bluuebunny/crossref_metadata_2025 huggingface dataset:
Intermolecular proteolytic processing of SPRING and Site-1-protease regulate SREBP signaling
Authors: Hendrix Sebastian , Tan Josephine M.E. , Ndoj Klevis , Valiloo Masoud , Zijlstra Lobke F. , Ottenhoff Roelof , Seidah Nabil G. , Loregger Anke , Zelcer Noam
Published: March 2023

The SREBP transcription factors are central regulators of fatty acid and cholesterol metabolism. Produced as membrane-resident precursor proteins in the ER, their transcriptional activation requires the cholesterol-dependent translocation to the Golgi, and subsequent proteolytic cleavage by S1P, a type-I transmembrane protein. S1P is produced as a proprotein convertase that needs to undergo autocatalytic cleavage to attain its mature form in the Golgi, in a process that is not fully elucidated. We have recently identified SPRING (C12ORF49) as a novel regulator of the SREBP pathway and reported that S1P activity and retrograde recycling of the SREBP chaperone SCAP are affected. Here, we demonstrate that SPRING and S1P interact and that in co-transfection experiments in mammalian cells this facilitates the autocatalytic activation of S1PA→Cform. Accordingly, S1PA→Cprocessing of stably overexpressed S1P in SPRINGKOcells is attenuated, but not abolished, and does not rescue SREBP signaling. Reciprocally, we identified a conserved S1P cleavage site in SPRING, and demonstrate that cleavage of SPRING results in secretion of the SPRING ectodomain. SPRING cleavage is S1P-specific and can be pharmacologically inhibited by S1P inhibitors or by mutating the S1P cleavage site. Functional analysis revealed that the SPRING ectodomain was sufficient to support S1PA→Cprocessing and SREBP signaling, but that SPRING cleavage is not a prerequisite for this. In conclusion, our study reveals a complex interplay between the proteolytic activation of S1P and SPRING yet suggests that this is not the primary mechanism underlying the role of SPRING in SREBP signaling.
Mitochondria induce anisotropy and delays in action potential conduction
Authors: Castelfranco Ann , Alcami Pepe
Published: March 2023

The internal resistance of axons to ionic current flow affects the speed of action potential propagation. As biological cables, axons contain mitochondria which are necessary to support axonal function with energy supply. Although we would expect mitochondria to increase the internal resistance to current flow, their impact on the conduction velocity of action potentials has remained elusive. To investigate the impact of mitochondria on action potential propagation in the small non-myelinated fibers found in the vertebrate brain, we combined computational modeling and electron microscopy from the axons found in the premotor pathway that controls the production of birdsong with submillisecond precision. Mitochondria occupancy of axonal cross-sections ranged from 5 to 73% (average: 29%) in the ∼ 0.2-0.7 μm diameter non-myelinated axons connecting song premotor nuclei HVC and RA in canaries. Interestingly, this occupancy depends on axonal diameter: axonal cross-section occupancy by mitochondria was larger in small axons, with an average occupancy of ∼46% for axons with diameters smaller than 300 nm and ∼21% for larger diameters. Computational modeling showed that when the propagating action potential meets a mitochondrion, the conduction velocity decreases and the action potential is delayed by tenths of microseconds to microseconds. This effect is stronger in small axons given their larger cross section mitochondrial occupancy and cumulates delays of tenths of milliseconds along the whole pathway linking HVC and RA. Finally, we modeled the impact of varying densities of mitochondria on action potential propagation along the songbird premotor pathway. In summary, our model shows that axonal mitochondria induce the anisotropic propagation of action potentials, and that this effect cumulates a typical delay in the order of tenths of milliseconds over distances of mms. By partially occupying axoplasm, mitochondria constitute a biological design constraint that delays information processing in the small-diameter unmyelinated axons found in the vertebrate brain.
A new ferrocene derivative blocks KRAS localization and function by oxidative modification at His95
Authors: Rehl Kristen M. , Selvakumar Jayaraman , Hoang Don , Arumugam Kuppuswamy , Gorfe Alemayehu A. , Cho Kwang-jin
Published: March 2023

Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers (NSCLCs) harboring oncogenic mutant K-Ras. Here, we developed and tested a novel ferrocene derivative on the growth of human pancreatic ductal adenocarcinoma (PDAC) and NSCLC. Our compound inhibited the growth of K-Ras-dependent PDAC and NSCLC and abrogated the PM binding and signaling of K-Ras, but not other Ras isoforms. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified K-Ras His95 residue in the G-domain as being involved in the ferrocene-induced K-Ras PM dissociation via oxidative modification. Together, our studies demonstrate that the redox system directly regulates K-Ras PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced metastasis in K-Ras-driven lung cancers.
Emergence of Bow-tie Architecture in Evolving Feedforward Networks
Authors: Itoh Thoma , Kondo Yohei , Aoki Kazuhiro , Saito Nen
Published: March 2023

Bow-tie architecture is a layered network structure that has a narrow middle layer with multiple inputs and outputs. Such structures are widely seen in the molecular networks in cells, suggesting that a universal evolutionary mechanism underlies the emergence of bow-tie architecture. The previous theoretical studies have implemented evolutionary simulations of the feedforward network to satisfy a given input–output goal, and proposed that the bow-tie architecture emerges when the ideal input– output relation is given as a rank-deficient matrix with mutations in network link strength in a multiplicative manner. Here, we report that the bow-tie network inevitably appears when the link intensities representing molecular interactions are small at the initial condition of the evolutionary simulation, regardless of the rank of the goal matrix. Our dynamical system analysis clarifies the mechanisms underlying the emergence of the bow-tie structure. Further, we demonstrate that the increase in the input–output matrix facilitates the emergence of bow-tie architecture even when starting from strong network links. Our data suggest that bow-tie architecture emerges as a side effect of evolution rather than as a result of evolutionary adaptation.

Author Summary

Many biological networks including gene regulatory networks, metabolic networks, and signaling networks, show a characteristic hierarchical structure known as the bow-tie architecture. This architecture consists of a narrow middle layer with multiple inputs and outputs. Understanding why bow-tie architecture has universally appeared through evolution may provide insight into the design principle of a network within a cell. The universality of the bow-tie structure has so far been explained by the adaptive advantages such as high evolvability and capability to classify the inputs. However, our computer simulation demonstrates that the bow-tie structure inevitably emerges even without functional advantages when the molecular interactions within the network are weak at the initial condition of the evolution. We also demonstrate that an increase in the number of inputs (i.e., receptors) and outputs (i.e., downstream genes) leads to the emergence of bow-tie architecture, even when evolution starts from a strong molecular interaction. Although many previous studies have discussed the adaptive properties of bow-tie architecture, our findings suggest that bow-tie architecture is a byproduct of evolution rather than a result of evolutionary adaptation.
The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasusL.) genome reveals insights into its segmental allopolyploid nature
Authors: Wöhner Thomas W. , Emeriewen Ofere F. , Wittenberg Alexander H.J. , Nijbroek Koen , Wang Rui Peng , Blom Evert-Jan , Keilwagen Jens , Berner Thomas , Hoff Katharina J. , Gabriel Lars , Thierfeldt Hannah , Almolla Omar , Barchi Lorenzo , Schuster Mirko , Lempe Janne , Peil Andreas , Flachowsky Henryk
Published: March 2023

Sour cherry (Prunus cerasusL.) is an economically important allotetraploid cherry species believed to have evolved in the Caspian Sea and Black Sea regions. How, when and where exactly the evolution of this species took place is unclear. It resulted from a hybridization of the tetraploid ground cherry (Prunus fruticosaPall.) and an unreduced (2n) pollen of the diploid ancestor sweet cherry (P. aviumL.). Some indications implement that the genome of sour cherry is segmental allopolyploid, but how it is structured and to what extent is unknown. To get an insight, the genome of the sour cherry cultivar ‘Schattenmorelle’ was sequenced at ~400x using Illumina NovaSeqTMshort-read and Oxford Nanopore long-read technologies (ONT R9.4.1 PromethION). Additionally, the transcriptome of ‘Schattenmorelle’ was sequenced using PacBio Sequel II SMRT cell sequencing at ~300x. The final assembly resulted in a ~629 Mbp long pseudomolecule reference genome, which could be separated into two subgenomes each split into eight chromosomes. SubgenomePceS_a which originates fromP. aviumhas a length of 269 Mbp, whereas subgenomePceS_f which originates fromP. fruticosahas a length of 299.5 Mbp. The length of unassembled contigs was 60 Mbp. The genome of the sour cherry shows a size-reduction compared to the genomes of its ancestral species. It also shows traces of homoeologous sequence exchanges throughout the genome. Comparative positional sequence and protein analyses provided evidence that the genome of sour cherry is segmental allotetraploid and that it has evolved in a very recent event in the past.
Changes in large-scale neural networks under stress are linked to affective reactivity to stress in real life
Authors: Tutunji Rayyan , Krentz Martin , Kogias Nikos , de Voogd Lycia , Krause Florian , Vassena Eliana , Hermans Erno J.
Published: March 2023

Controlled laboratory stress induction procedures are very effective in inducing physiological and subjective stress. However, whether such stress responses are representative for stress reactivity in real life is not clear. Using a combined within-subject functional MRI laboratory stress and ecological momentary assessment stress paradigm, we investigated dynamic shifts in large-scale neural network configurations under stress and how these relate to affective reactivity to stress in real life. Laboratory stress induction resulted in significantly increased cortisol levels, and shifts in task-driven neural activity including increased salience network (SN) activation in an oddball task and decreased default mode network activity in a memory retrieval task. Crucially, individuals showing increased SN reactivity specifically in the early phase of the acute stress response also expressed increased affective reactivity in real life. Our findings provide (correlational) evidence that real-life affective stress reactivity is driven primarily by vigilant attentional reorienting mechanisms associated with SN.
PRC domain-containing proteins modulate FtsZ-based archaeal cell division
Authors: Nußbaum Phillip , Kureisaite-Ciziene Danguole , Bellini Dom , van der Does Chris , Kojic Marko , Taib Najwa , Gribaldo Simonetta , Loose Martin , Löwe Jan , Albers Sonja-Verena
Published: March 2023

Dividing cells into two daughter cells is a complicated process that in bacteria and eukaryotes requires many proteins to work together. For archaea that divide via an FtsZ-based mechanism, only three proteins of the cell division machinery could so far be identified. These are two tubulin homologs, FtsZ1, FtsZ2 and the membrane anchor of FtsZ2, SepF. Here, we investigate additional archaeal cell division proteins that were identified by immunoprecipitation of SepF. These proteins comprise a single PRC-barrel domain and strictly co-occur with FtsZ. Two out of three PRC-barrel domain containing proteins found inHaloferax volcanii, CdpB1 and CdpB2 localize to the site of cell division in a SepF-dependent manner. Moreover, depletions and deletions cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1/2 deletion strains revealed that the divisome is unusually disordered and not organized into a distinct ring-like structure at the cell centre. Biochemical analysis of CdpB homologs from different archaeal species showed that SepF interacts directly with CdpB1, which in turn binds to CdpB2, forming a tripartite complex. A crystal structure of CdpB1 and B2 recapitulated these interactions and suggested how these proteins might form filaments, possibly aligning SepF and therefore the FtsZ2 ring during cell division. In summary, we demonstrate that PRC domain proteins play essential roles in FtsZ based cell division in archaea.
Bioregionalization: From Wallace and Humboldt to deep-time paleoregion dynamics
Authors: Briega-Álvarez Andrea , Siebert Heike , Rodríguez Miguel Ángel , Varela Sara
Published: March 2023

Bioregionalization methods allow us to classify and map biogeographic units using data on species composition and traits. Here, we reviewed the evolution of the field during the last 70 years, seeking to summarize its history, and identify gaps and future avenues for research. Our results show that the aim of the studies using bioregionalization methods changed in time. First, bioregionalization were used to unveil the drivers of the observed spatial patterns of biodiversity on Earth, and to understand the role of dispersal limitations on the evolutionary history of clades, but recently, these methods are mostly used for conservation management. Further, data used to map biodiversity regions, the ones that we are now defining conservation strategies, are taxonomically and geographically biased, with a large percentage of the papers using vertebrate data from developed continents/countries. Finally, we show how key papers in the field, the ones with most citations, heavily depend on expert criteria and non-reproducible workflows, preventing direct comparison of maps of bioregions from different papers. Following our findings, we identified 3 gaps for the advance in the field, 1) We need to move beyond maps of vertebrate composition. Ideally, we need to increase the taxonomic diversity of the studies, but also to add other type of information, like data on species traits, genetic diversity, or phylogenetic distances. 2) we need reproducible and standardized methods 3) we need to further explore the temporal dimension of bioregions, to understand how they evolved through time.
ZEB1-dependent modulation of fibroblast polarization governs inflammation and immune checkpoint blockade sensitivity in colorectal cancer
Authors: Schuhwerk Harald , Menche Constantin , Armstark Isabell , Gupta Pooja , Fuchs Kathrin , van Roey Ruthger , Mosa Mohammed H. , Geppert Carol I. , Bärthel Stefanie , Saur Dieter , Greten Florian R. , Brabletz Simone , Brabletz Thomas , Farin Henner F. , Stemmler Marc P.
Published: March 2023

The EMT-transcription factor ZEB1 is heterogeneously expressed in tumor cells and in cancer-associated fibroblasts (CAFs) in colorectal cancer (CRC). While ZEB1 in tumor cells regulates metastasis and therapy resistance, its role in CAFs is largely unknown. Combining fibroblast-specificZeb1deletion with immunocompetent mouse models of CRC, we observe that inflammation-driven tumorigenesis is accelerated, whereas invasion and metastasis in sporadic cancers is reduced upon fibroblast-specific loss ofZeb1. Single-cell transcriptomics, histological andin vitrocharacterization reveal a crucial role in CAF polarization, promoting myofibroblastic features whilst restricting inflammatory activation.Zeb1deficiency impairs collagen deposition and CAF barrier function but increases cytokine production, jointly promoting lymphocyte recruitment and immune checkpoint activation. Strikingly, theZeb1-deficient CAF repertoire sensitizes to immune checkpoint inhibition, pointing to a therapeutic opportunity of targeting ZEB1 in CAFs and its usage as a prognostic biomarker. Collectively, we demonstrate that ZEB1-dependent plasticity of CAFs suppresses anti-tumor immunity and promotes metastasis.
Exponential diversity-dependent diversification emerges from an individual-based model with Lotka-Volterra competition
Authors: Pannetier Théo , Brad Duthie A. , Etienne Rampal S.
Published: March 2023

Abstract

A long-standing question in macroevolution is whether diversification is governed by the same processes that structure diversity at ecological scales, particularly competition. This competition has led to the development of a model where diversification rates depend on diversity, analogous to density-dependence in population growth models. Various versions of this model have been widely used for inference, where the rate of speciation and/or extinction can be either a linear or a power function of species number. It is, however, unknown if either approximates the diversification process that arises from the general ecological setting proposed to lead to diversity-dependence. This is of concern for inference, as failure to include a model that appropriately represents the hypothesized scenario is likely to lead to erroneous inference. Here we use an individual-based model adapted from adaptive dynamics, where fitness is governed by resource availability and the density of competitors, to determine the shape of the diversity-dependence functions. We find that the diversity-dependent rate of speciation produced by the individual-based model is best approximated by an exponential function of species diversity, consistent with a view of macroevolution where diversity increases rapidly after mass extinctions or when new adaptive space becomes available. Although we do find diversity-dependence in the extinction rate, it remains low over the entire process and erases its own signal, so it cannot be recovered from reconstructed phylogenies. The support for a linear relationship for diversity-dependent diversification found in many empirical phylogenies suggests that either our adaptive dynamics model of speciation is inadequate or there is too little information contained in reconstructed phylogenies. We indeed find evidence for the latter when pruning extinct species from our simulated phylogenies, but this does not rule out the former.
Spatial structure, chemotaxis and quorum sensing shape biomass accumulation in complex systems
Authors: Scheidweiler David , Bordoloi Ankur Deep , Sentchilo Vladimir , Bollani Monica , Engel Philipp , de Anna Pietro
Published: March 2023

Biological tissues, sediments, or engineered systems are spatially structured media with a tortuous and porous structure that host the flow of fluids. Such complex environments can influence the spatial and temporal colonization patterns of bacteria by controlling the transport of individual bacterial cells, the availability of resources, and the distribution of chemical signals for communication. Yet, due to the multi-scale structure of these complex systems, it is hard to assess how different biotic and abiotic properties work together to control the accumulation of bacterial biomass. Here, we explore how flow mediated interactions allow the gut commensal Escherichia coli to colonize a porous structure that is composed of heterogenous dead-end pores (DEPs) and connecting percolating channels, i.e. transmitting pores (TPs), mimicking the structured surface of mammalian guts. We find that in presence of flow, gradients of the quorum sensing (QS) signaling molecule autoinducer-2 (AI-2) promote E. coli chemotactic accumulation in the DEPs. In this crowded environment, the combination of growth and cell-to-cell collision favors the development of suspended bacterial aggregates. This results in hot-spots of resource consumption, which, upon resource limitation, triggers the mechanical evasion of biomass from glucose and oxygen depleted DEPs. Our findings demonstrate that microscale medium structure and complex flow coupled with bacterial quorum sensing and chemotaxis control the heterogenous accumulation of bacterial biomass in a spatially structured environment, such as villi and crypts in the gut or in tortuous pores within soil and filters.
TheEscherichia colismall heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ32
Authors: Miwa Tsukumi , Taguchi Hideki
Published: March 2023

Small heat shock proteins (sHsps) act as ATP-independent chaperones that prevent irreversible aggregate formation by sequestering denatured proteins. IbpA, anEscherichia colisHsp, functions not only as a chaperone but also as a suppressor of its own expression through posttranscriptional regulation, contributing to negative feedback regulation. IbpA also regulates the expression of its paralog, IbpB, in a similar manner, but the extent to which IbpA regulates other protein expressions is unclear. We have discovered that IbpA downregulates the expression of many Hsps by repressing the translation of the heat shock transcription factor σ32. The IbpA regulation not only controls the σ32level but also contributes to the shut-off of the heat shock response. These results revealed an unexplored role of IbpA to regulate heat shock response at a translational level, which adds a new layer for tightly controlled and rapid expression of σ32on demand.

Significance Statement

To survive during heat shock, cells have a mechanism to induce the synthesis of Hsps and to restore normal levels when the stress subsides. The molecular mechanisms of the heat shock response inE. colihave been extensively studied over the years. The master heat shock transcriptional regulator, σ32, which is normally at low levels due to chaperone-mediated degradation, is increased upon heat shock. Our study has identified a previously unknown factor, IbpA, that regulates the level of σ32by suppressing its expression at a translational level, thereby contributing to the heat shock response regulation.
Click chemistry selectively activates an auristatin protodrug with either intratumoral or systemic tumor-targeting agents
Authors: McFarland Jesse M , Aleckovic Masa , Coricor George , Srinivasan Sangeetha , Tso Matthew , Lee John , Nguyen Tri-Hung , Oneto Jose M Mejia
Published: March 2023

The Click Activated Protodrugs Against Cancer (CAPACTM) platform enables activation of powerful cancer drugs at tumor sites, maximizing efficacy and minimizing systemic toxicity. CAPAC utilizes a potent click chemistry reaction between tetrazine and trans-cyclooctene, called tetrazine ligation. The reaction between the activator, linked to a tumor targeting agent, and the protodrug leads to targeted activation of the drug. In this study, activation is accomplished either by intratumoral injection of a tetrazine-modified hyaluronic acid biopolymer (SQL70) or by systemic infusion of a tetrazine-modified HER2-targeting antigen-binding fragment (SQT01). The drug used is monomethyl auristatin E (MMAE), a cytotoxic agent hindered in its clinical use by severe toxicity. MMAE modification with a trans-cyclooctene moiety to form the protodrug SQP22 reduced its cytotoxicity in vitro and in vivo. Treatment of SQP22 paired with SQL70 biopolymer demonstrated anti- tumor effects in Karpas 299 and RENCA murine tumor models, establishing the requirement of click chemistry for protodrug activation. Furthermore, SQP22 paired with SQT01 induced anti-tumor effects in the HER2-positive NCI-N87 murine tumor model, showing that activation could be accomplished by systemic dosing of a tumor-targeting antibody conjugate. Observed toxicities were limited to modest, transient myelosuppression and moderate body weight loss in these tumor models. This study further delineates the capabilities of the CAPAC platform by demonstrating anti-tumor activity of SQP22 with two differentiated targeting approaches and underscores the power of click chemistry to precisely control the activation of cancer drugs at tumor sites.
Delta-dependent Notch activation closes the early neuroblast temporal program to promote lineage progression and neurogenesis termination inDrosophila
Authors: Sood Chhavi , Nahid Md Ausrafuggaman , Branham Kendall R. , Pahl Matthew C. , Doyle Susan E. , Siegrist Sarah E.
Published: March 2023

Neuroblasts inDrosophiladivide asymmetrically, sequentially expressing a series of intrinsic factors to generate a diversity of neuron types. These intrinsic factors known as temporal factors dictate timing of neuroblast transitions in response to steroid hormone signaling and specify early versus late temporal fates in neuroblast neuron progeny. After completing their temporal programs, neuroblasts differentiate or die, finalizing both neuron number and type within each neuroblast lineage. From a screen aimed at identifying genes required to terminate neuroblast divisions, we identified Notch and Notch pathway components. When Notch is knocked down, neuroblasts maintain early temporal factor expression longer, delay late temporal factor expression, and continue dividing into adulthood. We find that Delta, expressed in cortex glia, neuroblasts, and after division, their GMC progeny, regulates neuroblast Notch activity. We also find that Delta in neuroblasts is expressed high early, low late, and is controlled by the intrinsic temporal program: early factor Imp promotes Delta, late factors Syp/E93 reduce Delta. Thus, in addition to systemic steroid hormone cues, forward lineage progression is controlled by local cell-cell signaling between neuroblasts and their cortex glia/GMC neighbors: Delta transactivates Notch in neuroblasts bringing the early temporal program and early temporal factor expression to a close.
Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing
Authors: Reedy Jennifer L. , Jensen Kirstine Nolling , Crossen Arianne J. , Basham Kyle J. , Ward Rebecca A. , Reardon Christopher M. , Harding Hannah Brown , Hepworth Olivia W. , Simaku Patricia , Kwaku Geneva N. , Tone Kazuya , Willment Janet A. , Reid Delyth M. , Stappers Mark H.T. , Brown Gordon D. , Rajagopal Jayaraj , Vyas Jatin M.
Published: March 2023

Respiratory infections caused by the human fungal pathogenAspergillus fumigatusare a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway bothin vitroandin vivo.Aspergillus-derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.
Bioenergetic costs and the evolution of noise regulation by microRNAs
Authors: Ilker Efe , Hinczewski Michael
Published: March 2023

Noise control, together with other regulatory functions facilitated by microRNAs (miRNAs), is believed to have played important roles in the evolution of multicellular eukaryotic organisms. miRNAs can dampen protein fluctuations via enhanced degradation of mRNAs, but this requires compensation by increased mRNA transcription to maintain the same expression levels. The overall mechanism is metabolically expensive, leading to questions about how it might have evolved in the first place. We develop a stochastic model of miRNA noise regulation, coupled with a detailed analysis of the associated metabolic costs. Additionally we calculate binding free energies for a range of miRNA seeds, the short sequences which govern target recognition. We argue that natural selection may have fine-tuned the Michaelis-Menten constantKMdescribing miRNA-mRNA affinity, and show supporting evidence from analysis of experimental data.KMis constrained by seed length, and optimal noise control (minimum protein variance at a given energy cost) is achievable for seeds of 6-7 nucleotides in length, the most commonly observed types. Moreover, at optimality the degree of noise reduction approaches the theoretical bound set by the Wiener-Kolmogorov linear filter. The results illustrate how selective pressure toward energy efficiency has potentially shaped a crucial regulatory pathway in eukaryotes.
Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport
Authors: Tong Alexander , Kuchroo Manik , Gupta Shabarni , Venkat Aarthi , San Juan Beatriz P. , Rangel Laura , Zhu Brandon , Lock John G. , Chaffer Christine L. , Krishnaswamy Smita
Published: March 2023

While single-cell technologies have allowed scientists to characterize cell states that emerge during cancer progression through temporal sampling, connecting these samples over time and inferring gene-gene relationships that promote cancer plasticity remains a challenge. To address these challenges, we developed TrajectoryNet, a neural ordinary differential equation network that learns continuous dynamics via interpolation of population flows between sampled timepoints. By running causality analysis on the output of TrajectoryNet, we compute rich and complex gene-gene networks that drive pathogenic trajectories forward. Applying this pipeline to scRNAseq data generated fromin vitromodels of breast cancer, we identify and validate a refined CD44hiEPCAM+CAV1+marker profile that improves the identification and isolation of cancer stem cells (CSCs) from bulk cell populations. Studying the cell plasticity trajectories emerging from this population, we identify comprehensive temporal regulatory networks that drive cell fate decisions between an epithelial-to-mesenchymal (EMT) trajectory, and a mesenchymal-to-epithelial (MET) trajectory. Through these studies, we identify and validate estrogen related receptor alpha as a critical mediator of CSC plasticity. We further apply TrajectoryNet to anin vivoxenograft model and demonstrate it’s ability to elucidate trajectories governing primary tumor metastasis to the lung, identifying a dominant EMT trajectory that includes elements of our newly-defined temporal EMT regulatory network. Demonstrated here in cancer, the TrajectoryNet pipeline is a transformative approach to uncovering temporal molecular programs operating in dynamic cell systems from static single-cell data.
Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities
Authors: Garg Vidur , Yang Yang , Nowotschin Sonja , Setty Manu , Kuo Ying-Yi , Sharma Roshan , Polyzos Alexander , Salataj Eralda , Murphy Dylan , Jang Amy , Pe’er Dana , Apostolou Effie , Hadjantonakis Anna-Katerina
Published: March 2023

Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonicENdoderm (XEN) stem cells –in vitrocounterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded byGata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mappingin vitrotrajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrEin vivostates without transitioning through the ICM.
Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era
Authors: Jin Ze-Tao , Hodel Richard G.J. , Ma Dai-Kun , Wang Hui , Liu Guang-Ning , Ren Chen , Ge Bin-Jie , Fan Qiang , Jin Shui-Hu , Xu Chao , Wu Jun , Liu Bin-Bin
Published: March 2023

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups identified to have pervasive reticulate evolution. The red-fruit genus,Stranvaesia, provides an ideal model for testing the effect of reticulation on generic circumscription when hybridization and allopolyploidy define a group’s evolutionary history. Here, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship ofStranvaesiaand its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of theStranvaesiaclade, a conclusion further bolstered by cytonuclear and gene tree discordance. The well-inferred phylogenetic backbone revealed an updated generic delimitation ofStranvaesiaand a new genus,Weniomeles, characterized by purple-black fruits, trunk and/or branches with thorns, and fruit core with multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Here, we highlight a broadly-applicable workflow for inferring how analyses of reticulate evolution in phylogenomic data can directly shape taxonomic revisions.
simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry
Authors: He Dongze , Patro Rob
Published: March 2023

Thealevin-fryecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as thealevin-fryecosystem itself expands and grows, it is becoming increasingly important to manage the complexity ofalevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introducesimpleaf, a program that simplifies the processing of single-cell data using tools from thealevin-fryecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.

Availability and implementation

Simpleafis written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repositoryhttps://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation forsimpleafis available athttps://simpleaf.readthedocs.io/en/latest/and tutorials forsimpleafare being developed that can be accessed athttps://combine-lab.github.io/alevin-fry-tutorials.
Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments
Authors: Kaufman M.H. , Torgeson J. , Stegen J. C.
Published: March 2023

We present a system for carrying out small batch reactor microbial metabolism experiments on water and sediment samples for environmental questions. In general, it provides several advantages that can help researchers achieve impactful experiments at relatively low costs and high data quality. In particular, it allows for multiple reactors to be operated and their oxygen concentrations to be measured simultaneously, providing high throughput and high time-resolution data, which can be advantageous. Most existing literature on similar small batch-reactor metabolic studies is limited to either only a few samples, or only a few time points per sample, which can restrict the ability for researchers to learn from their experiments.

The oxygen sensing system is based very directly on the work of Larsen, et al. [2011], and similar oxygen sensing technology is widely used in the literature. As such we do not delve deeply into the specifics of the fluorescent dye sensing mechanism. Instead, we focus on practical considerations. We describe the construction and operation of the calibration and experimental systems, and answer many of the questions likely to come up when other researchers choose to build and operate a similar system themselves (questions we ourselves had when we first built the system). In this way, we hope to provide an approachable and easy to use research article that can help other researchers construct and operate a similar system that can be tailored to ask their own research questions, with a minimum of confusion and missteps along the way.
AWC mediated behavioral plasticity inC. elegansagainstSalmonellaTyphimurium infection
Authors: Mallick Swarupa , Pradhan Jasmin , Negi Vidya Devi
Published: March 2023

Soil-dwelling nematodeCaenorhabditis elegans(C. elegans) is widely found in close vicinity with different types of microbes, including bacteria, fungus, viruses, etc. However, sensing environmental stress, they often undergo a dormant state called dauer for better survival. Our current study aims to decipher chemosensory responses of worms underSalmonellaTyphimurium (WT-STM) infection and how bacterial gene modulating worms’ chemosensory system to mediate dauer larvae development. We initially observed the olfactory preference ofC. eleganstoward the pathogenic WT-STM. Although prolonged exposure showed enhanced lawn occupancy of worms infepBmutantSalmonellastrain with better associative learning response compared to WT-STM counterpart. We also found strong participation of AWC neuron for sensing ΔfepBstrain and mediating worms’ behavioral plasticity. Overall out study implying a relationship between chemosensory neurons and bacteria emitted signals alter worms’ behavioral plasticity which help us to understand complex scenario of host-pathogen interaction.
Accurate long-read sequencing identified GBA variants as a major genetic risk factor in the Luxembourg Parkinson’s study
Authors: Peiris Sinthuja Pachchek , Landoulsi Zied , Pavelka Lukas , Schulte Claudia , Buena-Atienza Elena , Gross Caspar , Hauser Ann-Kathrin , Bobbili Dheeraj Reddy , Casadei Nicolas , May Patrick , Krüger Rejko
Published: March 2023

Heterozygous variants in the glucocerebrosidaseGBAgene are an increasingly recognized risk factor for Parkinson’s disease (PD). Due to the pseudogeneGBAP1that shares 96% sequence homology with theGBAcoding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape ofGBA-related PD. We established a novel long-read sequencing technology for assessing the full length of theGBAgene. We used subsequent regression models for genotype-phenotype analyses. We sequenced 752 patients with parkinsonism and 806 healthy controls of the Luxembourg Parkinson’s study. AllGBAvariants identified showed a 100% true positive rate by Sanger validation. We found 12% of unrelated PD patients carryingGBAvariants. Three novel variants of unknown significance (VUS) were identified. Using a structure-based approach, we defined a potential risk prediction method for VUS. This study describes the full landscape ofGBA-related parkinsonism in Luxembourg, showing a high prevalence ofGBAvariants as the major genetic risk for PD. Our approach provides an important advancement for highly accurateGBAvariant calling, which is essential for providing access to emerging causative therapies forGBAcarriers.
Comparison of the classification of HER2 from whole-slide images between pathologists and a deep learning model
Authors: Tsuneki Masayuki , Abe Makoto , Kanavati Fahdi
Published: March 2023

HER2 (human epidermal growth factor receptor 2) is a protein that is found on the surface of some cells, including breast cells. HER2 plays a role in cell growth, division, and repair, and when it is overexpressed, it can contribute to the development of certain types of cancer, particularly breast cancer. HER2 overexpression occurs in approximately 20% of cases, and it is associated with more aggressive tumor phenotypes and poorer prognosis. This makes its status an important factor in determining treatment options for breast cancer. While HER2 expression is typically diagnosed through a combination of immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) testing on breast cancer tissue samples, we sought to determine to what extent it is possible to diagnose from H&E-stained specimens. To this effect we trained a deep learning model to classify HER2-positive image patches using a dataset of 10 whole-slide images (5 HER2-positive, 5 HER2-negative). We evaluated the model on a different test set consisting of patches extracted from 10 WSIs (5 HER2-positive, 5 HER2-negative), and we compared the performance against two pathologists on 100 512×512 patches (50 HER2-positive, 50 HER2-negative). Overall, the model achieved an accuracy of 73% while the pathologists achieved 58% and 47%, respectively.
Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia
Authors: Chapman Lloyd AC , Aubry Maite , Maset Noémie , Russell Timothy W , Knock Edward S , Lees John A , Mallet Henri-Pierre , Cao-Lormeau Van-Mai , Kucharski Adam J
Published: March 2023

Estimation of the impact of vaccination and non-pharmaceutical interventions (NPIs) on COVID-19 incidence is complicated by several factors, including the successive emergence of SARS-CoV-2 variants of concern and changing population immunity resulting from vaccination and previous infection. We developed an age-structured multi-strain COVID-19 transmission model and inference framework that could estimate the impact of vaccination and NPIs while accounting for these factors. We applied this framework to French Polynesia, which experienced multiple large COVID-19 waves from multiple variants over the course of the pandemic, interspersed with periods of elimination. We estimated that the vaccination programme averted 49.6% (95% credible interval (CI) 48.7–50.5%) of the 5830 hospitalisations and 64.2% (95% CI 63.1–65.3%) of the 1540 hospital deaths that would have occurred in a baseline scenario without any vaccination up to May 2022. Vaccination also averted an estimated 34.8% (95% CI 34.5–35.2%) of 223,000 symptomatic cases in the baseline scenario. We estimated the booster campaign contributed 4.5%, 1.9% and 0.4% to overall reductions in cases, hospitalisations and hospital deaths respectively. Our results suggested that removing, or altering the timings of, the lockdowns during the first two waves had non-linear effects on overall incidence owing to the resulting effect on accumulation of population immunity. Our estimates of vaccination and booster impact differ from those for other countries due to differences in age structure, previous exposure levels and timing of variant introduction relative to vaccination, emphasising the importance of detailed analysis that accounts for these factors.
FADD- and RIPK3-mediated cell death ensures timely clearance of wound macrophages and promotes wound healing
Authors: Injarabian Louise , Willenborg Sebastian , Welcker Daniela , Pasparakis Manolis , Kashkar Hamid , Eming Sabine A
Published: March 2023

Cells of the monocyte/macrophage lineage are an integral component of the body’s innate ability to restore tissue function after injury. In parallel to mounting an inflammatory response, clearance of monocytes/macrophages from the wound site is critical to re-establish tissue functionality and integrity during the course of healing. The role of regulated cell death in macrophage clearance from damaged tissue and its implications for the outcome of the healing response is little understood. Here, we explored the role of macrophage-specific FADD-mediated cell death onRipk3-/-background in a mechanical skin injury model in mice. We found that combined inhibition of RIPK3-mediated necroptosis and FADD-caspase-8-mediated apoptosis in macrophages profoundly delayed wound healing. Importantly, RIPK3 deficiency alone did not considerably alter the wound healing process and macrophage population dynamics, arguing that inhibition of FADD-caspase-8-dependent death of macrophages is primarily responsible for the delayed wound closure. Notably, TNF blockade reversed the accumulation of Ly6Chighmacrophages induced by combined deficiency of FADD and RIPK3, indicating a critical dual role of TNF-mediated pro-survival and cell death signalling, particularly in this highly pro-inflammatory macrophage subset. Our findings reveal a previously uncharacterized cross-talk of inflammatory and cell death signalling in macrophages in regulating repair processes in the skin.
Modeling and predicting meat yield and growth performance using morphological features of narrow-clawed crayfish with machine learning techniques
Authors: Gültepe Yasemin , Berber Selçuk , Gültepe Nejdet
Published: March 2023

In this study, predictions of length-weight relationships and meat productivity were generated by machine learning models using measurement data of male and female crayfish in the narrow-clawed crayfish population living in Apolyont Lake. The data set was created using the growth performance and morphometric characters obtained from 1416 crayfish in different years to determine the length-weight relationship and length-meat yield. Statistical methods, artificial intelligence, and machine learning are used due to the difficulty of constructing mathematical models in multi-parameter and multivariate problems. In recent studies, artificial intelligence and machine learning methods give higher accuracy than other prediction methods in large data sets with complex structures. No previous studies have been conducted on such population parameters. The analysis results show that most of the models designed as an alternative to traditional estimation methods in future planning studies in sustainable fisheries, aquaculture, and natural sources management are valid for machine learning and artificial intelligence. Seven different machine learning algorithms were applied to the data set and the length-weight relationships and length-meat yields were evaluated for both male and female individuals. Support Vector Regression (SVR) has achieved the best prediction performance with 0.996 and 0.992 values for the length-weight of males and females, with 0.996 and 0.995 values for the length-meat yield of males and females. The results showed that the SVR outperforms the others for all scenarios regarding the accuracy, sensitivity, and specificity metrics.