bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications
Authors: Li Wenjin
Published: July 2022

Reactive flux can be largely non-zero in a nonequilibrium ensemble of trajectories and provide insightful information for reactive transitions from the reactant state to the product state. Based on the reactive flux, a theoretical framework is proposed here for two quantities, the potential energy weighted reactive flux and the total rate of change of potential energy, which are useful for the identification of mechanism from a nonequilibrium ensemble. From such quantities, two multidimensional free energy analogues can be derived in the subspace of collective variables and they are equivalent in the regions where the reactive flux is divergence-free. These free energy analogues are assumed to be closely related to the free energy in the subspace of collective variables and they are reduced in the one-dimensional case to be the ensemble average of the potential energy weighted with reactive flux intensity, which was proposed recently and could be decomposed into energy components at the per-coordinate level. In the subspace of collective variables, the decomposition of the multidimensional free energy analogues at the per-coordinate level is theoretically possible and is numerically difficult to be calculated. Interestingly, the total rate of change of potential energy is able to identify the location of the transition state ensemble or the stochastic separatrix, in addition to the locations of the reactant and product states. The total rate of change of potential energy can be decomposed at the per-coordinate level and its components can quantify the contribution of a coordinate to the reactive transition in the subspace of collective variables. We then illustrated the main insights and objects that can be provided by the approach in the application to the alanine peptide in vacuum in various nonequilibrium ensembles of short trajectories and the results from these ensembles were found to be consistent.
Partial protection from fluctuating selection leads to evolution toward wider population size fluctuation and a novel mechanism of balancing selection
Authors: Kim Yuseob
Published: July 2022

Classical theory predicted that natural selection favors a variant causing smaller fluctuation of population density. It is also known that if population is partially protected from fluctuating selection, as in the case of seed bank, the variance of fitness is further reduced and therefore the reproductive success of population is ensured. This study, exploring a mathematical model for coupled demographic and evolutionary dynamics, finds that such a ‘refuge’ from fluctuating selection even causes positive selection for a variant increasing the amplitude of population size fluctuation under weak or moderate regulation of population density. Under strong density regulation and constant carrying capacity, long-term maintenance of polymorphism known as the storage effect emerges. However, if the carrying capacity is changing either cyclically or randomly and the density regulation is strong, variants whose fitness fluctuates in phase with population size are positively selected to either fixation or oscillation at intermediate frequencies. The latter dynamics, arising when fitness fluctuates as expected under a simple life-history trade-off, is a novel form of balancing selection. These results highlight the importance of allowing in models the joint demographic and population genetic changes, the failure of which prevents the discovery of important and novel eco-evolutionary dynamics.
Bioelectronic microfluidic wound healing
Authors: Shaner Sebastian , Savelyeva Anna , Kvartuh Anja , Jedrusik Nicole , Matter Lukas , Leal José , Asplund Maria
Published: July 2022

This work delves into the impact of direct current (DC) stimulation on both healthy and diabetic in vitro wound healing models of keratinocytes, the most prevalent cell type of the skin. The augmentation of non-metal electrode materials and prudent microfluidic design allowed for a platform to study the effects of different sustained (12 hours DC) electric field configurations on wound closure dynamics. We found that electric guidance cues (≃ 200mVmm−1) enhance wound closure rate by nearly 3X for both healthy and diabetic-like keratinocyte sheets, compared to their respective controls. The motility-inhibited keratinocytes regained wound closure rates with stimulation (increase from 1.0 to 2.8% hr−1) comparable to healthy non-stimulated keratinocyte collectives (3.5% hr−1). Our results bring hope that electrical stimulation is a viable pathway to accelerate wound repair.
Two-point optical manipulation reveals mechanosensitive remodeling of cell-cell contacts in vivo
Authors: Nishizawa Kenji , Lin Shao-Zhen , Chardès Claire , Rupprecht Jean-François , Lenne Pierre-François
Published: July 2022

Biological tissues acquire reproducible shapes during development through dynamic cell behaviors. These events involve the remodeling of cell contacts driven by active cytoskeletal contractile forces. However how cell-cell contacts remodel remains poorly understood because of lack of tools to directly apply forces at cell-cell contacts to produce their remodeling. Here we develop a dual-optical trap manipulation method to impose different force patterns on cell-cell contacts in the early epithelium of the Drosophila embryo. Through different push and pull manipulations at the edges of junctions, the technique allows us to produce junction extension and junction shrinkage. We use these observations to constrain and specify vertex-based models of tissue mechanics, incorporating negative and positive mechanosensitive feedback depending on the type of remodeling. We show that Myosin-II activity responds to junction strain rate and facilitates full junction shrinkage. Altogether our work provides insight into how stress produces efficient deformation of cell-cell contacts in vivo and identifies unanticipated mechanosensitive features of their remodeling.

Significance statement

The highly organized tissues and organs that form our body emerge from internal dynamic activities at the cellular level. Among such activities, cell shape changes and cell rearrangement, cell extrusion and cell division sculpt epithelial tissues into elongated sheets, tubes and spherical cavities. Remodeling of cell-cell contacts, powered by actomyosin contractility, is key to all these transformations. Although much is known about the molecular machinery and biochemical signals that regulate remodeling of cell contacts, there is a lack of approaches to directly probe the mechanics of cell contacts and therefore assess their ability to resist or deform in response to mechanical loads. We developed an experimental technique to manipulate and exert contractile and extensile forces to cell-cell junctions. Our results lead to a specific physical model of junctional mechanics, with implications in the modeling of collective cell behavior in epithelial tissues.
Designing Single Cell RNA-Sequencing Experiments for Learning Latent Representations
Authors: Treppner Martin , Haug Stefan , Köttgen Anna , Binder Harald
Published: July 2022

To investigate the complexity arising from single-cell RNA-sequencing (scRNA-seq) data, researchers increasingly resort to deep generative models, specifically variational autoencoders (VAEs), which are trained by variational inference techniques. Similar to other dimension reduction approaches, this allows encoding the inherent biological signals of gene expression data, such as pathways or gene programs, into lower-dimensional latent representations. However, the number of cells necessary to adequately uncover such latent representations is often unknown. Therefore, we propose a single-cell variational inference approach for designing experiments (scVIDE) to determine statistical power for detecting cell group structure in a lower-dimensional representation. The approach is based on a test statistic that quantifies the contribution of every single cell to the latent representation. Using a smaller scRNA-seq data set as a starting point, we generate synthetic data sets of various sizes from a fitted VAE. Employing a permutation technique for obtaining a null distribution of the test statistic, we subsequently determine the statistical power for various numbers of cells, thus guiding experimental design. We illustrate with several data sets from various sequencing protocols how researchers can use scVIDE to determine the statistical power for cell group detection within their own scRNA-seq studies. We also consider the setting of transcriptomics studies with large numbers of cells, where scVIDE can be used to determine the statistical power for sub-clustering. For this purpose, we use data from the human KPMP Kidney Cell Atlas and evaluate the power for sub-clustering of the epithelial cells contained therein. To make our approach readily accessible, we provide a comprehensive Jupyter notebook at https://github.com/MTreppner/scVIDE.jl that researchers can use to design their own experiments based on scVIDE.
Differential ability of three bee species to move genes via pollen
Authors: Fragoso Fabiana P. , Brunet Johanne
Published: July 2022

Since the release of genetically engineered (GE) crops, there has been increased concern about the introduction of GE genes into non-GE fields of a crop and their spread to feral or wild cross-compatible relatives. More recently, attention has been given to the differential impact of distinct pollinators on gene flow, with the goal of developing isolation distances associated with specific managed pollinators. To examine the differential impact of bee species on gene movement, we quantified the relationship between the probability of getting a GE seed in a pod, and the order in which a flower was visited, or the cumulative distance travelled by a bee in a foraging bout. We refer to these relationships as ‘seed curves’ and compare these seeds curves among three bee species. The experiments used Medicago sativa L. plants carrying three copies of the glyphosate resistance (GR) allele as pollen donors, such that each pollen grain carried the GR allele, and conventional plants as pollen recipients. Different foraging metrics, including the number of GR seeds produced over a foraging bout, were also quantified and contrasted among bee species. Leafcutting bees produced the lowest number of GR genes in a foraging bout, and moved them the shortest distances, bumble bees the longest. Values for honey bees were intermediate. Seed curves correlated with field-based gene flow estimates. Thus, differential seed curves of bee species, reflecting within foraging bout patterns, translated into distinct abilities of bee species to move genes at a landscape level. Differences in seed curves reflected differences in foraging behavior among bee species, and helped explain their differential impact on gene flow and the spread of GE genes in insect-pollinated crops.
Phenotypic screening using waveform analysis of calcium dynamics in primary cortical cultures
Authors: Sakaguchi Richi , Nakamura Saki , Iha Hiroyuki , Tanaka Masaki
Published: July 2022

At present, in vitro phenotypic screening methods are widely used for drug discovery. In the field of epilepsy research, measurements of neuronal activity have been utilized for predicting efficacy of anti-epileptic drugs. Fluorescence measurements of calcium oscillations in neurons are commonly used for measurement of neuronal activities, and some anti-epileptic drugs have been evaluated using this assay technique. However, changes in waveforms were not quantified in previous reports. Here, we have developed a high-throughput screening system containing a new analysis method for quantifying waveforms, and our method has successfully enabled simultaneous measurement of calcium oscillations in a 96-well plate. Features of waveforms were extracted automatically and allowed the characterization of some anti-epileptic drugs using principal component analysis. Moreover, we have shown that trajectories in accordance with the concentrations of compounds in principal component analysis plots were unique to the mechanism of anti-epileptic drugs. We believe that an approach that focuses on the features of calcium oscillations will lead to better understanding of the characteristics of existing anti-epileptic drugs and allow prediction of the mechanism of action of novel drug candidates.
A single residue within the MCR-1 protein confers anticipatory resilience
Authors: Frantz Renate , Gwozdzinski Konrad , Gisch Nicolas , Doijad Swapnil Prakash , Hudel Martina , Wille Maria , Mraheil Mobarak Abu , Schwudke Dominik , Imirzalioglu Can , Falgenhauer Linda , Ehrmann Michael , Chakraborty Trinad
Published: July 2022

The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role towards antimicrobials but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here we report specific interactions between the two-component conjugative pilus expression (Cpx)RA signal transduction system and the recently described mobile colistin resistance (MCR-1) protein. Purified MCR-1 is specifically cleaved by the serine endoprotease DegP within a structurally conserved periplasmic bridging domain. Cleavage-site mutations in MCR-1 render derivatives either protease-resistant or degradation-susceptible with widely differing consequences for colistin resistance. Transfer of the degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli induces a Cpx-dependent ESR and imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. MCR-1 production impairs bacterial motility indicating dissipation of cytoplasmic transmembrane potential. Indeed, growth in media with low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A as well as colistin-resistance activity. In vitro transferase- and lipid A reconstitution-assays demonstrate that MCR-1 is highly active at acidic pH. Acquiring MCR-1 also renders strains more resistant to antimicrobial peptides. Thus, a conserved motif within MCR-1 induces components of the ESR to confer resilience to stimuili commonly encountered in the environment such as to changes in pH and towards antimicrobial peptides. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids indicating that a targeted strategy can lead to the elimination of transferable colistin resistance in Gram-negative bacteria.
Quantification of genetic variants in bacterial cultures by Sanger sequencing
Authors: Prakash Satya , Racovita Adrian , Petrucci Teresa , Galizi Roberto , Jaramillo Alfonso
Published: July 2022

Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify non-neutral mutations by selection or counter- selection, neutral mutations usually require DNA sequencing to be identified in a population, which are normally expensive and time-consuming. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counter- selection. We propose a novel methodology to quantify DNA using Sanger sequencing, that we validated experimentally with specially-engineered plasmids both in vitro and in co-transformed E. coli by and assessing our predictions with qPCR and fluorescence quantifications. The method relies on the alignment of the electropherograms from the query and reference samples, where we quantify the DNA concentration from the amplitude ratio of aligned electropherogram peaks. Our DNA quantification will allow quantifying genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with consistent reduction of costs compared to canonical approaches such as qPCR.
Architecture of the NADH:ferredoxin oxidoreductase RNF that drives Biological Nitrogen Fixation
Authors: Zhang Lin , Einsle Oliver
Published: July 2022

Biological nitrogen fixation requires substantial metabolic energy in form of ATP, as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotrophAzotobacter vinelandiitransfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryo-EM structure of the nitrogenase-associated RNF complex ofA. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.

One Sentence Summary

Biological nitrogen fixation requires electrons with a negative redox potential, and the diazotrophAzotobacter vinelandiican provide these through the evolutionarily ancient RNF complex that bridges the energy difference between NADH and a low-potential ferredoxin by exploiting the transmembrane proton gradient.
Random folding drives the emergence of topologically associating domains in chromatin three-dimensional structure
Authors: Meng Luming , Luo Qiong
Published: July 2022

Domains are units of genome organization. Due to the seemingly irreconcilable difference between topologically associating domains (TADs) revealed by population-based biochemical studies and domains (sTADs) by single-cell imaging, finding a mechanism that simultaneously shape TADs and sTADs is challenging. Here we propose that TADs and sTADs are underlied by random folding of chromatin fiber heterogeneous in DNA density. On the hypothesis, we develop a model, termed RCHC, to yield chromatin structure ensemble from chromatin accessibility data. Calculated ensemble enables our hypothesis to be validated by population-based and single-cell experiments. Our simulation confirms the independence between domain and compartment structures in genome organization and shows that RCHC can predict the chromatin reorganization during differentiation. We mechanistically prove that genome is organized randomly with biases introduced by DNA-encoded information.

One-Sentence Summary

The TADs emergence is underlied by random folding of heterogeneous chromatin fiber carrying nucleosome occupancy information.
Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses
Authors: Dremel Sarah E. , Koparde Vishal N. , Arbuckle Jesse H. , Hogan Chad H. , Kristie Thomas M. , Krug Laurie T. , Conrad Nicholas K , Ziegelbauer Joseph M.
Published: July 2022

Herpesviruses rely on the host transcriptional machinery for expression of their >100 different transcripts. To prioritize viral transcripts, herpesviruses affect significant changes in all stages of gene expression. Herein, we examined how herpesviruses alter circular RNA (circRNA) synthesis resulting in distinct characteristics for those expressed from the host or viral genome. CircRNA were identified with our Circrnas in Host And viRuses anaLysis pIpEline (CHARLIE) capable ofde novoannotation using aggregated calls from five distinct tools. Comparative profiling for Herpes Simplex Virus-1, Kaposi sarcoma-associated herpesvirus, and murine gammaherpesvirus 68 identified thousands of back splicing variants, including circRNA species commonly expressed in all phases of infection. CircRNA expression was highest during lytic infection, with a transcriptional density 500-fold greater than the host. We characterized cis- and trans-elements controlling back splicing and found viral circRNAs are generally resistant to spliceosome inhibition or depletion, with >90% lacking canonical splice donor-acceptor sites. Using eCLIP and 4sU-Sequencing, we determined that the viral RNA binding protein, ORF57, enhanced synthesis for a subset of viral and host circRNAs. Our work elucidates a unique splicing mechanism driven by late lytic replication and identifies a class of transcripts with potential to function in replication, persistence, or tumorigenesis.
IKKα promotes lung adenocarcinoma growth through activation of ERK signaling via DARPP-32-mediated inhibition of PP1 activity
Authors: Alam Sk. Kayum , Wang Li , Zhu Zhu , Hoeppner Luke H.
Published: July 2022

Non–small cell lung cancer (NSCLC) accounts for 80-85% cases of lung cancer cases. Diagnosis at advanced stages is common, after which therapy-refractory disease progression frequently occurs. Therefore, a better understanding of the molecular mechanisms that control NSCLC progression is necessary to develop new therapies. Overexpression of IκB kinase α (IKKα) in NSCLC correlates with poor patient survival. IKKα is an NF-κB-activating kinase that is important in cell survival and differentiation, but its regulation of oncogenic signaling is not well understood. We recently demonstrated that IKKα promotes NSCLC cell migration by physically interacting with dopamine- and cyclic AMP-regulated phosphoprotein, Mr 32000 (DARPP-32), and its truncated splice variant, t-DARPP. Here, we show that IKKα phosphorylates DARPP-32 at threonine 34, resulting in DARPP-32-mediated inhibition of protein phosphatase 1 (PP1), subsequent PP1-mediated dephosphorylation of ERK, and activation of ERK signaling to promote lung oncogenesis. Correspondingly, DARPP-32 ablation in human lung adenocarcinoma cells reduced their anchorage-independent growth in soft agar. Mice challenged with IKKα-ablated HCC827 cells exhibited less lung tumor growth than mice orthotopically administered control HCC827 cells. Our findings suggest that IKKα drives NSCLC growth through activation of ERK signaling via DARPP-32-mediated inhibition of PP1 activity.
Stochastic modelling of cell differentiation networks from partially-observed clonal tracking data
Authors: Del Core L. , Pellin D. , Grzegorczyk M. A. , Wit E. C.
Published: July 2022

Motivation

Clarifying how hematopoietic stem cells differentiate into mature cell types is important for understanding how they attain specific functions and offers the potential for therapeutic manipulation. Over the past decades, clonal tracking has proven to be capable of unveiling population dynamics and hierarchical relationships in vivo. For this reason, clonal tracking studies are required for safety and long-term efficacy assessment in gene therapy. However, many standard clonal tracking studies consider only a subset of cell-types and are subject to noise.

Results

In this work, we propose a stochastic framework that investigates the dynamics of cell differentiation from typical clonal tracking data subject to measurement noise, false-negative errors, and systematically unobserved cell types. Our framework is based on stochastic reaction networks combined with extended Kalman filtering and Rauch-Tung-Striebel smoothing. Our tool can provide statistical support to biologists in gene therapy clonal tracking studies to better understand clonal reconstitution dynamics.

Availability

The stochastic framework is implemented in the package Karen which is available for download at https://github.com/delcore-luca/Karen. The code that supports the findings of this study is openly available at https://github.com/delcore-luca/CellDifferentiationNetworks.

Contact

l.del.core@rug.nl
Bayesian Inference of RNA Velocity from Multi-Lineage Single-Cell Data
Authors: Gu Yichen , Blaauw David , Welch Joshua D.
Published: July 2022

Experimental approaches for measuring single-cell gene expression can observe each cell at only one time point, requiring computational approaches for reconstructing the dynamics of gene expression during cell fate transitions. RNA velocity is a promising computational approach for this problem, but existing inference methods fail to capture key aspects of real data, limiting their utility. To address these limitations, we developed VeloVAE, a Bayesian model for RNA velocity inference. VeloVAE uses variational Bayesian inference to estimate the posterior distribution of latent time, latent cell state, and kinetic rate parameters for each cell. Our approach addresses key limitations of previous methods by inferring a global time and cell state value for each cell; explicitly modeling the emergence of multiple cell types; incorporating prior information such as time point labels; using scalable minibatch optimization; and quantifying parameter uncertainty. We show that VeloVAE significantly outperforms previous approaches in terms of data fit and accuracy of inferred differentiation directions. VeloVAE can also capture qualitative features of expression dynamics neglected by previous methods, including late induction, early repression, transcriptional boosts, and bifurcations. These improvements allow VeloVAE to accurately model gene expression dynamics in complex biological systems, including hematopoiesis, induced pluripotent stem cell reprogramming, neurogenesis, and organogenesis. We find that the latent time automatically inferred using all cells can even outperform pseudotime inferred using manually chosen cell subsets and root cells. We further use the inferred parameters to construct cell type transition graphs and fit branching differential equation models that describe the effects of cell type bifurcations on kinetic rate parameters.
Interplay between MYZUS PERSICAE-INDUCED LIPASE 1 and OPDA signaling in controlling green peach aphid infestation on Arabidopsis thaliana
Authors: Archer Lani , Mondal Hossain A. , Behera Sumita , Twayana Moon , Louis Joe , Nalam Vamsi J. , Keereetaweep Jantana , Chowdhury Zulkarnain , Shah Jyoti
Published: July 2022

MYZUS PERSICAE-INDUCED LIPASE1 (MPL1) encodes a lipase in Arabidopsis thaliana that is required for controlling infestation by the green peach aphid (GPA; Myzus persicae), an important phloem sap-consuming insect pest. Previously, we demonstrated that MPL1 expression was upregulated in response to GPA infestation, and GPA fecundity was higher on the mpl1 mutant, compared to the wild-type (WT), and lower on 35S:MPL1 plants that constitutively expressed MPL1 from the 35S promoter. Here, we show that the MPL1 promoter is active in the phloem and expression of the MPL1 coding sequence from the phloem-specific SUC2 promoter is sufficient to restore resistance to the GPA in the mpl1 mutant. The GPA infestation-associated upregulation of MPL1 requires CYCLOPHILIN 20-3 (CYP20-3), which encodes a 12-oxo- phytodienoic acid (OPDA)-binding protein that is involved in OPDA signaling and is required for controlling GPA infestation. OPDA promotes MPL1 expression to limit GPA fecundity, a process that requires CYP20-3 function. These results along with our observation that constitutive expression of MPL1 from the 35S promoter restores resistance to the GPA in the cyp20-3 mutant, and MPL1 feedbacks to limit OPDA levels in GPA-infested plants, suggest that an interplay between MPL1, OPDA, and CYP20-3 contributes to resistance to the GPA.

Highlight

Interaction between MYZUS PERSICAE-INDUCED LIPASE 1 function in the phloem, and 12-oxo-phytodienoic acid (OPDA) and CYCLOPHILIN 20-3, which encodes an OPDA-binding protein that is involved in OPDA signaling, is involved in controlling green peach aphid infestation on Arabidopsis thaliana.
The rostral zona incerta: a subcortical integrative hub and potential DBS target for OCD
Authors: Haber Suzanne N. , Lehman Julia , Maffei Chiara , Yendiki Anastasia
Published: July 2022

Background

The zona incerta (ZI) is involved in mediating survival behaviors and is connected to a wide range of cortical and subcortical structures, including key basal ganglia nuclei. Based on these connections and their links to behavioral modulation, we propose the ZI is a connectional hub for in mediating between top-down and bottom-up control and a possible target for deep brain stimulation for obsessive compulsive disorder.

Methods

We analyzed the trajectory of cortical fibers to the ZI in nonhuman and human primates, based on tracer injections in monkeys and high-resolution diffusion MRI in humans. The organization of cortical and subcortical connections with the ZI were identified in the nonhuman primate studies.

Results

Monkey anatomic data and human dMRI data showed a similar trajectory of fibers/streamlines to the ZI. PFC/ACC terminals all converge within the rostral ZI (ZIr), with dorsal and lateral areas most prominent. Motor areas terminate caudally. Dense subcortical reciprocal connections included the thalamus, medial hypothalamus, substantia nigra/ventral tegmental area, reticular formation, and pedunculopontine nucleus and a dense nonreciprocal projection to the lateral habenula (LHb). Additional connections included amygdala, dorsal raphe nucleus, and periaqueductal grey.

Conclusions

Dense connections with dorsal and lateral PFC/ACC cognitive control areas and LHb and SN/VTA coupled with inputs from the amygdala, hypothalamus, and brainstem, suggests that the ZIr is a subcortical hub positioned to modulate between top-down and bottom-up control. A DBS electrode placed in the ZIr would involve both connections common to other DBS sites, but also would capture several critically distinctive connections.
Gene Trajectory Inference for Single-cell Data by Optimal Transport Metrics
Authors: Qu Rihao , Cheng Xiuyuan , Sefik Esen , Stanley Jay S. , Landa Boris , Strino Francesco , Platt Sarah , Garritano James , Odell Ian D. , Coifman Ronald , Flavell Richard A. , Myung Peggy , Kluger Yuval
Published: July 2022

Single-cell RNA-sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal-transport distances are calculated between gene distributions across the cell-cell graph to extract gene programs and define their gene pseudotemporal order. Here, we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory deconvolves key gene programs underlying mouse skin hair follicle dermal condensate differentiation that could not be resolved by cell trajectory approaches. GeneTrajectory facilitates discovery of gene programs that control the changes and activities of biological processes.
Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control
Authors: Nadler Franziska , Lavdovskaia Elena , Krempler Angelique , Cruz-Zaragoza Luis Daniel , Dennerlein Sven , Richter-Dennerlein Ricarda
Published: July 2022

Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We solve this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for almost 25 years, and lead to a comprehensive picture of translation termination in human mitochondria.
CeDAR: incorporating cell type hierarchy improves cell type specific differential analyses in bulk omics data
Authors: Chen Luxiao , Li Ziyi , Wu Hao
Published: July 2022

The bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell-type-specific inferences from bulk data. Our real data exploration suggests that the differential expression or methylation status are often correlated among cell types. Based on this observation, we develop a novel statistical method named CeDAR to incorporate the cell type hierarchy in cell-type-specific differential analyses in bulk data. Extensive simulation and real data analyses demonstrate that this approach significantly improves the accuracy and power in detecting cell-type-specific differential signals compared with existing methods, especially in low abundance cell types.
Development of genome-driven, lifestyle-informed primers for identification of the cereal-infecting pathogens Xanthomonas translucens pathovars undulosa and translucens
Authors: Román-Reyna Verónica , Curland Rebecca D. , Velez-Negron Yesenia , Ledman Kristi E. , Gutierrez Diego , Beutler Jonathan , Butchacas Jules , Brar Gurcharn Singh , Roberts Robyn , Dill-Macky Ruth , Jacobs Jonathan M.
Published: July 2022

Bacterial leaf streak, blight and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains and Upper Midwest; however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. We validated the primers across different Xanthomonas and non-Xanthomonas strains. To our knowledge, these are the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens.
Conservation of three-dimensional structure in Lepidoptera and Trichoptera L-fibroins for 290 million years
Authors: Stewart Russell J. , Frandsen Paul B. , Pauls Steffen U. , Heckenhauer Jacqueline
Published: July 2022

The divergence of sister orders, Trichoptera (caddisflies) and Lepidoptera (moths and butterflies), from a silk-spinning ancestor occurred around 290 million years ago. Trichoptera larvae are mainly aquatic and Lepidoptera larvae are almost entirely terrestrial, distinct habitats that required molecular adaptation of their silk for deployment in water versus air. The major protein components of their silks are Heavy chain and Light chain fibroins. In an effort to identify molecular changes in L-fibroins that may have contributed to the divergent use of silk in water versus air, we used the ColabFold implementation of AlphaFold2 to predict three-dimensional structures of L-fibroins from both orders. Comparison of the structures revealed that despite the ancient divergence, profoundly different habitats, and low sequence conservation, a 10-helix core structure was strongly conserved in L-fibroins from both orders. Previously known intra- and intermolecular disulfide linkages were accurately predicted. Structure variations observed outside of the core may represent molecular changes that contributed to the evolution of silks adapted to water or air. The distributions of electrostatic potential, for example, are not conserved and present distinct order-specific surfaces for potential interactions with or modulation by external factors. Also, the interactions of L-fibroins with the H-fibroin C-termini are different between the orders; lepidopteran L-fibroins have N-terminal insertions, not present in trichopteran L-fibroins, which form an unstructured ribbon in isolation but become part of an intermolecular β-sheet when folded with their corresponding H-fibroin C-termini. The results may serve as another example of protein structure prediction from deep sequence data of understudied proteins made possible by AlphaFold2.
Machine learning reveals conserved chromatin patterns determining meiotic recombination sites in plants
Authors: Wang Minghui , Shilo Shay , Zhou Adele , Zelkowski Mateusz , Olson Mischa A. , Azuri Ido , Shoshani-Hechel Nurit , Melamed-Bessudo Cathy , Marand Alexandre P. , Jiang Jiming , Schnable James C. , Underwood Charles J. , Henderson Ian R. , Sun Qi , Pillardy Jaroslaw , Kianian Penny M.A. , Kianian Shahryar F. , Chen Changbin , Levy Avraham A. , Pawlowski Wojciech P.
Published: July 2022

Distribution of meiotic recombination events in plants has been associated with local chromatin and DNA characteristics, chromosome landmark proximity, and other features1-7. However, relative importance of these characteristics is unclear and it is unknown if they are sufficient to unambiguously determine recombination landscape8. Here, we analyzed over 40 DNA sequence, chromatin, and chromosome location features of maize andArabidopsisrecombination sites using machine learning9,10. We discovered that a combination of just three features, CG methylation, CHG methylation, and nucleosome occupancy, enabled identification of exact crossover site with 90% accuracy. These results imply redundancy of most recombination site characteristics. Recombination takes place in a small fraction of the genome with chromatin features distinct from those of genome at large. Surprisingly, crossover sites show elevated heterochromatin histone marks despite low DNA methylation. Crossover site features show broad evolutionary conservation, which will enable creating genetic maps in species where conventional mapping is unfeasible.
A ripening-associated ethylene response factor ERF.D7 activates ARF2 orthologs to regulate tomato fruit ripening
Authors: Gambhir Priya , Parida Adwaita Prasad , Singh Vijendra , Raghuvanshi Utkarsh , Kumar Rahul , Sharma Arun Kumar
Published: July 2022

Despite the obligatory nature of ethylene to climacteric fruit ripening and the identification of 77 Ethylene Response Factors (ERFs) in the tomato genome, the role of only limited ERFs has been validated in the ripening process. Here, using a comprehensive morpho-physiological, molecular and biochemical approach, we demonstrate the regulatory role of SlERF.D7 in tomato fruit ripening. The expression of SlERF.D7 positively responds to exogenous ethylene and auxin treatments, most likely in a RIN-independent manner. Overexpression of SlERF.D7 promotes ripening and its silencing has the opposite effects. Alterations in its expression modulated ethylene production, pigment accumulation, and fruit firmness. Consistently, genes involved in ethylene biosynthesis and signalling, lycopene biosynthesis, and cell wall loosening were upregulated in the overexpression lines and downregulated in RNAi lines. These transgenic lines also accumulated altered levels of IAA at late-breaker stages. A positive correlation between ARF2 orthologs transcripts and SlERF.D7 mRNA levels and the fact that ARF2A and ARF2B are direct targets of SlERF.D7 underpinned the perturbed auxin-ethylene crosstalk for the altered ripening program observed in the transgenic fruits. Overall, this study uncovers that SlERF.D7 positively regulates SlARF2A/B abundance to amalgamate auxin and ethylene signalling pathways for controlling tomato fruit ripening.

Highlight

The present study identifies a new ripening regulator, SlERF.D7, that controls tomato fruit ripening by activating other known-ripening regulators, SlARF2A and SlARF2B.
An RNAi screen reveals common host-virus gene signatures: implication for anti-viral drug discovery
Authors: Shum David , Bhinder Bhavneet , Mahida Jeni , Radu Constantin , Calder Paul A. , Djaballah Hakim
Published: July 2022

Dengue is the most common mosquito-borne viral disease that in recent years has become a major international public health concern. Dengue is a tropical neglected disease with increasing global incidences, affecting millions of people worldwide, and without the availability of specific treatments to combat it. The identification of host-target genes essential for the virus life cycle, for which effective modulators may already exist, would provide an alternative path to a rapid drug development of the much needed anti-Dengue agents. For this purpose, we performed the first genome-wide RNAi screen, combining two high content readouts for DENV infection (FLUO) and host cell toxicity (NUCL), against an arrayed lentiviral based shRNA library covering 16,000 genes with a redundancy of at least 5 hairpins per gene. The screen identified 1,924 gene candidates in total; of which, 1,730 gene candidates abrogated Dengue infection, while 194 gene candidates were found to enhance its infectivity in HEK293 cells. A first pass clustering analysis of hits revealed a well orchestrated gene-network dependency on host cell homeostasis and physiology triggering distinct cellular pathways for infectivity, replication, trafficking and egress; a second analysis revealed a comprehensive gene signature of 331 genes common to hits identified in 28 published RNAi host-viral interactions screens. Taken together, our findings provide novel antiviral molecular targets with the potential for drug discovery and development.
SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA
Authors: Maharana Shovamayee , Kretschmer Stefanie , Hunger Susan , Yan Xiao , Kuster David , Traikov Sofia , Zillinger Thomas , Gentzel Marc , Chappidi Nagaraja , Lucas Nadja , Maser Katharina Isabell , Maatz Henrike , Rapp Alexander , Marchand Virginie , Iyer K. Venkatesan , Chhabra Akshita , Chang Young-Tae , Motorin Yuri , Hubner Norbert , Hartmann Gunther , Hyman Anthony , Alberti Simon , Lee-Kirsch Min Ae
Published: July 2022

Recognition of pathogen-derived foreign nucleic acids is central to innate immune defense. This requires discrimination between structurally highly similar self and nonself nucleic acids to avoid aberrant inflammatory responses as in the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). How vast amounts of self RNA are shielded from immune recognition to prevent autoinflammation is not fully understood. Here we show that SAM domain and HD domain-containing protein 1 (SAMHD1), one of the AGS-causing genes, functions as a single-stranded RNA (ssRNA) 3’exonuclease, the lack of which causes cellular RNA accumulation. Increased ssRNA in cells leads to dissolution of RNA-protein condensates, which sequester immunogenic double-stranded RNA (dsRNA). Release of sequestered dsRNA from condensates triggers activation of antiviral type I interferon via retinoic acid-inducible gene I-like receptors. Our results establish SAMHD1 as a key regulator of cellular RNA homeostasis and demonstrate that buffering of immunogenic self RNA by condensates regulates innate immune responses.
A universal dynamical metabolic model representing mixotrophic growth of Chlorella sp
Authors: Pessi Bruno Assis , Baroukh Caroline , Bacquet Anais , Bernard Olivier
Published: July 2022

An emerging idea is to couple wastewater treatment and biofuel production using microalgae to achieve higher productivities and lower costs. This paper proposes a metabolic modelling of Chlorella sp. growing on wastes in mixotrophic conditions, accounting also for the possible inhibitory substrates. A metabolic model considering several possible carbon substrates was developed and run. The addition of several organic carbon substrates such as acetate, butyrate or glucose were tested, along with glycerol, a more realistic substrate from an economical point of view. The metabolic model was built using DRUM framework and consists of 188 reactions and 176 metabolites. After a calibration phase, the model was successfully challenged with data from 122 experiments collected from scientific literature in autotrophic, heterotrophic and mixotrophic conditions. The optimal feeding strategy estimated with the model reduces the time to consume the volatile fatty acids from 16 days to 2 days. The high prediction capability of this model opens new routes for enhancing design and operation in waste valorisation using microalgae.

Author Summary

Waste valorisation is one of the current envisaged strategies to make renewable processes more economically advantageous. For example, wastewater treatment can be used to produce biohydrogen from bacteria, through a process called dark fermentation, and to cultivate microalgae for biofuel production. Dark fermentation has, as by-products, organic acids that have inhibitory effects on the growth of microalgae, increasing the time to completely treat the waste. Advances in metabolic knowledge and techniques allow for the deployment of new strategies to improve the efficiency of bioprocesses. In this work, we validate a mathematical model of the metabolism of the microalgae genus Chlorella using the DRUM framework for 122 experiments from the scientific literature. This model enables us to apply control and optimisation techniques to provide a strategy to treat wastes coming from dark fermentation processes, overcoming the inhibition of some organic acids. The strategy is able to reduce the time to treat the waste from 16 days to only 2 days. The high prediction capability of this model opens new routes for enhancing design and operation in waste valorisation using microalgae.
Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
Authors: Widen Sonya A. , Bes Israel Campo , Koreshova Alevtina , Krogull Daniel , Burga Alejandro
Published: July 2022

Horizontal gene transfer—the movement of genetic material between different species—has been reported across all major eukaryotic lineages, including vertebrates. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode C. briggsae, we discovered that Mavericks, ancient viral-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons—nature’s melting pot—causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.