bluuebunny/crossref_metadata_2025 huggingface dataset:
Strigolactones are chemoattractants for host tropism in Orobanchaceae parasitic plants
Authors: Ogawa Satoshi , Cui Songkui , White Alexandra R.F. , Nelson David C. , Yoshida Satoko , Shirasu Ken
Published: February 2022

Parasitic plants are worldwide threats that damage major agricultural crops. To initiate infection, parasitic plants have developed the ability to locate hosts and grow towards them. This ability, called host tropism, is critical for parasite survival, but its underlying mechanism remains mostly unresolved. To characterize host tropism, we used the model facultative root parasite Phtheirospermum japonicum, a member of the Orobanchaceae. Here, we show that strigolactones (SLs) function as host-derived chemoattractants. Chemotropism to SLs is also found in Striga hermonthica, a parasitic member of the Orobanchaceae, but not in non-parasites. Intriguingly, chemotropism to SLs in P. japonicum is attenuated in ammonium ion-rich conditions, where SLs are perceived, but the resulting asymmetrical accumulation of the auxin transporter PIN2 is diminished. P. japonicum encodes putative receptors that sense exogenous SLs, whereas expression of a dominant-negative form reduces its chemotropic ability. We propose a new function for SLs as navigators for parasite roots.
Interaction mechanism between the HSV-1 glycoprotein B and the antimicrobial peptide Amyloid-β
Authors: Bourgade Karine , Frost Eric H. , Dupuis Gilles , Witkowski Jacek M. , Laurent Benoit , Calmettes Charles , Ramassamy Charles , Desroches Mathieu , Rodrigues Serafim , Fülöp Tamás
Published: February 2022

Unravelling the mystery of Alzheimer’s Disease (AD) requires urgent resolution given the worldwide increase of the aging population. There is a growing concern that the current leading AD hypothesis, the amyloid cascade hypothesis, does not stand up to validation with respect to emerging new data. Indeed, several paradoxes are being discussed in the literature, for instance, both the deposition of the Amyloid-Beta peptide (Aβ) and the intracellular neurofibrillary tangles (NFTs) could occur within the brain without any cognitive pathology. Thus, these paradoxes suggest that something more fundamental is at play in the onset of the disease and other key and related pathomechanisms have to be investigated. The present study follows our previous investigations on the infectious hypothesis, which posits that some pathogens are linked to late onset AD. Our studies also build upon the shattering finding that Aβ is a powerful antimicrobial agent capable of inhibiting pathogens as observed in in vitro experiments. Herein, we ask what are the molecular mechanisms in play when Aβ neutralizes infectious pathogens? To answer this question, we probed at nanoscale lengths with FRET (Förster Resonance Energy Transfer), the interaction between Aβ peptides and glycoprotein B (responsible of virus-cell binding) within the HSV-1 virion. We concluded that there is indeed a close interaction, likely nonspecific or semi-specific, between the two types of molecules, which participate in virus neutralization.
Choosing variant interpretation tools for clinical applications: context matters
Authors: Aguirre Josu , Padilla Natàlia , Özkan Selen , Riera Casandra , Feliubadaló Lidia , de la Cruz Xavier
Published: February 2022

Our inability to solve the Variant Interpretation Problem (VIP) has become a bottleneck in the biomedical/clinical application of Next-Generation Sequencing. This situation has favored the development and use of bioinformatics tools for the VIP. However, choosing the optimal tool for our purposes is difficult because of the high variability of clinical contexts across and within countries.

Here, we introduce the use of cost models as a new approach to compare pathogenicity predictors that considers clinical context. An interesting feature of this approach, absent in standard performance measures, is that it treats pathogenicity predictors as rejection classifiers. These classifiers, commonly found in machine learning applications to healthcare, reject low-confidence predictions. Finally, to explore whether context has any impact on predictor selection, we have developed a computational procedure that solves the problem of comparing an arbitrary number of tools across all possible clinical scenarios.

We illustrate our approach using a set of seventeen pathogenicity predictors for missense variants. Our results show that there is no optimal predictor for all possible clinical scenarios. We also find that considering rejection gives a view of classifiers contrasting with that of standard performance measures. The Python code for comparing pathogenicity predictors across the clinical space using cost models is available to any interested user at:https://github.com/ClinicalTranslationalBioinformatics/clinical_space_partition

Summaries

Josu Aguirre earned his doctorate at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).

Natàlia Padilla earned is a post-doctoral researcher at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).

Selen Özkan is a Ph.D. student at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).

Casandra Riera earned her doctorate at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).

Lidia Feliubadalo earned her doctorate at the Universitat de Barcelona, presently she is a high-level technician working at the Catalan Institute of Oncology (ICO) in the diagnosis of hereditary cancers.

Xavier de la Cruz is ICREA Research Professor at the Vall d’Hebron Institute of Research (VHIR). His research interests revolve around the application of machine learning methods to healthcare problems.
Spatially resolved epigenomic profiling of single cells in complex tissues
Authors: Lu Tian , Ang Cheen Euong , Zhuang Xiaowei
Published: February 2022

The recent development of spatial omics methods enables single-cell profiling of the transcriptome and the 3D genome organization in a spatially resolved manner. Expanding the repertoire of spatial omics tools, a spatial epigenomics method will accelerate our understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved profiling of epigenomes in single cells using in-situ tagmentation and transcription followed by highly multiplexed imaging. We profiled histone modifications marking active promoters and enhancers, H3K4me3 and H3K27ac, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results further revealed putative promoter-enhancer pairs and enhancer hubs regulating the expression of developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
Nuclear envelope disruption triggers hallmarks of aging in lung alveolar macrophages
Authors: De Silva Nilushi S. , Nader Guilherme P.F. , Nadalin Francesca , de Azevedo Kevin , Couty Mickaël , Bhargava Anvita , Conrad Cécile , Maurin Mathieu , Fouillade Charles , Londono-Vallejo Arturo , Behrendt Rayk , Gallwitz Lisa , Saftig Paul , Fernández Beatriz Herrero , González-Granado José María , van Niel Guillaume , Boissonnas Alexandre , Piel Mathieu , Manel Nicolas
Published: February 2022

Aging is characterized by gradual immune dysfunction and increased risk for many diseases, including respiratory infections. Genomic instability is thought to play a central role in the aging process but the mechanisms that damage nuclear DNA in aging are insufficiently defined. Cells that migrate or reside within confined environments experience forces applied to their nucleus, leading to transient nuclear envelope (NE) ruptures. NE ruptures are associated with DNA damage, and Lamin A/C is required to limit these events. Here, we show that Lamin A/C protects lung alveolar macrophages from NE rupture and hallmarks of aging. Lamin A/C ablation in immune cells results in a selective depletion of lung alveolar macrophages (AM) and a heightened susceptibility to influenza infection. Lamin A/C-deficient AM that persist display constitutive nuclear envelope rupture marks, DNA damage and p53-dependent senescence. In wild-type mice, we found that AM migrate within constricted spaces in vivo, at heights that induce NE rupture and DNA damage. AM from aged wild-type mice and from Lamin A/C-deficient mice share an upregulated lysosomal signature with CD63 expression, and we find that CD63 is required to clear damaged DNA in macrophages. We propose that induction of genomic instability by NE disruption represents a mechanism of aging in alveolar macrophages.
Comparison of fitness effects in the earthworm Eisenia fetida after exposure to single or multiple anthropogenic pollutants
Authors: Holzinger Anja , Mair Magdalena M. , Lücker Darleen , Seidenath Dimitri , Opel Thorsten , Langhof Nico , Otti Oliver , Feldhaar Heike
Published: February 2022

Terrestrial ecosystems are exposed to many anthropogenic pollutants. Non-target effects of pesticides and fertilizers have put agricultural intensification in the focus as a driver for biodiversity loss. However, other pollutants, such as heavy metals, particulate matter, or microplastic also enter the environment, e.g. via traffic and industrial activities in urban areas. As soil acts as a potential sink for such pollutants, soil invertebrates like earthworms may be particularly affected by them. Under natural conditions soil invertebrates will likely be confronted with combinations of pollutants simultaneously, which may result in stronger negative effects if pollutants act synergistically.

Within this work we study how multiple pollutants affect the soil-dwelling, substrate feeding earthworm Eisenia fetida. We compared the effects of the single stressors, polystyrene microplastic fragments, polystyrene fibers, brake dust and soot, with the combined effect of these pollutants when applied as a mixture. Endpoints measured were survival, growth, reproductive fitness, and changes in three oxidative stress markers. We found that among single pollutant treatments, brake dust imposed the strongest negative effects on earthworms in all measured endpoints including increased mortality rates. Sub-lethal effects were found for all pollutants. Exposing earthworms to all four pollutants simultaneously led to effects on mortality and oxidative stress markers that were smaller than expected by the respective null models. These antagonistic effects are likely a result of the adsorption of toxic substances found in brake dust to the other pollutants. With this study we show that effects of combinations of pollutants cannot necessarily be predicted from their individual effects and that combined effects will likely depend on identity and concentration of the pollutants.
Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions and cell growth
Authors: Bellotto N. , Agudo-Canalejo J. , Colin R. , Golestanian R. , Malengo G. , Sourjik V.
Published: February 2022

Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli, and, for the faster-diffusing proteins, it is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
Molecular characteristics and laminar distribution of prefrontal neurons projecting to the mesolimbic system
Authors: Babiczky Ákos , Mátyás Ferenc
Published: February 2022

Prefrontal cortical influence over the mesolimbic system – including the nucleus accumbens (NAc) and the ventral tegmental area (VTA) - is implicated in various cognitive processes and behavioral malfunctions. The functional versatility of this system could be explained by an underlying anatomical complexity; however, the detailed characterization of the medial prefrontal cortical (mPFC) innervation of the NAc and VTA is still lacking. Therefore, combining classical retrograde and conditional viral tracing techniques with multiple fluorescent immunohistochemistry, we sought to deliver a precise, cell- and layer-specific anatomical description of the cortico-mesolimbic pathways. We demonstrated that NAc- (mPFCNAc) and VTA-projecting mPFC (mPFCVTA) populations show different laminar distribution (layers 2/3-5a and 5b-6, respectively) and express different molecular markers. Specifically, calbindin and Ntsr1 are specific to mPFCNAc neurons, while mPFCVTA neurons express high levels of Ctip2 and FoxP2, indicating that these populations are mostly separated at the cellular level. We directly tested this with double retrograde tracing and Canine adenovirus type 2-mediated viral labelling and found that there is indeed minimal overlap between the two populations. Furthermore, whole-brain analysis revealed that the projection patter of these populations is also different throughout the brain. Taken together, we demonstrated that the NAc and the VTA are innervated by two, mostly non-overlapping mPFC populations with different laminar distribution and molecular profile. These results can contribute to the advancement in our understanding of mesocorticolimbic functions and its disorders in future studies.
Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals
Authors: Turjeman Sondra , Pekarsky Sasha , Corl Ammon , Kamath Pauline L. , Getz Wayne M. , Bowie Rauri C. K. , Markin Yuri , Nathan Ran
Published: February 2022

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in microbial composition (alpha and beta diversity), which were not accounted for by noninvasive samples’ exposure to soil contaminants, as manually assessed by comparing differentially abundant taxa. They could result from trapped birds’ exposure to sedatives. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, stressing or sedation may unravel how trapping affects wildlife microbiota.
PKD-1 Signaling Is Required for the Maintenance of CSCs with Epithelial-mesenchymal Plasticity in Pancreatic Neuroendocrine Tumors
Authors: Guo Yichen , Jiang Yinan , Rose J. Bart , Jaskula-Sztul Renata , Hjelmeland Anita B. , Chen Herbert , Ren Bin
Published: February 2022

Pancreatic neuroendocrine tumors (pNETs) are extremely heterogeneous and highly vascularized neoplasms that arise from endocrine cells in the pancreas. pNETs harbor a subpopulation of stem cell-like cancer cells (cancer stem cells/CSCs), which contribute to intratumoral heterogeneity and promote tumor maintenance and recurrence. In this study we demonstrated that CSCs in human pNETs co-expressed PKD-1 and CD44. We further identified PKD-1 signaling as a critical pathway in the regulation of CSC maintenance in pNET cells. PKD-1 signaling regulated the expression of a CSC-related gene signature and promoted CSC self-renewal. Intriguingly, pharmacological or genetic disruption of PKD-1 signaling in human pNET cells impaired lysophosphatidic acid-induced expression of genes associated with epithelial to mesenchymal transition (EMT), specifically E-cadherin and vimentin. This study indicates that PKD-1 signaling is essential for the maintenance of a subpopulation of CSCs in pNETs at an intermediate state along the epithelial–mesenchymal spectrum, thereby leading to a CSC phenotype with plasticity and partial EMT. Inhibiting the PKD-1 pathway may facilitate the elimination of CSC subpopulations to curb pNET progression, therapeutic resistance and metastasis. Given that the signaling networks associated with CSC maintenance and EMT are complex and extend across multiple levels of gene regulation, this study provides insight into signaling regulation of partial EMT in determining CSC fate and aids in developing potential therapeutic strategies that target different subsets of CSCs in a variety of cancers.
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
Authors: Hoang Minh , Zheng Hongyu , Kingsford Carl
Published: February 2022

Minimizers are k-mer sampling schemes designed to generate sketches for large sequences that preserve sufficiently long matches between sequences. Despite their widespread application, learning an effective minimizer scheme with optimal sketch size is still an open question. Most work in this direction focuses on designing schemes that work well on expectation over random sequences, which have limited applicability to many practical tools. On the other hand, several methods have been proposed to construct minimizer schemes for a specific target sequence. These methods, however, require greedy approximations to solve an intractable discrete optimization problem on the permutation space of k-mer orderings. To address this challenge, we propose: (a) a reformulation of the combinatorial solution space using a deep neural network re-parameterization; and (b) a fully differentiable approximation of the discrete objective. We demonstrate that our framework, DeepMinimizer, discovers minimizer schemes that significantly outperform state-of-the-art constructions on genomic sequences.
Modulation of sleep by trafficking of lipids through the Drosophila blood brain barrier
Authors: Artiushin Gregory , Li Fu , Sehgal Amita
Published: February 2022

Endocytosis through Drosophila glia is a significant determinant of sleep amount and occurs preferentially during sleep in glia of the blood brain barrier (BBB). To identify metabolites whose trafficking is mediated by sleep-dependent endocytosis, we conducted metabolomic analysis of flies that have increased sleep due to a block in glial endocytosis. We report that acylcarnitines, molecules that conjugate with long chain fatty acids to promote their transport, accumulate in heads of these animals. In parallel, to identify transporters and receptors whose loss contributes to the sleep phenotype caused by blocked endocytosis, we screened genes enriched in barrier glia for effects on sleep. We find that knockdown of lipid transporters LRP1&2 as well as carnitine transporters ORCT1&2 increases sleep. In support of the idea that the block in endocytosis affects trafficking through specific transporters, knockdown of LRP or ORCT transporters also increases acylcarnitines in heads. We propose that lipid species, such as acylcarnitines, are trafficked through the BBB via sleep-dependent endocytosis, and their accumulation in the brain increases the need for sleep.
Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation
Authors: Kubo Shintaroh , Bui Khanh Huy
Published: February 2022

Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific for the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e. “tubulin code”, for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the stochastic stepping behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
Eurasian Stone-curlews Burhinus oedicnemus breeding in Italy show a remarkable inter and intra-population variability of migratory behaviour
Authors: Falchi Valentina , Barbon Andrea , Catoni Carlo , Cerritelli Giulia , Cutroneo Alice , Dell’omo Giacomo , Dragonetti Marco , Giovacchini Pietro , Meschini Angelo , Panzarin Lucio , Picciau Angela , Giunchi Dimitri
Published: February 2022

Migratory behaviour in birds shows a remarkable variability at species, population and individual levels. Short-distance migrants, in particular, often adopt a partial migratory strategy and tend to have a rather flexible migration schedule which allows them to respond more effectively to extreme environmental variations, like those due to climate change. Weather seasonality and environmental heterogeneity at regional and local scales have been reported as significant factors in the diversification of migratory behaviour for some species of Mediterranean migrants. Relatively few studies, however, investigated the migration patterns of non-passerine birds migrating within this area. In this study we investigated the migratory strategy of the Eurasian Stone-curlewBurhinus oedicnemususing data collected on 40 individuals tagged with geolocators and GPS-GSM tags, belonging to two continental and two Mediterranean populations of the Italian peninsula. The proportion of migrants was significantly higher in continental populations, but we observed a significant variability also within Mediterranean populations. GPS-tagged migrants traveled less than 1000 km, spending the winter within the Mediterranean basin. Continental Stone-curlews i) departed earlier in spring and later in autumn and ii) covered longer distances than those from Mediterranean areas. The speed of migration did not change between seasons for continental birds, while Mediterranean individuals tended to migrate faster in spring. The likelihood of departure for autumn migration of GPS-tagged birds significantly increased when temperatures were near or below 0 °C suggesting that Stone-curlews tend to delay departure weather conditions worsen abruptly. Thus it can be speculated that the frequency of migratory birds in the considered populations may decrease in the near future due to the effect of global warming in the Mediterranean. This could have a significant effect on the distribution of species throughout the year and should be taken into account when targeting conservation measures.
Deep phenotyping platform for microscopic plant-pathogen interactions
Authors: Lück Stefanie , Douchkov Dimitar
Published: February 2022

1

The initial phases of plant-pathogen interactions are critical since they are often decisive for the successful infection. However, these early stages of interaction are typically microscopic, making it challenging to study on a large scale.

For this reason, using the powdery mildew fungi of cereals as a model, we have developed an automated microscopy pipeline coupled with deep learning-based image analysis for the high-throughput phenotyping of plant-pathogen interactions.

The system can quantify fungal microcolony count and density, the precise area of the secondary hyphae of each colony, and different morphological parameters. Moreover, the high throughput and sensitivity allow quantifying rare microscopic phenotypes in a large sample size. One of these phenotypes is the cryptic infection of non-adapted pathogens, marking the hidden transition stages of pathogen adaptation and breaking the nonhost barrier. Thus, our tool opens the nonhost resistance phenomenon to genetics and genomics studies.

We have developed an open-source high-throughput automated microscopy system for phenotyping the initial stages of plant-pathogen interactions, extendable to other microscopic phenotypes and hardware platforms. Furthermore, we have validated the system’s performance in disease resistance screens of genetically diverse barley material and performed Genome-wide associations scans (GWAS), discovering several resistance-associated loci, including conferring nonhost resistance.
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
Authors: Muffato Matthieu , Louis Alexandra , Nguyen Nga Thi Thuy , Lucas Joseph , Berthelot Camille , Crollius Hugues Roest
Published: February 2022

Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic andin silicoreconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.
Abiotic conditions shape spatial and temporal morphological variation in North American birds
Authors: Youngflesh Casey , Saracco James F. , Siegel Rodney B. , Tingley Morgan W.
Published: February 2022

Abiotic environmental conditions play a key role in driving the size and shape of organisms. Quantifying environment-morphology relationships is important not only for understanding the fundamental processes driving phenotypic diversity within and among species (1), but also for predicting how species will respond to ongoing global change (2). Despite a clear set of expectations motivated by ecological theory (3), broad evidence in support of generalizable effects of abiotic conditions, such as temperature (4), on spatial and temporal intraspecific morphological variation has been limited. Using standardized data from over 250,000 captures of 105 landbird species, we assessed intraspecific shifts in bird morphology since 1989 while simultaneously measuring spatial morphological gradients across the North American continent. Across bird species, we found strong spatial and temporal trends in body size, with warmer temperatures associated with smaller body sizes both at more equatorial latitudes and in more recent years. The magnitude of these thermal effects varied both across and within species, with results suggesting it is the warmest, rather than the coldest, temperatures driving both spatial and temporal trends. Across elevation, we found that body size declines as relative wing length increases, likely due to the benefits that longer wings confer for flight in thin air environments. Our results provide support for both existing and new large-scale ecomorphological gradients and highlight how the response of functional tradeoffs to abiotic variation drives morphological change.

Significance Statement

Characterizing how the size and shape of organisms varies over space and time is key to understanding the processes that create ecological communities and for predicting how species will respond to climate change. Across more than 100 species of North American birds, we show that within species the size and shape of individuals varies substantially across space and time. Warmer temperatures are associated with smaller body sizes, likely due to the importance of body size for thermoregulation. As the climate continues to warm, these species will likely continue to shrink. We also provide the first large-scale evidence of an increase in wing length with elevation, a pattern that could be attributed to thinner air in high elevation environments.
Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data
Authors: Gervásio João , Ferreira Alice , Felicori Liza F.
Published: February 2022

Motivation

The next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets.

Results

To address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires.

Availability and implementation

YClon was implemented in Python3 and is freely available on GitHub

(https://github.com/jao321/YClon.git)

Contact:joaodgervasio@gmail.com,liza@icb.ufmg.br
Integrating Fossil Flowers into the Angiosperm Phylogeny using a Total Evidence Approach
Authors: López-Martínez Andrea M. , Schönenberger Jürg , von Balthazar Maria , González-Martínez César A. , Ramírez-Barahona Santiago , Sauquet Hervé , Magallón Susana
Published: February 2022

Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were sampled to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits.
Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge
Authors: Malhi Harman , Homad Leah J. , Wan Yu-Hsin , Poudel Bibhav , Fiala Brooke , Borst Andrew J. , Wang Jing Yang , Walkey Carl , Price Jason , Wall Abigail , Singh Suruchi , Moodie Zoe , Handa Simran , Correnti Colin , Stoddard Barry L. , Veesler David , Pancera Marie , Olson James , King Neil P. , McGuire Andrew T.
Published: February 2022

Summary/Abstract

Epstein-Barr virus (EBV) is a cancer-associated pathogen responsible for 140,000 deaths per year. EBV is also the etiological agent of infectious mononucleosis and is associated with multiple sclerosis and rheumatoid arthritis. Thus, an EBV vaccine could alleviate significant morbidity and mortality. EBV is orally transmitted and has tropism for both epithelial cells and B cells which are present in the oral cavity. Therefore, a prophylactic vaccine would need to prevent infection of both cell types. Passive transfer neutralizing monoclonal antibodies targeting the viral gH/gL glycoprotein complex prevent experimental EBV infection in humanized mice and rhesus macaques, suggesting that gH/gL is an attractive vaccine candidate. Here, we produced and evaluated the immunogenicity of several nanoparticle immunogens displaying gH/gL with distinct valencies and geometries. After one or two immunizations, all nanoparticles elicited superior binding and neutralizing titers relative to monomeric gH/gL. Antibodies elicited by a computationally designed self-assembling nanoparticle that displays 60 copies of the gH/gL protein conferred protection against a lethal dose of EBV in a humanized mouse challenge model, whereas antibodies elicited by monomeric gH/gL did not. Taken together, these data motivate further development of gH/gL nanoparticle vaccine candidates for EBV.
Asymmetric requirement for α-tubulin over β-tubulin
Authors: Wethekam Linnea C. , Moore Jeffrey K.
Published: February 2022

How cells regulate the supply of α- and β-tubulin monomers to meet the demand for αβ- heterodimers while avoiding consequences of monomer imbalance is not understood. We investigate the role of gene copy number in tubulin regulation and how shifting the expression of α- or β-tubulin genes impacts tubulin proteostasis and microtubule function. We find that α- tubulin gene copy number is important for maintaining an excess α-tubulin protein compared to β-tubulin protein and preventing accumulation of super-stoichiometric β-tubulin. Super- stoichiometric β-tubulin is toxic to cells, leading to loss of microtubules, formation of non- microtubule assemblies of tubulin, and disrupted cell proliferation. In contrast, decreased β- tubulin or increased α-tubulin has minor effects. We provide evidence that cells rapidly equilibrate the concentration of α-tubulin protein during shifts in α-tubulin isotype expression to maintain a ratio in excess of β-tubulin. We propose an asymmetric relationship between α- and β-tubulins, where α-tubulins are maintained in excess to supply αβ-heterodimers and limit the accumulation of β-tubulin monomers.
Nomograms of Human Hippocampal Volume Shifted by Polygenic Scores
Authors: Janahi Mohammed , Aksman Leon Michael , Schott Jonathan , Altmann Andre
Published: February 2022

Nomograms are important clinical tools applied widely in both developing and aging populations. They are generally constructed as normative models identifying cases as outliers to a distribution of healthy controls. Currently used normative models do not account for genetic heterogeneity. Hippocampal Volume (HV) is a key endophenotype for many brain disorders. Here, we examine the impact of genetic adjustment on HV nomograms and the translational ability to detect dementia patients.
Using imaging data from 35,686 healthy subjects aged 44 to 82 from the UK BioBank (UKBB), we built HV nomograms using gaussian process regression (GPR), extending the application age by 20 years, including dementia critical age ranges. Using HV Polygenic Scores (HV-PGS), we built genetically adjusted nomograms from participants stratified into the top and bottom 30% of HV-PGS. This shifted the nomograms in the expected directions by ~100 mm3 (2.3% of the average HV), which equates to 3 years of normal aging.
Clinical impact of genetically adjusted nomograms was investigated by comparing 818 subjects from the AD neuroimaging (ADNI) database diagnosed as either cognitively normal (CN), having mild cognitive impairment (MCI) or Alzheimers disease patients (AD). While no significant change in the survival analysis was found for MCI-to-AD conversion, an average of 4% decrease was found in intra-diagnostic-group variance, highlighting the importance of genetic adjustment in untangling phenotypic heterogeneity.
Density-dependent environments can select for extremes of body size
Authors: Coulson Tim , Felmy Anja , Passoni Gioele , Montgomery Robert A , Gaillard Jean-Michel , udson Peter HJ , Travis Joseph , Bassar Ronald D , Tuljapurkar Shripad , Marshall Dustin J , Clegg Sonya
Published: February 2022

Body size variation is an enigma. We do not understand why species achieve the sizes they do, and this means we also do not understand the circumstances under which gigantism or dwarfism is selected. We develop size-structured integral projection models to explore evolution of body size and life history speed. We make few assumptions and keep models simple: all functions remain constant across models except for the one that describes development of body size with age. We set sexual maturity to occur when size attains 80% of the asymptotic size, which is typical of a large mammal, and allow negative density dependence to only affect either reproduction or juvenile survival. Fitness – the quantity that is maximized by adaptive evolution – is carrying capacity in our models, and we are consequently interested in how it changes with size at sexual maturity, and how this association varies with development rate. The simple models generate complex dynamics while providing insight into the circumstances when extremes of body size evolve. The direction of selection leading to either gigantism or dwarfism crucially depends on the proportion of the population that is sexually mature, which in turn depends on how the development function determines the survivorship schedule. The developmental trajectories consequently interact with size-specific survival or reproductive rates to determine the best life history and the optimal body size emerges from that interaction. These dynamics result in trade-offs between different components of the life history, with the form of the trade-off that emerges depending upon where in the life history density dependence operates most strongly. Empirical application of the approach we develop has potential to help explain the enigma of body size variation across the tree of life.
Relative positioning of B and T cell epitopes drives immunodominance
Authors: Biavasco Riccardo , De Giovanni Marco
Published: February 2022

Humoral immunity is crucial for protection against invading pathogens. Broadly neutralizing antibodies (bnAbs) provide sterilizing immunity by targeting conserved regions of viral variants and represent the goal of most vaccination approaches. While antibodies can be selected to bind virtually any region of a given antigen, consistent induction of bnAbs in the context of influenza and HIV has been representing a major roadblock. Many possible explanations have been considered, however, none of the arguments proposed so far seems to fully recapitulate the observed counter-selection for broadly protective antibodies.

Antibodies can influence antigen presentation by enhancing the processing of CD4 epitopes adjacent to the binding region while suppressing the overlapping ones. We analyzed the relative positioning of dominant B and T cell epitopes in published antigens that elicit strong and poor humoral responses. In strong immunogenic antigens, regions bound by immunodominant antibodies are frequently adjacent to CD4 epitopes, potentially boosting their presentation. Conversely, poorly immunogenic regions targeted by bnAbs in HIV and influenza overlap with clusters of dominant CD4 epitopes, potentially conferring an intrinsic disadvantage for bnAb-bearing B cells in germinal centers.

Here we propose the theory of immunodominance relativity, according to which relative positioning of immunodominant B and CD4 epitopes within a given antigen drives immunodominance. Thus, we suggest that relative positioning of B-T epitopes may be one additional mechanism that cooperates with other previously described processes to influence immunodominance. If demonstrated, this theory can improve the current understanding of immunodominance, provide a novel explanation on HIV and influenza escape from humoral responses, and pave the way for new rational design of universal vaccines.
First comprehensive identification of proteins with increased O-GlcNAc levels during pressure overload hypertrophy
Authors: Zhu Wei Zhong , Palazzo Teresa , Zhou Mowei , Ledee Dolena , Olson Heather M , Paša-Tolić Ljiljana , Olson Aaron K.
Published: February 2022

Protein posttranslational modifications (PTMs) by O-GlcNAc globally rise during pressure-overload hypertrophy (POH). However, only a few specific proteins with altered O-GlcNAc levels during POH are known primarily because this PTM is easily lost during standard mass spectrometry (MS) conditions used for protein identification. Methodologies have recently emerged to stabilize the O-GlcNAc moiety for MS analysis. Accordingly, our goal was to determine the proteins undergoing changes in O-GlcNAc levels during POH. We used C57/Bl6 mice subjected to Sham or transverse aortic constriction (TAC) to create POH. From the hearts, we stabilized and labelled the O-GlcNAc moiety with tetramethylrhodamine azide (TAMRA) before enriching by TAMRA immunoprecipitation (IP). We used LC-MS to identify the captured O-GlcNAcylated proteins. We identified a total of 707 O-GlcNAcylated proteins in Sham and POH. Two hundred thirty-three of these proteins were significantly increased in POH over Sham whereas no proteins were significantly decreased in POH. We examined two MS identified proteins, CPT1B and PDH, to validate the MS data by immunoprecipitation. We corroborated increased O-GlcNAc levels during POH for the metabolic enzymes CPT1B and PDH. Enzyme activity assays showed higher O-GlcNAcylation increased CPT1 activity and decreased PDH activity. In summary, we generated the first comprehensive list of proteins with changes in O-GlcNAc levels during POH and, to our knowledge, the largest list for any cardiac pathology. Our results demonstrate the large number of proteins and cellular processes affected by O-GlcNAc during POH and serve as a guide for testing specific O-GlcNAc-regulated mechanisms.
Genome-wide analyses of histone modifications and chromatin accessibility reveal the distinct genomic compartments in the Irish potato famine pathogen Phytophthora infestans
Authors: Chen Han , Shu Haidong , Fang Yufeng , Song Wenrui , Li Zhi , Fang Yujie , Wang Yuanchao , Dong Suomeng
Published: February 2022

Phytophthora infestans, the causal agent of potato late blight, is a devastating plant disease that leads to Irish potato famine and threatens world-wide food security. Despite the genome of P. infestans has provided fundamental resource for studying the aggressiveness of this pandemic pathogen, the epigenomes remain poorly understood. Here, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS), we demonstrate post-translational modifications (PTM) at P. infestans core histone H3. The PTMs not only include these prevalent modifications in eukaryotes, and also some novel marks, such as H3K53me2 and H3K122me3. We focused on the trimethylations of H3K4, H3K9 and H3K27 and H3K36, and profiled P. infestans epigenomes employing Native Chromatin Immunoprecipitation followed by sequencing (N-ChIP-seq). In parallel, we mapped P. infestans chromomatin accessibility by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We found that adaptive genomic compartments display significantly higher levels of H3K9me3 and H3K27me3, and are generally in condense chromatin. Interestingly, we observed that genes encoding virulence factors, such as effectors, are enriched in open chromatin regions that barely have the four histone modifications. With a combination of genomic, epigenomic, transcriptomic strategies, our study illustrates the epigenetic states in P. infestans, which will help to study genomic functions and regulations in this pathogen.

Author summary

Epigenetics play an important role in various biological processes of eukaryotes, including pathogenicity of plant pathogens. However, the epigenetic landscapes are marginally known in oomycetes that are fungal-like organisms and comprise lots of destructive plant pathogens. In this study, using the Irish potato famine pathogen Phytophthora infestans as a model, we conducted genome-wide studies of histone post modifications and chromatin accessibility, and demonstrate the relationship of gene expression and evolution with the epigenetic marks. We found that one of the most important classes of virulence proteins, effectors, are enriched in open chromatin regions that barely have eu- and hetero-chromatic marks. This study provides an overview of the oomycete epigenetic atlas, and advances our understanding of the regulation of virulence factors in plant pathogens.