bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the Key Regulators of Cell Identity in Human Adult Pancreas
Authors: Vanheer Lotte , Fantuzzi Federica , To San Kit , Schiavo Andrea Alex , Van Haele Matthias , Haesen Tine , Yi Xiaoyan , Janiszewski Adrian , Chappell Joel , Rihoux Adrien , Sawatani Toshiaki , Roskams Tania , Pattou Francois , Kerr-Conte Julie , Cnop Miriam , Pasque Vincent
Published: September 2020

Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. Both BHLHE41 and JUND depletion seemed to increase the number of sc-enterochromaffin cells in hiPSC-derived islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity in the human adult pancreas. Furthermore, given that transcription factors are major regulators of embryo development and are often perturbed in diseases, a comprehensive understanding of how transcription factors work will be relevant in development and disease.

HIGHLIGHTS

Reconstruction of gene regulatory networks for human adult pancreatic cell types

An interactive resource to explore and visualize gene expression and regulatory states

Prediction of putative transcription factors that drive pancreatic cell identity

BHLHE41 depletion in primary islets induces apoptosis
Treeline ecotones shape the distribution of avian species richness and functional diversity in south temperate mountains
Authors: Altamirano Tomás A. , de Zwaan Devin R. , Ibarra José Tomás , Wilson Scott , Martin Kathy
Published: September 2020

Mountains produce distinct environmental gradients that may constrain or facilitate both the presence of avian species and/or specific combinations of functional traits. We addressed species richness and functional diversity to understand the relative importance of habitat structure and elevation in shaping avian diversity patterns in the south temperate Andes, Chile. During 2010-2018, we conducted 2,202 point-counts in four mountain habitats (successional montane forest, old-growth montane forest, subalpine, and alpine) from 211 to 1,768 m in elevation and assembled trait data associated with resource use for each species to estimate species richness and functional diversity and turnover. We detected 74 species. Alpine specialists included 16 species (22%) occurring only above treeline with a mean elevational range of 298 m, while bird communities below treeline (78%) occupied a mean elevational range of 1,081 m. Treeline was an inflection line, above which species composition changed by 91% and there was a greater turnover in functional traits (2–3 times greater than communities below treeline). Alpine birds were almost exclusively migratory, inhabiting a restricted elevational range, and breeding in rock cavities. We conclude that elevation and habitat heterogeneity structure avian trait distributions and community composition, with a diverse ecotonal sub-alpine and a distinct alpine community.
Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation
Authors: Shirinpour Sina , Hananeia Nicholas , Rosado James , Galanis Christos , Vlachos Andreas , Jedlicka Peter , Queisser Gillian , Opitz Alexander
Published: September 2020

Transcranial Magnetic Stimulation (TMS) is a non-invasive brain stimulation technique widely used in research and clinical applications. However, its mechanism of action and the neural response to TMS are still poorly understood. Multi-scale modeling can complement experimental research and provide a framework between the physical input parameters and the subcellular neural effects of TMS. At the macroscopic level, sophisticated numerical models exist to estimate the induced electric fields in whole-brain volume conductor models. However, multi-scale computational modeling approaches to predict TMS cellular and subcellular responses, crucial to understanding TMS plasticity inducing protocols, are not available so far. Here, we develop a multi-scaleNeuron Modeling for TMStoolbox (NeMo-TMS) that enables researchers to easily generate accurate neuron models from morphological reconstructions, couple them to the external electric fields induced by TMS, and to simulate the cellular and subcellular responses of the neurons. Both single-pulse and rTMS protocols can be simulated and results visualized in 3D. We openly share our toolbox and provide example scripts and datasets for the user to explore.NeMo-TMStoolbox (https://github.com/OpitzLab/NeMo-TMS) allows researchers a previously not available level of detail and precision in realistically modeling the physical and physiological effects of TMS.
Measuring Protein Insertion Areas in Lipid Monolayers by Fluorescence Correlation Spectroscopy
Authors: Auerswald Jan , Ebenhan Jan , Schwieger Christian , Scrima Andrea , Meister Annette , Bacia Kirsten
Published: September 2020

The insertion of protein domains into membranes is an important step in many membrane remodeling processes, for example in vesicular transport. The membrane area taken up by the protein insertion influences the protein binding affinity as well as the mechanical stress induced in the membrane and thereby its curvature. Total area changes in lipid monolayers can be measured on a Langmuir film balance. Finding the area per inserted protein however proves challenging for two reasons: The number of inserted proteins must be determined without disturbing the binding equilibrium and the change in the film area can be very small. Here we address both issues using Fluorescence Correlation Spectroscopy (FCS): Firstly, by labeling a fraction of the protein molecules fluorescently and performing FCS experiments directly on the monolayer, the number of inserted proteins is determinedin situwithout having to rely on invasive techniques, such as collecting the monolayer by aspiration. Secondly, by using another FCS color channel and adding a small fraction of fluorescent lipids, the reduction in fluorescent lipid density accompanying protein insertion can be monitored to determine the total area increase. Here, we use this method to determine the insertion area per molecule of Sar1, a protein of the COPII complex, which is involved in transport vesicle formation, in a lipid monolayer. Sar1 has an N-terminal amphipathic helix, which is responsible for membrane binding and curvature generation. An insertion area of (3.4 ± 0.8) nm2was obtained for Sar1 in monolayers from a lipid mixture typically used in reconstitution, in good agreement with the expected insertion area of the Sar1 amphipathic helix. By using the two-color approach, determining insertion areas relies only on local fluorescence measurements. No macroscopic area measurements are needed, giving the method the potential to be applied also to laterally heterogeneous monolayers and bilayers.

Statement of Significance

We show that two color Fluorescence Correlation Spectroscopy (FCS) measurements can be applied to the binding of a protein to a lipid monolayer on a Langmuir film balance in order to determine the protein insertion area. One labelling color was used to determine the number of bound proteins and the other one to monitor the area expansion of the lipid monolayer upon protein binding. A strategy for the FCS data analysis is provided, which includes focal area calibration by raster image correlation spectroscopy and a framework for applying z-scan FCS and including free protein in the aqueous subphase. This approach allows determining an area occupied by a protein in a quasi-planar model membrane from a local, non-invasive, optical measurement.
Understanding the emergence of contingent and deterministic exclusion in multispecies communities
Authors: Song Chuliang , Uricchio Lawrence H. , Mordecai Erin A. , Saavedra Serguei
Published: September 2020

Competitive exclusion can be classified as deterministic or as historically contingent. While competitive exclusion is common in nature, it has remained unclear when multispecies communities should be dominated by deterministic or contingent exclusion. Here, we provide a general theoretical approach to explain both the emergence and sources of competitive exclusion in multispecies communities. We illustrate our approach on an empirical competition system between annual and perennial plant species. First, we find that the life-history of perennial species increases the probability of observing contingent exclusion by increasing their effective intrinsic growth rates. Second, we find that the probability of observing contingent exclusion increases with weaker intraspecific competition, and not with the level of hierarchical competition. Third, we find a shift from contingent exclusion to dominance with increasing numbers of competing species. Our work provides a heuristic framework to increase our understanding about the predictability of species persistence within multispecies communities.
Hamilton’s rule, gradual evolution, and the optimal (feedback) control of phenotypically plastic traits
Authors: Avila Piret , Priklopil Tadeas , Lehmann Laurent
Published: September 2020

Most traits expressed by organisms, such as gene expression profiles, developmental trajectories, behavioural sequences and reaction norms are function-valued traits (colloquially “phenotypically plastic traits”), since they vary across an individual’s age and in response to various internal and/or external factors (state variables). Furthermore, most organisms live in populations subject to limited genetic mixing and are thus likely to interact with their relatives. We here formalise selection on genetically determined function-valued traits of individuals interacting in a group-structured population, by deriving the marginal version of Hamilton’s rule for function-valued traits. This rule simultaneously gives a condition for the invasion of an initially rare mutant function-valued trait and its ultimate fixation in the population (invasion thus implies substitution). Hamilton’s rule thus underlies the gradual evolution of function-valued traits and gives rise to necessary first-order conditions for their uninvadability (evolutionary stability). We develop a novel analysis using optimal control theory and differential game theory, to simultaneously characterise and compare the first-order conditions of (i) open-loop traits - functions of time (or age) only, and (ii) closed-loop (state-feedback) traits - functions of both time and state variables. We show that closed-loop traits can be represented as the simpler open-loop traits when individuals do no interact or when they interact with clonal relatives. Our analysis delineates the role of state-dependence and interdependence between individuals for trait evolution, which has implications to both life-history theory and social evolution.
Antimicrobial efficacy of neem and liquorice with chlorhexidine on Streptococcus sanguis, Streptococcus mutans, Lactobacillus and Actinomyces naeslundii – An In Vitro Study
Authors: Alqahtani Saad M
Published: September 2020

The study was to formulate 2% neem and 2% liquorice mouthwashes and to compare the antimicrobial efficacy of these mouthwashes with the standard 0.2% chlorhexidine mouthwash. Alcoholic solution was prepared and added to neem mixture and liquorice mixture separately and made up to a volume of 16000 ml with purified water. Nine dilutions of each drug were done with Brain heart infusion broth (BHI) for MIC. Culture suspension was added in each serially diluted tube of 200 μl. The tubes were incubated for 24 hours and observed for turbidity. Minimum inhibitory concentration (MIC) of 2% neem, 2% liquorice and 0.2% chlorhexidine against Lactobacillus, Actinomyces naeslundii, Streptococcus sanguis, Streptococcus mutans is determined by serial dilution analysis. Streptococcus mutans shows sensitivity to all three mouthwashes at a concentration starting from 0.2 μg/ml. Lactobacillus shows sensitivity to neem and chlorhexidine mouthwashes at a concentration starting from 1.6 μg/ml, whereas liquorice is effective at a concentration starting from 3.125 μg/ml. Streptococcus sanguis shows sensitivity to chlorhexidine and liquorice mouthwashes at a concentration starting from 25 μg/ml, whereas it shows sensitivity to neem at a concentration starting from 50 μg/ml. Actinomyces naeslundii shows sensitivity to chlorhexidine and neem mouthwashes at a concentration starting from 1.6 μg/ml, whereas it shows sensitivity to liquorice at a concentration starting from 3.125μg/ml. Analysis showed an inhibition of all the four strains by the mouthwashes. The MIC for the studied mouthwashes was found to be similar to that of 0.2% chlorhexidine.
Decoding representations of discriminatory and hedonic information during appetitive and aversive touch
Authors: Kryklywy James H. , Ehlers Mana R. , Beukers Andre O. , Moore Sarah R. , Todd Rebecca M. , Anderson Adam K.
Published: September 2020

Emotion is typically understood to be an internal subjective experience originating in the brain. Yet in the somatosensory system hedonic information is coded by mechanoreceptors at the point of sensory contact before it reaches the central nervous system. It remains unknown, however, how these distinct peripheral channels for tactile hedonic information contribute to representations of interoceptive states relative to exteroceptive experience. In this fMRI study we applied representational similarity analyses with pattern component modeling, a technique that deconstructs representational states into a weighted set of distinct predefined constructs, to dissociate how discriminatory vs. hedonic tactile information, carried by A- and C-/CT-fibers respectively, contributes to population code representations in the human brain. Results demonstrated that information about appetitive and aversive tactile sensation is represented separately from non-hedonic tactile information across cortical structures. Specifically, although hedonic touch originates as a peripheral signal, labeled at the point of contact, representations in somatosensory cortices are guided by experiences of non-hedonic touch, By contrast, representations in regions associated with interoception and affect encode signals of hedonic touch. This provides evidence of complex tactile encoding that involves both external-exteroceptive and internal-interoceptive dimensions. Importantly, hedonic touch contributes to representations of internal state as well as those of externally generated stimulation.
Novelty is not Surprise: Human exploratory and adaptive behavior in sequential decision-making
Authors: Xu He A. , Modirshanechi Alireza , Lehmann Marco P. , Gerstner Wulfram , Herzog Michael H.
Published: September 2020

Classic reinforcement learning (RL) theories cannot explain human behavior in response to changes in the environment or in the absence of external reward. Here, we design a deep sequential decision-making paradigm with sparse reward and abrupt environmental changes. To explain the behavior of human participants in these environments, we show that RL theories need to include surprise and novelty, each with a distinct role. While novelty drives exploration before the first encounter of a reward, surprise increases the rate of learning of a world-model as well as of model-free action-values. Even though the world-model is available for model-based RL, we find that human decisions are dominated by model-free action choices. The world-model is only marginally used for planning but is important to detect surprising events. Our theory predicts human action choices with high probability and allows us to dissociate surprise, novelty, and reward in EEG signals.
Influences of male age, mating history and starvation on female post mating aggression and feeding inDrosophila
Authors: Bath Eleanor , Buzzoni Daisy , Ralph Toby , Wigby Stuart , Sepil Irem
Published: September 2020

Mating changes female behaviour and physiology across a wide range of taxa, with important effects for male and female fitness. These changes are often induced by components of the male ejaculate, such as sperm and seminal fluid proteins.

However, males can vary significantly in their ejaculates, due to factors such as age, mating history, or nutritional status. This male variation may therefore lead to variation in the strength of responses males can stimulate in females, with alterations in fitness outcomes for both sexes.

Using the fruit fly,Drosophila melanogaster, we tested whether three aspects of male condition shape an important, but understudied, post-mating response – increased female-female aggression.

We found that females mated to old males fought less than females mated to young males. This effect was exacerbated in mates of old, sexually active males, but there was no effect of male starvation status on mating-induced female aggression. There was also a significant effect of age and mating history on female post-mating feeding duration.

Our results add to a growing body of literature that variation in male condition can shape sexual selection through post-mating responses in females, including female-female interactions. Studying such variation may therefore be useful for understanding how the condition of sex affects the behaviour of the other.
A survey of proximal methods for monitoring leaf phenology in temperate deciduous forests
Authors: Soudani Kamel , Delpierre Nicolas , Berveiller Daniel , Hmimina Gabriel , Pontailler Jean-Yves , Seureau Lou , Vincent Gaёlle , Dufrêne Éric
Published: September 2020

Tree phenology is a major driver of forest-atmosphere mass and energy exchanges. Yet tree phenology has historically not been recorded at flux measurement sites. Here, we used seasonal time-series of ground-based NDVI (Normalized Difference Vegetation Index), RGB camera GCC (Greenness Chromatic Coordinate), broad-band NDVI, LAI (Leaf Area Index),fAPAR (fraction of Absorbed Photosynthetic Active Radiation), CC (Canopy Closure),fRvis(fraction of Reflected Radiation) and GPP (Gross Primary Productivity) to predict six phenological markers detecting the start, middle and end of budburst and of leaf senescence in a temperate deciduous forest. We compared them to observations of budburst and leaf senescence achieved by field phenologists over a 13-year period. GCC, NDVI and CC captured very well the interannual variability of spring phenology (R2> 0.80) and provided the best estimates of the observed budburst dates, with a mean absolute deviation (MAD) less than 4 days. For the CC and GCC methods, mid-amplitude (50%) threshold dates during spring phenological transition agreed well with the observed phenological dates. For the NDVI-based method, on average, the mean observed date coincides with the date when NDVI reaches 25% of its amplitude of annual variation. For the other methods, MAD ranges from 6 to 17 days. GPP provides the most biased estimates. During the leaf senescence stage, NDVI- and CC-derived dates correlated significantly with observed dates (R2=0.63 and 0.80 for NDVI and CC, respectively), with MAD less than 7 days. Our results show that proximal sensing methods can be used to derive robust phenological indexes. They can be used to retrieve long-term phenological series at flux measurement sites and help interpret the interannual variability and decadal trends of mass and energy exchanges.

Highlights

We used 8 indirect methods to predict the timing of phenological events.

GCC, NDVI and CC captured very well the interannual variation of spring phenology.

GCC, NDVI and CC provided the best estimates of observed budburst dates.

NDVI and CC derived-dates correlated with observed leaf senescence dates.
Social networks strongly predict the gut microbiota of wild mice
Authors: Raulo Aura , Allen Bryony , Troitsky Tanya , Husby Arild , Firth Josh A , Coulson Tim , Knowles Sarah CL
Published: September 2020

The mammalian gut teems with beneficial microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains unexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected hub individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.
Soundscapes predict species occurrence in tropical forests
Authors: Sethi Sarab S. , Ewers Robert M. , Jones Nick S. , Sleutel Jani , Shabrani Adi , Zulkifli Nursyamin , Picinali Lorenzo
Published: September 2020

Accurate occurrence data is necessary for the conservation of keystone or endangered species, but acquiring it is usually slow, laborious, and costly. Automated acoustic monitoring offers a scalable alternative to manual surveys, but identifying species vocalisations requires large manually annotated training datasets, and is not always possible (e.g., for silent species). A new, intermediate approach is needed that rapidly predicts species occurrence without requiring extensive labelled data.

We investigated whether local soundscapes could be used to infer the presence of 32 avifaunal and seven herpetofaunal species across a tropical forest degradation gradient in Sabah, Malaysia. We developed a machine-learning based approach to characterise species indicative soundscapes, training our models on a coarsely labelled manual point-count dataset.

Soundscapes successfully predicted the occurrence of 34 out of the 39 species across the two taxonomic groups, with area under the curve (AUC) metrics of up to 0.87 (Bold-striped Tit-babblerMacronus bornensis). The highest accuracies were achieved for common species with strong temporal occurrence patterns.

Soundscapes were a better predictor of species occurrence than above-ground biomass – a metric often used to quantify habitat quality across forest degradation gradients.

Synthesis and applications: Our results demonstrate that soundscapes can be used to efficiently predict the occurrence of a wide variety of species. This provides a new direction for audio data to deliver large-scale, accurate assessments of habitat suitability using cheap and easily obtained field datasets.
Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
Authors: Jing Yihang , Montano Jose , Levy Michaella , Lopez Jeff , Kung Pei-Pei , Richardson Paul , Krajewski Krzysztof , Florens Laurence , Washburn Michael , Meier Jordan L.
Published: September 2020

Chemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the Coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based Sepharose pulldown resins differentiated by a single negatively charged residue, and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of ‘probe selectivity’ versus traditional ‘competitive chemical proteomics’. This reveals the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of pre-clinical therapeutic agents.
Effective control of a viral disease with a high transmission rate through selective predation
Authors: Chen Yonggui , Wang Muhua , Zhao Zhong , Weng Shaoping , Yang Jinchuan , Liu Shangyun , Liu Chang , Yuan Fenghua , Ai Bin , Zhang Haiqing , Zhang Mingyan , Lu Lirong , Yuan Kai , Yu Zhaolong , Mo Bibo , Zhong Zhiwei , Zheng Luwei , Feng Guocan , Li Shengwen Calvin , He Jianguo
Published: September 2020

Due to the limited understanding of the characteristics of predator-pathogen-prey interactions, few attempts to use selective predation for controlling diseases in prey populations have been successful. The global pandemic of white spot syndrome (WSS), caused by white spot syndrome virus (WSSV), causes devastating economic losses in farmed shrimp production. Currently, there is no effective control for WSS. Here, we determined the transmission dynamics of WSSV and the feeding ability and selectivity of fish on healthy, infected and dead shrimp by experiments and mathematical modeling. Accordingly, we developed a novel and convenient shrimp cultural ecosystem, which that effectively prevented WSS outbreaks, by introducing aquaculture fish species. This provides a scheme for developing control strategies for viral diseases with high transmission rate.
Altered basal lipid metabolism underlies the functional impairment of naive CD8+T cells in elderly humans
Authors: Nicoli Francesco , Cabral-Piccin Mariela P. , Papagno Laura , Gallerani Eleonora , Folcher Victor , Dubois Marion , Clave Emmanuel , Vallet Hélène , Frere Justin J. , Gostick Emma , Llewellyn-Lacey Sian , Price David A. , Toubert Antoine , Boddaert Jacques , Caputo Antonella , Gavioli Riccardo , Appay Victor
Published: September 2020

Background

Aging is associated with functional deficits in the naive T cell compartment, which compromise the generation ofde novoimmune responses against previously unencountered antigens. The mechanisms that underlie this phenomenon have nonetheless remained unclear.

Methods

Biochemical and functional properties of naive CD8+T cells were characterized and compared between middle aged and older individuals.

Findings

We identified an age-related link between altered basal lipid metabolism in naive CD8+T cells and their impaired responsiveness to stimulation, characterized by low proliferative potential and susceptibility to apoptosis. Reversal of the bioenergetic anomalies with lipid-altering drugs, such as rosiglitazone, improved the functional capabilities of naive CD8+T cells in elderly subjects.

Interpretation

Interventions that favor lipid catabolism may find utility as adjunctive therapies in the elderly to promote vaccine-induced immunity against emerging pathogens or tumors.

Funding

A full list of the funding sources is detailed in the Acknowledgment section of the manuscript.

RESEARCH IN CONTEXT

Evidence before this study

Old subjects are highly susceptible to infections and tumors and usually present with low responses to vaccine. This is mainly due to the age-related loss of primary immune resources, i.e. a quantitative decline of naive CD8+T cells. Nonetheless, few studies have also underlined, within this cell subset, qualitative defects in elderly subjects.

Added value of this study

Considering the well-demonstrated link between nutrient usage and lymphocyte functions, we characterized the bioenergetics features of old naïve CD8+T cells. Our data show an age-dependent altered basal metabolism in this cell subset, mostly at the levels of fatty acids and mitochondrial functions. These alterations were associated with functional defects which were partially reverted through the use of lipid-lowering strategies.

Implications of all the available evidence

This study highlights the potential role of an altered cellular lipid metabolism in immunosenescence, providing clues to understand the epidemiological profile of emerging infections or tumors and to develop preventive and therapeutic strategies based on metabolic manipulation.
Surface condensation of a pioneer transcription factor on DNA
Authors: Morin Jose A. , Wittmann Sina , Choubey Sandeep , Klosin Adam , Golfier Stefan , Hyman Anthony A. , Jülicher Frank , Grill Stephan W.
Published: September 2020

In the last decade, extensive studies on the properties of non-membrane-bound compartments in the cellular cytoplasm have shown that concepts in phase separation drawn from physical chemistry can describe their formation and behaviour1–4. Current evidence also suggests that phase separation plays a role in the organization inside the cell nucleus5–8. However, the influence and role of DNA on the physical chemistry of phase separation is not well understood. Here, we are interested in the role of interactions between phase separating proteins and the DNA surface. The interaction of liquid phases with surfaces has been extensively studied in soft matter physics, in the context of macroscopic surfaces and non-biological liquids9–11. The conditions in the nucleus are different from those studied in conventional soft matter physics because DNA with a diameter of about 2 nm12provides a microscopic surface, and liquid-like phases are complex mixtures of proteins subject to a myriad of biochemical modifications13. Transcriptional condensates, which are thought to serve as regulatory hubs in gene expression14–21, provide an accessible system to investigate the physics of condensates that emerge from DNA-protein and protein-protein interactions. These condensates are typically small22, and the mechanisms that determine their size are unknown. Whether they can be understood as phase separated compartments has been subject to debate23–26. Here, we use optical tweezers to directly observe the condensation of the pioneer transcription factor Klf427,28on DNAin vitro. We demonstrate that Klf4 forms microphases that are enabled by interaction with the DNA surface. This sets their typical size and allows them to form below the saturation concentration for liquid-liquid phase separation. We combine experiment with theory to show that these microphases can be understood as forming by surface condensation on DNA via a switch-like transition similar to prewetting. Polymer surface mediated condensation reconciles several observations that were previously thought to be at odds with the idea of phase separation as an organizing principle in the nucleus.
A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis
Authors: Stamboulian Moses , Doak Thomas G. , Ye Yuzhen
Published: September 2020

1

Background

Recent advances in genome and metagenome sequencing have dramatically enriched the collection of genomes of bacterial species related to human health and diseases. In metagenomic studies phylogenetic trees are commonly used to depict, describe, and compare the bacterial members of the community under study. The most accurate tree-building algorithms now use large sets of marker genes taken from across genomes. However, many of the current bacterial genomes were assembled from metagenomic datasets (i.e., metagenome assembled genomes, MAGs), and often contain missing information. It is therefore important to study how well the phylogeny approach performs on such genomes. Further, phylogeny methods are not perfect and it is important to know how reliable an inferred tree is.

Results

Here we examined the impact of incompleteness of the genomes on the tree reconstruction, and we showed that phylogeny approaches including RAxML (which handles missing data explicitly) and FastTree generally performed well on simulated collection of 400 genomes with missing information. As RAxML is computationally prohibitive for the much larger collections of gut genomes, we chose FastTree to build a unified tree of human-gut associated bacterial species (referred to as gut tree), including more than 3000 genomes, most of which are incomplete. We developed two downstream applications of the gut tree: peptide-centric analysis of metaproteomics datasets; and taxonomic characterization of metagenomic sequences. In both applications, the gut tree provided the basis for quantification of species composition at various taxonomic resolutions.

Conclusions

The gut tree presented in this study provides a useful framework for taxonomic profiling of human gut microbiome. Including MAGs in the tree provides more comprehensive representation of microbial species diversity associated with human gut, important for studying the taxonomic composition of gut microbiome.

Availability and Implementation

The tree construction pipeline and downstream applications of the gut tree are freely available athttps://github.com/mgtools/guttree.
The soybean (Glycine maxL.) cytokinin oxidase/dehydrogenase multigene family; identification of natural variations for altered cytokinin content and seed yield
Authors: Nguyen Hai Ngoc , Kambhampati Shrikaar , Kisiala Anna , Seegobin Mark , Emery RJ Neil
Published: September 2020

Cytokinins (CKs) play a fundamental role in regulating dynamics of organ source/sink relationships during plant development, including flowering and seed formation stages. As a result, CKs are key drivers of seed yield. The cytokinin oxidase/dehydrogenase (CKX) is one of the critical enzymes responsible for regulating plant CK levels by causing their irreversible degradation. Variation ofCKXgene activity is significantly correlated with seed yield in many crop species while in soybean (Glycine maxL.), the possible associations betweenCKXgene family members (GFMs) and yield parameters have not yet been assessed. In this study, seventeenGmCKXGFMs were identified, and natural variations amongGmCKXgenes were probed among soybean cultivars with varying yield characteristics. The keyCKXgenes responsible for regulating CK content during seed filling stages of reproductive development were highlighted using comparative phylogenetics, gene expression analysis and CK metabolite profiling. Five of the seventeen identifiedGmCKXGFMs, showed natural variations in the form of single nucleotide polymorphisms (SNPs). The geneGmCKX14, with high expression during critical seed filling stages, was found to have a non-synonymous mutation (H105Q), on one of the active site residues, Histidine 105, previously reported to be essential for co-factor binding to maintain structural integrity of the enzyme. Soybean lines with this mutation had higher CK content and desired yield characteristics. The potential for marker-assisted selection based on the identified natural variation withinGmCKX14, is discussed in the context of hormonal control that can result in higher soybean yield.

Key Message

Natural variations in soybean cytokinin oxidase/dehydrogenase gene,GmCKX14, with high expression during seed development, were linked to increased sink strength via altered cytokinin profiles in high yielding cultivars.
Chickpea (Cicer arietinumL.) root system architecture adaptation to initial soil moisture improves seed development in dry-down conditions
Authors: Bontpart Thibaut , Robertson Ingrid , Giuffrida Valerio , Concha Cristobal , Scorza Livia C. T. , McCormick Alistair J. , Fikre Asnake , Tsaftaris Sotirios A. , Doerner Peter
Published: September 2020

Soil water deficit (WD) impacts vascular plant phenology, morpho-physiology, and reproduction. Chickpea, which is mainly grown in semi-arid areas, is a good model plant to dissect mechanisms involved in drought resistance.

We used a rhizobox-based phenotyping system to simultaneously and non-destructively characterise root system architecture (RSA) dynamics and water use (WU) patterns. We compared the drought-adaptive strategies of ‘Teketay’ to the drought-sensitive genotype ICC 1882 in high and low initial soil moisture without subsequent irrigation.

WD restricted vegetative and reproductive organ biomass for both genotypes. Teketay displayed greater adaptability for RSA dynamics and WU patterns and revealed different drought adaptive strategies depending on initial soil moisture: escape when high, postponement when low. These strategies were manifested in distinct RSA dynamics: in low initial soil moisture, its reduced root growth at the end of the vegetative phase was followed by increased root growth in deeper, wetter soil strata, which facilitated timely WU for seed development and produced better-developed seeds.

We demonstrate that RSA adaptation to initial soil moisture is one mechanism by which plants can tolerate WD conditions and ensure reproduction by producing well-developed seeds. Our approach will help in identifying the genetic basis for large plasticity of RSA dynamics which enhances the resilience with which crops can optimally adapt to various drought scenarios.

Highlight

Root system architecture and water use patterns change dynamically for distinct drought adaptation strategies in chickpea.
The ER chaperones BiP and Grp94 regulate the formation of insulin-like growth factor 2 (IGF2) oligomers
Authors: Jin Yi , Kotler Judy L.M. , Wang Shiyu , Huang Bin , Halpin Jackson C. , Street Timothy O.
Published: September 2020

While cytosolic Hsp70 and Hsp90 chaperones have been extensively studied, less is known about how the ER Hsp70 and Hsp90 paralogs (BiP and Grp94) recognize clients and influence their folding. Here, we examine how BiP and Grp94 influence the folding of insulin-like growth factor 2 (IGF2). Full-length proIGF2 is composed of an insulin-like hormone and an E-peptide that has sequence characteristics of an intrinsically disordered region. We find that the E-peptide region allows proIGF2 to form oligomers. BiP and Grp94 influence both the folding and the oligomerization of proIGF2. BiP and Grp94 exert a similar holdase function on proIGF2 folding by preferentially binding the proIGF2 unfolded state, rather than stabilizing specific folding intermediates and changing the proIGF2 folding process. In contrast, BiP and Grp94 exert counteracting effects on proIGF2 oligomerization. BiP suppresses proIGF2 oligomerization under both ADP and ATP conditions. Interestingly, Grp94 can enhance proIGF2 oligomerization when Grp94 adopts an open conformation (ADP conditions), but not when Grp94 is in the closed conformation (ATP conditions). We propose that BiP and Grp94 regulate the assembly of proIGF2 oligomers, and that regulated oligomerization may enable proIGF2 to be effectively packaged for export from the ER to the Golgi.
Super-relaxed state of myosin in human skeletal muscle is fiber-type dependent
Authors: Phung Lien A. , Foster Aurora D. , Miller Mark S. , Lowe Dawn A. , Thomas David D.
Published: September 2020

The myosin super-relaxed state (SRX) in skeletal muscle is hypothesized to play an important role in regulating muscle contractility and thermogenesis in humans, but has only been examined in model organisms. Here we report the first human skeletal muscle SRX measurements, using quantitative epifluorescence microscopy of fluorescent 2’/3’-O-(N-methylanthraniloyl) ATP (mantATP) single-nucleotide turnover. Myosin heavy chain (MHC) isoform expression was determined using gel electrophoresis for each permeabilized vastus lateralis fiber, to allow for novel comparisons of SRX between fiber-types. We find that the fraction of myosin in SRX is less in MHC IIA fibers than in MHC I and IIAX fibers (p = 0.008). ATP turnover of SRX is faster in MHC IIAX fibers compared to MHC I and IIA fibers (p = 0.001). We conclude that SRX biochemistry is measurable in human skeletal muscle, and our data indicate that SRX depends on fiber type as classified by MHC isoform. Extension from this preliminary work would provide further understanding regarding the role of SRX in human muscle physiology.
Lamprey Lecticans Link New Vertebrate Genes to the Origin and Elaboration of Vertebrate Tissues
Authors: Root Zachary D. , Jandzik David , Allen Cara , Brewer Margaux , Romášek Marek , Square Tyler , Medeiros Daniel M.
Published: September 2020

The evolution of vertebrates from an invertebrate chordate ancestor involved the evolution of new organs, tissues, and cell types. It was also marked by the origin and duplication of new gene families. If, and how, these morphological and genetic innovations are related is an unresolved question in vertebrate evolution. Hyaluronan is an extracellular matrix (ECM) polysaccharide important for water homeostasis and tissue structure. Vertebrates possess a novel family of hyaluronan binding proteins called Lecticans, and studies in jawed vertebrates (gnathostomes) have shown they function in many of the cells and tissues that are unique to vertebrates. This raises the possibility that the origin and/or expansion of this gene family helped drive the evolution of these vertebrate novelties. In order to better understand the evolution of thelecticangene family, and its role in the evolution of vertebrate morphological novelties, we investigated the phylogeny, genomic arrangement, and expression patterns of alllecticansin the sea lamprey (Petromyzon marinus), a jawless vertebrate. Though bothP. marinusand gnathostomes have fourlecticans, our phylogenetic and syntenic analyses suggest lampreylecticansare the result of one or more cyclostome-specific duplications. Despite the independent expansion of the lamprey and gnathostomelecticanfamilies, we find highly conserved expression oflecticansin vertebrate-specific and mesenchyme-derived tissues. We also find that, unlike gnathostomes, lamprey expresses itslecticanparalogs in distinct subpopulations of head skeleton precursors, potentially reflecting an ancestral diversity of skeletal tissue types. Together, these observations suggest that the ancestral pre-duplicationlecticanhad a complex expression pattern, functioned to support mesenchymal histology, and likely played a role in the evolution of vertebrate-specific cell and tissue types.
Single-cell characterization of transcriptomic heterogeneity in lymphoblastoid cell lines
Authors: SoRelle Elliott D. , Dai Joanne , Zhou Jeffrey Y. , Giamberardino Stephanie N. , Bailey Jeffrey A. , Gregory Simon G. , Chan Cliburn , Luftig Micah A.
Published: September 2020

Lymphoblastoid Cell Lines (LCLs) are generated by transforming primary B cells with Epstein-Barr Virus (EBV) and are used extensively as model systems in viral oncology, immunology, and human genetics research. In this study, we characterized single-cell transcriptomic profiles of five LCLs and present a simple discrete-time simulation to explore the influence of stochasticity on LCL clonal evolution. Single-cell RNA sequencing revealed substantial phenotypic heterogeneity within and across LCLs with respect to immunoglobulin isotype; virus-modulated host pathways involved in survival, proliferation, and differentiation; viral replication state; and oxidative stress. This heterogeneity is likely attributable to intrinsic variance in primary B cells and host-pathogen dynamics. Stochastic simulations demonstrate that initial primary cell heterogeneity, random sampling, time in culture, and even mild differences in phenotype-specific fitness can contribute substantially to dynamic diversity in populations of nominally clonal cells.
Molecular characterization revealed the role of thaumatin-like proteins in stress response in bread wheat
Authors: Sharma Alok , Sharma Himanshu , Rajput Ruchika , Pandey Ashutosh , Upadhyay Santosh Kumar
Published: September 2020

Thaumatin-like proteins (TLPs) are related to the pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93TLPgenes were identified in the genome ofTriticum aestivum.Further, we identified 26, 27, 39 and 37TLPgenes in theBrachypodium distachyon,Oryza sativa,Sorghum bicolorandZea maysgenomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles ofTLPsin plant development and abiotic and fungal stress response. Recombinant expression ofTaTLP2-BinSaccharomyces cerevisiaeprovided significant tolerance against cold, heat, drought and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.
Primary saturation of α, β-unsaturated carbonyl containing fatty acids does not abolish electrophilicity
Authors: Snyder Nathaniel W. , O’Brien James , Singh Bhupinder , Buchan Gregory , Arroyo Alejandro D. , Liu Xiaojing , Bostwick Anna , Varner Erika L. , Angajala Anusha , Sobol Robert W. , Blair Ian A. , Mesaros Clementina , Wendell Stacy G.
Published: September 2020

Metabolism of polyunsaturated fatty acids results in the formation of hydroxylated fatty acids that can be further oxidized by dehydrogenases, often resulting in the formation of electrophilic, α,β-unsaturated ketone containing fatty acids. As electrophiles are associated with redox signaling, we sought to investigate the metabolism of the oxo-fatty acid products in relation to their double bond architecture. Using an untargeted liquid chromatography mass spectrometry approach, we identified mono- and di-saturated products of the arachidonic acid-derived 11-oxoeicosatetraenoic acid (11-oxoETE) and mono-saturated metabolites of 15-oxoETE and docosahexaenoic acid-derived 17-oxodocosahexaenoinc acid (17-oxoDHA) in both human A549 lung carcinoma and umbilical vein endothelial cells. Notably, mono-saturated oxo-fatty acids maintained their electrophilicity as determined by nucleophilic conjugation to glutathione while a second saturation of 11-oxoETE resulted in a loss of electrophilicity. These results would suggest that prostaglandin reductase (PTGR1), known for its reduction of the α,β-unsaturated double bond, was not responsible for the saturation of oxo-fatty acids. Surprisingly, knockdown of PTGR1 expression by shRNA confirmed its participation in the formation of 15-oxoETE and 17-oxoDHA mono-saturated metabolites. Furthermore, overexpression of PTGR1 in A549 cells increased the rate and total amount of oxo-fatty acid saturation. These findings will further facilitate the study of electrophilic fatty acid metabolism and signaling in the context of inflammatory diseases and cancer where they have been shown to have anti-inflammatory and anti-proliferative signaling properties.

Highlights

Primary saturation of electrophilic fatty acids does not abolish biological activity.

Prostaglandin reductase 1 reduces double bonds in fatty acids that are structurally similar to 15-keto-prostaglandin E2.

Prostaglandin reductase 1 reduces non-carbonyl adjacent double bonds.