-yield performance
Authors: Gosa Sanbon Chaka , Koch Amit , Shenhar Itamar , Hirschberg Joseph , Zamir Dani , Moshelion Menachem
Published: March 2021

To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zetaz2083and tangerinet3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY:r2= 0.9 and 0.77, respectively) and plant vegetative weight (PW:r2= 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.
A novel Mycobacterium tuberculosis-specific subunit vaccine provides synergistic immunity upon co-administration with Bacillus Calmette-Guérin
Authors: Woodworth Joshua S. , Clemmensen Helena Strand , Battey Hannah , Dijkman Karin , Lindenstrøm Thomas , Laureano Raquel Salvador , Taplitz Randy , Morgan Jeffrey , Aagaard Claus , Rosenkrands Ida , Lindestam Arlehamn Cecilia S. , Andersen Peter , Mortensen Rasmus
Published: March 2021

Tuberculosis (TB) remains a global health crisis. Following encouraging clinical results of subunit vaccination and revaccination with Bacillus Calmette-Guérin (BCG), it has been suggested to combine BCG and subunit vaccines for increased efficacy. Current subunit vaccines are almost exclusively designed as BCG boosters. The goal of this study was to design a subunit vaccine that does not share antigens with BCG and explore the advantages of a BCG+subunit vaccine co-administration strategy, where the two vaccines do not cross-react. Eight protective antigens were selected to create a Mycobacterium tuberculosis (Mtb)-specific subunit vaccine, named H107. Whereas subunit vaccines with BCG-shared antigens displayed cross-reactivity to BCG in vivo in both mice and humans, H107 showed no cross-reactivity and did not inhibit BCG colonization in mice. Encouragingly, co-administering H107 with BCG (BCG+H107) led to increased adaptive immune responses against both H107 and BCG leading to improved BCG-mediated immunity. In contrast to subunit vaccines with BCG-shared antigens, ‘boosting’ BCG with H107 led to substantial expansion of clonal diversity in the T cell repertoire, and BCG+H107 co-administration conferred significantly increased Th17 responses and less differentiated CD4 T cells. CD4 T cells induced by BCG+H107 maintained functional superiority after Mtb infection, and BCG+H107 provided significantly increased long-term protection compared to both BCG and H107 alone, as well as, BCG co-administered with a subunit vaccine composed of antigens shared with BCG. Overall, we identify several advantages of combining an Mtb-specific subunit vaccine with BCG and introduce H107 as a BCG-complementing vaccine with distinctive value for co-administration with BCG.
BATL: Bayesian annotations for targeted lipidomics
Authors: Chitpin Justin G. , Surendra Anuradha , Nguyen Thao T. , Taylor Graeme P. , Xu Hongbin , Alecu Irina , Ortega Roberto , Tomlinson Julianna J. , Crawley Angela M. , McGuinty Michaeline , Schlossmacher Michael G. , Saunders-Pullman Rachel , Cuperlovic-Culf Miroslava , Bennett Steffany A.L. , Perkins Theodore J.
Published: March 2021

Motivation

Bioinformatic tools capable of annotating, rapidly and reproducibly, large, targeted lipidomic datasets are limited. Specifically, few programs enable high-throughput peak assessment of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) data acquired in either selected or multiple reaction monitoring (SRM and MRM) modes.

Results

We present here Bayesian Annotations for Targeted Lipidomics (BATL), a Gaussian naïve Bayes classifier for targeted lipidomics that annotates peak identities according to eight features related to retention time, intensity, and peak shape. Lipid identification is achieved by modelling distributions of these eight input features across biological conditions and maximizing the joint posterior probabilities of all peak identities at a given transition. When applied to sphingolipid and glycerophosphocholine SRM datasets, we demonstrate over 95% of all peaks are rapidly and correctly identified.

Availability and implementation

BATL software is freely accessible online athttps://complimet.ca/batl/and is compatible with Safari, Firefox, Chrome and Edge.

Supplementary information

Supplementary data are available atBioinformaticsonline.
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data
Authors: Amblard Elise , Bac Jonathan , Chervov Alexander , Soumelis Vassili , Zinovyev Andrei
Published: March 2021

Background

Single-cell RNA-seq datasets are characterized by large ambient dimensionality, and their analyses can be affected by various manifestations of the dimensionality curse. One of these manifestations is the hubness phenomenon, i.e. existence of data points with surprisingly large incoming connectivity degree in the neighbourhood graph. Conventional approach to dampen the unwanted effects of high dimension consists in applying drastic dimensionality reduction. It remains unexplored if this step can be avoided thus retaining more information than contained in the low-dimensional projections, by correcting directly hubness.

Results

We investigate the phenomenon of hubness in scRNA-seq data in spaces of increasing dimensionality. We also link increased hubness to increased levels of dropout in sequencing data. We show that hub cells do not represent any visible technical or biological bias. The effect of various hubness reduction methods is investigated with respect to the visualization, clustering and trajectory inference tasks in scRNA-seq datasets. We show that hubness reduction generates neighbourhood graphs with properties more suitable for applying machine learning methods; and that it outperforms other state-of-the-art methods for improving neighbourhood graphs. As a consequence, clustering, trajectory inference and visualisation perform better, especially for datasets characterized by large intrinsic dimensionality.

Conclusion

Hubness is an important phenomenon in sequencing data. Reducing hubness can be beneficial for the analysis of scRNA-seq data with large intrinsic dimensionality in which case it can be an alternative to drastic dimensionality reduction.
Amelioration of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration
Authors: Chen Xi , Niu Xuran , Liu Yang , Zheng Rui , Wang Liren , Yang Lei , Lu Jian , Yin Shuming , Shao Yanjiao , Wei Yu , Pan Jiahao , Sayed Ahmed , Ma Xueyun , Liu Meizhen , Jing Fengxiang , Liu Mingyao , Hu Jiazhi , Zhang Xiaohui , Li Dali
Published: March 2021

Site-specific integration of exogenous gene through genome editing is a promising strategy for gene therapy. However, homology-directed repair (HDR) only occurring in proliferating cells is inefficient especiallyin vivo. To investigate the efficacy of Cas9-induced homology-independent targeted integration (HITI) strategy for gene therapy, a rat hemophilia B model was generated and employed. Through HITI, a DNA sequence encoding the last exon of ratAlbumin(rAlb) gene fused with a high-specific-activity Factor IX variant (R338L) using T2A, was inserted into the last intron of rAlbvia recombinant adeno-associated viral (rAAV). The knock-in efficiency reached up to 3.66% determined by ddPCR. The clotting time was reduced to normal level 4 weeks after treatment, and the circulating FIX level was gradually increased up to 52% of normal during 9 months even after partial hepatectomy, demonstrating the amelioration of hemophilia. Through PEM-seq, no significant off-targeting effect was detected. Moreover, this study provides a promising therapeutic approach for hereditary diseases.
A two-type branching process model of gene family evolution
Authors: Zwaenepoel Arthur , Peer Yves Van de
Published: March 2021

Phylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption of these models is the constant per-gene loss rate in any particular family. Because of the possibility of partial functional redundancy among gene family members, gene loss dynamics are however likely to be dependent on the number of genes in a family, and different variations of commonly employed BDP models indeed suggest this is the case. We propose a simple two-type branching process model to better approximate the stochastic evolution of gene families by gene duplication and loss and perform Bayesian statistical inference of model parameters in a phylogenetic context. We evaluate the statistical methods using simulated data sets and apply the model to gene family data forDrosophila, yeasts and primates, providing new quantitative insights in the long-term maintenance of duplicated genes.
Plasma Membrane Calcium ATPase (PMCA) Regulates Stoichiometry of CD4+T-cell Compartments
Authors: Merino-Wong Maylin , Niemeyer Barbara A. , Alansary Dalia
Published: March 2021

Immune responses involve mobilization of T cells within naïve and memory compartments. Tightly regulated Ca2+levels are essential for balanced immune outcomes. How Ca2+contributes to regulating compartment stoichiometry is unknown. Here, we show that plasma membrane Ca2+ATPase 4 (PMCA4) is differentially expressed in human CD4+T compartments yielding distinct store operated Ca2+entry (SOCE) profiles. Modulation of PMCA4 yielded a more prominent increase of SOCE in memory than in naïve CD4+T cell. Interestingly, downregulation of PMCA4 reduced the effector compartment fraction and led to accumulation of cells in the naïve compartment.In silicoanalysis and chromatin immunoprecipitation unraveled Ying Yang 1 (YY1) as a transcription factor regulating PMCA4 expression. Analyses of PMCA and YY1 expression patterns following activation and of PMCA promoter activity following downregulation of YY1 highlight repressive role of YY1 on PMCA expression. Our findings show that under the transcriptional control by YY1, PMCA4 adapts Ca2+levels to cellular requirements during effector and quiescent phases and thereby represent a potential target to intervene with the outcome of the immune response.
Evolutionary determinants of non-seasonal breeding in wild chacma baboons
Authors: Dezeure Jules , Baniel Alice , Burtschell Lugdiwine , Carter Alecia J. , Godelle Bernard , Cowlishaw Guy , Huchard Elise
Published: March 2021

Animal reproductive phenology varies from strongly seasonal to non-seasonal, sometimes among closely related or sympatric species. While the extent of reproductive seasonality is often attributed to environmental seasonality, this fails to explain many cases of non-seasonal breeding in seasonal environments. We investigated the evolutionary determinants of non-seasonal breeding in a wild primate, the chacma baboon (Papio ursinus), living in a seasonal environment with high climatic unpredictability. We tested three hypotheses proposing that non-seasonal breeding has evolved in response to (1) climatic unpredictability, (2) reproductive competition between females favouring birth asynchrony, and (3) individual, rank-dependent variations in optimal reproductive timing. We found strong support for an effect of reproductive asynchrony modulated by rank: (i) birth synchrony is costly to subordinate females, lengthening their interbirth intervals, and (ii) females delay their reproductive timings (fertility periods and conceptions) according to other females in the group to stagger conceptions. These results indicate that reproductive competition generates reproductive asynchrony, weakening the intensity of reproductive seasonality at the population level. This study emphasizes the importance of sociality in mediating the evolution of reproductive phenology in gregarious organisms, a result of broad significance for understanding key demographic parameters driving population responses to increasing climatic fluctuations.
Long-term patterns of an interconnected core marine microbiota
Authors: Krabberød Anders K. , Deutschmann Ina M. , Bjorbækmo Marit F. M. , Balagué Vanessa , Giner Caterina R. , Ferrera Isabel , Garcés Esther , Massana Ramon , Gasol Josep M. , Logares Ramiro
Published: March 2021

Background

Ocean microbes constitute ∼70% of the marine biomass, are responsible for ∼50% of the Earth’s primary production, and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade.

Results

Core microbes were defined as those present in >30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1,411 strong and mostly positive (∼95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities.

Conclusions

We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
On the genetic architecture of rapidly adapting and convergent life history traits in guppies
Authors: Whiting James R , Paris Josephine R , Parsons Paul J , Matthews Sophie , Reynoso Yuridia , Hughes Kimberly A. , Reznick David , Fraser Bonnie A
Published: March 2021

The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.
Discovery of a Novel Non-Narcotic Analgesic Derived from the CL-20 Explosive: Synthesis, Pharmacology and Target Identification of Thio-wurtzine, a Potent Inhibitor of the Opioid Receptors and the Voltage-Dependent Calcium Channels
Authors: Aguero Stephanie , Megy Simon , Fournier Mailys , Kulagina Daria A. , Sysolyatin Sergey V. , Kalashnikov Alexander I. , Krylova Svetlana G. , Vorozhtsov Alexander B. , Zhdanov Vadim V. , Terreux Raphael
Published: March 2021

The number of candidate molecules for new non-narcotic analgesics is extremely limited. Here we report the identification of thiowurtzine, a new potent analgesic molecule with promising application in chronic pain treatment. We describe the chemical synthesis of this unique compound derived from the hexaazaisowurtzitane (CL-20) explosive molecule. Then we use animal experiments to assess its analgesic activityin vivoupon chemical, thermal and mechanical exposures, compared to the effect of several reference drugs. Finally, we investigate the potential receptors of thiowurtzine in order to better understand its complex mechanism of action. We use docking, molecular modeling and molecular dynamics simulations to identify and characterize the potential targets of the drug and confirm the results of the animal experiments. Our findings finally indicate that thiowurtzine may have a complex mechanism of action, by targeting the mu, kappa, delta and ORL1 opioid receptors, and the voltage-gated calcium channels as well.
The archaeal triphosphate tunnel metalloenzymeSaTTM defines structural determinants for the diverse activities in the CYTH protein family
Authors: Vogt Marian S. , Nguepbeu Roi R. Ngouoko , Mohr Michael K. F. , Albers Sonja-Verena , Essen Lars-Oliver , Banerjee Ankan
Published: March 2021

CYTH is a large protein superfamily that is conserved in all three domains of life with its unique triphosphate tunnel metalloenzyme (TTM) fold. Besides phosphatase functions, e.g. as RNA triphosphatase, inorganic polyphosphatase or thiamine triphosphatase, some CYTH orthologs cyclize nucleotide triphosphates to 3’,5’-cyclic nucleotides. So far, archaeal CYTH proteins are annotated as adenylyl cyclases although experimental evidence is lacking. To address this gap, we characterized a CYTH ortholog,SaTTM, from the crenarchaeoteSulfolobus acidocaldarius. Our initialin silicostudies suggested a close relationship between archaeal CYTH enzymes and class IV adenylyl cyclases compared to the other CYTH-subclasses, but biochemical data showed no cyclic nucleotide production. Instead, our structural and functional analyses show a classical TTM behavior. The Ca2+-inhibited Michaelis complex indicates a two-metal ion reaction mechanism analogous to other TTMs. Different co-crystal structures ofSaTTM further reveal conformational dynamics inSaTTM, let us to assume feedback inhibition in TTMs due to tunnel closure in the product state. Combining our structural insights with sequence-similarity network basedin silicoanalysis, we further set out a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases.

Major highlights

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CyaB-like class IV adenylyl cyclase homologs in archaea are triphosphatases.

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The co-crystal structure ofSaTTM in sulfate and triphosphate bound state revealed conformational transition of the TTM tunnel during catalysis.

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Atomic insights into TTM inhibition by calcium and pyrophosphate.

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In silicoand structure-function analysis revealed the molecular determinant for functional diversification among CYTH proteins.
Transcriptional condensates formed by phase-separated ALOG family proteins control shoot meristem maturation for flowering
Authors: Huang Xiaozhen , Xiao Nan , Xie Yue , Tang Lingli , Zhang Yueqin , Yu Yuan , Xu Cao
Published: March 2021

Plants have evolved remarkable diversity in inflorescence architecture. At the center of this diversity lies a meristem maturation program featured by transition of stem cell populations from a vegetative state into a reproductive growth, determining when, where, and how many flowers are produced on inflorescences. Here we identified a new meristem maturation regulatorTMF FAMILY MEMBER3(TFAM3) that encodes an ALOG family transcription factor. Loss ofTFAM3results in early flowering and simplified inflorescences with fewer flowers. Genetic analysis by creating high-order mutants ofTFAM3with three key regulators of tomato shoot meristem maturation,TERMINATING FLOWER(TMF),TMF FAMILY MEMBER1(TFAM1) andTMF FAMILY MEMBER2(TFAM2), suggested that they synergistically control flowering transition and inflorescence architecture. The four paralogous ALOG proteins share the prion-like properties and undergo liquid-liquid phase separationin vitro. Strikingly, TMF can recognize cognate TFAM proteins and selectively recruit them into phase separated condensates. Supporting this, they interact with themselves and each other to form biomolecular condensates in the nucleus. Their interaction induces formation of transcriptional condensates that directly repress expression of floral identity geneANANTHA. Our study revealed a selective-recruitment phase separation mechanism for transcriptional condensation by which plants achieve optimal coordination of functional overlapped paralogs within a protein family to enable precise control of shoot meristem maturation for flowering and production of compound inflorescences.
Variants with the N501Y mutation extend SARS-CoV-2 host range to mice, with contact transmission
Authors: Montagutelli Xavier , Prot Matthieu , Levillayer Laurine , Salazar Eduard Baquero , Jouvion Grégory , Conquet Laurine , Beretta Maxime , Donati Flora , Albert Mélanie , Gambaro Fabiana , Behillil Sylvie , Enouf Vincent , Rousset Dominique , Mouquet Hugo , Jaubert Jean , Rey Felix , van der Werf Sylvie , Simon-Loriere Etienne
Published: March 2021

Receptor recognition is a major determinant of viral host range, infectivity and pathogenesis. Emergences have been associated with serendipitous events of adaptation upon encounters with novel hosts, and the high mutation rate of RNA viruses may explain their frequent host shifts. SARS-CoV-2 extensive circulation in humans results in the emergence of variants, including variants of concern (VOCs) with diverse mutations notably in the spike, and increased transmissibility or immune escape. Here we show that, unlike the initial and Delta variants, the three VOCs bearing the N501Y mutation can infect common laboratory mice. Contact transmission occurred from infected to naive mice through two passages. This host range expansion likely results from an increased binding of the spike to the mouse ACE2. Together with the observed contact transmission, it raises the possibility of wild rodent secondary reservoirs enabling the emergence of new variants.
The N-terminal domain of RfaH plays an active role in protein fold-switching
Authors: Galaz-Davison Pablo , Román Ernesto A. , Ramírez-Sarmiento César A.
Published: March 2021

The bacterial elongation factor RfaH promotes the expression of virulence factors by specifically binding to RNA polymerases (RNAP) stalled at a DNA signal known asops. This behavior is unlike that of its paralog NusG, the major representative of the protein family to which RfaH belongs. Both proteins have an N-terminal domain (NTD) bearing an RNAP binding site, yet NusG C-terminal domain (CTD) is folded as a β-barrel while RfaH CTD is forming an α-hairpin blocking such site. Upon recognition of theopsexposed by RNAP, RfaH is activated via interdomain dissociation and complete CTD structural rearrangement into a β-barrel structurally identical to NusG CTD.

Although RfaH transformation has been extensively characterized computationally, most studies employ tertiary biases towards each native state, hampering the analysis of sequence-encoded interactions on fold-switching. Here, we used Associative Water-mediated Structure and Energy Model (AWSEM) molecular dynamics to characterize the transformation of RfaH, spotlighting the sequence-dependent effects of NTD on CTD fold stabilization. Umbrella sampling simulations guided by native contacts recapitulate the thermodynamic equilibrium experimentally observed for RfaH and its isolated CTD. Temperature refolding simulations of full-length RfaH show a high success towards α-folded CTD, whereas the NTD interferes with βCTD folding, becoming trapped in a β-barrel intermediate. Meanwhile, NusG CTD refolding is unaffected by the presence of RfaH NTD, showing that these NTD-CTD interactions are encoded in RfaH sequence. Altogether, these results suggest that the NTD of RfaH favors the α-folded RfaH by specifically orienting the αCTD upon interdomain binding and also by favoring β-barrel rupture into an intermediate from which fold-switching proceeds.
Critical behaviour of the stochastic Wilson-Cowan model
Authors: de Candia Antonio , Sarracino Alessandro , Apicella Ilenia , de Arcangelis Lucilla
Published: March 2021

Spontaneous brain activity is characterized by bursts and avalanche-like dynamics, with scale-free features typical of critical behaviour. The stochastic version of the celebrated Wilson-Cowan model has been widely studied as a system of spiking neurons reproducing non-trivial features of the neural activity, from avalanche dynamics to oscillatory behaviours. However, to what extent such phenomena are related to the presence of a genuine critical point remains elusive. Here we address this central issue, providing analytical results in the linear approximation and extensive numerical analysis. In particular, we present results supporting the existence of a bona fide critical point, where a second-order-like phase transition occurs, characterized by scale-free avalanche dynamics, scaling with the system size and a diverging relaxation time-scale. Moreover, our study shows that the observed critical behaviour falls within the universality class of the mean-field branching process, where the exponents of the avalanche size and duration distributions are, respectively, −3/2 and −2. We also provide an accurate analysis of the system behaviour as a function of the total number of neurons, focusing on the time correlation functions of the firing rate in a wide range of the parameter space.

Author summary

Networks of spiking neurons are introduced to describe some features of the brain activity, which are characterized by burst events (avalanches) with power-law distributions of size and duration. The observation of this kind of noisy behaviour in a wide variety of real systems led to the hypothesis that neuronal networks work in the proximity of a critical point. This hypothesis is at the core of an intense debate. At variance with previous claims, here we show that a stochastic version of the Wilson-Cowan model presents a phenomenology in agreement with the existence of a bona fide critical point for a particular choice of the relative synaptic weight between excitatory and inhibitory neurons. The system behaviour at this point shows all features typical of criticality, such as diverging timescales, scaling with the system size and scale-free distributions of avalanche sizes and durations, with exponents corresponding to the mean-field branching process. Our analysis unveils the critical nature of the observed behaviours.
Brain Water as a Function of Age and Weight in Normal Rats
Authors: Gottschalk Allan , Scafidi Susanna , Toung Thomas J. K.
Published: March 2021

Rats are frequently used to study water content of normal and injured brain, as well as changes in response to various osmotherapeutic regimens. Magnetic resonance imaging in humans has shown that brain water content declines with age as a result of progressive myelination. The purpose of this study was to quantify changes in brain water content during rat development and aging. Brain water content was measured by standard techniques in 129 normal male Sprague-Dawley rats that ranged in age (weight) from 13 to 149 days (18 to 759 g). Overall, the results demonstrated a decrease from 85.59% to 76.56% water content with increasing age (weight). Nonlinear allometric functions relating brain water to age and weight were determined. These findings provide age-related context for prior rat studies of brain water, emphasize the importance of using similarly aged controls in studies of brain water, and indicate that age-related changes in brain water content are not specific to humans.
Large-scale computational discovery and analysis of virus-derived microbial nanocompartments
Authors: Andreas Michael P. , Giessen Tobias W.
Published: March 2021

Protein compartments represent an important strategy for subcellular spatial control and compartmentalization. Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. This has hampered progress in understanding the distribution and functional diversity of encapsulins. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We report the discovery and analysis of over 6,000 encapsulin-like systems in 31 bacterial and 4 archaeal phyla, including two novel encapsulin families as well as many new operon types that fall within the two already known families. We formulate hypotheses about the biological functions and biomedical relevance of newly identified operons which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. We conduct an evolutionary analysis of encapsulins and related HK97-type virus families and show that they share a common ancestor. We conclude that encapsulins likely evolved from HK97-type bacteriophages. Our study sheds new light on the evolutionary interplay of viruses and cellular organisms, the recruitment of protein folds for novel functions, and the functional diversity of microbial protein organelles.
EMBED: Essential Microbiome Dynamics, a dimensionality reduction approach for longitudinal microbiome studies
Authors: Shahin Mayar , Ji Brian , Dixit Purushottam D.
Published: March 2021

Dimensionality reduction can offer unique insights into high dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa level are not currently available. To that end, we present EMBED:EssentialMicroBiomE Dynamics, a probabilistic non-linear tensor factorization approach. Similar to normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. A very small number of ECNs can accurately approximate microbiome dynamics across multiple data sets. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.
Angiotensin II disrupts the cytoskeletal architecture of human urine-derived podocytes and results in activation of the renin-angiotensin system
Authors: Erichsen Lars , Bohndorf Martina , Rahman Md. Shaifur , Wruck Wasco , Adjaye James
Published: March 2021

High blood pressure is one of the major public health problems which causes severe disorders in several tissues including the human kidney. One of the most important signaling pathways associated with the regulation of blood pressure is the renin-angiotensin system (RAS), with its main mediator angiotensin II (ANGII). Elevated levels of circulating and intracellular ANGII and aldosterone lead to pro-fibrotic, -inflammatory and -hypertrophic milieu that causes remodelling and dysfunction in cardiovascular and renal tissues. Furthermore, ANGII has been recognized as major risk factor for the induction of apoptosis in podocytes, ultimately leading to chronic kidney disease (CDK).

In the past, disease modeling of kidney-associated malignancies was extremely difficult, as the derivation of kidney originated cells is very challenging. Here we describe a differentiation protocol for reproducible differentiation of SIX2-positive urine derived renal progenitor cells (UdRPCs) into mature podocytes bearing typical foot processes. The UdRPCs-derived podocytes show the ability to execute Albumin endocytosis and the activation of the renin-angiotensin system by being responsive to ANGII stimulation. Our data reveals the ANGII dependent downregulation ofNPHS1andSYNPO, resulting in the disruption of the complex podocyte cytoskeletal architecture, as shown by immunofluorescence-based detection of α–ACTININ. In the present manuscript we confirm and propose UdRPCs as a unique cell type useful for studying nephrogenesis and associated diseases. Furthermore, the responsiveness of UdRPCs-derived podocytes to ANGII implies potential applications in nephrotoxicity studies and drug screening.