bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Lactate in the Regulation of Transcriptional Activity of Breast Cancer-Related Genes and Epithelial-to-Mesenchymal Transition Proteins: A Compassion of MCF7 and MDA-MB-231 Cancer Cell Lines
Authors: San-Millan Inigo , Martinez Janel L. , Pickard Shivaun Lueke , Yu Hui , Hirsch Fred R. , Rivard Christopher J. , Brooks George A. 
Published: March 2023

ABSTRACTThe Warburg Effect is characterized by accelerated glycolytic metabolism and lactate production and under fully aerobic conditions is a hallmark of cancer cells. Recently, we have demonstrated the role of endogenous, glucose-derived lactate as an oncometabolite which regulates gene expression in the estrogen receptor positive (ER+) MCF7 cell line cultivated in glucose media. Presently, with the addition of a triple negative breast cancer (TNBC) cell line, MDA-MB-231, we further confirm the effect of lactate on gene expression patterns and extend results to include lactate effects on protein expression. As well, we report effects of lactate on the expression of E-cadherin and vimentin, proteins associated with epithelial-to-mesenchymal transition (EMT). Endogenous lactate regulates the expression of multiple genes involved in carcinogenesis. In MCF7 cells, lactate increased the expression of EGFR, VEGF, HIF-1a, KRAS, MIF, mTOR, PIK3CA, TP53, and CDK4 as well as decreased the expression of ATM, BRCA1, BRCA2, E2F1, MET, MYC, and RAF mainly after 48h of exposure. On the other hand, in the MDA-MB-231 cell line, lactate increased the expressions of PIK3CA, VEGF, EGFR, mTOR, HIF-1α, ATM, E2F1, TP53 and decreased the expressions of BRCA1, BRCA2, CDK4, CDK6, MET, MIF, MYC, and RAF after 48h of exposure. In response to endogenous lactate, changes in protein expression of representative genes corroborated changes in mRNA expressions. Finally, lactate exposure decreased E-cadherin protein expression in MCF7 cells and increased vimentin expression in MDA-MB-231 cells. Further-more, by genetically silencing LDHA in MCF7 cells, we show suppression of protein expression of EGFR and HIF-1α, while full protein expression occurred under glucose and glucose + exogenous lactate exposure. Hence, endogenous, glucose-derived lactate, and not glucose, elicited changes in gene and protein expression levels.In this study, we demonstrate that endogenous lactate produced under aerobic conditions (Warburg Effect) elicits important changes in gene and protein expression in both ER+ and TNBC cell lines. The widespread regulation of multiple genes by lactate and involves those involved in carcinogenesis including DNA repair, cell growth, proliferation, angiogenesis, and metastasis. Furthermore, lactate affected the expression of two relevant EMT biomarkers, E-cadherin and vimentin, which could contribute to the complex process of EMT and a shift towards a more mesenchymal phenotype in the two cancer cell lines studied.
THE FACTOR STRUCTURE OF THE PATIENT HEALTH QUESTIONNAIRE-9 IN STROKE: A COMPARISON WITH A NON-STROKE POPULATION
Authors: Blake J.J. , Munyombwe T. , Fischer F. , Quinn T.J , Van der Feltz-Cornelis C.M. , De Man-van Ginkel J.M. , Santos I.S. , Jeon H.J. , Köhler S. , Schram M.T. , Stehouwer C.D.A. , Wang Jianli , Levin-Aspenson H.F. , Whooley M.A. , Hobfoll S.E , Patten S.B. , Simning A. , Gracey F. , Broomfield N.M. 
Published: March 2023

ABSTRACTBackgroundThere are concerns that the measurement of depression by the Patient Health Questionnaire-9 (PHQ-9), a self-report screening questionnaire, is biased by comorbid stroke sequelae. We, therefore, aimed to investigate these concerns in stroke, benchmarked against a non-stroke comparison sample, using factor analysis.MethodsThe secondary data sample constituted 787 stroke and 12,016 non-stroke participants, in a cross-sectional design. A subsample of 1,574 non-stroke participants was selected via propensity score matching. Dimensionality was assessed by comparing fit statistics of one-factor, two-factor, and bi-factor models. Between-group differences in factor structure were identified using measurement invariance.ResultsA two-factor model, consisting of somatic and cognitive-affect factors, had a superior fit to a unidimensional model (CFI = .984 versus CFI =.974, p<.001), but the high correlation between the factors indicated unidimensionality (r = .866). Configural invariance between stroke and non-stroke was supported (CFI = .983, RMSEA = .080), as were invariant thresholds (p = .092) and loadings (p = .103) for all items. Strong invariance was violated (p < .001, ΔCFI = -.003), indicating non-invariant item intercepts. Partially invariant models indicated responsibility of the tiredness and appetite intercepts, and latent depression severity was significantly overestimated in stroke, relative to the general population, using a summed score approach (Cohen’s d=.434).ConclusionsThe findings suggest that the PHQ-9 measures a single latent factor in stroke. However, the presence of non-invariant intercepts means that PHQ-9 total scores may be disproportionately influenced by fatigue in post-stroke vs. non-stroke patients and that total scores are incomparable between groups.
Non-linearity in motor unit velocity twitch dynamics: Implications for ultrafast ultrasound source separation
Authors: Lubel Emma , Sgambato Bruno Grandi , Rohlén Robin , Ibáñez Jaime , Barsakcioglu Deren Y , Tang Meng-Xing , Farina Dario 
Published: March 2023

AbstractUltrasound (US) muscle image series can be used for peripheral human-machine interfacing based on global features, or even on the decomposition of US images into the contributions of individual motor units (MUs). With respect to state-of-the-art surface electromyography (sEMG), US provides higher spatial resolution and deeper penetration depth. However, the accuracy of current methods for direct US decomposition, even at low forces, is relatively poor. These methods are based on linear mathematical models of the contributions of MUs to US images. Here, we test the hypothesis of linearity by comparing the average velocity twitch profiles of MUs when varying the number of other concomitantly active units. We observe that the velocity twitch profile has a decreasing peak-to-peak amplitude when tracking the same target motor unit at progressively increasing contraction force levels, thus with an increasing number of concomitantly active units. This observation indicates non-linear factors in the generation model. Furthermore, we directly studied the impact of one MU on a neighboring MU, finding that the effect of one source on the other is not symmetrical and may be related to unit size. We conclude that a linear approximation is limiting the decomposition methods to decompose full velocity twitch trains from velocity images, highlighting the need for more advanced models and methods for US decomposition than those currently employed.
xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data
Authors: Gong Jing , Hao Minsheng , Zeng Xin , Liu Chiming , Ma Jianzhu , Cheng Xingyi , Wang Taifeng , Zhang Xuegong , Song Le 
Published: March 2023

AbstractThe advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions in single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for human with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGene, which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we increase the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell classification, perturb-seq effect prediction, and drug combination prediction.
Structural development of the human fetal kidney: new stages and cellular dynamics in nephrogenesis
Authors: Schumacher Anika , Nguyen Tri Q. , Broekhuizen Roel , van Griensven Martijn , LaPointe Vanessa 
Published: March 2023

AbstractResearch on the ultrastructural development of the kidney is limited, and research on rodent kidneys prevails. Yet, large differences between rodent and human nephrogenesis exist and therefore translation between species is not desirable. At the same time, there is an increasing demand for human research, in addition to assessing the potential of novel therapies such as renal organoids. We therefore generated an interactive atlas of large transmission electron microscopy tile scans of first trimester human kidneys, specifically Carnegie stage 20 until post-conceptional week 12. Analysis identified key ultrastructural features of proximal and distal progenitor cells such as cell shape, microvilli and luminal budding in the renal vesicle. Regarding glomerular development, we identified a new W-shaped body stage and three distinct sub-stages of the well-known capillary loop stage. Chromatin organization, nuclear shape and location were used to describe tubule cell identity and maturity, indicating a specific order of tubular maturation. The greatest congruence with adult tissue was seen in proximal tubules and the least in distal tubules. Finally, cytoplasmic glycogen depositions in collecting duct cells, which are absent in adult tissue, were found to be an early feature distinguishing distal tubules from collecting ducts as well as differentiating cortical from medullary collecting ducts. The findings of this research provide new fundamental insights for researchers who aim to understand and recreate kidney development.
A model for the gradual evolution of dioecy and heterogametic sex determination
Authors: Lesaffre Thomas , Pannell John R. , Mullon Charles 
Published: March 2023

AbstractIn plants with separate sexes, the development of an individual as male or female is controlled by a dominant allele at a sex-determining locus - the fundamental basis of XY and ZW systems. The many independent transitions from hermaphroditism to dioecy that have taken place in flowering plants must therefore often have entailed the emergence of such a locus. One proposition is that this evolution occurs in two steps, with the initial invasion of a male-sterility mutation at one locus followed by mutations causing female sterility at a second closely linked locus. Here, we show how dioecy with heterogametic sex determination can also emerge in a gradual adaptive process, involving the co-evolution of resource allocation to different sexual functions jointly with its genetic architecture. Our model reveals that whether an XY or a ZW system evolves depends on the mating system of the ancestral hermaphrodites as well as the trade-off they face between allocation to male and female functions. In particular, the evolution of dioecy in response to selection to avoid selfing and inbreeding depression favours the emergence of XY systems, which characterise the vast majority of dioecious flowering plants. Selection favouring female specialisation also favours XY over ZW sex determination. Taken together, our results throw new light on the possible origins of dioecy from hermaphroditism by revealing a hitherto unrecognised link between the ecology and economics of sex allocation and the genetic basis of sex determination.
Massive genome reduction occurred prior to the origin of coral algal symbionts
Authors: Shah Sarah , Dougan Katherine E. , Chen Yibi , Lo Rosalyn , Laird Gemma , Fortuin Michael D. A. , Rai Subash K. , Murigneux Valentine , Bellantuono Anthony J. , Rodriguez-Lanetty Mauricio , Bhattacharya Debashish , Chan Cheong Xin 
Published: March 2023

AbstractDinoflagellates in the Family Symbiodiniaceae (Order Suessiales) are diverse, predominantly symbiotic lineages that associate with taxa such as corals and jellyfish. Their ancestor is believed to have been free-living, and the establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution. Among Symbiodiniaceae taxa, the genusEffreniumis an early diverging, free-living lineage that is phylogenetically positioned between two robustly supported groups of genera within which symbiotic taxa have emerged. The lack of symbiogenesis inEffreniumsuggests that the ancestral features of Symbiodiniaceae may have been retained in this lineage. Here we presentde novoassembled genomes and associated transcriptome data from three isolates ofEffrenium voratum. We compared theEffreniumgenomes (1.2-1.9 Gbp in size) and gene features with those of 16 Symbiodiniaceae taxa and other outgroup dinoflagellates. Surprisingly, we find that genome reduction, which is often associated with a symbiotic lifestyle, predates the origin of Symbiodiniaceae. We postulate that adaptation to an extreme habitat (e.g., as inPolarella glacialis) or life in oligotrophic conditions resulted in the Suessiales ancestor having a haploid genome size<2Gbp, which was retained (or reduced) among all extant algae in this lineage. Nonetheless, our data reveal that the free-living lifestyle distinguishesEffreniumfrom symbiotic Symbiodiniaceae vis-à-vis their longer introns, more-extensive mRNA editing, fewer (∼30%) lineage-specific gene families, and lower (∼10%) level of pseudogenisation. These results demonstrate how genome reduction and the adaptation to symbiotic versus free-living lifestyles intersect, and have driven the diversification and genome evolution of Symbiodiniaceae.
Mid-cell migration of the chromosomal terminus is coupled to origin segregation inEscherichia coli
Authors: Sadhir Ismath , Murray Seán M. 
Published: March 2023

AbstractBacterial chromosomes are dynamically and spatially organised within cells. In slow-growingEscherichia coli, the chromosomal terminus is initially located at the new pole and must therefore migrate to midcell during replication to reproduce the same pattern in the daughter cells. Here, we use high-throughput time-lapse microscopy to quantify this transition, its timing and its relationship to chromosome segregation. We find that terminus centralisation is a rapid discrete event that occurs ~25 min after initial separation of duplicated origins and ~50 min before the onset of bulk nucleoid segregation but with substantial variation between cells. Despite this variation, its movement is tightly coincident with the completion of origin segregation, even in the absence of its linkage to the divisome, suggesting a coupling between these two events. Indeed, we find that terminus centralisation does not occur if origin segregation away from mid-cell is disrupted, which results in daughter cells having an inverted chromosome organisation. Overall, our study quantifies the choreography of origin-terminus positioning and identifies an unexplored connection between these loci, furthering our understanding of chromosome segregation in this bacterium.
Super-Resolved FRET and Co-Tracking in pMINFLUX
Authors: Cole Fiona , Zähringer Jonas , Bohlen Johann , Schröder Tim , Steiner Florian , Stefani Fernando D. , Tinnefeld Philip 
Published: March 2023

SummarySingle-molecule FRET (smFRET) is widely used to investigate dynamic (bio) molecular interactions taking place over distances of up to 10 nm. With the advent of recent super-resolution methods such as MINFLUX, MINSTED or RASTMIN, the spatiotemporal resolution of these techniques advanced towards the smFRET regime. While these methods do not suffer from the spatial restriction of FRET, they only visualize one emitter at a time, thus rendering fast dynamics of interactions out of reach. Here, we describe two approaches to overcome this limitation in pMINFLUX using its intrinsic fluorescence lifetime information. First, we combined pMINFLUX with smFRET. This enabled us to track a FRET donor fluorophore and simultaneously colocalize its FRET acceptor with nanometer precision. To extend co-localized tracking beyond the FRET range, we developed pMINFLUX lifetime multiplexing, a method to simultaneously track two fluorophores with similar spectral properties but distinct fluorescence lifetimes. We demonstrated its application on both static and dynamic DNA origami systems with a precision better than 2 nm. Within the FRET range, pMINFLUX lifetime multiplexing additionally uses a novel combined phasor-microtimegating approach. This paves the way for nanometer precise co-localized tracking for inter-dye distances between 4 nm and 100 nm, closing the resolution gap between smFRET and co-tracking.Graphical Abstract
Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor
Authors: Twentyman Joy , Khalifeh Anthony , Felton Abby L. , Emerman Michael , OhAinle Molly 
Published: March 2023

AbstractHuman immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral proteins, called restriction factors, constrain lentivirus replication and transmission is key to understanding the emergence of pandemic viruses like HIV-1. Human TRIM34, a paralogue of the well-characterized lentiviral restriction factor TRIM5α, was previously identified by our lab via CRISPR-Cas9 screening as a restriction factor of certain HIV and SIV capsids. Here, we show that diverse primate TRIM34 orthologues from non-human primates can restrict a range of Simian Immunodeficiency Virus (SIV) capsids including SIVAGM-SAB, SIVAGM-TANand SIVMACcapsids, which infect sabaeus monkeys, tantalus monkeys, and rhesus macaques, respectively. All primate TRIM34 orthologues tested, regardless of species of origin, were able to restrict this same subset of viral capsids. However, in all cases, this restriction also required the presence of TRIM5α. We demonstrate that TRIM5α is necessary, but not sufficient, for restriction of these capsids, and that human TRIM5α functionally interacts with TRIM34 from different species. Finally, we find that both the TRIM5α SPRY v1 loop and the TRIM34 SPRY domain are essential for TRIM34-mediated restriction. These data support a model in which TRIM34 is a broadly-conserved primate lentiviral restriction factor that acts in tandem with TRIM5α, such that together, these proteins can restrict capsids that neither can restrict alone.
Inferring CpG methylation signatures accumulated along human history from genetic variation catalogs
Authors: Si Yichen , Zöllner Sebastian 
Published: March 2023

AbstractUnderstanding the DNA methylation patterns in the human genome is a key step to decipher gene regulatory mechanisms and model mutation rate heterogeneity in the human genome. While methylation rates can be measured e.g. with bisulfite sequencing, such measures do not capture historical patterns. Here we present a new method, Methylation Hidden Markov Model (MHMM), to estimate the accumulated germline methylation signature in human population history leveraging two properties: (1) Mutation rates of cytosine to thymine transitions at methylated CG dinucleotides are orders of magnitude higher than that in the rest of the genome. (2) Methylation levels are locally correlated, so the allele frequencies of neighboring CpGs can be used jointly to estimate methylation status. We applied MHMM to allele frequencies from the TOPMed and the gnomAD genetic variation catalogs. Our estimates are consistent with whole genome bisulfite sequencing (WGBS) measured human germ cell methylation levels at 90% of CpG sites, but we also identified ∼ 442, 000 historically methylated CpG sites that could not be captured due to sample genetic variation, and inferred methylation status for ∼ 721, 000 CpG sites that were missing from WGBS. Hypo-methylated regions identified by combining our results with experimental measures are 1.7 times more likely to recover known active genomic regions than those identified by WGBS alone. Our estimated historical methylation status can be leveraged to enhance bioinformatic analysis of germline methylation such as annotating regulatory and inactivated genomic regions and provide insights in sequence evolution including predicting mutation constraint.
Clonal differences underlie variable responses to sequential and prolonged treatment
Authors: Schaff Dylan L. , Fasse Aria J. , White Phoebe E. , Vander Velde Robert J. , Shaffer Sydney M. 
Published: March 2023

SummaryCancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA-sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor.
The conserved protein CBA1 is required for vitamin B12uptake in different algal lineages
Authors: Sayer Andrew P. , Llavero-Pasquina Marcel , Geisler Katrin , Holzer Andre , Bunbury Freddy , Mendoza-Ochoa Gonzalo I. , Lawrence Andrew D. , Warren Martin J. , Mehrshahi Payam , Smith Alison G. 
Published: March 2023

AbstractMicroalgae play an essential role in global net primary productivity and global biogeochemical cycling, but despite their phototrophic lifestyle, over half of algal species depend on a supply of the corrinoid vitamin B12(cobalamin) for growth. This essential organic micronutrient is produced only by a subset of prokaryotic organisms, which implies that for algal species to use this compound, they must first acquire it from external sources. Previous studies have identified protein components involved in vitamin B12uptake in bacterial species and humans. However, little is known about how it is taken up in algae. Here, we demonstrate the essential role of a protein, CBA1 (for cobalamin acquisition protein 1), in B12uptake inPhaeodactylum tricornutum, using CRISPR-Cas9 to generate targeted knockouts, and inChlamydomonas reinhardtii, by insertional mutagenesis. In both cases, CBA1 knockout lines are no longer able to take up exogenous vitamin B12. Complementation of theC. reinhardtiimutants with the wildtypeCBA1gene restores B12uptake, and regulation ofCBA1expression via a riboswitch element can be used to control the phenotype. When visualised by confocal microscopy, a YFP-fusion withC. reinhardtiiCBA1 shows association with membranes. A bioinformatics analysis found that CBA1-like sequences are present in all the major eukaryotic phyla. Its presence is correlated with B12-dependent enzymes in many, although not all, taxa, suggesting CBA1 has a conserved role. Our results thus provide insight into the molecular basis of algal B12acquisition, a process that likely underpins many interactions in aquatic microbial communities.One sentence summaryKnockout mutants and physiological studies demonstrate that the CBA1 protein is essential for uptake of vitamin B12in bothChlamydomonas reinhardtiiand the unrelatedPhaeodactylum tricornutum.