bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation
Authors: Caspi Itamar , Meir Moran , Nun Nadav Ben , Yakhini Uri , Stern Adi , Ram Yoav 
Published: January 2023

AbstractRNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full length genomes of an evolving virus population. Our approach employsneural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial-passaging experiment with the MS2 bacteriophage. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem-loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over and under-expression of lysis that leads to this pattern of epistasis. To summarize, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors, and used it to reveal features governing MS2 evolution.
Mapping the auditory space ofCulex pipiensfemale mosquito in 3D
Authors: Lapshin Dmitry. N. , Vorontsov Dmitry. D. 
Published: January 2023

AbstractThe task of directional hearing faces most of the animals that possess ears. They approach this task in different ways, but the common trait is the usage of the binaural cues to find the direction to the source of sound. In insects, the task is further complicated by their small size and, hence, minute temporal and level differences between two ears. A way to overcome this problem is to receive the particle velocity component of sound rather than the pressure, as the former naturally involves directionality. However, even in this case, one ear is not enough for directional hearing: a single symmetric flagellar particle velocity receiver cannot discriminate between the two opposite directions along the vector of the sound wave. Insects that use flagellar auditory organs, and mosquitoes in particular, possess a pair of receivers, which presumes the usage of binaural hearing. Its mechanisms are expected to be significantly different from the ones typical for the pressure receivers. However, the directionality of flagellar auditory organs has received little attention. Here we measured the in-flight orientation of a female mosquito antennae and obtained detailed physiological mapping of the Johnston’s organ directionality at the level of individual sensory units. By combining these data, we provided a three-dimensional model of the mosquito’s auditory space. The natural orientation of the antennae together with angular distribution of sensory units in each of the Johnston’s organs was found to be optimal for binaural hearing focused primarily in front of, above and below a flying mosquito.
Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis?
Authors: Nogueira Marilise , Enfissi Eugenia M. A. , Price Elliott J. , Menard Guillaume N. , Venter Eudri , Eastmond Peter J. , Bar Einat , Lewinsohn Efraim , Fraser Paul D. 
Published: January 2023

SUMMARYPlants are sessile and therefore have developed an extraordinary capacity to adapt to external signals. Here, the focus is on the plasticity of the plant cell to respond to new intracellular cues. Ketocarotenoids are high-value natural red pigments with potent antioxidant activity. In the present study, system level analyses have revealed that the heterologous biosynthesis of ketocarotenoids in tomato initiated a series of cellular and metabolic mechanisms to cope with the formation of metabolites that are non-endogenous to the plant. The broad multilevel changes were linked to, among others, (i) the remodelling of the plastidial membrane, where the synthesis and storage of ketocarotenoids occurs, (ii) the recruiting of core metabolic pathways for the generation of metabolite precursors and energy, and (iii) redox control. The role of the metabolites as regulators of cellular processes shown here, reinforces their pivotal role suggested in the remodelled “central dogma” concept.
Native Triboelectric Nanogenerator Ion Mobility-Mass Spectrometry of Egg Proteins Relevant to Objects of Cultural Heritage at Picoliter and Nanomolar Quantities
Authors: Vallejo Daniel D. , Popowich Aleksandra , Arslanoglu Julie , Tokarski Caroline , Fernández Facundo M. 
Published: January 2023

ABSTRACTNative mass spectrometry (nMS) has found widespread success in measuring native-like protein structures in the gas-phase and, when combined with ion mobility (IM), is capable of measuring protein collision cross sections (CCS) and stabilities. These methods are well validated, but often rely on samples that are abundantly available through repeated recombinant protein expression. For ultra-precious and irreplaceable samples from cultural heritage objects, protein content can be far below the micromolar and microliter levels required for robust protein experiments, a major hurdle in characterizing protein higher order structure and degradation mechanisms. Combining triboelectric nanogenerators (TENG) and IM-MS enables measuring protein size and stability rapidly from ultra-small sample quantities. Here, TENG IM-MS is implemented with standard and sub-micron emitters to characterize proteins relevant to cultural heritage objects, and demonstrates native structures can be obtained even at nanomolar concentrations and picoliter quantities.
Phosphatidylinositol-4-phosphate signaling regulates dense granule biogenesis and exocytosis inToxoplasma gondii
Authors: Arabiotorre Angela , Formanowicz Megan , Bankaitis Vytas A. , Grabon Aby 
Published: January 2023

ABSTRACTPhosphoinositide metabolism defines the foundation of a major signaling pathway that is conserved throughout the eukaryotic kingdom. The 4-OH phosphorylated phosphoinositides such as phosphatidylinositol-4-phosphate (PtdIns4P) and phosphatidylinositol-4,5-bisphosphate are particularly important molecules as these execute intrinsically essential activities required for the viability of all eukaryotic cells studied thus far. Using intracellular tachyzoites of the apicomplexan parasiteToxoplasma gondiias model for assessing primordial roles for PtdIns4P signaling, we demonstrate the presence of PtdIns4P pools in Golgi/trans-Golgi (TGN) system and in post-TGN compartments of the parasite. Moreover, we show that deficits in PtdIns4P signaling result in structural perturbation of compartments that house dense granule cargo with accompanying deficits in dense granule exocytosis. Taken together, the data report a direct role for PtdIns4P in dense granule biogenesis and exocytosis. The data further indicate that the biogenic pathway for secretion-competent dense granule formation inT. gondiiis more complex than simple budding of fully matured dense granules from the TGN.
A comparative analysis of microglial inducible Cre lines
Authors: Faust Travis E. , Feinberg Philip A. , O’Connor Ciara , Kawaguchi Riki , Chan Andrew , Strasburger Haley , Masuda Takahiro , Amann Lukas , Knobeloch Klaus-Peter , Prinz Marco , Schaefer Anne , Schafer Dorothy P. 
Published: January 2023

SummaryCre/LoxP technology has revolutionized genetic studies and allowed for spatial and temporal control of gene expression in specific cell types. The field of microglial biology has particularly benefited from this technology as microglia have historically been difficult to transduce with virus or electroporation methods for gene delivery. Here, we interrogate four of the most widely available microglial inducible Cre lines. We demonstrate varying degrees of recombination efficiency and spontaneous recombination, depending on the Cre line and loxP distance. We also establish best practice guidelines and protocols to measure recombination efficiency in microglia, which could be extended to other cell types. There is increasing evidence that microglia are key regulators of neural circuit structure and function. Microglia are also major drivers of a broad range of neurological diseases. Thus, reliable manipulation of their function in vivo is of utmost importance. Identifying caveats and benefits of all tools and implementing the most rigorous protocols are crucial to the growth of the field of microglial biology and the development of microglia-based therapeutics.
A multi-scale clutch model for adhesion complex mechanics
Authors: Venturini C. , Sáez P. 
Published: January 2023

AbstractCell-matrix adhesion is a central mechanical function to a large number of phenomena in physiology and disease, including morphogenesis, wound healing and tumor cell invasion. Today, how single cells responds to different extracellular cues has been comprehensibly studied. However, how the mechanical behavior of the main individual molecules that form an adhesion complex cooperatively respond to force within the adhesion complex has not been addressed. This is a key aspect in cell adhesion because how these cell adhesion molecules respond to force determines not only cell-matrix behavior but, ultimately, cell function. To answer this question, we develop a multi-scale computational model for adhesion complexes mechanics. Based on the classical clutch hypothesis, we model individual adhesion chains made of a contractile actin network, a talin rod and an integrin molecule that binds at individual adhesion sites on the extracellular matrix. We explore several scenarios of integrins dynamics and analyze the effects of diverse extracellular matrices on the behavior of the adhesion molecules and on the whole adhesion complex. Our results explains how every single component of the adhesion chain mechanically responds to the contractile actomyosin force and show how they control the tractions forces exerted by the cell on the extracellular space. Importantly, our computational results are in agreement with previous experimental data both at the molecular and cell level. Our multi-scale clutch model presents a step forward not only to further understand adhesion complexes mechanics but also to, e.g., engineer better biomimetic materials, repair biological tissues or arrest invasive tumor migration.Author summaryCell-matrix adhesions are directly implicated in key biological processes such as tissue development, regeneration and tumor cell invasion. These cell functions are determined by how adhesion complexes feel and respond to mechanical forces. Still, how forces are transmitted through the individual cell adhesion molecules that integrate the adhesion complex is poorly understood. To address this issue, we develop a multi-scale clutch model for adhesion complexes where individual adhesion chains, made of integrin and talin molecules, are considered within classical clutch models. This approach provides a rich mechanosensivity insight of how the mechanics of cell adhesion works. It allows to integrate accurate biophysical models of individual adhesion molecules into whole adhesion complex models. Our multi-scale clutch approach allows to extend our current knowledge of adhesion complexes for physiology and disease, e.g., the regeneration of biological tissues or arrest invasive tumor migration, and for engineering better biomimetic materials.
Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into genetic variants in candidate genes for disease resistance
Authors: Das Ashutosh , Gupta Mukta Das , Shaha Mishuk , Lima Arjuman , Miazi Omar Faruk , Das Goutam Buddha 
Published: January 2023

AbstractDetection of genome-wide genetic variation is one of the primary goals in bovine genomics. Genomes of several cattle breeds have been sequenced so far to understand the genetic variation associated with important phenotypes. Red Chittagong Cattle (RCC) is a locally adopted and disease-resistant indicine cattle breed in Bangladesh. In this study, we describe the first genome sequence of the RCC breed and in silico analyses of identified functional variants. Deep sequencing of a RCC bull genome on the NanoBall sequencing platform generated approximately 110 Gb paired-end data, resulting in 31X of genome coverage. Quality filtering retained 360,711,803 paired-end reads. Of the filtered reads, 99.8% were mapped to the bovine reference genome (ARSUCD1.2). A total of 17. 8 million Single nucleotide variants (SNVs) and 2.1 insertions and deletions (INDELs) were identified in the RCC genome. Ts/Tv ratio was computed and found to be 2.21. In total, 332 4621 variants were novel compared with dbSNP data (NCBI dbSNP bovine build 150). Functional annotation identified 54961 SNVs exonic regions, 63.75% of which were synonymous, whereas 30.42% were non-synonymous changes. The percentage of coding INDELs was 0.25% (Frameshift deletion 0.19% and Frameshift insertion 0.06%). We identified 120 variants in 26 candidates for five diseases-foot and mouth disease (FMD), Mastitis, Parasite, para-tuberculosis, and tick. Of the 120 variants, 50 were non-synonymous / frameshift (NS/FS), while 70 were synonymous/non-frameshift (SS/NFS). The identified catalog of genomic variants in RCC may establish a paradigm for cattle research in Bangladesh by filling the void and providing a database for genome-wide variation for future functional studies in RCC.
Humanized CD36 mouse model supports the preclinical evaluation of therapeutic candidates targeting CD36
Authors: Xie Xiulong , Niu Zhenlan , Wang Linlin , Zhou Xiaofei , Yu Xingyan , Jing Hongyan , Yang Yi 
Published: January 2023

AbstractCD36 (also known as scavenger receptor B2) is a multifunctional receptor that mediates lipid uptake, advanced oxidation protein products, and immunological recognition, and has roles in lipid accumulation, apoptosis, as well as in metastatic colonization in cancer. CD36 is involved in tumor immunity, metastatic invasion, and therapy resistance through various molecular mechanisms. Targeting CD36 has emerged as an effective strategy for tumor immunotherapy. In this study, we have successfully generated a novel CD36 humanized mouse strain where the sequences encoding the extracellular domains of the mouseCd36gene were replaced with the corresponding human sequences. The results showed that CD36 humanized mice expressed only human CD36, and the proportion of each lymphocyte was not significantly changed compared with wild-type mice. Furthermore, CD36 monoclonal antibody could significantly inhibit tumor growth after treatment. Therefore, the CD36 humanized mice provided a validated preclinical mouse model for the evaluation of tumor immunotherapy targeting CD36.
Direct visualization of emergent metastatic features within anex vivomodel of the tumor microenvironment
Authors: Anandi Libi , Garcia Jeremy , Ros Manon , Janská Libuše , Liu Josephine , Carmona-Fontaine Carlos 
Published: January 2023

ABSTRACTMetabolic conditions such as hypoxia, nutrient starvation, and media acidification, together with interactions with stromal cells are critical drivers of metastasis. Since these conditions arise deep within tumor tissues with poor access to the bloodstream, the observation of nascent metastasesin vivois exceedingly challenging. On the other hand, conventional cell culture studies cannot capture the complex nature of metastatic processes. We thus designed and implemented anex vivomodel of the tumor microenvironment to study the emergence of metastatic features in tumor cells in their native 3-dimensional (3D) context. In this system, named 3MIC, tumor cells spontaneously create ischemic-like conditions, and it allows the direct visualization of tumor-stroma interactions with high spatial and temporal resolution. We studied how 3D tumor spheroids evolve in the 3MIC when cultured under different metabolic environments and in the presence or absence of stromal cells. Consistent with previous experimental and clinical data, we show that ischemic environments increase cell migration and invasion. Importantly, the 3MIC allowed us to directly observe the emergence of these pro-metastatic features with single-cell resolution allowing us to track how changes in tumor motility were modulated by macrophages and endothelial cells. With these tools, we determined that the acidification of the extracellular media was more important than hypoxia in the induction of pro-metastatic tumor features. We also illustrate how the 3MIC can be used to test the effects of anti-metastatic drugs on cells experiencing different metabolic conditions. Overall, the 3MIC allows us to directly observe the emergence of metastatic tumor features in a physiologically relevant model of the tumor microenvironment. This simple and cost-effective system can dissect the complexity of the tumor microenvironment to test perturbations that may prevent tumors from becoming metastatic.
FastRecomb: Fast inference of genetic recombination rates in biobank scale data
Authors: Naseri Ardalan , Yue William , Zhang Shaojie , Zhi Degui 
Published: January 2023

AbstractWhile rates of recombination events across the genome (genetic maps) are fundamental to genetic research, the majority of current studies only use one standard map. There is evidence suggesting population differences in genetic maps, and thus estimating population-specific maps are of interest. While the recent availability of biobank-scale data offers such opportunities, current methods are not efficient at leveraging very large sample sizes. The most accurate methods are still linkage-disequilibrium (LD)-based methods that are only tractable for a few hundred samples. In this work, we propose a fast and memory-efficient method for estimating genetic maps from population genotyping data. Our method, FastRecomb, leverages the efficient positional Burrows-Wheeler transform (PBWT) data structure for counting IBD segment boundaries as potential recombination events. We used PBWT blocks to avoid redundant counting of pairwise matches. Moreover, we used a panel smoothing technique to reduce the noise from errors and recent mutations. Using simulation, we found that FastRecomb achieves state-of-the-art performance at 10k resolution, in terms of correlation coefficients between the estimated map and the ground truth. This is mainly due to the fact that FastRecomb can effectively take advantage of large panels comprising more than hundreds of thousands of haplotypes. At the same time, other methods lack the efficiency to handle such data. We believe further refinement of FastRecomb would deliver more accurate genetic maps for the genetics community.
DNA-origami line-actants control domain organisation and fission in synthetic membranes
Authors: Rubio-Sánchez Roger , Mognetti Bortolo Matteo , Cicuta Pietro , Di Michele Lorenzo 
Published: January 2023

AbstractCells can precisely program the shape and lateral organisation of their membranes using protein machinery. Aiming to replicate a comparable degree of control, here we introduce DNA-Origami Line-Actants (DOLAs) as synthetic analogues of membrane-sculpting proteins. DOLAs are designed to selectively accumulate at the line-interface between co-existing domains in phase-separated lipid membranes, modulating the tendency of the domains to coalesce. With experiments and coarse-grained simulations, we demonstrate that DOLAs can reversibly stabilise two-dimensional analogues of Pickering emulsions on synthetic giant liposomes, enabling dynamic programming of membrane lateral organisation. The control afforded over membrane structure by DOLAs extends to three-dimensional morphology, as exemplified by a proof-of-concept synthetic pathway leading to vesicle fission. With DOLAs we lay the foundations for mimicking, in synthetic systems, some of the critical membrane-hosted functionalities of biological cells, including signalling, trafficking, sensing, and division.
Multifaceted roles of a light-responsive factor LhWRKY44 in promoting anthocyanin accumulation in Asiatic hybrid lilies (Liliumspp.)
Authors: Bi Mengmeng , Liang Rui , Qu Yuxiao , Wang Jiawen , Cao Yuwei , Liu Xin , He Guoren , Zhang Wenliang , Yang Yue , Tang Yuchao , Yang Panpan , Xu Leifeng , Ming Jun 
Published: January 2023

AbstractThe coloration of Asiatic hybrid lily results mostly from anthocyanin accumulation in flowers. Although anthocyanin accumulation-related genes and MBW complexes are well studied, the transcriptional regulation of WRKY transcription factors involved in anthocyanin accumulation remains poorly understood.Here, we identified a lily WRKY protein, LhWRKY44, whose expression is highly expressed downstream of LhHY5 by light and positively correlated with anthocyanin accumulation.LhWRKY44overexpression enhanced anthocyanin accumulation and silencing decreased anthocyanin accumulation in flowers. As a trans-acting regulator, LhWRKY44 activited the anthocyanin biosynthesis pathway-related genesPALandF3Hby binding to the their promoters. And the encoded TF also participates in anthocyanin transport and targets the intracellular anthocyanin transport proteinGSTpromoters. Additionally, a novel dual activity of LhWRKY44 and LhMYBSPLATTER regulatory module, with LhWRKY44 binds to the promoter ofLhMYBSPLATTERand interacts with LhMYBSPLATTER, strongly enhanced the interaction of LhMYBSPLATTER and LhbHLH2, indirectly enhancingDFR, UFGTandGSTexpression targeted by LhMYBSPLATTER. These results show a regulatory mode for light-induced anthocyanin accumulation enhancement by LhWRKY44 in lily, expanding our understanding of the complex transcriptional regulatory hierarchy modulating anthocyanin accumulation.