bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D osteocyte lacunar morphometry of human bone biopsies with high resolution microCT: from monoclonal gammopathy to newly diagnosed multiple myeloma
Authors: Moreno-Jiménez Inés , Heinig Sharen , Heras Unai , Maichl Daniela Simone , Strifler Susanne , Leich Ellen , Blouin Stéphane , Fratzl Peter , Fratzl-Zelman Nadja , Jundt Franziska , Cipitria Amaia 
Published: July 2023

AbstractOsteocytes are mechanosensitive, bone-embedded cells which are connected via dendrites in a lacuno-canalicular network and regulate bone resorption and formation balance. Alterations in osteocyte lacunar volume, shape and density have been identified in conditions of aging, osteoporosis and osteolytic bone metastasis, indicating patterns of impaired bone remodeling, osteolysis and disease progression. Osteolytic bone disease is a hallmark of the hematologic malignancy multiple myeloma (MM), in which monoclonal plasma cells in the bone marrow disrupt the bone homeostasis and induce excessive resorption at local and distant sites. Qualitative and quantitative changes in the 3D osteocyte lacunar morphometry have not yet been evaluated in MM, nor in the precursor conditions monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). In this study, we characterized the osteocyte lacunar morphology in trabecular bone of the iliac crest at the ultrastructural level using high resolution microCT in human bone biopsy samples of three MGUS, two SMM and six newly diagnosed MM. In MGUS, SMM and MM we found a trend for lower lacunar density and a shift towards larger lacunae with disease progression (higher 50% cutoff of the lacunar volume cumulative distribution) in the small osteocyte lacunae 20-900 μm3range compared to control samples. In the larger lacunae 900-3000 μm3range, we detected significantly higher lacunar density and microporosity in the MM group compared to the MGUS/SMM group. Regarding the shape distribution, the MGUS/SMM group showed a trend for flatter, more elongated and anisotropic osteocyte lacunae compared to the control group. Altogether, our findings suggest that osteocytes in human MM bone disease undergo changes in their lacunae density, volume and shape, which could be an indicator for osteolysis and disease progression. Future studies are needed to understand whether alterations of the lacunae architecture affect the mechanoresponsiveness of osteocytes and ultimately bone adaptation and fracture resistance in MM and its precursors conditions.
Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images
Authors: Daviet Benoit , Fournier Christian , Cabrera-Bosquet Llorenç , Simonneau Thierry , Cafier Maxence , Romieu Charles 
Published: July 2023

AbstractBackgroundGrapevine berries undergo asynchronous growth and ripening dynamics within the same bunch. Due to the lack of efficient methods to perform sequential non-destructive measurements on a representative number of individual berries, the genetic and environmental origins of this heterogeneity, as well as its impacts on both vine yield and wine quality, remain nearly unknown. To address these limitations, we propose to track the growth and coloration kinetics of individual berries on time-lapse images of grapevine bunches.ResultFirst, a deep-learning approach is used to detect berries with at least 50±10% of visible contours, and infer the shape they would have in the absence of occlusions. Second, a tracking algorithm was developed to assign a common label to shapes representing the same berry along the time-series. Training and validation of the methods were performed on challenging image datasets acquired in a robotised high-throughput phenotyping platform. Berries were detected on various genotypes with a F1-score of 91.8%, and segmented with a mean absolute error of 4.1% on their area. Tracking allowed to label and retrieve the temporal identity of more than half of the segmented berries, with an accuracy of 98.1%. This method was used to extract individual growth and colour kinetics of various berries from the same bunch, allowing us to propose the first statistically relevant analysis of berry ripening kinetics, with a time resolution lower than one day.ConclusionsWe successfully developed a fully-automated open-source method to detect, segment and track overlapping berries in time-series of grapevine bunch images. This makes it possible to quantify fine aspects of individual berry development, and to characterise the asynchrony within the bunch. The interest of such analysis was illustrated here for one genotype, but the method has the potential to be applied in a high throughput phenotyping context. This opens the way for revisiting the genetic and environmental variations of the ripening dynamics. Such variations could be considered both from the point of view of fruit development and the phenological structure of the population, which would constitute a paradigm shift.
Single-molecule digital sizing of proteins in solution
Authors: Krainer Georg , Jacquat Raphael P.B. , Schneider Matthias M. , Welsh Timothy J. , Fan Jieyuan , Peter Quentin A. E. , Andrzejewska Ewa A. , Šneiderienė Greta , Czekalska Magdalena A. , Ausserwoeger Hannes , Chai Lin , Arter William E. , Saar Kadi L. , Herling Therese W. , Franzmann Titus M. , Kosmoliaptsis Vasilis , Alberti Simon , Hartl F.-Ulrich , Lee Steven F. , Knowles Tuomas P.J. 
Published: July 2023

AbstractProteins constitute the molecular machinery of life and exert their biological function by interacting with other proteins, as well as by assembling into biomolecular complexes and higher order structures. Characterizing the sizes, interactions, and assembly states of proteins is thus key for understanding the normal functional behavior of proteins and for elucidating aberrant processes and interactions that can lead to dysfunction and disease. However, the physical characterization of proteins has remained a challenging problem due to the inherent compositional heterogeneity of protein mixtures as well as the polydisperse nature of protein complexes. Here, we address this challenge by demonstrating measurements of molecular diffusivity of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. The approach, termed single-molecule microfluidic diffusional sizing (smMDS), allows individual molecules to be counted directly, that is, in a digital manner, to enable calibration-free single-molecule diffusional-sizing-based monitoring of protein hydrodynamic radii even within heterogenous multicomponent mixtures. Applying smMDS to a variety of protein systems, we show that the high sensitivity provided by smMDS enables ultrasensitive sizing of proteins down to the femtomolar concentration range. We further demonstrate the applicability of the approach towards affinity profiling of protein interactions at the single-molecule level and illustrate the potential of smMDS in resolving different assembly states of high- and low-molecular weight protein oligomers. Furthermore, we highlight the digital nature of the detection process by sizing multiple protein species within complex aggregation mixtures. Finally, we apply the approach to characterize nanoscale clusters of a phase separating protein system. Taken together, smMDS constitutes a versatile approach for digital, in-solution characterization of the sizes, interactions, and assembly states of proteins. We anticipate that smMDS will facilitate the discovery of new biomolecular mechanisms of proteins and will find broad applicability in the analysis of protein complexes in the biological, biophysical, and biomedical sciences, and beyond.
Mechanisms of Innate Immune Injury in Arrhythmogenic Cardiomyopathy
Authors: Chelko Stephen P. , Penna Vinay , Engel Morgan , Landim-Vieira Maicon , Cannon Elisa N. , Lavine Kory , Saffitz Jeffrey E. 
Published: July 2023

ABSTRACTInhibition of nuclear factor kappa-B (NFκB) signaling prevents disease inDsg2mut/mutmice, a model of arrhythmogenic cardiomyopathy (ACM). Moreover, NFκB is activated in ACM patient-derived iPSC-cardiac myocytes under basal conditionsin vitro. Here, we used genetic approaches and sequencing studies to define the relative pathogenic roles of immune signaling in cardiac myocytes vs. inflammatory cells inDsg2mut/mutmice. We found that NFκB signaling in cardiac myocytes drives myocardial injury, contractile dysfunction, and arrhythmias inDsg2mut/mutmice. It does this by mobilizing cells expressing C-C motif chemokine receptor-2 (CCR2+ cells) to the heart, where they mediate myocardial injury and arrhythmias. Contractile dysfunction inDsg2mut/mutmice is caused both by loss of heart muscle and negative inotropic effects of inflammation in viable muscle. Single nucleus RNA sequencing and cellular indexing of transcriptomes and epitomes (CITE-seq) studies revealed marked pro-inflammatory changes in gene expression and the cellular landscape in hearts ofDsg2mut/mutmice involving cardiac myocytes, fibroblasts and CCR2+ cells. Changes in gene expression in cardiac myocytes and fibroblasts inDsg2mut/mutmice were modulated by actions of CCR2+ cells. These results highlight complex mechanisms of immune injury and regulatory crosstalk between cardiac myocytes, inflammatory cells, and fibroblasts in the pathogenesis of ACM.BRIEF SUMMARYWe have uncovered a therapeutically targetable innate immune mechanism regulating myocardial injury and cardiac function in a clinically relevant mouse model of Arrhythmogenic Cardiomyopathy (ACM).
PP2A inhibition instructs spliceosome phosphorylation to create splicing vulnerability in colon adenocarcinoma
Authors: Dias Matheus H. , Liudkovska Vladyslava , Bleijerveld Onno B. , Velds Arno , Bernards René , Cieśla Maciej 
Published: July 2023

SUMMARYProtein phosphatase 2A (PP2A) is a versatile enzyme affecting many aspects of cellular physiology. However, it remains unclear which of the cellular processes are most perturbed upon PP2A inhibition and how these perturbations could be exploited therapeutically. We report an unanticipated sensitivity of the splicing machinery to phosphorylation changes in response to PP2A inhibition by LB-100 in colorectal adenocarcinoma. We observe enrichment for differentially phosphorylated sites within cancer-critical splicing nodes of U2 snRNP, SRSF and hnRNP proteins. Altered phosphorylation endows LB-100-treated colorectal adenocarcinoma cells with differential splicing patterns. In PP2A-inhibited cells, over 1000 events of exon skipping and intron retention affect regulators of genomic integrity. Finally, LB-100-evoked alternative splicing is predicted to be a source of neoantigens that can improve cancer treatment responses to immune modulators. Our findings provide a potential explanation for the pre-clinical and clinical observations that PP2A inhibition sensitizes cancer cells to immune checkpoint blockade and genotoxic agents.
BNIP3-mediated mitophagy boosts the competitive dominant growth of lenvatinib resistant cells via reprogramming energy metabolism in HCC
Authors: Wang Sikai , Cheng Hongxia , Li Miaomiao , Wu Haoran , Zhang Shanshan , Gao Dongmei , Huang Yilan , Guo Kun 
Published: July 2023

AbstractAlthough increasing studies has demonstrated that cell competition widely involved in the growth and homeostasis of multicellular organisms is closely linked to tumorigenesis and development, the mechanistic contributions to the association between tumor cell competition-driven heterogeneity and drug resistance remains ill-defined. In our study, lenvitinib-resistant hepatocellular carcinoma (HCC) cells display obviously competitive growth dominance against sensitive cells through reprogramming energy metabolism. Mechanistically, when BCL2 interacting protein3 (BNIP3) overexpression activates mitophagy activity in lenvatinib-resistant HCC cells, energy imbalance signal caused by reduced mitochondrial oxidative phosphorylation levels provokes the phosphorylation of AMP-activated protein kinase (AMPK) sensor; subsequently, enabled AMPK specifically targets enolase 2 (ENO2) to enhance glycolysis and eventually promots the competitive capacity and dominant growth. Of note, BNIP3 deficiency shows certain inhibition of cell competition outcome. Our findings emphasize a vital role for BNIP3-AMPK-ENO2 signaling in maintaining the competitive outcome of lenvitinib-resistant HCC cells via regulating energy metabolism; meanwhile this work recognaizes BNIP3 as a promising target to overcome HCC drug resistance.
Teosinte Pollen Driveguides maize diversification and domestication by RNAi
Authors: Berube Benjamin , Ernst Evan , Cahn Jonathan , Roche Benjamin , Alves Cristiane de Santis , Lynn Jason , Scheben Armin , Siepel Adam , Ross-Ibarra Jeffrey , Kermicle Jerry , Martienssen Rob 
Published: July 2023

AbstractMeiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describeTeosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosintemexicana(Zea mays ssp. mexicana), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin inmexicanadepend onDicer-Like 2 (Dcl2)and targetTeosinte Drive Responder 1 (Tdr1),which encodes a lipase required for pollen viability.Dcl2,Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression ofmexicanainto early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion inmexicanaspans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosintemexicanareveals correlated patterns of admixture among unlinked genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids.Teosinte Pollen Drivelikely played a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of “self” small RNAs in the germlines of plants and animals.
Modular and integrative activity reporters enhance biochemical studies in the yeast ER
Authors: Martinusen Samantha G , Slaton Ethan W , Nelson Sage E , Pulgar Marian A , Besu Julia T , Simas Cassidy F , Denard Carl A 
Published: July 2023

AbstractThe yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.
Host obesity impacts genetic variation in influenza A viral populations
Authors: Knoll Marissa , Honce Rebekah , Meliopoulos Victoria , Schultz-Cherry Stacey , Ghedin Elodie , Gresham David 
Published: July 2023

AbstractObesity is a chronic health condition characterized by excess adiposity leading to a systemic increase in inflammation and dysregulation of metabolic hormones and immune cell populations. Obesity is well established as a risk factor for many noncommunicable diseases; however, its consequences for infectious disease are poorly understood. Influenza A virus (IAV) is a highly infectious pathogen responsible for seasonal and pandemic influenza. Host risk factors, including compromised immunity and pre-existing health conditions, can contribute to increased infection susceptibility and disease severity. During viral replication in a host, the negative sense single stranded RNA genome of IAV accumulates genetic diversity that may have important consequences for viral evolution and transmission. Here, we investigated the impact of host obesity on IAV genetic variation using a diet induced obesity ferret model. We infected obese and lean male ferrets with the A/Hong Kong/1073/1999 (H9N2) IAV strain. Using a co-caging study design, we investigated the maintenance, generation, and transmission of intrahost IAV genetic variation by sequencing viral genomic RNA obtained from nasal wash samples over multiple days of infection. We found evidence for an enhanced role of positive selection acting onde novomutations in obese hosts that led to nonsynonymous changes that rose to high frequency. In addition, we identified numerous cases of recurrent low-frequency mutations throughout the genome that were specific to obese hosts. Despite these obese-specific variants, overall viral genetic diversity did not differ significantly between obese and lean hosts. This is likely due to the high supply rate ofde novovariation and common evolutionary adaptations to the ferret host regardless of obesity status, which we show are mediated by variation in the hemagglutinin (HA) and polymerase genes (PB2 and PB1). As with single nucleotide variants, we identified a class of defective viral genomes (DVGs) that were found uniquely in either obese or lean hosts, but overall DVG diversity and dynamics did not differ between the two groups. Our study provides the first insight into the consequences of host obesity on viral genetic diversity and adaptation, suggesting that host factors associated with obesity alter the selective environment experienced by a viral population, thereby impacting the spectrum of genetic variation.
Evolution of Evolvability In Rapidly Adapting Populations
Authors: Ferrare James T. , Good Benjamin H. 
Published: July 2023

AbstractMutations can alter the short-term fitness of an organism, as well as the rates and benefits of future mutations. While numerous examples of these evolvability modifiers have been observed in rapidly adapting microbial populations, existing theory struggles to predict when they will be favored by natural selection. Here, we develop a mathematical framework for predicting the fates of genetic variants that modify the rates and benefits of future mutations in linked genomic regions. We derive analytical expressions showing how the fixation probabilities of these variants depend on the size of the population and the diversity of competing mutations. We find that competition between linked mutations can dramatically enhance selection for modifiers that increase the benefits of future mutations, even when they impose a strong direct cost on fitness. However, we also find that modest direct benefits can be sufficient to drive evolutionary dead-ends to fixation. Our results suggest that subtle differences in evolvability could play an important role in shaping the long-term success of genetic variants in rapidly evolving microbial populations.
A dual Purkinje cell rate and synchrony code sculpts reach kinematics
Authors: Nashef Abdulraheem , Spindle Michael S. , Calame Dylan J. , Person Abigail L. 
Published: July 2023

AbstractCerebellar Purkinje cells (PCs) encode movement kinematics in their population firing rates. Firing rate suppression is hypothesized to disinhibit neurons in the cerebellar nuclei, promoting adaptive movement adjustments. Debates persist, however, about whether a second disinhibitory mechanism, PC simple spike synchrony, is a relevant population code. We addressed this question by relating PC rate and synchrony patterns recorded with high density probes, to mouse reach kinematics. We discovered behavioral correlates of PC synchrony that align with a known causal relationship between activity in cerebellar output. Reach deceleration was positively correlated with both Purkinje firing rate decreases and synchrony, consistent with both mechanisms disinhibiting target neurons, which are known to adjust reach velocity. Direct tests of the contribution of each coding scheme to nuclear firing using dynamic clamp, combining physiological rate and synchrony patterns ex vivo, confirmed that physiological levels of PC simple spike synchrony are highly facilitatory for nuclear firing. These findings suggest that PC firing rate and synchrony collaborate to exert fine control of movement.
Gene expression variation underlying tissue-specific responses to copper stress inDrosophila melanogaster
Authors: Everman Elizabeth R , Macdonald Stuart J 
Published: July 2023

AbstractCopper is one of a handful of biologically necessary heavy metals that is also a common environmental pollutant. Under normal conditions, copper ions are required for many key physiological processes. However, in excess, copper quickly results in cell and tissue damage that can range in severity from temporary injury to permanent neurological damage. Because of its biological relevance, and because many conserved copper-responsive genes also respond to other non-essential heavy metal pollutants, copper resistance inDrosophila melanogasteris a useful model system with which to investigate the genetic control of the response to heavy metal stress. Because heavy metal toxicity has the potential to differently impact specific tissues, we genetically characterized the control of the gene expression response to copper stress in a tissue- specific manner in this study. We assessed the copper stress response in head and gut tissue of 96 inbred strains from theDrosophilaSynthetic Population Resource (DSPR) using a combination of differential expression analysis and expression quantitative trait locus (eQTL) mapping. Differential expression analysis revealed clear patterns of tissue-specific expression, primarily driven by a more pronounced gene expression response in gut tissue. eQTL mapping of gene expression under control and copper conditions as well as for the change in gene expression following copper exposure (copper response eQTL) revealed hundreds of genes with tissue- specific localcis-eQTL and many distanttrans-eQTL. eQTL associated withMtnA,Mdr49,Mdr50, andSod3exhibited genotype by environment effects on gene expression under copper stress, illuminating several tissue- and treatment-specific patterns of gene expression control. Together, our data build a nuanced description of the roles and interactions between allelic and expression variation in copper-responsive genes, provide valuable insight into the genomic architecture of susceptibility to metal toxicity, and highlight many candidate genes for future functional characterization.