bluuebunny/crossref_metadata_2025_split huggingface dataset:
Speed modulation of hippocampal theta frequency and power predicts water maze learning
Authors: Young Calvin K. , Ruan Ming , McNaughton Neil 
Published: April 2020

AbstractTheta oscillations in the hippocampus have many behavioural correlates, with the magnitude and vigour of ongoing movement being the most salient. Many consider correlates of locomotion with hippocampal theta to be a confound in delineating theta contributions to cognitive processes. But, theory and empirical experiments suggest theta-movement relationships are important if spatial navigation is to support higher cognitive processes. In the current study, we tested if variations in speed modulation of hippocampal theta can predict spatial learning rates in the water maze. Using multi-step regression, we find the magnitude and robustness of hippocampal theta frequency versus speed scaling can predict water maze learning rates. Using generalised linear models, we also demonstrate that speed and water maze learning are the best predictors of hippocampal theta frequency and power. Theta oscillations recorded from the supramammillary area showed much weaker, or non-existent, relationships, which supports the idea that hippocampal theta has specific roles in speed representation and spatial learning. Our findings suggest movement-speed correlations with hippocampal theta frequency may be actively used in spatial learning.
Oxygen-glucose deprivation and reoxygenation on human cerebral organoids alters expression related to lipid metabolism
Authors: Iwasa Naoki , Matsui Takeshi K. , Morikawa Naritaka , Sakaguchi Yoshihiko M. , Shiota Tomo , Iguchi Naohiko , Nishimura Yuhei , Mori Eiichiro , Sugie Kazuma 
Published: April 2020

AbstractIschemic stroke is one of the most common neurological disease. However, the impact of ischemic stroke on human cerebral tissue remains largely unknown; due to a lack of ischemic human brain samples. In this study, we used cerebral organoids derived from human induced pluripotent stem cells to evaluate the effect of oxygen-glucose deprivation/reoxygenation (OGD/R). We identified 15 differentially expressed genes (DEGs); and found that all the DEGs were downregulated. Pathway analysis showed the relationship of vitamin digestion and absorption, fat digestion and absorption, peroxisome proliferator-activated receptor signaling pathway, and complement and coagulation cascades. These findings indicate the mechanisms underlying ischemic injury in human cerebral tissue.
CPPred-sORF: Coding Potential Prediction of sORF based on non-AUG
Authors: Tong Xiaoxue , Hong Xu , Xie Juan , Liu Shiyong 
Published: April 2020

AbstractIn recent years, researchers have discovered thousands of sORFs that can encode micropeptides, and more and more discoveries that non-AUG codons can be used as translation initiation sites for these micropeptides. On the basis of our previous tool CPPred, we develop CPPred-sORF by adding two features and using non-AUG as the starting codon, which makes a comprehensive evaluation of sORF. The database of CPPred-sORF are constructed by small coding RNA and lncRNA as positive and negative data, respectively. Compared to the small coding RNAs and small ncRNAs, lncRNAs and small coding RNAs are less distinguishable. This is because the longer the sequences, the easier to include open reading frames. We find that the sensitivity, specificity and MCC value of CPPred-sORF on the independent testing set can reach 88.22%, 88.84% and 0.768, respectively, which shows much better prediction performance than the other methods.
Learning-related population dynamics in the auditory thalamus
Authors: Gilad Ariel , Maor Ido , Mizrahi Adi 
Published: April 2020

AbstractLearning to associate sensory stimuli with a chosen action has been classically attributed to the cortex. Whether the thalamus, considered mainly as an upstream area relative to cortex, encodes learning-related information is still largely unknown. We studied learning-related activity in the dorsal and medial regions of the medial geniculate body (MGB), part of the non-lemniscal auditory pathway. Using fiber photometry, we continuously imaged population calcium dynamics as mice learned a go/no-go auditory discrimination task. The MGB was tuned to frequency shortly after stimulus onset and responded to cognitive features like the choice of the mouse several hundred milliseconds later. Encoding of choice in the MGB increased with learning, and was highly correlated with the learning curves of the mice. MGB also encoded motor parameters of the mouse during the task. These results provide evidence that the MGB encodes task- motor- and learning-related information.
Chromatin 3D interaction analysis of theSTARD10locus unveilsFCHSD2as a new regulator of insulin secretion
Authors: Hu Ming , Cebola Inês , Carrat Gaelle , Jiang Shuying , Nawaz Sameena , Khamis Amna , Canouil Mickael , Froguel Philippe , Schulte Anke , Solimena Michele , Ibberson Mark , Marchetti Piero , Cardenas-Diaz Fabian L. , Gadue Paul J. , Hastoy Benoit , Alemeida-Souza Leonardo , McMahon Harvey , Rutter Guy A. 
Published: April 2020

SUMMARYGenome-wide association studies have identified thousands of genetic variants associated with type 2 diabetes (T2D) risk. Using chromatin conformation capture we show that an enhancer cluster in theSTARD10T2D locus forms a defined 3D chromatin domain. A 4.1 Kb region within this region, carrying five disease-associated variants, physically interacts with CTCF-binding regions and with an enhancer possessing strong transcriptional activity. Analysis of human islet 3D chromatin interaction maps identifiesFCHSD2gene as an additional target of the enhancer cluster. CRISPR-Cas9-mediated deletion of the variant region, or of an associated enhancer, in human pancreatic beta cells impaired glucose-stimulated insulin secretion. Expression of bothSTARD10andFCHSD2, but notARAP1, was reduced in cells harboring CRISPR deletions, and expression ofSTARD10andFCHSD2was associated with the possession of variant alleles in human islets. Finally, CRISPR-Cas9-mediated loss ofSTARD10orFCHSD2impaired regulated insulin secretion. Thus, multiple genes at theSTARD10locus influence β cell function.
Can genetic polymorphisms predict response variability to anodal transcranial direct current stimulation of the primary motor cortex?
Authors: Pellegrini Michael , Zoghi Maryam , Jaberzadeh Shapour 
Published: April 2020

AbstractGenetic mediation of cortical plasticity and the role genetic variants play in previously observed response variability to transcranial direct current stimulation (tDCS) have become important issues in the tDCS literature in recent years. This study investigated whether inter-individual variability to tDCS was in-part genetically mediated. In sixty-one healthy males, anodal-tDCS (a-tDCS) and sham-tDCS were administered to the primary motor cortex at 1mA for 10-minutes via 6×4cm active and 7×5cm return electrodes. Twenty-five single-pulse transcranial magnetic stimulation (TMS) motor evoked potentials (MEP) were recorded to represent corticospinal excitability (CSE).Twenty-five paired-pulse MEPs were recorded with 3ms inter-stimulus interval (ISI) to assess intracortical inhibition (ICI) via short-interval intracranial inhibition (SICI) and 10ms ISI for intracortical facilitation (ICF). Saliva samples tested for specific genetic polymorphisms in genes encoding for excitatory and inhibitory neuroreceptors. Individuals were sub-grouped based on a pre-determined threshold and via statistical cluster analysis. Two distinct subgroups were identified, increases in CSE following a-tDCS (i.e. Responders) and no increase or even reductions in CSE (i.e. Non-responders). No changes in ICI or ICF were reported. No relationships were reported between genetic polymorphisms in excitatory receptor genes and a-tDCS responders. An association was reported between a-tDCS responders and GABRA3 gene polymorphisms encoding for GABA-A receptors suggesting potential relationships between GABA-A receptor variations and capacity to undergo tDCS-induced cortical plasticity. In the largest tDCS study of its kind, this study presents an important step forward in determining the contribution genetic factors play in previously observed inter-individual variability to tDCS.
Eco-evolutionary interaction in competing phytoplankton: genotype sorting likely explains dominance shift and species responses to CO2
Authors: Listmann Luisa , Hattich Giannina S. I. , Matthiessen Birte , Reusch Thorsten B.H. 
Published: April 2020

AbstractHow ecological and evolutionary processes interact and together determine species and community responses to climate change is poorly understood. We studied long-term dynamics (over approximately 200 asexual generations) in two phytoplankton species, a coccolithophore (Emiliania huxleyi) and a diatom (Chaetoceros affinis), to increased CO2growing alone or competing with one another in co-occurrence. To allow for rapid evolutionary responses, the experiment started with a standing genetic variation of nine genotypes in each of the species. Under co-occurrence of both species, we observed a dominance shift fromC. affinistoE. huxleyiafter about 120 generations in both CO2treatments, but more pronounced under high CO2. Associated with this shift, we only found weak adaptation to high CO2in the diatom and none in the coccolithophore in terms of species’ growth rates. In addition, no adaptation to interspecific competition could be observed by comparing the single to the two-species treatments in reciprocal assays, regardless of the CO2treatment. Nevertheless, highly reproducible genotype sorting left only one genotype remaining for each of the species among all treatments. This strong evolutionary selection coincided with the dominance shift fromC. affinistoE. huxleyi. Since all other conditions were kept constant over time, the most parsimonious explanation for the dominance shift is that the strong evolutionary selection potentially altered competitive ability of the two species. Thus, here observed changes in the simplest possible two-species phytoplankton “community” demonstrated that eco-evolutionary interactions can be critical for predicting community responses to climate change in rapidly dividing organisms such as phytoplankton.
Substrate sensing institutes sequential and asymmetric electron transfer in the nitrogenase-like DPOR complex
Authors: Corless Elliot I. , Bennett Brian , Antony Edwin 
Published: April 2020

AbstractDark-operative protochlorophyllide oxidoreductase (DPOR) catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key penultimate step in the biosynthesis of bacteriochlorophyll. DPOR shares structural homology with nitrogenase and is made of electron donor (BchL) and electron acceptor (BchNB) component proteins. ATP driven assembly of the BchL and BchNB proteins drives electron transfer and Pchlide reduction. BchNB is composed of two subunits each of BchN and BchB arranged as an α2ß2 heterotetramer. Here, we describe extensive allosteric communication between the two identical active sites in BchNB that drives sequential and asymmetric electron transfer. Pchlide binding and electron transfer activities in one half of the BchNB tetramer allosterically regulates activities in the other half. Pchlide binding is sensed and recognizedin transby an Asp274 from the opposing half and is positioned in the active site to likely serve as the initial proton donor. An Asp274 to Ala substituted DPOR binds to two Pchlide molecules in the BchNB complex but is unable to conformationally poise one Pchlide molecule. Thus, stalling Pchlide reduction in both active sites. The [4Fe-4S] cluster of the BchNB protein is pre-reduced and donates the first electron to Pchlide, a mechanism similar to the deficit-spending model observed in nitrogenase. In half-reactive DPOR complexes, incapacitating proton donation in one half generates a stalled intermediate and Pchlide reduction in both halves is abolished. The results showcase long-range allosteric communication and sequential ET in the two symmetric halves. The findings shed light on the functional advantages imparted by the oligomeric architecture found in many electron transfer enzymes.
Genome and time-of-day transcriptome ofWolffia australianalink morphological extreme minimization with un-gated plant growth
Authors: Michael Todd P. , Ernst Evan , Hartwick Nolan , Chu Philomena , Bryant Douglas , Gilbert Sarah , Ortleb Stefan , Baggs Erin L. , Sree K. Sowjanya , Appenroth Klaus J. , Fuchs Joerg , Jupe Florian , Sandoval Justin P. , Krasileva Ksenia V. , Borisjuk Ljudmylla , Mockler Todd C. , Ecker Joseph R. , Martienssen Robert A. , Lam Eric 
Published: April 2020

AbstractWolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than a day. Wolffia has a dramatically reduced body plan, primarily growing through a continuous, budding-type asexual reproduction with no obvious phase transition. Most plants are bound by the 24-hour light-dark cycle with the majority of processes such as gene expression partitioned or phased to a specific time-of-day (TOD). However, the role that TOD information and the circadian clock plays in facilitating the growth of a fast-growing plant is unknown. Here we generated draft reference genomes forWolffia australiana(Benth.) Hartog & Plas to monitor gene expression over a two-day time course under light-dark cycles.Wolffia australianahas the smallest genome size in the genus at 357 Mb and has a dramatically reduced gene set at 15,312 with a specific loss of root (WOX5), vascular (CASP), circadian (TOC1), and light-signaling (NPH3) genes. Remarkably, it has also lost all but one of the NLR genes that are known to be involved in innate immunity. In addition, only 13% of its genes cycle, which is far less than in other plants, with an overrepresentation of genes associated with carbon processing and chloroplast-related functions. Despite having a focused set of cycling genes, TOD cis-elements are conserved inW. australiana, consistent with the overall conservation of transcriptional networks. In contrast to the model plantsArabidopsis thalianaandOryza sativa, the reduction in cycling genes correlates with fewer pathways under TOD control in Wolffia, which could reflect a release of functional gating. Since TOD networks and the circadian clock work to gate activities to specific times of day, this minimization of regulation may enable Wolffia to grow continuously with optimal economy. Wolffia is an ideal model to study the transcriptional control of growth and the findings presented here could serve as a template for plant improvement.
Emotional responsiveness task in emotional distress: correlated of functional neuroimaging in anorexia and bulimia
Authors: D’Agata Federico , Caroppo Paola , Spalatro Angela , Lavagnino Luca , Daga Giovanni Abbate , Boghi Andrea , Bergui Mauro , Cicerale Alessandro , Vitiello Benedetto , Fassino Secondo , Derntl Birgit , Amianto Federico 
Published: April 2020

AbstractAimThe present study aims to extend the knowledge of the neural correlates of emotion processing in first episode subjects affected by anorexia nervosa (AN) or bulimia nervosa (BN). We applied an emotional distress paradigm targeting negative emotions thought to be relevant for interpersonal difficulties and therapeutic resistance mechanisms.MethodsThe current study applied a neuroimaging paradigm eliciting affective responses to 44 female participants with newly diagnosed AN or BN and 20 matched controls. The measurements also included an extensive assessment comprised of clinical scales, neuropsychological tests, measures of emotion processing and empathy.ResultsAN and BN did not differ from controls in terms of emotional response, emotion matching, self-reported empathy and cognitive performance. However, scores of eating disorder and psychopathological clinical scores, as well alexithymia levels, were increased in AN and BN. On a neural level, no significant group differences emerged, even when focusing on a region of interest selected a priori: the amygdala.ConclusionsOur data are against the hypothesis that participants with AN or BN display a reduced emotional responsiveness. This supports the hypothesis that relational difficulties, as well as therapeutic resistance, are not secondary to simple difficulty in feeling and identifying basic negative emotions in AN and BN participants.
Detecting tropical selective logging with SAR data requires a time series approach
Authors: Hethcoat MG , Carreiras JMB , Edwards DP , Bryant RG , Quegan S 
Published: April 2020

AbstractSelective logging is the primary driver of forest degradation in the tropics and reduces the capacity of forests to harbour biodiversity, maintain key ecosystem processes, sequester carbon, and support human livelihoods. While the preceding decade has seen a tremendous improvement in the ability to monitor forest disturbances from space, advances in forest monitoring have almost universally relied on optical satellite data from the Landsat program, whose effectiveness is limited in tropical regions with frequent cloud cover. Synthetic aperture radar (SAR) data can penetrate clouds and have been utilized in forest mapping applications since the early 1990s, but no study has exclusively used SAR data to map tropical selective logging. A detailed selective logging dataset from three lowland tropical forest regions in the Brazilian Amazon was used to assess the effectiveness of SAR data from Sentinel-1, RADARSAT-2 and PALSAR-2 for monitoring tropical selective logging. We built Random Forest models in an effort to classify pixel-based differences in logged and unlogged areas. In addition, we used the BFAST algorithm to assess if a dense time series of Sentinel-1 imagery displayed recognizable shifts in pixel values after selective logging. Random Forest classification with SAR data (Sentinel-1, RADARSAT-2, and ALOS-2 PALSAR-2) performed poorly, having high commission and omission errors for logged observations. This suggests little to no difference in pixel-based metrics between logged and unlogged areas for these sensors. In contrast, the Sentinel-1 time series analyses indicated that areas under higher intensity selective logging (> 20 m3ha−1) show a distinct spike in the number of pixels that included a breakpoint during the logging season. BFAST detected breakpoints in 50% of logged pixels and exhibited a false alarm rate of approximately 10% in unlogged forest. Overall our results suggest that SAR data can be used in time series analyses to detect tropical selective logging at high intensity logging locations within the Amazon (> 20 m3ha−1). These results have important implications for current and future abilities to detect selective logging with freely available SAR data from SAOCOM 1A, the planned continuation missions of Sentinel-1 (C and D), ALOS PALSAR-1 archives (expected to be opened for free access in 2020), and the upcoming launch of NISAR.
Regulation of light harvesting in Chlamydomonas: two protein phosphatases are involved in state transitions
Authors: Cariti Federica , Chazaux Marie , Lefebvre-Legendre Linnka , Longoni Paolo , Ghysels Bart , Johnson Xenie , Goldschmidt-Clermont Michel 
Published: April 2020

ABSTRACTProtein phosphorylation plays important roles in short-term regulation of photosynthetic electron transfer. In a mechanism known as state transitions, the kinase STATE TRANSITION 7 (STT7) ofChlamydomonas reinhardtiiphosphorylates components of light-harvesting antenna complex II (LHCII). This reversible phosphorylation governs the dynamic allocation of a part of LHCII to photosystem I or photosystem II, depending on light conditions and metabolic demands. Little is however known in the green alga on the counteracting phosphatase(s). In Arabidopsis, the homologous kinase STN7 is specifically antagonized by PROTEIN PHOSPHATASE 1/THYLAKOID-ASSOCIATED PHOSPHATASE 38 (PPH1/TAP38). Furthermore, the paralogous kinase STN8 and the countering phosphatase PHOTOSYSTEM II PHOSPHATASE (PBCP), which count subunits of PSII amongst their major targets, influence thylakoid architecture and high-light tolerance. Here we analyze state transitions inC. reinhardtiimutants of the two homologous phosphatases, CrPPH1 and CrPBCP. The transition from state 2 to state 1 is retarded inpph1, and surprisingly also inpbcp. However both mutants can eventually return to state 1. In contrast, the double mutantpph1;pbcpappears strongly locked in state 2. The complex phosphorylation patterns of the LHCII trimers and of the monomeric subunits are affected in the phosphatase mutants. Their analysis indicates that the two phosphatases have different yet overlapping sets of protein targets. The dual control of thylakoid protein de-phosphorylation and the more complex antenna phosphorylation patterns in Chlamydomonas compared to Arabidopsis are discussed in the context of the stronger amplitude of state transitions and the more diverse LHCII isoforms in the alga.
The Na+/K+ATPase Regulates Glycolysis and Modifies Immune Metabolism in Tumors
Authors: Sanderson Sydney M. , Xiao Zhengtao , Wisdom Amy J. , Bose Shree , Liberti Maria V. , Reid Michael A. , Hocke Emily , Gregory Simon G. , Kirsch David G. , Locasale Jason W. 
Published: April 2020

AbstractCancer therapies targeting metabolism have been limited due to a lack of understanding of the controlling properties of vulnerable pathways. The Na+/K+ATPase is responsible for a large portion of cellular energy demands but how these demands influence metabolism and create metabolic liabilities are not known. Using metabolomic approaches, we first show that digoxin, a cardiac glycoside widely used in humans, acts through disruption to central carbon metabolism via on target inhibition of the Na+/K+ATPase that was fully recovered by expression of an allele resistant to digoxin. We further show in vivo that administration of digoxin inhibits glycolysis in both malignant and healthy cells, particularly within clinically relevant cardiac tissue, while exhibiting tumor-specific cytotoxic activity in an allografted soft tissue sarcoma. Single-cell expression analysis of over 31,000 cells within the sarcoma shows that acute Na+/K+ATPase inhibition shifts the immune composition of the tumor microenvironment, leading to selective alterations to metabolic programs in specific immune cells thus acting both through tumor cell and microenvironmental (e.g. macrophage) cells. These results provide evidence that altering energy demands can be used to regulate glycolysis with cell-type specific consequences in a multicellular environment of biomedical interest.