bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome and DNA methylome dynamics reveal differential characteristics of inflorescence development between two ecotypes in Panicum hallii
Authors: Weng Xiaoyu , Song Haili , Sreedasyam Avinash , Haque Taslima , Zhang Li , Chen Cindy , Yoshinaga Yuko , Williams Melissa , O’Malley Ronan C. , Grimwood Jane , Schmutz Jeremy , Juenger Thomas E. 
Published: March 2022

AbstractThe morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation and fitness. Cytosine methylation is an epigenetic mark that contributes to gene expression regulation during inflorescence development. Panicum hallii is a wild perennial grass in the subfamily Panicoideae that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the two major ecotypes in P. hallii, the upland ecotype with compact inflorescence and large seed and the lowland ecotype with an open inflorescence and small seed. Here we performed a comparative transcriptome and DNA methylome analysis across different stages of inflorescence between these two divergent ecotypes of P. hallii. Global transcriptome analysis identified differentially expressed genes (DEGs) involved in panicle divergence, stage-specific expression, and co-expression modules underlying inflorescence development. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of the P. hallii inflorescence. We found that most differentially methylated regions (DMRs) occurred within the flanking regulatory regions of genes, especially the promoter. Integrative analysis of DEGs and DMRs characterized the global features of DMR-associated DEGs in the divergence of P. hallii inflorescence, which includes homologs of important inflorescence and seed developmental genes that have been previously identified in domesticated crops. Evolutionary analysis measured by Ka/Ks ratio suggested that most DMR-associated DEGs are under relatively strong purifying selection. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a novel genomic resource for perennial grass biology.One sentence summary:A comparative transcriptome and DNA methylome analysis of inflorescence between upland and lowland ecotypes reveal gene expression and DNA methylation variation underlying inflorescence divergence in Panicum hallii.
Magnetoencephalography can reveal deep brain network activities linked to memory processes
Authors: López-Madrona Víctor J. , Villalon Samuel Medina , Badier Jean-Michel , Trébuchon Agnès , Jayabal Velmurugan , Bartolomei Fabrice , Carron Romain , Barborica Andrei , Vulliémoz Serge , Alario F. Xavier , Bénar Christian G. 
Published: March 2022

ABSTRACTRecording from deep neural structures such as hippocampus non-invasively and yet with high temporal resolution remains a major challenge for human neuroscience. Although it has been proposed that deep neuronal activity might be recordable during cognitive tasks using magnetoencephalography (MEG), this remains to be demonstrated as the contribution of deep structures to MEG recordings may be too small to be detected or might be eclipsed by the activity of large-scale neocortical networks. In the present study, we disentangled mesial activity and large-scale networks from the MEG signals thanks to blind source separation (BSS). We then validated the MEG BSS components using intracerebral EEG signals recorded simultaneously in patients during their presurgical evaluation of epilepsy. In the MEG signals obtained during a memory task involving the recognition of old and new images, we identified with BSS a putative mesial component, which was present in all patients and all control subjects. The time course of the component selectively correlated with SEEG signals recorded from hippocampus and rhinal cortex, thus confirming its mesial origin. This finding complements previous studies with epileptic activity and opens new possibilities for using MEG to study deep brain structures in cognition and in brain disorders.
Astrocyte-targeted gene delivery of interleukin 2 specifically increases brain-resident regulatory T cell numbers and protects against pathological neuroinflammation
Authors: Yshii Lidia , Pasciuto Emanuela , Bielefeld Pascal , Mascali Loriana , Lemaitre Pierre , Marino Marika , Dooley James , Kouser Lubna , Verschoren Stijn , Lagou Vasiliki , Kemps Hannelore , Gervois Pascal , de Boer Antina , Burton Oliver T. , Wahis Jérôme , Verhaert Jens , Tareen Samar , Roca Carlos P. , Singh Kailash , Whyte Carly E. , Kerstens Axelle , Callaerts-Vegh Zsuzsanna , Poovathingal Suresh , Prezzemolo Teresa , Wierda Keimpe , Dashwood Amy , Xie Junhua , Van Wonterghem Elien , Creemers Eline , Aloulou Meryem , Gsell Willy , Abiega Oihane , Munck Sebastian , Vandenbroucke Roosmarijn E. , Bronckaers Annelies , Lemmens Robin , De Strooper Bart , Van Den Bosch Ludo , Himmelreich Uwe , Fitzsimons Carlos P. , Holt Matthew G. , Liston Adrian 
Published: March 2022

AbstractThe ability of immune-modulating biologics to prevent and reverse pathology has transformed recent clinical practice. Full utility in the neuroinflammation space, however, requires identification of both effective targets for local immune-modulation and a delivery system capable of crossing the blood-brain-barrier. The recent identification and characterization of a small population of regulatory T cells (Tregs) resident in the brain presents one such potential therapeutic target. Here we identified brain IL2 levels as a limiting factor for brain-resident Tregs. We developed a gene-delivery approach for astrocytes, with a small-molecule on-switch to allow temporal control, and enhanced production in reactive astrocytes to spatially-direct delivery to inflammatory sites. Mice with brain-specific IL2 delivery were protected from traumatic brain injury, stroke and multiple sclerosis models, without impacting the peripheral immune system. These results validate brain-specific IL2 gene-delivery as effective protection against neuroinflammation, and provide a versatile platform for delivery of diverse biologics to neuroinflammatory patients.
Human hippocampal responses to network intracranial stimulation vary with theta phase
Authors: Lurie Sarah M. , Kragel James E. , Schuele Stephan U. , Voss Joel L. 
Published: March 2022

AbstractHippocampal-dependent memory is thought to be supported by distinct connectivity states, with strong input to the hippocampus benefitting encoding and weak input benefitting retrieval. Previous research in rodents suggests that the hippocampal theta oscillation orchestrates the transition between these states, with opposite phase angles predicting minimal versus maximal input. We investigated whether this phase dependence exists in humans using network-targeted intracranial stimulation. Intracranial local field potentials were recorded from individuals with epilepsy undergoing medically necessary stereotactic electroencephalographic recording. In each subject, biphasic bipolar direct electrical stimulation was delivered to lateral temporal sites with demonstrated connectivity to hippocampus. Lateral temporal stimulation evoked ipsilateral hippocampal potentials with distinct early and late components. Using evoked component amplitude to measure functional connectivity, we assessed whether the phase of hippocampal theta predicted relatively high versus low connectivity. We observed an increase in the continuous phase-amplitude relationship selective to the early and late components of the response evoked by lateral temporal stimulation. The maximal difference in these evoked component amplitudes occurred across 180 degrees of separation in the hippocampal theta rhythm; i.e., the greatest difference in component amplitude was observed when stimulation was delivered at theta peak versus trough. The pattern of theta phase dependence observed for hippocampus was not identified for control locations. These findings demonstrate that hippocampal receptivity to input varies with theta phase, suggesting that theta phase reflects connectivity states of human hippocampal networks. These findings confirm a putative mechanism by which neural oscillations modulate human hippocampal function.
New Insights on the Evolutionary Relationships Between the Major Lineages of Amoebozoa
Authors: Tekle Yonas I. , Wang Fang , Wood Fiona C. , Anderson O. Roger , Smirnov Alexey 
Published: March 2022

AbstractThe supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages recalcitrant to modern phylogenetics. Deep divergences, taxonomic placement of some key taxa and character evolution in the group largely remain poorly elucidated or controversial. We surveyed available Amoebozoa genomes and transcriptomes to mine conserved putative single copy genes, which were used to enrich gene sampling and generate the largest supermatrix (824 genes) in the group to date. We recovered a well-resolved and supported tree of Amoebozoa, revealing novel deep level relationships and resolving placement of enigmatic lineages congruent with morphological data. In our analysis the deepest branching group is Tubulinea. A recent proposed major clade Tevosa, uniting Evosea and Tubulinea, is not supported. Based on the new phylogenetic tree, paleoecological and paleontological data as well as data on the biology of presently living amoebozoans, we hypothesize that the evolution of Amoebozoa probably was driven with the need to disrupt and graze on microbial mats - a dominant ecosystem of the mid-Proterozoic period of the Earth history.
Chronic obstructive pulmonary disease and cigarette smoke exposure lead to dysregulated MAIT cell activation by bronchial epithelial cells
Authors: Huber Megan E. , Larson Emily , Lust Taylor N. , Heisler Chelsea M. , Harriff Melanie J. 
Published: March 2022

AbstractChronic obstructive pulmonary disease (COPD) is associated with airway inflammation, increased infiltration by CD8+ T lymphocytes, and infection-driven exacerbations. COPD is most commonly caused by cigarette smoke (CS), however the mechanisms driving development of COPD in some smokers but not others are incompletely understood. Lung-resident mucosal-associated invariant T (MAIT) cells play a role in both microbial infections and inflammatory diseases. MAIT cell frequency is reduced in the peripheral blood of individuals with COPD, however the role of MAIT cells in COPD pathology is unknown. Here, we examined MAIT cell activation in response to CS-exposed primary human bronchial epithelial cells (BEC) from healthy, COPD, or smoker donors. We observed significantly higher MAIT cell responses to COPD BEC than healthy BEC. However, COPD BEC stimulated a smaller fold-increase in MAIT cell response despite increased microbial infection. For all donor groups, CS-exposed BEC elicited reduced MAIT cell responses; conversely, CS exposure increased ligand-mediated MR1 surface translocation in healthy and COPD BEC. Our data demonstrate MAIT cell activation is dysregulated in the context of CS and COPD. MAIT cells could contribute to CS- and COPD-associated inflammation through both inappropriate activation and reduced early recognition of bacterial infection, contributing to microbial persistence and COPD exacerbations.
Mutations in Parkinsonism-linked endocytic proteins synaptojanin1 and auxilin have synergistic effects on dopaminergic axonal pathology
Authors: Ng Xin Yi , Wu Yumei , Lin Youneng , Yaqoob Sidra Mohamed , Greene Lois E. , Camilli Pietro De , Cao Mian 
Published: March 2022

AbstractParkinson’s disease (PD) is a neurodegenerative disorder characterized by defective dopaminergic (DAergic) input to the striatum. Mutations in two genes encoding synaptically enriched clathrin-uncoating factors, synaptojanin 1 (SJ1) and auxilin, have been implicated in atypical Parkinsonism. SJ1 knock-in (SJ1-KIRQ) mice carrying a disease-linked mutation display neurological manifestations reminiscent of Parkinsonism. Here we report that auxilin knockout (Aux-KO) mice display dystrophic changes of a subset of nigrostriatal DAergic terminals similar to those of SJ1-KIRQmice. Furthermore, Aux-KO/SJ1-KIRQdouble mutant mice have shorter lifespan and more severe synaptic defects than single mutant mice. These include increase in dystrophic striatal nerve terminals positive for DAergic markers and for the PD risk protein SV2C, as well as adaptive changes in striatal interneurons. The synergistic effect of the two mutations demonstrates a special lability of DAergic neurons to defects in clathrin uncoating, with implications for PD pathogenesis in at least some forms of this condition.
Protein-protein interaction map in pre-eclampsia through the interaction of hub genes, transcription factors and microRNAs
Authors: Guttula Praveen Kumar , Agrawal Kirti , Gupta Mukesh Kumar 
Published: March 2022

AbstractPre-eclampsia causes complications in pregnancy and characterized by uremia, proteinuria and hypertension in unattended cases. Blood biomarkers for pre-eclampsia are lacking. In this study, microarray gene expression data from peripheral blood of pre-eclampsia women was analyzed. In our study we developed a combined network approach for hub node prediction regulated by transcription factors and microRNAs corresponding to pre-eclampsia. Differentially expressed genes (DEGs) interaction map was constructed using STRING database. JUN, RPL35, NDUFB2, ATP5I, UQCRQ, COX7C, and FN1 were predicted as potential novel hub genes. Pathway analysis showed metabolic pathways, cytokine signaling in the immune system, Wnt, and MAPK signaling pathways involvement in pre-eclampsia. Regulatory network analysis showed that transcription factors JUN and STAT1 were connected with hub nodes, and microRNAs (miRNAs) like hsa-miR-26b-5p and hsa-miR-155-5p. In conclusion, the expression pattern of hub genes, analyzed deciphers a molecular signature for understanding the pathophysiology of pre-eclampsia and prediction of biomarkers for diagnosis.
Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice
Authors: McKinney Andrew , Hu Ming , Hoskins Amber , Mohammadyar Arian , Naeem Nabeeha , Jing Junzhan , Patel Saumil S. , Sheth Bhavin R. , Jiang Xiaolong 
Published: March 2022

AbstractThe locus coeruleus (LC) houses the vast majority of noradrenergic neurons in the brain and regulates many fundamental functions including fight and flight response, attention control, and sleep/wake cycles. While efferent projections of the LC have been extensively investigated, little is known about its local circuit organization. Here, we performed large-scale multi-patch recordings of noradrenergic neurons in adult mouse LC to profile their morpho-electric properties while simultaneously examining their interactions. LC noradrenergic neurons are diverse and could be classified into two major morpho-electric types. While fast excitatory synaptic transmission among LC noradrenergic neurons was not observed in our preparation, these mature LC neurons connected via gap junction at a rate similar to their early developmental stage and comparable to other brain regions. Most electrical connections form between dendrites and are restricted to narrowly spaced pairs or small clusters of neurons of the same type. In addition, more than two electrically coupled cell pairs were often identified across a cohort of neurons from individual multi-cell recording sets that followed a chain-like organizational pattern. The assembly of LC noradrenergic neurons thus follows a spatial and cell type-specific wiring principle that may be imposed by a unique chain-like rule.
Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading IdentifiesLINC00881as an Essential Regulator of Calcium Handling in the Cardiomyocyte
Authors: Liao Xianghai , Kennel Peter J. , Liu Bohao , Nash Trevor R. , Zhuang Richard , Godier-Furnemont Amandine F. , Xue Chenyi , Lu Rong , Colombo Paolo C. , Uriel Nir , Reilly Muredach P. , Marx Steven O. , Vunjak-Novakovic Gordana , Topkara Veli K. 
Published: March 2022

AbstractBackgroundHuman heart failure is characterized by global alterations in the myocardial DNA methylation profile, yet little is known about epigenetic regulation of non-coding transcripts and potential reversibility of DNA methylation with left ventricular assist device (LVAD) support.MethodGenome-wide mapping of myocardial DNA methylation was performed in 36 patients with end-stage heart failure at the time of LVAD implant, 8 patients at the time of LVAD explant, and 7 non-failing controls using high-density bead array platform. Transcriptomic and functional studies were performed in human induced pluripotent stem cell derived cardiomyocytes (iPSCs).ResultsEtiology-specific analysis revealed 2079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in non-ischemic cardiomyopathy (NICM). 192 DMPs were common to ICM and NICM. Analysis of paired samples before and after LVAD support demonstrated reverse methylation of only 3.2% of HF-specific DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FAM65A, FBXO16, EFCAB13, AKAP13, RPTOR) or hypermethylated and downregulated (TBX3) in ICM and NICM patients. A novel cardiac-specific super-enhancer lncRNA (LINC00881) is hypermethylated and downregulated in the failing human heart.LINC00881is an upstream regulator of sarcomere and calcium channel gene expression includingMYH6, CACNA1C, andRYR2. LINC00881knockdown significantly reduced peak calcium amplitude in the beating human iPSCs.ConclusionsFailing human heart exhibits etiology-specific changes in DNA methylation including coding and non-coding regions, which are minimally reversible with mechanical unloading. Epigenetic reprogramming may be necessary to achieve transcriptional normalization and sustained clinical recovery from heart failure.
FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer
Authors: Rise Kjersti , Tessem May-Britt , Drabløs Finn , Rye Morten B. 
Published: March 2022

AbstractMitochondrial activity in cancer cells has been central to cancer research since Otto Warburg first published his thesis on the topic in 1956. Although Warburg proposed that oxidative phosphorylation in the tricarboxylic acid (TCA) cycle was perturbed in cancer, later research has shown that oxidative phosphorylation is activated in most cancers, including prostate cancer (PCa). However, more detailed knowledge on mitochondrial metabolism and metabolic pathways in cancers is still lacking. In this study we expand our previously developed method for analyzing functional homologous proteins (FunHoP), which can provide a more detailed view of metabolic pathways. FunHoP uses results from differential expression analysis of RNA-Seq data to improve pathway analysis. By adding information on subcellular localization based on experimental data and computational predictions we can use FunHoP to differentiate between mitochondrial and non-mitochondrial processes in cancerous and normal prostate cell lines. Our results show that mitochondrial pathways are upregulated in PCa and that splitting metabolic pathways into mitochondrial and non-mitochondrial counterparts using FunHoP adds to the interpretation of the metabolic properties of PCa cells.
EEG evidence that morally relevant autobiographical memories can be suppressed
Authors: Satish Akul , Hellerstedt Robin , Anderson Michael C. , Bergström Zara M. 
Published: March 2022

AbstractRemembering unpleasant events can trigger negative feelings. Fortunately, research indicates that unwanted memories can be suppressed to prevent them from intruding into awareness, improving our mental state. The current scientific understanding of memory suppression is, however, based mostly on simpler memories such as associations between words or pictures, which may not reflect how people control unpleasant memory intrusions in everyday life. Here, we investigated the neural and behavioural dynamics of suppressing personal and emotional autobiographical memories using a modified version of the Think/No-Think task. We asked participants to suppress memories of their own past immoral actions, which were hypothesised to be both highly intrusive and motivating to suppress. We report novel evidence from behavioural, ERP and EEG oscillation measures that autobiographical memory retrieval can be suppressed and suggest that autobiographical suppression recruits similar neurocognitive mechanisms as suppression of simple laboratory associations. Suppression did fail sometimes, and EEG oscillations indicated that such memory intrusions occurred from lapses in sustained control. Importantly however, participants improved at limiting intrusions with repeated practice. Furthermore, both behavioural and EEG evidence indicated that intentional suppression may be more difficult for memories of our morally wrong actions than memories of our morally right actions. The findings elucidate the neurocognitive correlates of autobiographical retrieval suppression and have implications for theories of morally motivated memory control.
PRL1 and CK2 collaborate to time morning and evening phase in short photoperiods
Authors: Lear Bridget C. , Kula-Eversole Ela , Allada Ravi 
Published: March 2022

AbstractThe TIMELESS (TIM) phosphatase, Phosphatase of Regenerating Liver-1 (PRL-1), is required for setting behavioral phase especially under short photoperiod conditions. Yet the circadian clock neurons and underlying mechanisms important for these effects are unknown. Here we demonstrate that PRL-1 function in PDF neurons is necessary and sufficient for timing morning and evening phase under short photoperiod (6:18) conditions. In standard (12:12) photoperiod, we find that PRL-1 rescue or blocking PRL-1 knockdown in PDF neurons restores wild-type morning phase. Expression of the TIM kinase shaggy (sgg) in PDF neurons suppresses in an additive manner PRL-1 period lengthening and delayed morning phase further underscoring the role of PDF neurons. In contrast to knockdown in all clock neurons, knockdown of PRL-1 selectively in PDF clock neurons does not alter the timing of morning or evening phase under standard photoperiod conditions, suggesting PRL-1 function in non-PDF neurons may also be important. In contrast to SGG effects, we find that phase delay of evening onset due to expression of a dominant negative version of the TIM kinase CK2 (CK2alphaTik) requires PRL-1. Given that TIM is a substrate of both the PRL-1 phosphatase and CK2 kinase, we hypothesize that PRL-1 dephosphorylation at specific sites may be necessary for subsequent CK2 phosphorylation to time behavior.
The GEF-GAP pair Solo and DLC3 balances Rho activity during endocytic transport
Authors: Lungu Cristiana , Meyer Florian , Hörning Marcel , Steudle Jasmin , Braun Anja , Noll Bettina , Benz David , Fränkle Felix , Schmid Simone , Eisler Stephan A. , Olayioye Monilola A. 
Published: March 2022

ABSTRACTThe control of intracellular membrane trafficking by Rho GTPases is central to cellular homeostasis. How defined pairs of guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) come together to locally balance GTPase activation cycles in this process is nevertheless largely unclear. By performing a microscopy-based RNAi screen we here identify the RhoGEF protein Solo as a counterpart of DLC3, a RhoGAP protein with established roles in membrane trafficking. Biochemical, imaging and optogenetics assays further uncover Solo as a novel regulator of endosomal RhoB. Remarkably, we find that the interplay between Solo and DLC3 controls not only the activity but also total protein levels of RhoB. Together, the results of our study uncover the first functionally connected RhoGAP-RhoGEF pair at endomembranes and place the Solo-DLC3 axis at the core of endocytic trafficking.