bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep Representation Learning Determines Drug Mechanism of Action from Cell Painting Images
Authors: Wong Daniel R. , Logan David J. , Hariharan Santosh , Stanton Robert , Kiruluta Andrew
Published: November 2022

Fluorescent-based microscopy screens carry a broad range of phenotypic information about how compounds affect cellular biology. From changes in cellular morphology observed in these screens, one key area of medicinal interest is determining a compound’s mechanism of action. However, much of this phenotypic information is subtle and difficult to quantify. Hence, creating quantitative embeddings that can measure cellular response to compound perturbation has been a key area of research. Here we present a deep learning enabled encoder called MOAProfiler that captures phenotypic features for determining mechanism of action from Cell Painting images. We compared our method with both a traditional computer vision means of feature encoding via CellProfiler and a deep learning encoder called DeepProfiler. The results, on two independent and biologically different datasets, indicated that MOAProfiler encoded MOA-specific features that allowed for more accurate clustering and classification of compounds over hundreds of different MOAs.
Chromosomal inversions and the demography of speciation inDrosophila montanaandDrosophila flavomontana
Authors: Poikela N. , Laetsch D. R. , Hoikkala V. , Lohse K. , Kankare M
Published: November 2022

Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analysed long- and short-read whole-genome data from sympatric and allopatric populations of twoDrosophila virilisgroup species,D. montanaandD. flavomontana, to understand if inversions have contributed to their divergence. We identified three large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and non-inverted (colinear) chromosomal regions suggest that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) fromD. montanatoD. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population, and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process ofD. montanaandD. flavomontana, since they harbour strong genetic incompatibilities that were detected in a recent study of experimental introgression.

Significance

Chromosomal inversions, genomic rearrangements with reversed gene order, have been extensively studied, but it remains unclear whether and how inversions play a role in species divergence. Analysis of long- and short-read whole-genome data for twoDrosophilasister species,D. montanaandD. flavomontana, revealed five alternatively fixed inversions. Modelling the demographic history of these inversions shows that they were segregating already in the common ancestor of the species and that they have reduced gene exchange between these sister taxa both before and after the onset of species divergence. These results are compatible with a scenario in which ancestrally polymorphic inversions aid species divergence by protecting divergently selected loci from erosion via gene flow during the earliest stages of speciation.
PSMC2 and CXCL8-Modulated Four Critical Gene Biomarkers and Druggable and Vaccinable Targets for Colorectal Cancer
Authors: Liu Yongjun , Xu Yuqing , Li Xiaoxing , Chen Mengke , Wang Xueqin , Zhang Ning , Zhang Xiaofei , Zheng Wei , Zhang Heping , Zhang Zhengjun
Published: November 2022

Transcriptomic studies have reported numerous differentially expressed genes in colorectal carcinoma (CRC) versus noncancerous tissues. Given the large number of genes identified, it is unclear which ones are the key genes that drive cancer development. To address the issue, we conducted a large-scale study of eight cohorts with thousands of tumor and nontumor samples, analyzed transcriptomic data, and identified the most miniature set of differentially expressed genes (DEGs) that can nearly perfectly describe the overall features of CRC at the genomic level. The analytical framework was built on a recently proven powerful max-linear competing risk factor model. We first analyzed six public transcriptomic datasets and identified four critical DEGs (i.e., CXCL8, PSMC2, APP, and SLC20A1) with nearly perfect (close to 100%) predictive power. The findings were further validated in a newly collected Chinese cohort and another public dataset. Among the four DEGs, PSMC2 and CXCL8 appeared to play a central role, and CXCL8 alone could serve as a biomarker for early-stage CRC. They rise as druggable and vaccinable targets for CRC. This work represents a pioneering effort to identify critical colorectal-specific genes and their interactions that have not been discovered in previous endeavors.

Simple Summary

Human knowledge of cancer is still limited. There don’t exist reliable genomic biomarkers for cancer diagnosis, and truly functional and druggable genomic (gene) targets haven’t been reported. One of the main reasons is due to lack of powerful discovery tools to discover the best possible and accurate miniature set of genes to fight against the cancer war. Our research was motivated by such an urgent need, and we hope our findings can fill up gaps in the literature and medical practice. We focus on colorectal cancers in this paper.
Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis
Authors: Pontius W. Dean , Hong Ellen S. , Faber Zachary J. , Gray Jeremy , Peacock Craig , Bayles Ian , Lovrenert Katreya , Bartels Cynthia F. , Scacheri Peter C.
Published: November 2022

The metastasis-invasion cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor and ultimately grow within a secondary organ. Despite metastasis being a dynamic, multistep process, most omics studies to date have focused on comparing primary tumors to the metastatic deposits that define end-stage disease. This static approach means we lack information about the genomic and epigenomic changes that occur during the majority of tumor progression. One particularly understudied phase of tumor progression is metastatic colonization, during which cells must adapt to the new microenvironment of the secondary organ. Through temporal profiling of chromatin accessibility and gene expressionin vivo, we identify dynamic changes in the epigenome that occur as osteosarcoma tumors form and grow within the lung microenvironment. Furthermore, we show through pairedin vivoandin vitroCRISPR drop-out screens and pharmacological validation that the upstream transcription factors represent a class of metastasis-specific dependency genes. While current models depict lung colonization as a discrete step within the metastatic cascade, our study shows it is a defined trajectory through multiple epigenetic states, revealing new therapeutic opportunities undetectable with standard approaches.
Conformational epistasis impairs AlphaFold structural predictions
Authors: Sawicki Luciana Rodriguez , Benitez Guillermo , Carletti Matias , Palopoli Nicolas , Fornasari Maria Silvina , Parisi Gustavo
Published: November 2022

Protein structures have been massively predicted using homologous sequence information. AlphaFold2 (AF2) is a recent breakthrough to predict 3D models using machine learning approaches that reached an outstanding accuracy in recent quality evaluations. However, information derived from extant homologous sequences, as those used by AF2, might not contain enough information to accurately predict protein structure. This limitation could be related to the process known as epistasis, which describes the differential effect of a mutation on the evolutionary trajectory. Clear evidence of conformational epistasis, which has a specific impact on protein structure, was characterized in the evolutionary origin of the glucocorticoid receptor (GR) specificity during its functional divergence from the mineralocorticoid (MR) receptor. In this work we explore how AF2 can reproduce conformations derived from epistatic effects. Using structural clustering and principal component analysis to analyze the structural similarities in 16 and 13 extant GR and MR conformers, respectively, we found that AF2 models for human GR failed to reproduce extant GR conformations. Interestingly, AF2 models for human MR, for which no conformational epistasis was reported, were almost indistinguishable from extant MR. Our results showcase the importance of evolutionary trajectories to predict accurate 3D models.
A synthetic lethal screen for Snail-induced enzalutamide resistance identifies JAK/STAT signaling as a therapeutic vulnerability in prostate cancer
Authors: Ware Kathryn E. , Thomas Beatrice C. , Olawuni Pelumi , Sheth Maya U. , Hawkey Nathan , Yeshwanth M , Miller Brian C. , Vietor Katherine J. , Jolly Mohit Kumar , Kim So Young , Armstrong Andrew J. , Somarelli Jason A.
Published: November 2022

Despite substantial improvements in the treatment landscape of prostate cancer, the evolution of hormone therapy-resistant and metastatic prostate cancer remains a major cause of cancer-related death globally. The mainstay of treatment for advanced prostate cancer is targeting of androgen receptor signaling, including androgen deprivation therapy plus second-generation androgen receptor blockade (e.g., enzalutamide, apalutamide, darolutamide), and/or androgen synthesis inhibition (abiraterone). While these agents have significantly prolonged the lives of patients with advanced prostate cancer, the evolution of resistance to these treatments in nearly universal. This therapy resistance is mediated by diverse mechanisms, including both androgen receptor-dependent mechanisms, such as androgen receptor mutations, amplifications, alternatively spliced isoforms, and structural rearrangements, as well as non-androgen receptor-mediated mechanisms, such as lineage plasticity toward neuroendocrine-like or epithelial-mesenchymal transition (EMT)-like lineages. Our prior work identified the EMT transcriptional regulator Snail as critical to hormonal therapy resistance and commonly detected in human metastatic prostate cancer. In the current study, we sought to interrogate the actionable landscape of EMT-mediated hormone therapy-resistant prostate cancer to identify synthetic lethality and collateral sensitivity approaches to treating this aggressive disease state. Using a combination of high-throughput drug screens and multi-parameter phenotyping by confluence imaging, ATP production, and phenotypic plasticity reporters of EMT, we identified candidate synthetic lethalities to Snail-mediated EMT in prostate cancer. These analyses identified multiple actionable targets, such as XPO1, PI3K/mTOR, aurora kinases, c-MET, polo-like kinases, and JAK/STAT as synthetic lethalities in Snail+ prostate cancer. We validated these targets in a subsequent validation screen in an LNCaP-derived model of resistance to sequential androgen deprivation and enzalutamide. This follow-up screen provided validation of inhibitors of JAK/STAT and PI3K/mTOR as therapeutic vulnerabilities for Snail+ and enzalutamide-resistant prostate cancer.
LXR-inducible host E3 ligase IDOL targets a human cytomegalovirus reactivation determinant
Authors: Mlera Luwanika , Collins-McMillen Donna , Zeltzer Sebastian , Buehler Jason C. , Moy Melissa , Zarrella Kristen , Caviness Katie , Cicchini Louis , Tafoya David J. , Goodrum Felicia
Published: November 2022

Liver X receptor (LXR) signaling broadly restricts virus replication; however, the mechanisms of restriction are poorly defined. Here, we demonstrate that the LXR-inducible cellular E3 ligase IDOL (inducible degrader of low-density lipoprotein receptor, LDLR) targets the human cytomegalovirus (HMCV) UL136p33 protein for turnover.UL136encodes multiple proteins that differentially impact latency and reactivation. UL136p33 is a determinant of reactivation. UL136p33 is targeted for rapid turnover by the proteasome and its stabilization by mutation of lysine residues to arginine results in a failure to quiet replication for latency. We show that IDOL targets UL136p33 for turnover, but not the stabilized variant. IDOL is highly expressed in undifferentiated hematopoietic cells where HCMV establishes latency, but is sharply downregulated upon differentiation, a stimulus for reactivation. We hypothesize that IDOL maintains low levels of UL136p33 for the establishment of latency. Consistent with this, knockdown of IDOL impacts viral gene expression in WT HCMV infection, but not in infection where UL136p33 has been stabilized. Further, induction of LXR signaling restricts WT HCMV reactivation from latency, but does not affect replication of a recombinant virus expressing a stabilized variant of UL136p33. This work establishes the UL136p33-IDOL interaction as a key regulator of the bistable switch between latency and reactivation. It further suggests a model whereby a key viral determinant of HCMV reactivation is regulated by a host E3 ligase and acts as a sensor at the tipping point between the decision to maintain the latent state or exit latency for reactivation.

Importance

Herpesviruses establish life-long latent infections, which pose an important risk for disease particularly in the immunocompromised. Our work is focused on the beta-herpesvirus, human cytomegalovirus (HCMV) that latently infects the majority of the population worldwide. Defining the mechanisms by which HCMV establishes latency or reactivates from latency is important to controlling viral disease. Here, we demonstrate that the cellular inducible degrader of low-density lipoprotein receptor, IDOL, targets a HCMV determinant of reactivation for degradation. The instability of this determinant is important for the establishment of latency. This work defines a pivotal virus-host interaction that allows HCMV to sense changes in host biology to navigate decisions to establish latency or replicate.
The CWI pathway is activated through high hydrostatic pressure, enhancing glycerol efflux via the aquaglyceroporin Fps1 inSaccharomyces cerevisiae
Authors: Mochizuki Takahiro , Tanigawa Toshiki , Shindo Seiya , Suematsu Momoka , Oguchi Yuki , Mioka Tetsuo , Kato Yusuke , Fujiyama Mina , Hatano Eri , Yamaguchi Masashi , Chibana Hiroji , Abe Fumiyoshi
Published: November 2022

The fungal cell wall is the initial barrier for the fungi against diverse external stresses, such as osmolarity changes, harmful drugs, and mechanical injuries. This study explores the roles of osmoregulation and the cell wall integrity (CWI) pathway in response to high hydrostatic pressure in the yeastSaccharomyces cerevisiae. We demonstrate the roles of the transmembrane mechanosensor Wsc1 and aquaglyceroporin Fps1 in a general mechanism to maintain cell growth under high-pressure regimes. The promotion of water influx into cells at 25 MPa, as evident by an increase in cell volume and a loss of the plasma membrane eisosome structure, promotes the activation of Wsc1, an activator of the CWI pathway. The downstream mitogen-activated protein kinase Slt2 was hyperphosphorylated at 25 MPa. Glycerol efflux increases via Fps1 phosphorylation, which is initiated by downstream components of the CWI pathway and contributes to the reduction in intracellular osmolarity under high pressure. The elucidation of the mechanisms underlying adaption to high pressure through the well-established CWI pathway could potentially translate to mammalian cells and provide novel insights into cellular mechanosensation.
Feeling lucky? Prospective and retrospective cues for sensorimotor confidence
Authors: Fassold Marissa E. , Locke Shannon M. , Landy Michael S.
Published: November 2022

On a daily basis, humans interact with the outside world using judgments of sensorimotor confidence, constantly evaluating our actions for success. We ask, what sensory and motorexecution cues are used in making these judgements and when are they available? Two sources of temporally distinct information are prospective cues, available prior to the action (e.g., knowledge of motor noise and past performance), and retrospective cues specific to the action itself (e.g., proprioceptive measurements). We investigated the use of these two cues in two tasks, a secondary motor-awareness task and a main task in which participants reached toward a visual target with an unseen hand and then made a continuous judgment of confidence about the success of the reach. Confidence was reported by setting the size of a circle centered on the reach-target location, where a larger circle reflects lower confidence. Points were awarded if the confidence circle enclosed the true endpoint, with fewer points returned for larger circles. This incentivized accurate reaches and attentive reporting to maximize the score. We compared three Bayesian-inference models of sensorimotor confidence based on either prospective cues, retrospective cues, or both sources of information to maximize expected gain (i.e., an ideal-performance model). Our findings showed two distinct strategies: participants either performed as ideal observers, using both prospective and retrospective cues to make the confidence judgment, or relied solely on prospective information, ignoring retrospective cues. Thus, participants can make use of retrospective cues, evidenced by the behavior observed in our motorawareness task, but these cues are not always included in the computation of sensorimotor confidence.

Author Summary

Sensorimotor confidence is a secondary judgment about how successful we feel a motor action was with relation to the goal. To make this judgment we can draw on information available before we execute an action such as our past experiences and knowledge of the environment, as well as after the action including visual feedback and proprioception, a sense of where our body is in space. In this study, we inquired as to how the information available before and after an action is weighted when considering the final feeling of sensorimotor confidence. To do so we asked participants to make reaches to visually cued targets in an unseen hand task, then report their confidence in how successful they were at hitting the target. We measured each participant’s reach accuracy and proprioceptive sensitivity in a separate task. Using mathematical models to fit our data we tested if a given participant depended more heavily on prior information or retrospective information when making their confidence judgment. We found that participants with high proprioceptive uncertainty were more likely to focus on prior knowledge while those with a more exact sense of proprioception incorporated information from both time points.
Gene Expression Detection in Developing Mouse Tissue Using In Situ Hybridization and µCT Imaging
Authors: Väänänen Vilma , Christensen Mona M. , Suhonen Heikki , Jernvall Jukka
Published: November 2022

High resolution and noninvasiveness have made soft tissue X-ray microtomography (µCT) a widely applicable three-dimensional (3D) imaging method in studies of morphology and development. However, scarcity of molecular probes to visualize gene activity with µCT has remained a challenge. Here we apply horseradish peroxidase -assisted reduction of silver and catalytic gold enhancement of the silver deposit toin situhybridization in order to detect gene expression in developing tissues with µCT (here called GECT, Gene Expression CT). We show that GECT detects expression patterns ofcollagen type II alpha 1 (Col2a1) andsonic hedgehog (Shh) in developing mouse tissues comparably with an alkaline phosphatase-based detection method. After detection, expression patterns are visualized with laboratory µCT, demonstrating that GECT is compatible with varying levels of gene expression and varying sizes of expression regions. Additionally, we show that the method is compatible with prior phosphotungstic acid (PTA) staining, a conventional contrast staining approach in µCT imaging of soft tissues. Overall, GECT is a method that can be integrated with existing laboratory routines to obtain spatially accurate 3D detection of gene expression.
Evidence for a putative isoprene reductase inAcetobacterium wieringae
Authors: Kronen Miriam , Vázquez-Campos Xabier , Wilkins Marc R. , Lee Matthew , Manefield Michael J
Published: November 2022

Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome assembled genome (MAG) of the most abundant (89% rel. abundance) lineage in the enrichment,Acetobacterium wieringae, was obtained. Comparative proteogenomics and RT-PCR identified a putative five-gene operon from theA. wieringaeMAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 x HypA-like, HypB-like) and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, FAD and two pairs of [4Fe-4S]-clusters. Other knownAcetobacteriumstrains do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (∼47–49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across theFirmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, BacteroidetesandProteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons.

Importance

Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene reducing enrichment culture, dominated byAcetobacterium wieringae, with genomes of otherAcetobacteriumlineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
Emergence of division of labor in tissues through cell interactions and spatial cues
Authors: Adler Miri , Moriel Noa , Goeva Aleksandrina , Avraham-Davidi Inbal , Mages Simon , Adams Taylor S , Kaminski Naftali , Macosko Evan Z , Regev Aviv , Medzhitov Ruslan , Nitzan Mor
Published: November 2022

Most cell types in multicellular organisms can perform multiple functions. However, not all functions can be optimally performed simultaneously by the same cells. Functions incompatible at the level of individual cells can be performed at the cell population level, where cells divide labor and specialize in different functions. Division of labor can arise due to instruction by tissue environment or through self-organization. Here, we develop a computational framework to investigate the contribution of these mechanisms to division of labor within a cell-type population. By optimizing collective cellular task performance under trade-offs, we find that distinguishable expression patterns can emerge from cell-cell interactionsvs. instructive signals. We propose a method to construct ligand-receptor networks between specialist cells and use it to infer division-of-labor mechanisms from single-cell RNA-seq and spatial transcriptomics data of stromal, epithelial, and immune cells. Our framework can be used to characterize the complexity of cell interactions within tissues.
Insights into the structure-function relationship of the NorQ/NorD chaperones fromParacoccus denitrificansreveal shared principles of interacting MoxR AAA+/VWA domain proteins
Authors: Kahle Maximilian , Appelgren Sofia , Elofsson Arne , Carroni Marta , Ädelroth Pia
Published: November 2022

NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (FeB) cofactor insertion into cytochromec-dependent nitric oxide reductase (cNOR).cNOR catalyzes the NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed FeBinsertion, and the general mechanism of the MoxR/VWA interacting protein families. We show that NorQ-catalyzed ATP hydrolysis, an intact VWA-domain in NorD and specific surface carboxylates oncNOR are all features required forcNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that ‘plugs’ the NorQ ring pore to the VWA domain of NorD with a protruding ‘finger’ inserting through the pore, and suggest this binding mode to be general for MoxR/VWA couples. We present a tentative model for the mechanism of NorQD-catalyzedcNOR remodelling and suggest many of its features to be applicable to the whole MoxR/VWA family.
Release site plasticity via Unc13A regulatory domains mediates synaptic short-term facilitation and homeostatic potentiation
Authors: Jusyte Meida , Blaum Natalie , Böhme Mathias A. , Berns Manon M. M. , Bonard Alix E. , Kobbersmed Janus R. L. , Walter Alexander M.
Published: November 2022

Chemical synaptic transmission relies on neurotransmitter release from presynaptic release sites and on transmitter-sensing by the postsynaptic cell. Presynaptic plasticity increasing neurotransmitter release achieves two fundamental nervous system functions: It tunes some synapses to be more responsive to millisecond repetitive activation and it maintains signals when postsynaptic transmitter sensitivity is reduced. How enhanced neurotransmitter release is achieved in these phenomena, termed short-term facilitation and homeostatic potentiation, remains unknown. We combine mathematical modeling and experimental analysis ofDrosophilaneuromuscular junction model synapses to elucidate the molecular mechanisms underlying these forms of plasticity. Our results indicate that both phenomena depend on a rapid increase in the participation of neurotransmitter release sites which is controlled by the regulatory domains of the evolutionarily conserved (M)Unc13A protein that bind Ca2+/Calmodulin and diacylglycerol. Mutation of the Calmodulin binding (CaM) domain increased baseline transmission and impaired both short-term facilitation and acute homeostatic potentiation. Mathematical modeling indicated that these defects result from too many release sites participating at rest combined with the inability to plastically further increase their number. Super-resolution microscopy revealed that this coincided with a redistribution of Unc13A’s functionally essential MUN domain closer to the synaptic plasma membrane, which may constitute the molecular switch to increase release site participation. Similar consequences (enhanced baseline transmission, block of both short-term facilitation and homeostatic potentiation) were caused by the acute pharmacological activation of the C1 domain of wildtype Unc13A using phorbol esters. This treatment had no effect on Unc13A CaM domain mutants, indicating that both the CaM and C1 domains activate a binary release site switch. Thus, our findings indicate that Unc13A regulatory domains are tuned to integrate a multitude of signals on various timescales to switch release site participation for synaptic plasticity.
The Alternate Ligand Jagged Enhances the Robustness of Notch Signaling Patterns
Authors: Mukherjee Mrinmoy , Levine Herbert
Published: November 2022

The Notch pathway, an example of juxtacrine signaling, is an evolutionary conserved cell-cell communication mechanism. It governs emergent spatiotemporal patterning in tissues during development, wound healing and tumorigenesis. Communication occurs when Notch receptors of one cell bind to either of its ligands, Delta/Jagged of neighboring cell. In general, Delta-mediated signaling drives neighboring cells to have an opposite fate (lateral inhibition) whereas Jagged-mediated signaling drives cells to maintain similar fates (lateral induction). Here, By deriving and solving a reduced set of 12 coupled ordinary differential equations for Notch-Delta-Jagged system on a hexagonal grid of cells, we determine the allowed states across different parameter sets. We also show that Jagged (at low dose) acts synergistically with Delta to enable more robust pattern formation, despite of its lateral induction property; this effect is due to competition with Delta over binding with Notch, as experimentally observed in the case of chick inner ear development. Finally, we show that how Jagged can help to expand the bistable (both Uniform and Hexagon phases are stable) region, where a local perturbation can spread over time in a ordered manner to create a biologically relevant, defect-free lateral inhibition pattern.
Inferring the distributions of fitness effects and proportions of strongly deleterious mutations
Authors: Charmouh Anders P. , Bocedi Greta , Hartfield Matthew
Published: November 2022

The distribution of fitness effects is a key property in evolutionary genetics as it has implications for several evolutionary phenomena including the evolution of sex and mating systems, the rate of adaptive evolution, and the prevalence of deleterious mutations. Despite the distribution of fitness effects being extensively studied, the effects of strongly deleterious mutations are difficult to infer since such mutations are unlikely to be present in samples of haplotypes, so genetic data may contain very little information about them. Recent work has attempted to correct for this issue by expanding the classic gamma-distributed model to explicitly account for strongly deleterious mutations. Here, we use simulations to investigate one such method, adding a parameter (plth) to capture the proportion of strongly deleterious mutations. We show thatplthcan improve the model fit when applied to individual species but can underestimate the true proportion of strongly deleterious mutations. The parameter can also artificially maximize the likelihood when used to jointly infer a distribution of fitness effects from multiple species. Asplthand related parameters are used in current inference algorithms, our results are relevant with respect to avoiding model artifacts and improving future tools for inferring the distribution of fitness effects.
Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells
Authors: Dunjić Marko , Jonas Felix , Yaakov Gilad , More Roye , Mayshar Yoav , Rais Yoach , Barkai Naama , Stelzer Yonatan
Published: November 2022

Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central epigenetic determinant. Here, we define the genome-wide incorporation and exchange pattern of canonical and non-canonical histone variants in mouse embryonic stem cells by implementing a recently established, genetically encoded exchange sensor. While exchange of all measured variants scales with transcription, we describe variant-specific associations with transcription elongation and Polycomb binding. We found considerable exchange of H3.1 and H2B variants in heterochromatin and repeat elements, contrasting the stable incorporation and little exchange of H3.3 in these regions. This unexpected association between H3.3 incorporation and exchange of canonical variants is also evident in active promoters and enhancers, and further validated by reduced H3.1 dynamics following depletion of the HIRA H3.3-specific chaperone. The sensor system provides a powerful tool for studying regulation of histone dynamics toward understanding its role in shaping the epigenetic landscapein vivo.
Embryonic signals mediate extracellular vesicle biogenesis and trafficking at the embryo–maternal interface
Authors: Guzewska Maria M. , Myszczynski Kamil , Heifetz Yael , Kaczmarek Monika M.
Published: November 2022

Extracellular vesicles (EVs) are membrane-coated nanoparticles secreted by almost all cell types in living organisms. EVs, as paracrine mediators, are involved in intercellular communication, immune response, and several reproductive events, including the maintenance of pregnancy. Using a domestic animal model (Sus scrofa) with an epitheliochorial, superficial type of placentation, we focused on EV biogenesis pathway at the embryo–maternal interface, when the embryonic signaling occurs for maternal recognition and the maintenance of pregnancy. Transmission electron microscopy was used during early pregnancy to visualize different populations of EVs and apocrine and/or merocrine pathways of secretion. Immunofluorescent staining localized proteins responsible for EV biogenesis and cell polarization at the embryo–maternal interface. The expression profiles of genes involved in biogenesis and the secretion of EVs pointed at the possible modulation of endometrial expression by embryonic signals. Further in vitro studies showed that factors of embryonic origin can regulate the expression of the ESCRT-II complex and EV trafficking in luminal epithelial cells. Moreover, miRNA-mediated rapid negative regulation of gene expression was abolished by delivered embryonic signals. Our findings demonstrated that embryonic signals are potent modulators of EV-mediated secretory activity of the endometrium during the critical stages of early pregnancy.
Real-time library search increases cross-link identification depth across all levels of sample complexity
Authors: Ruwolt Max , He Yi , Lima Diogo Borges , Barshop William , Broichhagen Johannes , Huguet Romain , Viner Rosa , Liu Fan
Published: November 2022

Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactionsin vitroandin vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intactE. colicells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.
Multi-‘Omic Integration via Similarity Network Fusion to Detect Molecular Subtypes of Aging
Authors: Yang Mu , Matan-Lithwick Stuart , Wang Yanling , De Jager Philip L , Bennett David A , Felsky Daniel
Published: November 2022

Background

Molecular subtyping of brain tissue provides insights into the heterogeneity of common neurodegenerative conditions, such as Alzheimer’s disease (AD). However, existing subtyping studies have mostly focused on single data modalities and only those individuals with severe cognitive impairment. To address these gaps, we applied Similarity Network Fusion (SNF), a method capable of integrating multiple high-dimensional multi-’omic data modalities simultaneously, to an elderly sample spanning the full spectrum of cognitive aging trajectories.

Methods

We analyzed human frontal cortex brain samples characterized by five ‘omic modalities: bulk RNA sequencing (18,629 genes), DNA methylation (53,932 cpg sites), histone H3K9 acetylation (26,384 peaks), proteomics (7,737 proteins), and metabolomics (654 metabolites). SNF followed by spectral clustering was used for subtype detection, and subtype numbers were determined by eigen-gap and rotation cost statistics. Normalized Mutual Information (NMI) determined the relative contribution of each modality to the fused network. Subtypes were characterized by associations with 13 age-related neuropathologies and cognitive decline.

Results

Fusion of all five data modalities (n=111) yielded two subtypes (nS1=53, nS2=58) which were nominally associated with diffuse amyloid plaques; however, this effect was not significant after correction for multiple testing. Histone acetylation (NMI=0.38), DNA methylation (NMI=0.18) and RNA abundance (NMI=0.15) contributed most strongly to this network. Secondary analysis integrating only these three modalities in a larger subsample (n=513) indicated support for both 3- and 5-subtype solutions, which had significant overlap, but showed varying degrees of internal stability and external validity. One subtype showed marked cognitive decline, which remained significant even after correcting for tests across both 3- and 5-subtype solutions (pBonf=5.9×10−3). Comparison to single-modality subtypes demonstrated that the three-modal subtypes were able to uniquely capture cognitive variability. Comprehensive sensitivity analyses explored influences of sample size and cluster number parameters.

Conclusion

We identified highly integrative molecular subtypes of aging derived from multiple high dimensional, multi-’omic data modalities simultaneously. Fusing RNA abundance, DNA methylation, and H3K9 acetylation measures generated subtypes that were associated with cognitive decline. This work highlights the potential value and challenges of multi-’omic integration in unsupervised subtyping of postmortem brain.
Comparative Mucomic Analysis of Three Functionally DistinctCornu aspersumSecretions
Authors: Cerullo Antonio R. , McDermott Maxwell B. , Pepi Lauren E. , Liu Zhi-Lun , Barry Diariou , Zhang Sheng , Chen Xi , Azadi Parastoo , Holford Mande , Braunschweig Adam B.
Published: November 2022

Every animal secretes mucus, placing them among the most diverse biological materials. Mucus hydrogels are complex mixtures of water, ions, carbohydrates, and proteins. Uncertainty surrounding their composition and how interactions between components contribute to mucus function complicates efforts to exploit their properties. There is substantial interest in commercializing mucus from the garden snail,Cornu aspersum, for skincare, drug delivery, tissue engineering, and composite materials.C. asperumsecretes three mucus — one shielding the animal from environmental threats, one adhesive mucus from the pedal surface of the foot, and another pedal mucus that is lubricating. It remains a mystery how compositional differences account for their substantially different properties. Here, we characterize mucus proteins, glycosylation, ion content, and mechanical properties to understand structure-function relationships through an integrative “mucomics” approach. We identify new macromolecular components of these hydrogels, including a novel protein class termed Conserved Anterior Mollusk Proteins (CAMPs). Revealing differences betweenC. aspersummucus shows how considering structure at all levels can inform the design of mucus-inspired materials.
Repulsive interaction and secondary structure of highly charged proteins in regulating biomolecular condensation
Authors: Tan Cheng , Niitsu Ai , Sugita Yuji
Published: November 2022

Biomolecular condensation is involved in various cellular processes both functional and dysfunctional. Regulation of the condensation is thus crucial to avoid pathological protein aggregation and to maintain stable cellular environments. Recently, a class of highly charged intrinsically disordered proteins (IDPs), which are called the heat-resistant obscure (Hero) proteins, are shown to protect other client proteins from pathological aggregation. Besides the potential importance of this function, molecular mechanisms for how Hero proteins can protect other proteins from aggregation are not still known. Here we perform multiscale molecular dynamics (MD) simulations of Hero11, one of the Hero proteins, and the C-terminal region of TDP-43, as a target protein of Hero11, at various conditions to examine how they interact with each other. Based on the simulation results, three possible mechanisms have been proposed: (i) TDP-43 and Hero11 in dense phase reduces contacts with each other and shows faster diffusion due to the repulsive Hero11-Hero11 interactions, (ii) the amount of TDP-43 in dilute phase increases and their sizes become greater upon the attractive Hero11-TDP-43 interactions, and (iii) Hero-11 on the surface of small TDP-43 condensates avoids their fusions with the repulsive interactions. We also examine possible Hero-11 structures in atomistic and coarse-grained MD simulations and found disordered Hero-11 tend to assemble on the surface of the condensates, avoiding the droplet fusion effectively. The proposed mechanisms give us new insight into the regulation of biomolecular condensation in the cells and other conditions.
Clonal amplification-enhanced gene expression for cell-free directed evolution
Authors: Abil Zhanar , Restrepo Sierra Ana Maria , Danelon Christophe
Published: November 2022

In cell-free gene expression, low input DNA concentration severely limits the phenotypic output, which may impair in vitro protein evolution efforts. We address this challenge by developing CADGE, a strategy that is based on clonal isothermal amplification of a linear gene-encoding dsDNA template by the minimal Φ29 replication machinery and in situ transcription-translation. We demonstrate the utility of CADGE in bulk and in clonal liposome microcompartments to boost up the phenotypic output of soluble and membrane-associated proteins, as well as to facilitate the recovery of encapsulated DNA. Moreover, we report that CADGE enables the enrichment of a DNA variant from a mock gene library either via a positive feedback loop-based selection or high-throughput screening. This new biological tool can be implemented for cell-free protein engineering and the construction of a synthetic cell.
Spatiotemporal neural dynamics of object recognition under uncertainty in humans
Authors: Wu Yuan-hao , Podvalny Ella , He Biyu J.
Published: November 2022

While there is a wealth of knowledge about core object recognition—our ability to recognize clear, high-contrast object images, how the brain accomplishes object recognition tasks under increased uncertainty remains poorly understood. We investigated the spatiotemporal neural dynamics underlying object recognition under increased uncertainty by combining MEG and 7 Tesla fMRI in humans during a threshold-level object recognition task. We observed an early, parallel rise of recognition-related signals across ventral visual and frontoparietal regions that preceded the emergence of category-related information. Recognition-related signals in ventral visual regions were best explained by a two-state representational format whereby brain activity bifurcated for recognized and unrecognized images. By contrast, recognition-related signals in frontoparietal regions exhibited a reduced representational space for recognized images, yet with sharper category information. These results provide a spatiotemporally resolved view of neural activity supporting object recognition under uncertainty, revealing a pattern distinct from that underlying core object recognition.
The professional identity of accountants – an empirical analysis of job advertisements
Authors: Ott Christian
Published: November 2022

Purpose

The purpose of this study is to investigate to what extent the professional identity of accountants, as manifested in a set of advanced cognitive, emotional and social intelligence competencies relevant to their professional activities, varies with the respective accounting position.

Design/methodology/approach

The systematically developed, formally clearly structured job advertisements for accounting positions provide content-rich representations of those holding the advertised position and thus contribute to revealing the professional identity. This study conducts a content analysis of 600 profiles of accountants presented in job advertisements of German organizations to identify the characteristic set of advanced cognitive, emotional and social intelligence competencies, juxtaposing different accounting positions at various stages of professional life. German organizations were targeted because they traditionally clearly differentiate between financial accounting and management accounting.

Findings

The job advertisements suggest that accountants develop a multifaceted professional identity reflecting their area of specialization and their level of entry. Financial accountants are more likely to be team-oriented than management accountants, and non-executive accountants are more likely than executive accountants. Analytical thinking seems to characterize management accountants rather than financial accountants. An independent way of working appears to be more pronounced among financial accountants than among management accountants.

Originality/value

This study refines the understanding of the professional identity of accountants by exploring the recruitment of accountants, the initial step of professional socialization. It identifies the most relevant advanced cognitive, emotional and social intelligence competencies based on a broad sample of job advertisements for accounting positions in organizations of different sizes and industries. By contrasting the competencies relevant to different positions and at different stages of their professional lives, it becomes evident that distinct professional identities of accountants coexist. The relevant competencies may be developed during higher education and continuing professional education. They may also be incorporated into individual performance evaluations and used as the basis for promotion decisions.