bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy Body diseases
Authors: Feleke Rahel , Reynolds Regina H. , Smith Amy , Tilley Bension , Gagliano Taliun Sarah A. , Hardy John , Matthews Paul M. , Gentleman Steve , Owen David , Johnson Michael R. , Srivastava Prashant , Ryten Mina 
Published: April 2021

AbstractParkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular “window” of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.
Platelet HMGB1 in Platelet-Rich Plasma Promotes Tendon Wound Healing
Authors: Zhang Jianying , Li Feng , Augi Tyler , Williamson Kelly M. , Onishi Kentaro , Hogan MaCalus V. , Neal Matthew D. , Wang James H-C. 
Published: April 2021

AbstractPlatelet-rich plasma (PRP) is a widely used autologous treatment for tendon injuries in clinics, but clinical trials often produce conflicting results. Platelets (PLTs) are a major source of high mobility group box1 (HMGB1) that is gaining attention as a chemoattractant that can recruit stem cells to the wound area to enhance healing; however, the contribution of PLT HMGB1 in wounded tendon healing remains unexplored. This study investigated the effect of PLT HMGB1 within PRP to enhance healing in an acute patellar tendon injury model in PLT HMGB1 knockout (KO) mice and GFP mice. A window defect was created in the patellar tendons of both groups of mice, and wounds were treated with either saline, PRP isolated from PLT HMGB1 KO mice, or PRP isolated from GFP mice. Seven days post-treatment, animals were sacrificed and analyzed by gross inspection, histology, and immunostaining for characteristic signs of tendon healing and repair. Our results showed that in comparison to mice treated with PRP from PLT HMGB1-KO mice, wounds treated with PRP from GFP mice healed faster and exhibited a better organization in tendon structure. Mice treated with PRP from PLT HMGB1-KO mice produced tendon tissue with large premature wound areas and low cell densities. However, wounds of PLT HMGB1 KO mice showed better healing with PRP from HMGB1 KO mice compared to saline treatment. Moreover, wounds treated with PRP from GFP mice had increased extracellular HMGB1, decreased CD68, increased stem cell markers CD146 and CD73, and increased collagen III protein expression levels compared to those treated with PRP from PLT HMGB1 KO mice. Thus, PLT HMGB1 within PRP plays an important role in the healing of wounded tendon. Our findings also suggest that the efficacy of PRP treatment for tendon injuries in clinics may be affected by PLT HMGB1 within PRP preparations.
Identification of heat responsive genes in pea stipules and anthers through transcriptional profiling
Authors: Huang Shaoming , Kishore Krishna K. , Lachagari Reddy V.B. , Chakravartty Navajeet , Bueckert Rosalind A. , Tar’an Bunyamin , Warkentin Thomas D. 
Published: April 2021

AbstractField pea (Pisum sativumL.), a cool-season legume crop, is known for poor heat tolerance. Our previous work identified PR11-2 and PR11-90 as heat tolerant and susceptible lines in a recombinant inbred population. CDC Amarillo, a Canadian elite pea variety, was considered as another heat tolerant variety based on its similar field performance as PR11-2. This study aimed to characterize the differential transcription. Plants of these three varieties were stressed for 3h at 38°C prior to self-pollination, and RNAs from heat stressed anthers and stipules on the same flowering node were extracted and sequenced via the Illumina NovaSeq platform for the characterization of heat responsive genes.In silicoresults were further validated by qPCR assay. Differentially expressed genes (DEGs) were identified at log2 fold change, the three varieties shared 588 DEGs which were up-regulated and 220 genes which were down-regulated in anthers when subjected to heat treatment. In stipules, 879 DEGs (463/416 upregulation/downregulation) were consistent among varieties. The above heat-induced genes of the two plant organs were related to several biological processes i.e., response to heat, protein folding and DNA templated transcription. Ten gene ontology (GO) terms were over-represented in the consistently down-regulated DEGs of the two organs, and these terms were mainly related to cell wall macromolecule metabolism, lipid transport, lipid localization, and lipid metabolic processes. GO enrichment analysis on distinct DEGs of individual pea varieties suggested that heat affected biological processes were dynamic, and variety distinct responses provide insight into molecular mechanisms of heat-tolerance response. Several biological processes, e.g., cellular response to DNA damage stimulus in stipule, electron transport chain in anther that were only observed in heat induced PR11-2 and CDC Amarillo, and their relevance to field pea heat tolerance is worth further validation.
Nonlinear control of transcription through enhancer-promoter interactions
Authors: Zuin Jessica , Roth Gregory , Zhan Yinxiu , Cramard Julie , Redolfi Josef , Piskadlo Ewa , Mach Pia , Kryzhanovska Mariya , Tihanyi Gergely , Kohler Hubertus , Meister Peter , Smallwood Sebastien , Giorgetti Luca 
Published: April 2021

AbstractChromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs)1–4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. To address this question we use a novel assay to position an enhancer at a large number of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. Quantitative analysis of hundreds of cell lines reveal that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a non-linear relationship. Mathematical modeling and validation against experimental data further provide evidence that nonlinearity arises from transient enhancer-promoter interactions being memorized into longer-lived promoter states in individual cells, thus uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism for how enhancers control transcription across large genomic distances despite rarely meeting their target promoters, and for how TAD boundaries can block distal enhancers. We finally show that enhancer strength additionally determines not only absolute transcription levels, but also the sensitivity of a promoter to CTCF-mediated functional insulation. Our unbiased, systematic and quantitative measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.
Grandmaternal smoking during pregnancy is associated with differential DNA methylation in their grandchildren
Authors: Watkins Sarah Holmes , Iles-Caven Yasmin , Pembrey Marcus , Golding Jean , Suderman Matthew 
Published: April 2021

AbstractThe idea that information can be transmitted to subsequent generation(s) by epigenetic means has been studied for decades but remains controversial in humans. Epidemiological studies have established that grandparental exposures are associated with health outcomes in their grandchildren, often with sex-specific effects; however the mechanism of transmission is still unclear. We conducted Epigenome Wide Association Studies (EWAS) to test whether grandmaternal smoking during pregnancy is associated with altered DNA methylation (DNAm) in their adolescent grandchildren. We used data from a birth cohort, with discovery and replication datasets of 1225 and 708 individuals (respectively), aged 15-17 years, and tested replication in the same individuals at birth and 7 years. We show for the first time that DNAm at a small number of loci is associated with grandmaternal smoking in humans, and their locations in the genome suggest hypotheses of transmission. We observe and replicate sex-specific associations at two sites on the X chromosome, one located in an imprinting control region and both within transcription factor binding sites (TFBSs). In fact, we observe enrichment for TFBSs among the CpG sites with the strongest associations, suggesting that TFBSs may be a mechanism by which grandmaternal exposures influence offspring DNA methylation. There is limited evidence that these associations appear at earlier timepoints, so effects are not static throughout development. The implication of this work is that effects of smoking during pregnancy may induce DNAm changes in later generations and that these changes are often sex-specific, in line with observational associations.
Immune cell networks uncover candidate biomarkers of cancer immunotherapy response
Authors: Vo Duong H.T. , McGleave Gerard , Overton Ian M. 
Published: April 2021

AbstractTherapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types, and application to interrogate control of nivolumab response in advanced melanoma cohorts. Results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, ‘immune hot’ status, including T cell proliferation, confers good response to first line ICI therapy. Genes regulated in NK, dendritic and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights B cell genes as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.
RNA beacons for detecting the human testis-determining factor
Authors: Joseph Diego F. , Nakamoto Jose Alberto , Milón Pohl 
Published: April 2021

AbstractThe testis-determining factor (TDF) is an essential transcriptional protein for male differentiation in mammals, expressed along spermatids to early zygotes and, to some extent, in diverse cellular lines. In this study, we developed fluorescent biosensors capable of indicating the presence of TDF. We usedin vitroevolution techniques to produce RNA aptamers that bind the recombinantly expressed HMG-box, the DNA binding domain of TDF. Bioinformatic analysis alongin vitroevolution setup suggested two predominant aptamer clusters with distinctive motifs. The top ranked aptamer from each cluster, M1 and M2, showed specific binding to TDF. Aptamers were fluorescently modified as molecular beacons. Pre-steady-state kinetics indicated the beacons bind rapidly, within 50 seconds, yet M1 showed better signal to noise ratios than M2. Structural predictions of the aptamer interaction indicated that M1 is composed by three stem loops and likely interact with the HMG-box of TDF through the pocket formed by the three loops. Molecular modelling of M1 beacon shows that binding to TDF entails a conformational change of the sensor resulting in the measured fluorescence changes. To our knowledge, this is the first work describing an RNA beacon for detecting the essential TDF. Potential applications and advantages over alternative methods are provided and discussed.
The trade-off between pulse duration and power in optical excitation of midbrain dopamine neurons approximates Bloch’s law
Authors: Pallikaras Vasilios , Carter Francis , Martínez David Natanael Velázquez , Arvanitogiannis Andreas , Shizgal Peter 
Published: April 2021

AbstractBackgroundOptogenetic experiments reveal functional roles of specific neurons. However, such inferences have been restricted by widespread adoption of a fixed set of stimulation parameters. Broader exploration of the parameter space can deepen insight into the mapping between selective neural activity and behavior. In this way, characteristics of the activated neurons, such as temporal integration, can be inferred.ObjectiveTo determine whether an equal-energy principle accounts for the interaction of pulse duration and optical power in optogenetic excitation.MethodsSix male TH::Cre rats worked for optogenetic (ChannelRhodopsin-2) stimulation of Ventral Tegmental Area dopamine neurons. We used a within-subject design to describe the trade-off between pulse duration and optical power in determining reward seeking. Parameters were customized for each subject on the basis of behavioral effectiveness.ResultsWithin a useful range of powers (~12.6-31.6 mW) the product of optical power and pulse duration required to produce a given level of reward seeking was roughly constant. Such reciprocity is consistent with Bloch’s law, which posits an equal-energy principle of temporal summation over short durations in human vision. The trade-off between pulse duration and power broke down at higher powers.ConclusionsOptical power can be substituted for pulse duration to scale the region of neuronal excitation in behavioral optogenetic experiments. Power and duration can be adjusted reciprocally for brief durations and lower powers. The findings demonstrate the utility of within-subject and trade-off designs in optogenetics and of parameter adjustment based on functional endpoints instead of physical properties of the stimulation.HighlightsWe provide behaviorally derived intensity-duration curves for ChannelRhodopsin-2.Duration trades off almost perfectly with power within useful ranges.This trade-off breaks down at high optical powers.Pulse duration and optical power scale the area of neuronal excitation equivalently.Behaviorally derived trade-offs can reveal optogenetic excitation mechanisms.
Actin polymerization and crosslinking drive left-right asymmetry in single cell and cell collectives
Authors: Tee Y. H. , Goh W. J. , Yong X. , Ong H. T. , Hu J. , Tay I. Y. Y. , Shi S. , Jalal S. , Barnett S. F. H. , Kanchanawong P. , Huang W. , Yan J. , Thiagarajan V. , Bershadsky A. D. 
Published: April 2021

AbstractDeviations from mirror symmetry in the development of bilateral organisms are highly stereotypic and genetically predetermined, but their mechanisms are not sufficiently understood. At the cellular level, self-organization of the actin cytoskeleton results in chiral actin swirling, and cells in groups confined to micropatterns demonstrate chiral cell alignment. The relationship between individual and collective cell chirality is unclear, and molecular players involved remain essentially unidentified. Here, by screening major actin-associated proteins and deep-learning-based morphometric analysis of actin patterns, we found that knockdowns of specific actin polymerization regulators, such as mDia1, ARPC2, and cofilins 1&2, abolished chiral actin swirling, while depletion of profilin 1 and CapZβ, reversed its direction in an actin crosslinker α-actinin1-dependent manner. Analysis of these and other knockdowns and pharmacological treatments revealed a robust correlation between their effects on the chirality of individual cells and confined cell groups. Thus, actin-driven cell chirality may underlie tissue and organ asymmetry.One Sentence SummaryCell chirality determined by specific regulators of actin polymerization drives left-right asymmetry emergence in cell groups
Associations between MHC class II variation and phenotypic traits in a free-living sheep population
Authors: Huang Wei , Dicks Kara L , Ballingall Keith T , Johnston Susan E , Sparks Alexandra M , Watt Kathryn , Pilkington Jill G. , Pemberton Josephine M 
Published: April 2021

AbstractPathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC diversity and phenotypic traits which include direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five representative phenotypic traits measured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasiteTeladorsagia circumcinctain a free-living population of Soay sheep. We found no association between MHC class II variation and August weight or strongyle faecal egg count. We did however find associations between MHC class II variation and immunoglobulin levels which varied with age, isotype and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as body weight and highlight a useful role of MHC-antibody associations in examining selection on MHC genes.
Chronic Presence of Blood Circulating Anti-NMDAR1 Autoantibodies Impairs Cognitive Function in Mice
Authors: Yue William , Caldwell Sorana , Risbrough Victoria , Powell Susan , Zhou Xianjin 
Published: April 2021

AbstractHigh titers of anti-NMDAR1 autoantibodies in brain cause anti-NMDAR1 encephalitis that displays psychiatric symptoms of schizophrenia and/or other psychiatric disorders in addition to neurological symptoms. Low titers of anti-NMDAR1 autoantibodies are reported in the blood of a subset of the general human population and psychiatric patients. Since ∼0.1-0.2% of blood circulating antibodies cross the blood-brain barriers and antibodies can persist for months and years in human blood, it is important to investigate whether chronic presence of these blood circulating anti- NMDAR1 autoantibodies may impair human cognitive functions and contribute to the development of psychiatric symptoms. Here, we generated mice carrying low titers of anti-NMDAR1 autoantibodies in blood against a single antigenic epitope of mouse NMDAR1. Mice carrying the anti-NMDAR1 autoantibodies are healthy and display no differences in locomotion, sensorimotor gating, and contextual memory compared to controls. Chronic presence of the blood circulating anti-NMDAR1 autoantibodies, however, is sufficient to specifically impair T-maze spontaneous alternation in the integrity of blood-brain barriers across all 3 independent mouse cohorts, indicating a robust cognitive deficit in spatial working memory and/or novelty detection. Our studies implicate that chronic presence of low titers of blood circulating anti-NMDAR1 autoantibodies may impair cognitive functions in both the general healthy human population and psychiatric patients.
Expression of fatty acyl-CoA ligase drives one-pot de novo synthesis of membrane-bound vesicles in a cell free transcription-translation system
Authors: Bhattacharya Ahanjit , Cho Christy J. , Brea Roberto J. , Devaraj Neal K. 
Published: April 2021

AbstractDespite the central importance of lipid membranes in cellular organization, it is challenging to reconstitute their de novo formation from minimal chemical and biological elements. Here we describe a chemoenzymatic route to membrane-forming non-canonical phospholipids in which cysteine-modified lysolipids undergo spontaneous coupling with fatty acyl-CoA thioesters generated enzymatically by a fatty acyl-CoA ligase. Due to the high efficiency of the reaction, we were able to optimize phospholipid membrane formation in a cell-free transcription-translation (TX-TL) system. Combining DNA encoding for the fatty acyl-CoA ligase with suitable lipid precursors, enabled spontaneous one-pot de novo synthesis of membrane-bound vesicles. Non-canonical sphingolipid synthesis was also possible by using a cysteine-modified lysosphingomyelin as a precursor. When the sphingomyelin-interacting protein lysenin is co-expressed alongside the acyl CoA ligase, the in situ assembled membranes were spontaneously modified with protein. Our strategy of coupling gene expression with membrane lipid synthesis in a one-pot fashion could facilitate the generation of proteoliposomes and brings us closer to the bottom-up generation of synthetic cells using recombinant synthetic biology platforms.
Directed Evolution of Enzymes based on in vitro Programmable Self-Replication
Authors: Dramé-Maigné Adèle , Espada Rocío , McCallum Giselle , Sieskind Rémi , Rondelez Yannick 
Published: April 2021

AbstractHigh-throughput directed evolution, implemented in well-controlled in vitro conditions, provides a powerful route for enzyme engineering. Most existing technologies are based on activity screening and require the sequential observation and sorting of each individual variant. By contrast, approaches based on autonomous feedback loops, linking phenotype to genotype replication, enable autonomous selection without screening. However, these approaches are only possible in vivo, or applicable to very specific activities, such as polymerases or ligases. Here, we leverage synthetic molecular networks to create a programmable in vitro feedback loop linking a target enzymatic activity to gene amplification. After encapsulation and lysis of up to 107 transformed variants, the genes present in each droplet are amplified according to the activity of the encoded enzyme, resulting in the autonomous enrichment of interesting sequences. Applied to a nicking enzyme with thermal or kinetic selection pressures, this method reveals detailed mutational landscapes and provides improved variants.