bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in Placental microRNA Expression Associates with Familial Cardiovascular Disease
Authors: Tehrani Jesse M. , Kennedy Elizabeth M. , Tian Fu-Ying , Everson Todd M. , Deyssenroth Maya , Burt Amber , Hermetz Karen , Hao Ke , Chen Jia , Koestler Devin C. , Marsit Carmen J. 
Published: February 2021

AbstractIn the United States, cardiovascular disease is the leading cause of death, and the rate of maternal mortality remains among the highest of any industrialized nation. Maternal cardiometabolic health throughout gestation and postpartum is representative of placental health and physiology. Both proper placental functionality and placental microRNA expression are essential to successful pregnancy outcomes, and both are highly sensitive to genetic and environmental sources of variation. While placental pathologies, such as preeclampsia, are associated with maternal cardiovascular health and may contribute to the developmental programming of cardiovascular disease, the role of more subtle alterations to placental function and microRNA expression in this relationship remains poorly understood. To develop a more comprehensive understanding of how cardiometabolic health influences placental microRNA expression, and how this shapes placental functionality, we performed small RNA sequencing to investigate microRNA in the placentae from the Rhode Island Child Health Study (n=230). We modeled microRNA counts on maternal family history of cardiovascular disease using negative binomial generalized linear models, and identified microRNAs that were differential expressed (DEmiRs) at a false discovery rate (FDR) less than 0.10. Utilizing parallel mRNA sequencing data and bioinformatic target prediction software, we identified potential mRNA targets of these DEmiRs. We identified 9 DEmiRs, with predicted targets of those miRNA enriched overwhelmingly in the TGFβ signaling pathway but also in pathways involving cellular metabolism and immunomodulation. Overall, we identified a robust association existing between familial cardiovascular disease and placental microRNA expression which may be implicated in both placental insufficiencies and the developmental programming of cardiovascular disease.
Stage-specific, morphological and molecular markers of encystation inGiardia lamblia
Authors: Thomas Elizabeth B. , Sutanto Renaldo , Johnson Richard S. , Shih Han-Wei , Krtková Jana , MacCoss Michael J. , Paredez Alexander R. 
Published: February 2021

AbstractDifferentiation into environmentally resistant cysts is required for transmission of the ubiquitous intestinal parasiteGiardia lamblia. Encystation inGiardiarequires the production, processing and transport of Cyst Wall Proteins (CWPs) in developmentally-induced, Golgi-like, Encystation Specific Vesicles (ESVs). Progress through this trafficking pathway can be followed by tracking CWP localization over time. However, there is no recognized system to distinguish the advancing stages of this process which can complete at variable rates depending how encystation is induced. Here we propose a staging system for encystingGiardiabased on the morphology of CWP1-stained ESVs. We demonstrate the molecular distinctiveness of maturing ESVs at these stages by followingGlRab GTPases through encystation. Previously, we established thatGiardia’s sole Rho family GTPase,GlRac, associates with ESVs and has a role in regulating their maturation and the secretion of their cargo. As a proof of principle, we delineate the relationship betweenGlRac and ESV stages. Through proteomic studies, we identify putative interactors ofGlRac that could be used as additional stage-specific ESV markers. This staging system provides a common descriptor of ESV maturation regardless of the source of encysting cells. Furthermore, the identified set of molecular markers for ESV stages will be a powerful tool for characterizing trafficking mutants that impair ESV maturation and morphology.ImportanceGiardiasisis a diarrheal disease that affects 280 million people worldwide. It is caused byGiardia lamblia, a protozoan parasite which rely on differentiating from host-dwelling trophozoites to environmentally-resistant cysts for transmission and survival. This encystation process requires the transport of Cyst Wall Proteins (1-3) within membrane-bound compartments called Encystation Specific Vesicles (ESV) from the endoplasmic reticulum to the surface of the cell. The whole process takes 24 hours to complete and these compartments are the only recognizable equivalent of Golgi apparatus in this minimalistic organism. Progress of this trafficking pathway can be followed by localizing Cyst Wall Protein 1 over time post induction of encystation but this can be ambiguous when specific molecular events need to be specified. Here we propose a staging system that is based on ESV morphology changes by capitalizing on the secretory/processing events we already know they represent. We validate the molecular distinctiveness of these stages by followingGiardiaRabs through the pathway and characterize putative interactors of an established regulator of encystation,GlRac, to provide additional stage-specific molecular markers. This staging system will provide a definitive, yet adaptable, framework to map out functions of yet-to-be discovered players of this important pathway.
Transport engineering for improving production and secretion of valuable alkaloids inEscherichia coli
Authors: Yamada Yasuyuki , Urui Miya , Oki Hidehiro , Inoue Kai , Matsui Haruyuki , Ikeda Yoshito , Nakagawa Akira , Sato Fumihiko , Minami Hiromichi , Shitan Nobukazu 
Published: February 2021

AbstractMetabolic engineering of microorganisms to produce specialized plant metabolites has been established. However, these methods are limited by low productivity and the intracellular accumulation of metabolites. Here, we aimed to use transport engineering for producing reticuline, an important intermediate in the alkaloid biosynthetic pathway. We established a reticuline-producingEscherichia colistrain and introduced a multidrug and toxic compound extrusion transporter,ArabidopsisAtDTX1, into it. AtDTX1 was selected due to its suitable expression inE. coliand its reticuline-transport activity. Expression of AtDTX1 significantly enhanced reticuline production by 11-fold; produced reticuline was secreted into the medium. AtDTX1 expression conferred high plasmid stability, and up- or downregulated genes associated with biological processes including metabolic pathways for reticuline biosynthesis, leading to a high production and secretion of reticuline. The successful application of a transporter for alkaloid production suggests that the transport engineering approach may improve the biosynthesis of specialized metabolites via metabolic engineering.
Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla
Authors: Hua Xin , Song Wei , Wang Kangzong , Yin Xue , Hao Changqi , Duan Baozhong , Xu Zhichao , Su Tongbing , Xue Zheyong 
Published: February 2021

ABSTRACTThe genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network inParis polyphyllawith a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges ofOSC, CYP, andUGTgenes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin inP. polyphylla. This study provides a idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants.
DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING
Authors: Dimond James L. , Nguyen Nhung , Roberts Steven B. 
Published: February 2021

ABSTRACTSymbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyteElliptochloris marinaon methylation in the sea anemoneAnthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis withE. marinawas, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
The impact of distributional assumptions in gene-set and pathway analysis: how far can it go wrong?
Authors: Ho Chi-Hsuan , Huang Yu-Jyun , Lai Ying-Ju , Mukherjee Rajarshi , Hsiao Chuhsing Kate 
Published: February 2021

ABSTRACTGene-set analysis (GSA) has been one of the standard procedures for exploring potential biological functions when a group of differentially expressed genes have been derived. The development of its methodology has been an active research topic in recent decades. Many GSA methods, when newly proposed, rely on simulation studies to evaluate their performance with a common implicit assumption that the multivariate expression values are normally distributed. The validity of this assumption has been disputed in several studies but no systematic analysis has been carried out to assess the influence of this distributional assumption. Our goal in this study is not to propose a new GSA method but to first examine if the multi-dimensional gene expression data in gene sets follow a multivariate normal distribution (MVN). Six statistical methods in three categories of MVN tests were considered and applied to a total of twenty-two datasets of expression data from studies involving tumor and normal tissues, with ten signaling pathways chosen as the gene sets. Second, we evaluated the influence of non-normality on the performance of current GSA tools, including parametric and non-parametric methods. Specifically, the scenario of mixture distributions representing the case of different tumor subtypes was considered. Our first finding suggests that the MVN assumption should be carefully dealt with. It does not hold true in many applications tested here. The second investigation of the GSA tools demonstrates that the non-normality does affect the performance of these GSA methods, especially when subtypes exist. We conclude that the use of the inherent multivariate normality assumption should be assessed with care in evaluating new GSA tools, since this MVN assumption cannot be guaranteed and this assumption affects strongly the performance of GSA methods. If a newly proposed GSA method is to be evaluated, we recommend the incorporation of multivariate non-normal distributions or sampling from large databases if available.
Role of transmembrane spanning domain 1 in cystic fibrosis transmembrane conductance regulator folding
Authors: Patrick Anna E. , Millen Linda , Thomas Philip J. 
Published: February 2021

AbstractCystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) protein that disrupt its folding pathway. The most common mutation causing CF is a deletion of phenylalanine at position 508 (ΔF508). CFTR contains five domains that each form cotranslational structures that interact with other domains as they are produced and folded. CFTR is comprised of two transmembrane spanning domains (TMDs), two nucleotide binding domains (NBDs) and a unique regulatory region (R). The first domain translated, TMD1, forms interdomain interactions with the other domains in CFTR. In TMD1, long intracellular loops extend into the cytoplasm and interact with both NBDs via coupling helices and with TMD2 via transmembrane spans (TMs). We examined mutations in TMD1 to determine the impact on individual domain and multidomain constructs. We found that mutations in a TM span or in the cytosolic ICLs interfere with specific steps in the hierarchical folding of CFTR. TM1 CF-causing mutants, G85E and G91R, directly affect TMD1, whereas most ICL1 and ICL2 mutant effects become apparent in the presence of TMD2. A single mutant in ICL2 worsened CFTR trafficking in the presence of NBD2, supporting its role in the ICL2-NBD2 interface. Mutation of hydrophobic residues in ICL coupling helices tended to increased levels of pre-TMD2 biogenic intermediates but caused ER accumulation in the presence of TMD2. This suggests a tradeoff between transient stability during translation and final structure. NBD2 increased the efficiency of mutant trafficking from the ER, consistent with stabilization of the full-length constructs. While the G85E and G91R mutants in TM1 have immediately detectable effects, most of the studied mutant effects and the ΔF508 mutant are apparent after production of TMD2, supporting this intermediate as a major point of recognition by protein quality control.
Protein lactylation induced by neural excitation
Authors: Hagihara Hideo , Shoji Hirotaka , Otabi Hikari , Toyoda Atsushi , Katoh Kaoru , Namihira Masakazu , Miyakawa Tsuyoshi 
Published: February 2021

AbstractLactate is known to have diverse roles in the brain at the molecular and behavioral levels under both physiological and pathophysiological conditions, such as learning and memory and regulation of mood. Recently, a novel post-translational modification called lysine lactylation has been found in histone H3 of mouse macrophages, and the lactylation levels paralleled the intracellular lactate levels1. However, it is unknown whether lysine lactylation occurs in brain cells, and if it does, whether lactylation is induced by the stimuli that accompany changes in lactate levels. Herein, we reveal that lysine lactylation in brain cells is regulated by systemic changes in lactate levels, neural excitation, and behaviorally relevant stimuli. Lysine lactylation levels were increased by lactate treatment and by high-potassium-induced depolarization in cultured primary neurons; these increases were attenuated by pharmacological inhibition of monocarboxylate transporter 2 and lactate dehydrogenase, respectively, suggesting that both cell-autonomous and non-cell-autonomous neuronal mechanisms are involved in overall lysine lactylation.In vivo, electroconvulsive stimulation increased lysine lactylation levels in the prefrontal cortices of mice, and its levels were positively correlated with the expression levels of the neuronal activity marker c-Fos on an individual cell basis. In the social defeat stress model of depression in which brain lactate levels increase, lactylation levels were increased in the prefrontal cortices of the defeated mice, which was accompanied by increased c-Fos expression, decreased social behaviors, and increased anxiety-like behaviors, suggesting that stress-induced neuronal excitation may induce lysine lactylation, thereby affecting mood-related behaviors. Further, we identified 63 candidate lysine-lactylated proteins in the mouse cortex and found that lactylation levels in histone H1 increased in response to defeat stress. This study may open up an avenue for exploration of a novel role of neuronal activity-induced lactate mediated by protein lactylation in the brain.
Sorghum pan-genome explores the functional utility to accelerate the genetic gain
Authors: Ruperao Pradeep , Thirunavukkarasu Nepolean , Gandham Prasad , S. Sivasubramani , M Govindaraj , Nebie Baloua , Manyasa Eric , Gupta Rajeev , Das Roma Rani , Gandhi Harish , Edwards David , Deshpande Santosh P. , Rathore Abhishek 
Published: February 2021

AbstractSorghum (Sorghum bicolorL.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
Resolving phylogenetic and biochemical barriers to functional expression of heterologous iron-sulphur cluster enzymes
Authors: Shomar Helena , Garcia Pierre Simon , Fernández-Fueyo Elena , D’Angelo Francesca , Pelosse Martin , Manuel Rita Rebelo , Büke Ferhat , Liu Siyi , van den Broek Niels , Duraffourg Nicolas , de Ram Carol , Pabst Martin , Gribaldo Simonetta , Py Beatrice , de Choudens Sandrine Ollagnier , Bokinsky Gregory , Barras Frédéric 
Published: February 2021

AbstractMany of the most promising applications of synthetic biology, including engineering of microbes for renewable chemical production, relies upon the ability of genetically-tractable hosts to express heterologous enzymes from foreign species. While countless methods for facilitating heterologous enzyme expression have been developed, comparable tools for facilitating heterologous enzyme activity are generally lacking. Such tools are needed to fully exploit the biosynthetic potential of the natural world. Here, using the model bacterium Escherichia coli, we investigate why iron-sulphur (Fe-S) enzymes are often inactive when heterologously expressed. By applying a simple growth complementation assay with collections of Fe-S enzyme orthologs from a wide range of prokaryotic diversity, we uncover a striking correlation between phylogenetic distance and probability of functional expression. Moreover, co-expression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be functionally expressed. On the other hand, we find that heterologous Fe-S enzymes that require specific electron carrier proteins within their natural host are rarely functionally expressed unless their specific reducing partners are identified and co-expressed. We demonstrate in vitro that such selectivity in part derives from a need for low-potential electron donors. Our results clarify how phylogenetic distance and electron transfer biochemistry each separately impact functional heterologous expression and provide insight into how these barriers can be overcome for successful microbial engineering involving Fe-S enzymes.
Angiotensin-II modulates GABAergic neurotransmission in the mouse substantia nigra
Authors: Singh Maibam R. , Vigh Jozsef , Amberg Gregory C. 
Published: February 2021

ABSTRACTGABAergic projections neurons of the substantia nigra reticulata (SNr), through an extensive network of dendritic arbors and axon collaterals, provide robust inhibitory input to neighboring dopaminergic neurons in the substantia nigra compacta (SNc). Angiotensin-II (Ang-II) receptor signaling increases SNc dopaminergic neuronal sensitivity to insult, thus rendering these cells susceptible to dysfunction and destruction. However, the mechanisms by which Ang-II regulates SNc dopaminergic neuronal activity are unclear. Given the complex relationship between SN dopaminergic and GABAergic neurons, we hypothesized that Ang-II could regulate SNc dopaminergic neuronal activity directly and indirectly by modulating SNr GABAergic neurotransmission. Herein, using transgenic mice, slice electrophysiology, and optogenetics, we provide evidence of an AT1 receptor-mediated signaling mechanism in SNr GABAergic neurons where Ang-II suppresses electrically-evoked neuronal output by facilitating postsynaptic GABAA receptors and prolonging the action potential duration. Unexpectedly, Ang-II had no discernable effects on the electrical properties of SNc dopaminergic neurons. Also, and indicating a nonlinear relationship between electrical activity and neuronal output, following phasic photoactivation of SNr GABAergic neurons, Ang-II paradoxically enhanced the feedforward inhibitory input to SNc dopaminergic neurons. In sum, our observations describe an increasingly complex and heterogeneous response of the SN to Ang-II by revealing cell-specific responses and nonlinear effects on intranigral GABAergic neurotransmission. Our data further implicate the renin-angiotensin-system as a functionally relevant neuromodulator in the basal ganglia, thus underscoring a need for additional inquiry.SIGNIFICANCE STATEMENTAngiotensin II (Ang-II) promotes dopamine release in the striatum and, in the substantia nigra compacta (SNc), exacerbates dopaminergic cell loss in animal models of Parkinson’s disease. Despite a potential association with Parkinson’s disease, the effects of Ang-II on neuronal activity in the basal ganglia is unknown. Here we describe a novel AT1 receptor-dependent signaling mechanism in GABAergic projection neurons of the SN reticulata (SNr), a major inhibitory regulator of SNc dopaminergic neurons. Specifically, Ang-II suppresses SNr GABAergic neuronal activity, subsequently altering GABAergic modulation of SNc dopaminergic neurons in a nonlinear fashion. Altogether, our data provide the first indication of Ang-II-dependent modulation of GABAergic neurotransmission in the SN, which could impact output from the basal ganglia in health and disease.