bluuebunny/crossref_metadata_2025 huggingface dataset:
PHF6 suppresses self-renewal of leukemic stem cells in AML
Authors: Jalnapurkar Sapana S. , Pawar Aishwarya , George Subin S. , Antony Charles , Grana Jason , Gurbuxani Sandeep , Paralkar Vikram R.
Published: January 2024

Acute myeloid leukemia is characterized by uncontrolled proliferation of self-renewing myeloid progenitors. PHF6 is a chromatin-binding protein mutated in myeloid leukemias, and its loss increases mouse HSC self-renewal without malignant transformation. We report here thatPhf6knockout increases the aggressiveness ofHoxa9-driven AML over serial transplantation, and increases the frequency of leukemia initiating cells. We define thein vivohierarchy ofHoxa9-driven AML and identify a population that we term the ‘LIC-e’ (leukemia initiating cells enriched) population. We find thatPhf6loss has context-specific transcriptional effects, skewing the LIC-e transcriptome to a more stem-like state. We demonstrate that LIC-e accumulation inPhf6knockout AML occurs not due to effects on cell cycle or apoptosis, but due to an increase in the fraction of its progeny that retain LIC-e identity. Overall, our work indicates thatPhf6loss increases AML self-renewal through context-specific effects on leukemia stem cells.

Statement of Significance

Leukemia stem cell self-renewal is critical to the pathophysiology of AML.Phf6deletion accelerates mouse AML by increasing LSC self-renewal, specifically by increasing the fraction of LSC progeny that retain LSC identity. Our work shows how a repressor of HSC self-renewal is inactivated in AML to drive LSC stemness.
An adaptive numerical method for multi–cellular simulations of tissue development
Authors: Osborne James M.
Published: January 2024

In recent years, multi–cellular models, where cells are represented as individual interacting entities, are becoming ever popular. This has led to a proliferation of novel methods and simulation tools. The first aim of this paper is to review the numerical methods utilised by multi–cellular modelling tools and to demonstrate which numerical methods are appropriate for simulations of tissue and organ development and disease. The second aim is to introduce an adaptive time–stepping algorithm and to demonstrate it’s efficiency and accuracy. We focus on off–lattice, mechanics based, models where cell movement is defined by a series of first order ordinary differential equations, derived by assuming over–damped motion and balancing forces. We see that many numerical methods have been used, ranging from simple Forward Euler approaches through to higher order single–step methods like Runge–Kutta 4 and multi–step methods like Adams–Bashforth 2. Through a series of exemplar multi–cellular simulations, we see that if: care is taken to have events (births deaths and re–meshing/re–arrangements) occur on common time–steps; and boundaries are imposed on all sub–steps of numerical methods or implemented using forces, then all numerical methods can converge with the correct order. We introduce an adaptive time–stepping method and demonstrate that the best compromise betweenL∞error and run–time is to use Runge–Kutta 4 with an increased time–step and moderate adaptivity. We see that a judicious choice of numerical method can speed the simulation up by a factor of 10–60 from the Forward Euler methods seen in Osborneet. al. [2017,https://doi.org/10.1371/journal.pcbi.1005387] and a further speed up by a factor of 4 can be achieved by using an adaptive time–step.
A network toxicology approach for mechanistic modelling of nanomaterial hazard and adverse outcomes
Authors: del Giudice Giusy , Serra Angela , Pavel Alisa , Maia Marcella Torres , Saarimäki Laura Aliisa , Fratello Michele , Federico Antonio , Alenius Harri , Fadeel Bengt , Greco Dario
Published: January 2024

Hazard assessment is the first step in evaluating the potential adverse effects of chemicals. Traditionally, toxicological assessment has focused on the exposure, overlooking the impact of the exposed system on the observed toxicity. However, systems toxicology emphasises how system properties significantly contribute to the observed response. Hence, systems theory states that interactions store more information than individual elements, leading to the adoption of network based models to represent complex systems in many fields of life sciences. Here, we developed a network-based approach to characterise toxicological responses in the context of a biological system, inferring biological system specific networks. We directly linked molecular alterations to the adverse outcome pathway (AOP) framework, establishing connections with toxicologically relevant phenotypic events. We applied this framework on a dataset including 31 engineered nanomaterials with different physicochemical properties in two differentin vitroand onein vivomodels and demonstrated how the biological system is the driving force of the observed response. This work highlights the potential of network-based methods to significantly improve our understanding of toxicological mechanisms from a systems biology perspective, guiding the hazard assessment of nanomaterials and other advanced materials.
The Subcortical Atlas of the Marmoset (“SAM”) monkey based on high-resolution MRI and histology
Authors: Saleem Kadharbatcha S , Avram Alexandru V , Glen Daniel , Schram Vincent , Basser Peter J
Published: January 2024

A comprehensive three-dimensional digital brain atlas of cortical and subcortical regions based on MRI and histology has a broad array of applications for anatomical, functional, and clinical studies. We first generated aSubcorticalAtlas of theMarmoset, called the “SAM,” from 251 delineated subcortical regions (e.g., thalamic subregions, etc.) derived from the high-resolution MAP-MRI, T2W, and MTR imagesex vivo. We then confirmed the location and borders of these segmented regions in MRI data using matched histological sections with multiple stains obtained from the same specimen. Finally, we estimated and confirmed the atlas-based areal boundaries of subcortical regions by registering thisex vivoatlas template toin vivoT1- or T2W MRI datasets of different age groups (single vs. multisubject population-based marmoset control adults) using a novel pipeline developed within AFNI. Tracing and validating these important deep brain structures in 3D improves neurosurgical planning, anatomical tract tracer injections, navigation of deep brain stimulation probes, fMRI and brain connectivity studies, and our understanding of brain structure-function relationships. This newex vivotemplate and atlas are available as volumes in standard NIFTI and GIFTI file formats and are intended for use as a reference standard for marmoset brain research.
A Dimerization-dependent Allosteric Activation for Receptor-like Kinase in Plants
Authors: Chen Jia , Cai Dan , Zhang Yunxuan , Chen Lin , Yu Feng
Published: January 2024

Receptor-like kinases (RLKs) are essential in plants and phosphorylation is a critical step for their function. Interestingly, RLKs have many non-catalytic kinases/ pseudokinases and the biochemical basis for these pseudokinases remains unclear. FERONIA (FER) is an RLK with kinase activity, but the necessity of its kinase activity for genetic functions has been debated. Here, we uncovered that the kinase-deficient variant FERK565Rcan activate kinase activity in FER and its homologous through homo/heterodimerization-dependent allosteric activation. We further showed that reactive oxygen species (ROS) significantly promote the dimerization of FER family members. Next, we revealed that mutating the FER P740 within the αG-αH loop reduces FER dimerization and disrupts its allosteric activation, thus attenuating FER’s transphosphorylation for its substrate. This disruption in allosteric activation abolishes the genetic function of FERK565R, impacting ROS production and ABA-mediated stomatal movements. Additionally, we found that MEDOS1 (MDS1), a member of the FER family, is incapable of catalyzing phosphotransfer, but can boost the kinase activity of FER and HERK1 through allosteric activation. These findings settle the debate on FER’s inactivated forms, and reveal a new mechanism for allosteric activation of RLKs via redox signaling, enhancing our understanding of pseudokinases in plants.

One-sentence summary

FER activates kinase activity of homologous family members through allosteric activation.
CAP peptide artificially induces insect gall
Authors: Hirano Tomoko , Sakamoto Tomoaki , Kimura Seisuke , Nakayama Takumi , Sato Mitsuhiko P. , Shirasawa Kenta , Sato Masa H.
Published: January 2024

Galls caused by gall-inducing insects in their host plants clearly illustrate the concept of ‘extended phenotype’, which refers to traits expressed in a host organism when manipulated by a parasite. Candidate effector molecules involved in gall formation, such as phytohormones, amino acids, and proteins, have been reported in numerous studies. However, to date, no attempts to artificially regenerate gall structures using effector candidates have been reported. In this study, we tested the peptide fromCysteine-rich secretory proteins,Antigen 5, andPathogenesis-related 1 proteins, CAP peptide as a gall-inducing effector candidate obtained from transcripts isolated from the horned gall aphid, (Schlechtendalia chinensis) through in silico screening and the Arabidopsis-based gall-forming assay, which is a bioassay system for analysing the molecular mechanisms of gall formation. Furthermore, we succeeded in generating an artificial gall in the host plantVeronica peregrina,without any insect parasitism, using three minimal effector elements: CAP peptide, auxin, and cytokinin. Given the strong similarities observed in organ structure with a central cavity and three types of tissue and gene expression patterns between the native and artificial galls, we concluded that CAP peptide is a general gall-inducing effector peptide secreted by gall-inducing insects.
Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists
Authors: Pawnikar Shristi , Magenheimer Brenda S. , Joshi Keya , Munoz Ericka Nevarez , Haldane Allan , Maser Robin L. , Miao Yinglong
Published: January 2024

Polycystin-1 (PC1) is the membrane protein product of the PKD1 gene whose mutation is responsible for 85% of the cases of autosomal dominant polycystic kidney disease (ADPKD). ADPKD is primarily characterized by the formation of renal cysts and potential kidney failure. PC1 is an atypical G protein-coupled receptor (GPCR) consisting of 11 transmembrane helices and an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal (NTF) and membrane-embedded C-terminal (CTF) fragments. Recently, signaling activation of the PC1 CTF was shown to be regulated by a stalk tethered agonist (TA), a distinct mechanism observed in the adhesion GPCR family. A novel allosteric activation pathway was elucidated for the PC1 CTF through a combination of Gaussian accelerated molecular dynamics (GaMD), mutagenesis and cellular signaling experiments. Here, we show that synthetic, soluble peptides with 7 to 21 residues derived from the stalk TA, in particular, peptides including the first 9 residues (p9), 17 residues (p17) and 21 residues (p21) exhibited the ability to re-activate signaling by a stalkless PC1 CTF mutant in cellular assays. To reveal molecular mechanisms of stalk peptide-mediated signaling activation, we have applied a novel Peptide GaMD (Pep-GaMD) algorithm to elucidate binding conformations of selected stalk peptide agonists p9, p17 and p21 to the stalkless PC1 CTF. The simulations revealed multiple specific binding regions of the stalk peptide agonists to the PC1 protein including an “intermediate” bound yet inactive state. Our Pep-GaMD simulation findings were consistent with the cellular assay experimental data. Binding of peptide agonists to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of the PC1 CTF signaling activation mechanism. Using sequence covariation analysis of PC1 homologs, we further showed that the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. Therefore, structural dynamic insights into the mechanisms of PC1 activation by stalk-derived peptide agonists have enabled an in-depth understanding of PC1 signaling. They will form a foundation for development of PC1 as a therapeutic target for the treatment of ADPKD.
Unbiased identification of cell identity in dense mixed neural cultures
Authors: De Beuckeleer Sarah , Van De Looverbosch Tim , Van Den Daele Johanna , Ponsaerts Peter , De Vos Winnok H.
Published: January 2024

Induced pluripotent stem cell (iPSC) technology is revolutionizing cell biology. However, the variability between individual iPSC lines and the lack of efficient technology to comprehensively characterize iPSC-derived cell types hinder its adoption in routine preclinical screening settings. To facilitate the validation of iPSC-derived cell culture composition, we have implemented an imaging assay based on cell painting and convolutional neural networks to recognize cell types in dense and mixed cultures with high fidelity. We have benchmarked our approach using pure and mixed cultures of neuroblastoma and astrocytoma cell lines and attained a classification accuracy above 96%. Through iterative data erosion we found that inputs containing the nuclear region of interest and its close environment, allow achieving equally high classification accuracy as inputs containing the whole cell for semi-confluent cultures and preserved prediction accuracy even in very dense cultures. We then applied this regionally restricted cell profiling approach to evaluate the differentiation status of iPSC-derived neural cultures, by determining the ratio of postmitotic neurons and neural progenitors. We found that the cell-based prediction significantly outperformed an approach in which the time in culture was used as classification criterion (96%vs.86%, resp.). In mixed iPSC-derived neuronal cultures, microglia could be unequivocally discriminated from neurons, regardless of their reactivity state. A tiered strategy, allowed for discriminating microglial cell states as well, albeit with lower accuracy. Thus, morphological single cell profiling provides a means to quantify cell composition in complex mixed neural cultures and holds promise for use in quality control of iPSC-derived cell culture models.
Negative allosteric modulation of cannabinoid CB1receptor signaling suppresses opioid-mediated tolerance and withdrawal without blocking opioid antinociception
Authors: Iyer Vishakh , Saberi Shahin A. , Pacheco Romario , Sizemore Emily Fender , Stockman Sarah , Kulkarni Abhijit , Cantwell Lucas , Thakur Ganesh A. , Hohmann Andrea G.
Published: January 2024

The direct blockade of CB1cannabinoid receptors produces therapeutic effects as well as adverse side-effects that limit their clinical potential. CB1negative allosteric modulators (NAMs) represent an indirect approach to decrease the affinity and/or efficacy of orthosteric cannabinoid ligands or endocannabinoids at CB1. We recently reported that GAT358, a CB1-NAM, blocked opioid-induced mesocorticolimbic dopamine release and reward via a CB1-allosteric mechanism of action. Whether a CB1-NAM dampens opioid-mediated therapeutic effects such as analgesia or alters other unwanted side-effects of opioids remain unknown. Here, we characterized the effects of GAT358 on nociceptive behaviors in the presence and absence of morphine. We examined the impact of GAT358 on formalin-evoked pain behavior and Fos protein expression, a marker of neuronal activation, in the lumbar dorsal horn. We also assessed the impact of GAT358 on morphine-induced slowing of colonic transit, tolerance, and withdrawal behaviors. GAT358 attenuated morphine antinociceptive tolerance without blocking acute antinociception. GAT358 also reduced morphine-induced slowing of colonic motility without impacting fecal boli production. GAT358 produced antinociception in the presence and absence of morphine in the formalin model of inflammatory nociception and reduced the number of formalin-evoked Fos protein-like immunoreactive cells in the lumbar spinal dorsal horn. Finally, GAT358 mitigated the somatic signs of naloxone-precipitated, but not spontaneous, opioid withdrawal following chronic morphine dosing in mice. Our results support the therapeutic potential of CB1-NAMs as novel drug candidates aimed at preserving opioid-mediated analgesia while preventing their unwanted side-effects. Our studies also uncover previously unrecognized antinociceptive properties associated with an arrestin-biased CB1-NAMs.

Highlights

CB1negative allosteric modulator (NAM) GAT358 attenuated morphine tolerance

GAT358 reduced morphine-induced slowing of colonic motility but not fecal production

GAT358 was antinociceptive for formalin pain alone and when combined with morphine

GAT358 reduced formalin-evoked Fos protein expression in the lumbar spinal cord

GAT358 mitigated naloxone precipitated withdrawal after chronic morphine dosing
Poor decision making and sociability impairment following central serotonin reduction in inducible TPH2-knockdown rats
Authors: Alonso Lucille , Peeva Polina , Fernández del valle Alquicira Tania , Erdelyi Narda , Gil-Nolskog Ángel , Bader Michael , Winter York , Alenina Natalia , Rivalan Marion
Published: January 2024

Serotonin is an essential neuromodulator for mental health and animals’ socio-cognitive abilities. However, we previously found that a constitutive depletion of central serotonin did not impair rat cognitive abilities in stand-alone tests. Here we investigated how a mild and acute decrease of brain serotonin would affect rats’ cognitive abilities. Using a novel rat model of inducible serotonin depletion via the genetic knock-down of tryptophan hydroxylase 2 (TPH2), we achieved 20% decrease of serotonin levels in the hypothalamus after three weeks of non-invasive oral doxycycline administration. Decision making in the Rat Gambling Task and the Probability Discounting Task, cognitive flexibility and social recognition memory were tested in low-serotonin (Tph2-kd) and control rats. Our results showed that the Tph2-kd rats were more prone to choose disadvantageously on the long term (poor decision making) and that only the low-serotonin poor decision makers were more sensitive to probabilistic discounting and had poorer social recognition memory than other low-serotonin and control individuals. Flexibility was unaffected by the acute brain serotonin reduction. Poor social recognition memory was the most central characteristic of the behavioral network of low-serotonin poor decision makers, suggesting a key role of social recognition in expression of their profile. The acute decrease of brain serotonin appeared to specifically amplify cognitive impairments of the subgroup of individuals also identified as poor decision makers in the population. This study highlights the great opportunity Tph2-kd rat model offers to study inter-individual susceptibilities to develop cognitive impairment following mild variations of brain serotonin in otherwise healthy individuals. These transgenic and differential approaches together could be critical for the identification of translational markers and vulnerabilities in the development of mental disorders.
Leveraging engineeredPseudomonas putidaminicells for bioconversion of organic acids into short-chain methyl ketones
Authors: Kozaeva Ekaterina , Nieto-Domínguez Manuel , Tang Kent Kang Yong , Nikel Pablo Iván
Published: January 2024

Methyl ketones, key building-blocks widely used in diverse industrial applications, largely depend on oil-derived chemical methods for their production. Here, we investigated bio-based production alternatives for short-chain ketones, adapting the solvent-tolerant soil bacteriumPseudomonas putidaas a host for ketone biosynthesis either by whole-cell biocatalysis or using engineered minicells, chromosome-free bacterial vesicles. Organic acids (acetate, propanoate and butyrate) were selected as the main carbon substrate to drive the biosynthesis of acetone, 2-butanone and 2-pentanone. Pathway optimization identified efficient enzyme variants fromClostridium acetobutylicumandEscherichia coli, which were tested under both constitutive and inducible expression of the cognate genes. By implementing these optimized pathways inP.putidaminicells, which can be prepared through a simple 3-step purification protocol, the feedstock was converted into the target short-chain methyl ketones, remaining catalytically functional for >4 months. These results highlight the value of combining morphology and pathway engineering of non-canonical bacterial hosts to establish alternative bioprocesses for toxic chemicals that are difficult to produce by conventional approaches.

GRAPHICAL ABSTRACT
Comparison of urine proteome between obese people and normal weight people
Authors: Wang Haitong , Wei Lilong , Zhou Yun , Cao Yongtong , Gao Youhe
Published: January 2024

Objective

To explore whether urine proteome can reflect the difference between obese and normal weight people.

Methods

Urine samples from obese and normal weight people were collected and identified by non-label quantitative proteomics using high performance liquid chromatography tandem mass spectrometry (LC-MS/MS). The difference proteins of urine proteome between obese and normal weight people were screened for protein function and biological pathway analysis. The urine proteome of obese individuals was compared with that of normal weight people, and the common differential proteins were counted to analyze the protein function and biological pathways. Reported biomarkers of obesity were searched in the urine proteome of obese individuals.

Results

38 different proteins can be identified in the urine proteome of obese people compared with normal weight people, some of which have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. 8 common differential proteins in the urine proteome of obese individuals and normal weight people, among which some proteins have been reported to be related to metabolism and obesity, and the biological processes of differential proteins are also related to metabolism and other processes. Among the differential proteins in the urine proteome of obese individuals compared with the normal weight people, the reported obesity biomarkers can be matched.

Conclusions

The urine proteome can distinguish the obese people from the normal weight people, and the differential proteins in the urine proteome have key proteins that are known to be related to obesity and metabolism, and the biological processes of differential proteins also related biological processes such as nutrition and metabolism. Urine proteome has the potential to explore the pathogenesis of obesity and provide personalized treatment.
Dynamic cytoophidia duringDrosophilalate oogenesis
Authors: Zhang Shi-Qi , Liu Ji-Long
Published: January 2024

CTP synthase (CTPS) catalyzes the final step of de novo synthesis of CTP. CTPS was first discovered to form filamentous structures termed cytoophidia inDrosophilaovarian cells. Subsequent studies have shown that cytoophidia are widely present in cells of three life domains. In theDrosophilaovary model, our previous studies mainly focused on the early and middle stages, with less involvement in the later stages. In this work, we focus on the later stages of female germline cells inDrosophila. We use live cell imaging to capture the continuous dynamics of cytoophidia in Stages 10-12. We notice the heterogeneity of cytoophidia in the two types of germline cells (nurse cells and oocytes), manifested in significant differences in morphology, distribution, and dynamics. Surprisingly, we also find that neighboring nurse cells in the same egg chamber exhibit multiple dynamic patterns of cytoophidia over time. Our observation provides a systematic understanding of the dynamics of cytoophidia duringDrosophilalate oogenesis.
WITHDRAWN: BBB recovery after stroke by self-replenishing E-pericytes transdifferentiated from local endothelial cells
Authors: Li Tingbo , Tu Jiaqi , Gao Qingzhu , Li Xuzhao , Zhu Zhu , Jin Yuxiao , Zhang Yiyi , Xie Jiongfang , Zhu Peiran , Zhao Bingrui , Jia Jie-Min
Published: January 2024

Withdrawal statement

The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2023/570712. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/2023.12.07.570712.
Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics
Authors: Wang James , Seo Jai Woong , Kare Aris J. , Schneider Martin , Tumbale Spencer K. , Wu Bo , Raie Marina N. , Pandrala Mallesh , Iagaru Andrei , Brunsing Ryan L. , Charville Gregory W. , Park Walter G. , Ferrara Katherine W.
Published: January 2024

We apply spatial transcriptomics and proteomics to select pancreatic cancer surface receptor targets for molecular imaging and theranostics using an approach that can be applied to many cancers. Selected cancer surfaceome epithelial markers were spatially correlated and provided specific cancer localization, whereas the spatial correlation between cancer markers and immune- cell or fibroblast markers was low. While molecular imaging of cancer-associated fibroblasts and integrins has been proposed for pancreatic cancer, our data point to the tight junction protein claudin-4 as a theranostic target. Claudin-4 expression increased ∼16 fold in cancer as compared with normal pancreas, and the tight junction localization conferred low background for imaging in normal tissue. We developed a peptide-based molecular imaging agent targeted to claudin-4 with accumulation to ∼25% injected activity per cc (IA/cc) in metastases and ∼18% IA/cc in tumors. Our work motivates a new approach for data-driven selection of molecular targets.
Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration
Authors: Obata Tomohiro , Mizoguchi Satoshi , Greaney Allison M. , Adams Taylor , Yuan Yifan , Edelstein Sophie , Leiby Katherine L. , Rivero Rachel , Wang Nuoya , Kim Haram , Yang Junchen , Schupp Jonas C. , Stitelman David , Tsuchiya Tomoshi , Levchenko Andre , Kaminski Naftali , Niklason Laura E. , Raredon Micha Sam Brickman
Published: January 2024

Tissue homeostasis is controlled by cellular circuits governing cell growth, organization, and differentation. In this study we identify previously undescribed cell-to-cell communication that mediates information flow from mechanosensitive pleural mesothelial cells to alveolar-resident stem-like tuft cells in the lung. We find mesothelial cells to express a combination of mechanotransduction genes and lineage-restricted ligands which makes them uniquely capable of responding to tissue tension and producing paracrine cues acting on parenchymal populations. In parallel, we describe a large population of stem-like alveolar tuft cells that express the endodermal stem cell markers Sox9 and Lgr5 and a receptor profile making them uniquely sensitive to cues produced by pleural Mesothelium. We hypothesized that crosstalk from mesothelial cells to alveolar tuft cells might be central to the regulation of post-penumonectomy lung regeneration. Following pneumonectomy, we find that mesothelial cells display radically altered phenotype and ligand expression, in a pattern that closely tracks with parenchymal epithelial proliferation and alveolar tissue growth. During an initial pro-inflammatory stage of tissue regeneration, Mesothelium promotes epithelial proliferation via WNT ligand secretion, orchestrates an increase in microvascular permeability, and encourages immune extravasation via chemokine secretion. This stage is followed first by a tissue remodeling period, characterized by angiogenesis and BMP pathway sensitization, and then a stable return to homeostasis. Coupled with key changes in parenchymal structure and matrix production, the cumulative effect is a now larger organ including newly-grown, fully-functional tissue parenchyma. This study paints Mesothelial cells as a key orchestrating cell type that defines the boundary of the lung and exerts critical influence over the tissue-level signaling state regulating resident stem cell populations. The cellular circuits unearthed here suggest that human lung regeneration might be inducible through well-engineered approaches targeting the induction of tissue regeneration and safe return to homeostasis.
AXOLOTL: an accurate method for detecting aberrant gene expression in rare diseases using coexpression constraints
Authors: Leng Fei , Liu Yang , Zhang Jianzhao , Shen Yansheng , Liu Xiangfu , Wang Yi , Xu Wenjian
Published: January 2024

Background

The assessment of aberrant transcription events in patients with rare diseases holds promise for significantly enhancing the prioritization of causative genes, a practice already widely employed in clinical settings to increase diagnostic accuracy. Nevertheless, the entangled correlation between genes presents a substantial challenge for accurate identification of causal genes in clinical diagnostic scenarios. Currently, none of the existing methods are capable of effectively modeling gene correlation.

Methods

We propose a novel unsupervised method, AXOLOTL, to identify aberrant gene expression events in an RNA expression matrix. AXOLOTL effectively addresses biological confounders by incorporating coexpression constraints.

Results

We demonstrated the superior performance of AXOLOTL on representative RNA-seq datasets, including those from the GTEx healthy cohort, mitochondrial disease cohort and Collagen VI-related dystrophy cohort. Furthermore, we applied AXOLOTL to real case studies and demonstrated its ability to accurately identify aberrant gene expression and facilitate the prioritization of pathogenic variants.
Data-driven system matrix manipulation enabling fast functional imaging and intra-image nonrigid motion correction in tomography
Authors: Hu Peng , Tong Xin , Lin Li , Wang Lihong V.
Published: January 2024

Tomographic imaging modalities are described by large system matrices. Sparse sampling and tissue motion degrade system matrix and image quality. Various existing techniques improve the image quality without correcting the system matrices. Here, we compress the system matrices to improve computational efficiency (e.g., 42 times) using singular value decomposition and fast Fourier transform. Enabled by the efficiency, we propose (1) fast sparsely sampling functional imaging by incorporating a densely sampled prior image into the system matrix, which maintains the critical linearity while mitigating artifacts and (2) intra-image nonrigid motion correction by incorporating the motion as subdomain translations into the system matrix and reconstructing the translations together with the image iteratively. We demonstrate the methods in 3D photoacoustic computed tomography with significantly improved image qualities and clarify their applicability to X-ray CT and MRI or other types of imperfections due to the similarities in system matrices.
Neural precursor cells rescue symptoms of Rett syndrome by activation of the Interferon γ pathway
Authors: Frasca Angelisa , Miramondi Federica , Butti Erica , Indrigo Marzia , Arenas Maria Balbontin , Postogna Francesca M. , Piffer Arianna , Bedogni Francesco , Pizzamiglio Lara , Cambria Clara , Borello Ugo , Antonucci Flavia , Martino Gianvito , Landsberger Nicoletta
Published: January 2024

The beneficial effects of Neural Precursor Cell (NPC) transplantation in several neurological disorders are well established and they are generally mediated by the secretion of immunomodulatory and neurotrophic molecules. We therefore investigated whether Rett syndrome (RTT), that represents the first cause of severe intellectual disability in girls, might benefit from an NPC-based therapy.

Usingin vitroco-cultures, we demonstrate that, by sensing the pathological context, NPC-secreted factors induce the recovery of morphological and synaptic defects typical ofMecp2deficient neurons.In vivo,we prove that intracerebral transplantation of NPCs in RTT mice significantly ameliorates neurological functions. To uncover the molecular mechanisms underpinning the mediated benefic effects, we analysed the transcriptional profile of the cerebellum of transplanted animals, disclosing the possible involvement of the Interferon γ (IFNγ) pathway. Accordingly, we report the capacity of IFNγ to rescue synaptic defects, as well as motor and cognitive alterations inMecp2deficient models, thereby suggesting this molecular pathway as a potential therapeutic target for RTT.
Interaction BetweenYersinia pestisAil Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin
Authors: Vasseur Laurine , Barbault Florent , Monari Antonio
Published: January 2024

Yersinia pestis, the causative agent of plague, is capable to evade human immune system response by recruiting the plasma circulating vitronectin proteins, which acts as a shield and avoids its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding fromY. pestisouter membrane. By using all atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents.

TOC ABSTRACT
Turmeric shortens lifespan in houseflies
Authors: Laurie Sophie , Ainslie Leah , Mitchell Sharon , Morimoto Juliano
Published: January 2024

Climate change poses a significant threat to food security and global public health with the increasing likelihood of insect pest outbreaks. Alternative ways to control insect populations, preferably using environmental-friendly compounds, are needed. Turmeric has been suggested as a natural insecticide with toxicity properties in some insect groups. However, empirical evidence of the effects turmeric – and their interaction with other ecological factors such as diet – on insect survival has been limited. Here, we tested the effects of turmeric and its interactions with diets differing in protein source in the common housefly,Musca domestica. We found that turmeric shortened lifespan independent of diet and sex. Females in turmeric diets were heavier at death, which was likely driven by a combination of relatively lower rates of body mass loss during their lifetime and a higher percentage of water content at death. Each sex responded differently to the protein source in the diet, and the magnitude of the difference in lifespan between sexes were greatest in diets in which protein source was hydrolysed yeast; individuals from both sexes lived longest in sucrose-milk diets and shortest in diets with hydrolysed yeast. There was no evidence of an interaction between turmeric and diet, suggesting that the toxicity effects are independent of protein source in the diet. Given the seemingly opposing effects of turmeric in insects and mammals being uncovered in the literature, our findings provide further evidence in support of turmeric as a potential natural insecticide.
A BODIPY-naphtholimine-BF2dyad for precision photodynamic therapy, targeting and dual imaging of endoplasmic reticulum and lipid droplets in cancer
Authors: Chauhan Nitish , Koli Mrunesh , Ghosh Rajib , Majumdar Ananda Guha , Ghosh Ayan , Ghanty Tapan Kumar , Mula Soumyaditya , Patro Birija Sankar
Published: January 2024

Currently effective therapeutic modalities for pancreatic ductal adenocarcinoma (PDAC) is not available, leading to gloomy prognosis and ~6-months median patient survival. Recent advances showed the promise of photodynamic therapy (PDT) for PDAC patients. Next generation photosensitizers (PS) are based on “organelle-targeted-PDT” and provides new paradigm in the field of precision medicines to address the current challenge for treating PDAC. In this investigation, we have constructed a novel PS, named asNbB, for precise targeting of endoplasmic reticulum (ER) and lipid droplets (LD) in PDAC, as malignant PDAC cells are heavily relying on ER for hormone synthesis. Our live cell imaging and fluorescence recovery after photobleaching (FRAP) experiments revealed thatNbBis instantly targeted to ER and LD and show simultaneous dual fluorescence colour due to polar and non-polar milieu of ER and LD. Interestingly, the same molecule generates triplet state and singlet oxygen efficiently and cause robust ER stress and apoptosis in two different PDAC cells in the presence of light. Together, we present, for the first time, a potential next generation precision medicine for ER-LD organelle specific imaging and PDT of pancreatic cancer.
High-Resolution Molecular-Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)
Authors: Delobelle Quentin , Inizan Théo Jaffrelot , Adjoua Olivier , Lagardère Louis , Célerse Frédéric , Maréchal Vincent , Piquemal Jean-Philip
Published: January 2024

Glucose metabolism plays a pivotal role in physiological processes and cancer growth. The final stage of glycolysis, converting phosphoenolpyruvate (PEP) into pyruvate, is catalyzed by the pyruvate kinase (PK) enzyme. Whereas PKM1 is mainly expressed in cells with high energy requirements, PKM2 is preferentially expressed in proliferating cells, including tumor cells. Structural analysis of PKM1 and PKM2 is essential to design new molecules with antitumoral activity. To understand their structural dynamics, we performed extensive high-resolution molecular dynamics (MD) simulations using adaptive sampling techniques coupled to the polarizable AMOEBA force field. Performing more than 6 µs of simulation, we considered all oligomerization states of PKM2 and propose structural insights for PKM1 to further study the PKM2-specific allostery. We focused on key sites including the active site and the natural substrate Fructose Bi-Phosphate (FBP) fixation pocket. Additionally, we present the first MD simulation of biologically active PKM1 and uncover important similarities with its PKM2 counterpart bound to FBP. We also analysed TEPP-46’s fixation, a pharmacological activator binding a different pocket, on PKM2 and highlighted the structural differences and similarities compared to PKM2 bound to FBP. Finally, we determined potential new cryptic pockets specific to PKM2 for drug targeting.

Entry for the Table of Contents

Producing more than 6µs of cumulated simulation time with the AMOEBA polarizable force field, we determined key structural properties of the PKM2 (catalytic, FBP and TEPP) and PKM1 enzymes binding sites to determine new cryptic pockets for further antiviral/antitumoral drug design.
Genetic Toolbox forPhotorhabdusandXenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling
Authors: Rill Alexander , Zhao Lei , Bode Helge B.
Published: January 2024

Background

Bacteria of the genusPhotorhabdusandXenorhabdusare motile, Gram-negative bacteria that live in symbiosis with entomopathogenic nematodes. Due to their complex life cycle, they produce a large number of specialized metabolites (natural products) encoded in biosynthetic gene clusters (BGC). Genetic tools for this genus have been rare and applicable to only a few strains. In the past, several tools have been developed for the activation of BGCs and the deletion of individual genes. However, these often have limited efficiency or are time consuming. Among the limitations, it is essential to have versatile expression systems and genome editing tools that could facilitate the practical work.

Results

In the present study, we developed several expression vectors and a CRISPR-Cpf1 genome editing vector for genetic manipulations inPhotorhabdusandXenorhabdususing SEVA plasmids. The SEVA collection is based on modular vectors that allow exchangeability of different elements (e.g. origin of replication and antibiotic selection markers with the ability to insert desired sequences for different end applications. Initially, we tested different SEVA vectors containing the broad host range origins and three different resistance genes for kanamycin, gentamycin and chloramphenicol, respectively. We demonstrated that these vectors are replicative not only in well-known representatives, e.g.Photorhabdus laumondiiTTO1, but also in other rarely described strains likeXenorhabdussp. TS4. For our CRISPR/Cpf1-based system, we used the pSEVA231 backbone to delete not only small genes but also large parts of BGCs. Furthermore, we were able to activate and refactor BGCs to obtain high production titers of high value compounds such as safracin B, a semisynthetic precursor for the anti-cancer drug ET-743.

Conclusions

The results of this study provide new inducible expression vectors and a CRISPR/CPf1 encoding vector all based on the SEVA (Standard European Vector Architecture) collection, which can improve genetic manipulation and genome editing processes inPhotorhabdusandXenorhabdus.
Interactions between saccades and smooth pursuit eye movements in marmosets
Authors: Pattadkal Jagruti J. , Barr Carrie , Priebe Nicholas J.
Published: January 2024

Animals use a combination of eye movements to track moving objects. These different eye movements need to be coordinated for successful tracking, requiring interactions between the systems involved. Here, we study the interaction between the saccadic and smooth pursuit eye movement systems in marmosets. Using a single target pursuit task, we show that saccades cause an enhancement in pursuit following a saccade. Using a two-target pursuit task, we show that this enhancement in pursuit is selective towards the motion of the target selected by the saccade, irrespective of any biases in pursuit prior to the saccade. These experiments highlight the similarities in the functioning of saccadic and smooth pursuit eye movement systems across primates.

SIGNIFICANCE STATEMENT

We study the coordination between the smooth-pursuit and saccadic eye movement systems in marmosets using single and multiple object motions. We find that saccade to a target increases pursuit velocity towards the target. If multiple objects are visible, saccade choice makes pursuit more selective towards the saccade target. Our results show that coordination between different eye movement systems to successfully track moving objects is similar between marmosets and primates.
MUM, a maternal unknown message, inhibits early establishment of the medio-lateral axis in the embryo of the kelpSaccharina latissima
Authors: Boscq Samuel , Billoud Bernard , Theodorou Ioannis , Joemmanbaks Tanweer , Charrier Bénédicte
Published: January 2024

Brown algae are multicellular photosynthetic organisms that have evolved independently of plants and other algae. Apart from studies on the polarisation of theFucuszygote in the 1990s, little is known about the mechanisms controlling the embryogenesis of these organisms. Here, we studied the determinism of embryogenesis in the kelpSaccharina latissima,focusing on the formation of its body axes. This alga initially develops an oblong embryo formed of a cell monolayer, which subsequently thickens; growth axes are then established in temporally distinct stages, starting with the formation of a dominant apico-basal axis. Our experiments focused on the role of the stalk, an empty cell that retains the embryo attached to the maternal tissue, in the development of the growth axes in mature embryos. In response to the removal of the stalk, the embryos developed as a monolayered disc rather than an elongated blade, demonstrating that attachment to the stalk inhibits the formation of the medio-lateral axis at the onset of embryogenesis. In addition, compared with embryos attached to the stalk, the cells of detached embryos were smaller and displayed an altered shape. The topology of the tissue was also disrupted, as cells had a higher number of cell neighbours. Observation of cell division patterns just after removal of the stalk showed that the stalk represses longitudinal cell divisions, thereby reinforcing the establishment of the main apico-basal axis. This unique quantitative study of brown algal embryogenesis revealed that, in kelps, a signal from maternal tissue (MUM for maternal unknown message) is necessary for the establishment of growth axes at the onset of embryogenesis and of the organisation of growing embryonic tissues. In addition, we discovered that, although the stalk persists for several weeks until the embryo reaches at least 500 cells, MUM is emitted in the first 4 days after fertilisation only, before the embryo reaches the 8-cell stage. Finally, transplantation experiments indicated that MUM does not diffuse in seawater, but requires contact between the embryo and the stalk. The potential chemical or mechanical nature of MUM is discussed.
Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430modifications
Authors: Polêto Marcelo D. , Allen Kylie D. , Lemkul Justin A.
Published: January 2024

Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrapyrrole derivative. Additionally, a few modified versions of F430have been discovered, including the 172-methylthio-F430(mt-F430) that functions with ANME-1 MCR. This study employs molecular dynamics (MD) simulations to unravel the intricacies of the active-site dynamics of MCR fromMethanosarcina acetivoransand ANME-1 when bound to the canonical F430compared to 172-thioether coenzyme F430variants and substrates for methane formation. Overall, our simulations indicate that each MCR active site is optimized for a given version of F430and support the importance of the Gln to Val substitution in accommodating the 172methylthio modification. Notably, modifications in the 172position disrupt the canonical coordination among cofactors inM. acetivoransMCR, implicating structural perturbations, but evidence of active site reorganization to maintain substrate positions suggest that the modified F430s could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the significance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active-site dynamics, the enzyme’s organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics. This work not only advances our comprehension of MCR functionality but also provides a foundation for future investigations employing sophisticated models to capture the complex electronic properties of MCR active sites quantitatively.