bluuebunny/crossref_metadata_2025_split huggingface dataset:
Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts
Authors: Atkinson Nicky , Mao Yuwei , Chan Kher Xing , McCormick Alistair J. 
Published: October 2020

SummaryPhotosynthetic CO2 fixation in plants is limited by the inefficiency of the CO2-assimilating enzyme Rubisco (D-ribulose-1,5-bisphosphate carboxylase/ oxygenase)1–3. In plants possessing the C3 pathway, which includes most major staple crops, Rubisco is typically evenly distributed throughout the chloroplast stroma. However, in almost all eukaryotic algae Rubisco aggregates within a microcompartment known as the pyrenoid, in association with a CO2-concentrating mechanism that improves photosynthetic operating efficiency under conditions of low inorganic carbon4. Recent work has shown that the pyrenoid matrix is a phase-separated, liquid-like condensate5. In the alga Chlamydomonas reinhardtii, condensation is mediated by two components: Rubisco and the linker protein EPYC1 (Essential Pyrenoid Component 1)6,7. Here we show that expression of mature EPYC1 and a plant-algal hybrid Rubisco leads to spontaneous condensation of Rubisco into a single phase-separated compartment in Arabidopsis chloroplasts, with liquid-like properties similar to a pyrenoid matrix. The condensate displaces the thylakoid membranes and is enriched in hybrid Rubisco containing the algal Rubisco small subunit required for phase separation. Promisingly, photosynthetic CO2 fixation and growth is not impaired in stable transformants compared to azygous segregants. These observations represent a significant initial step towards enhancing photosynthesis in higher plants by introducing an algal CO2-concentrating mechanism, which is predicted to significantly increase the efficiency of photosynthetic CO2 uptake8,9.
The Big Five personality traits and CNS arousal in the resting state
Authors: Jawinski Philippe , Markett Sebastian , Sander Christian , Huang Jue , Ulke Christine , Hegerl Ulrich , Hensch Tilman 
Published: October 2020

AbstractBased on Eysenck’s pioneering work, CNS arousal has long been considered an encouraging biological candidate that may explain individual differences in human personality. Yet, results from empirical studies remained inconclusive. Notably, the vast majority of published results have been derived from small samples, and EEG alpha power has usually served as exclusive indicator for CNS arousal. In this study, we selectedN= 468 individuals of the LIFE-Adult cohort and investigated the associations between the Big Five personality traits and CNS arousal by using the low-resolution electromagnetic tomography-based analysis tool VIGALL. Our analyses revealed that subjects who reported higher levels of extraversion and openness to experience, respectively, exhibited lower levels of CNS arousal in the resting state. Bayesian and frequentist analysis results were especially convincing for openness to experience. Among the lower-order personality traits, we obtained strongest evidence for neuroticism facet ‘impulsivity’ and reduced CNS arousal. We regard these findings as well in line with the postulations of Eysenck and Zuckerman and consistent with the assumptions of the ‘arousal regulation model’. Our results also agree with meta-analytically derived effect sizes in the field of individual differences research, highlighting the need for large studies with at least several hundreds of subjects.
The Social Role of Self-Control
Authors: Dunbar R.I.M. , Shultz Susanne 
Published: October 2020

AbstractThe capacity to inhibit prepotent actions (inhibitory self-control) plays an important role in many aspects of the behaviour of birds and mammals. Although a number of studies have used it as an index of foraging skills, inhibition is also crucial for maintaining the temporal and spatial coherence of bonded social groups. Using three different sets of comparative data, we show that, across primate species, the capacity for self-control correlates better with the demands of social contexts than with the demands of foraging contexts, whereas a more generalised capacity for causal reasoning correlates better with foraging contexts. In addition, we confirm the Passingham-Wise Conjecture that the capacity for self-control is unique to anthropoid primates. These results suggest that the capacity for self-control most likely evolved because it was crucial for the evolution of bonded social groups.Significance StatementThe capacity for self-control has commonly been viewed as an index of foraging skills. In fact, it plays a much more important role in the social domain by enabling groups of animals to maintain social cohesion as they travel through time and space. In this respect, it is particularly important for species that live in stable bonded social groups (congregations). We show that, in this respect, it is uniquely characteristic of the anthropoid primates, in contrast to other kinds of reasoning tasks such as causal reasoning on which primates often perform no better than other birds and mammals.
Impact of the expectation on memory reconsolidation using a post retrieval extinction paradigm
Authors: Marinos Julia , Ashbaugh Andrea 
Published: October 2020

AbstractObjectiveThe present study examined if the expectation for learning enhances reconsolidation of conditioned fear memories using the post-retrieval extinction paradigm in an undergraduate sample (n = 48).MethodsThe study took place over three consecutive days. The expectation for learning was manipulated through oral instructions prior to memory reactivation. On day one, participants underwent differential fear conditioning to two spider images (CS+ and CS-). On day two, participants were assigned to either a reactivation with expectation for learning group, a reactivation with no expectation for learning group, or a no reactivation group. On day three, return of fear in response to the CS+ spider image was measured following reinstatement (i.e., four shocks). Fear potentiated startle (FPS) and skin conductance response (SCR) were taken as measures of fear.ResultsThe study found evidence that the expectation for learning may enhanced reconsolidation with FPS as a measure of fear as it was only the expectation for learning group in which FPS to the CS+ remained stable following reinstatement, however this effect was small and non-robust. In contrast, no evidence of reconsolidation was observed for SCR, as all participants exhibited a return of fear following reinstatement.ImplicationsThese findings suggest that a verbal manipulation of the expectation for learning may not be salient enough to induce reconsolidation as measured by SCR but may be sufficient as measured by FPS. Additionally, given in the inconsistent findings between SCR and FPS, the study’s results bring into question whether the post-retrieval extinction paradigm is appropriate to investigate reconsolidation using both physiological measures concurrently.
Integrating indigenous knowledge, ontology, and molecular barcoding to characterize spider monkey (Ateles paniscus) filariasis
Authors: Milstein Marissa S. , Shaffer Christopher A. , Lindsey Laramie L. , Wolf Tiffany M. , Suse Philip , Marawanaru Elisha , Kipp Evan J. , Garwood Tyler , Travis Dominic A. , Terio Karen A. , Larsen Peter A. 
Published: October 2020

AbstractZoonotic disease risk is greatly influenced by cultural practices and belief systems. Yet, few studies have integrated traditional ecological knowledge and ontology with western ways of knowing to better understand potential zoonoses. Here, we integrate molecular phylogenetics, histopathology, and ethnography to characterize a filarial nematode found within the abdominal cavity of spider monkeys (Ateles paniscus). The filarid is recognized as ‘spider monkey cotton’ by indigenous Waiwai in the Konashen Community Owned Conservation Area, Guyana. Ethnographic data revealed that the Waiwai perceive of ‘spider monkey cotton’ as a normal characteristic within the ‘spider monkey person.’ Further, the Waiwai indicated that ‘cotton’ was ubiquitous with spider monkeys and is not understood to be infectious nor zoonotic. This distinction is in contrast to other internal parasites found within spider monkeys that the Waiwai know to cause disease in both monkeys and humans. Our morphological and molecular characterization support the classification of the filarid asDipetalonema caudispina, a minimally studied and seemingly non-zoonotic parasite, consistent with Waiwai beliefs. Thus, our findings allow us to establish commensurability between scientific knowledge and indigenous ontology. More broadly, this work highlights the importance of integrating multiple knowledge systems and leveraging advanced genomics to better understand and prevent emerging zoonotic diseases.
Deep-learning based identification, tracking, pose estimation, and behavior classification of interacting primates and mice in complex environments
Authors: Marks Markus , Qiuhan Jin , Sturman Oliver , von Ziegler Lukas , Kollmorgen Sepp , von der Behrens Wolfger , Mante Valerio , Bohacek Johannes , Yanik Mehmet Fatih 
Published: October 2020

AbstractThe quantification of behaviors of interest from video data is commonly used to study brain function, the effects of pharmacological interventions, and genetic alterations. Existing approaches lack the capability to analyze the behavior of groups of animals in complex environments. We present a novel deep learning architecture for classifying individual and social animal behavior, even in complex environments directly from raw video frames, while requiring no intervention after initial human supervision. Our behavioral classifier is embedded in a pipeline (SIPEC) that performs segmentation, identification, pose-estimation, and classification of complex behavior, outperforming the state of the art. SIPEC successfully recognizes multiple behaviors of freely moving individual mice as well as socially interacting non-human primates in 3D, using data only from simple mono-vision cameras in home-cage setups.
Deep learning enables fast and dense single-molecule localization with high accuracy
Authors: Speiser Artur , Müller Lucas-Raphael , Matti Ulf , Obara Christopher J. , Legant Wesley R. , Kreshuk Anna , Macke Jakob H. , Ries Jonas , Turaga Srinivas C. 
Published: October 2020

ABSTRACTSingle-molecule localization microscopy (SMLM) has had remarkable success in imaging cellular structures with nanometer resolution, but the need for activating only single isolated emitters limits imaging speed and labeling density. Here, we overcome this major limitation using deep learning. We developed DECODE, a computational tool that can localize single emitters at high density in 3D with highest accuracy for a large range of imaging modalities and conditions. In a public software benchmark competition, it outperformed all other fitters on 12 out of 12 data-sets when comparing both detection accuracy and localization error, often by a substantial margin. DECODE allowed us to take live-cell SMLM data with reduced light exposure in just 3 seconds and to image microtubules at ultra-high labeling density. Packaged for simple installation and use, DECODE will enable many labs to reduce imaging times and increase localization density in SMLM.
A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment
Authors: Zhou Wenbin , Soghigian John , (Jenny) Xiang Qiu-yun 
Published: October 2020

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies ofHamamelis(the witch-hazels) andCastanea(chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs,Castanea,Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]
Slowing the Body slows down Time (Perception)
Authors: De Kock Rose , Zhou Weiwei , Joiner Wilsaan Mychal , Wiener Martin 
Published: October 2020

AbstractInterval timing is a fundamental component action, and is susceptible to motor-related temporal distortions. Previous studies have shown that movement biases temporal estimates, but have primarily considered self-modulated movement only. However, real-world encounters often include situations in which movement is restricted or perturbed by environmental factors. In the following experiments, we introduced viscous movement environments to externally modulate movement and investigated the resulting effects on temporal perception. In two separate tasks, participants timed auditory intervals while moving a robotic arm that randomly applied four levels of viscosity. Results demonstrated that higher viscosity led to shorter perceived durations. Using a drift-diffusion model and a Bayesian observer model, we confirmed these biasing effects arose from perceptual mechanisms, instead of biases in decision making. These findings suggest that environmental perturbations are an important factor in movement-related temporal distortions, and enhance the current understanding of the interactions of motor activity and cognitive processes.
Ca2+signaling driving pacemaker activity in submucosal interstitial cells of Cajal in the colon
Authors: Baker Salah A. , Leigh Wesley A. , De Yturriaga Inigo F. , Ward Sean M. , Cobine Caroline A. , Drumm Bernard T. , Sanders Kenton M. 
Published: October 2020

AbstractInterstitial cells of Cajal (ICC) generate pacemaker activity responsible for phasic contractions in colonic segmentation and peristalsis. ICC along the submucosal border (ICC-SM) contributing to mixing and more complex patterns of colonic motility. We show the complex patterns of Ca2+signaling in ICC-SM and the relationship between ICC-SM Ca2+transients and activation of SMCs using optogenetic tools. ICC-SM displayed rhythmic firing of Ca2+transients ∼15 cpm and paced adjacent SMCs. The majority of spontaneous activity occurred in regular Ca2+ transients clusters (CTCs) that propagated through the network. CTCs were organized and dependent upon Ca2+entry through voltage-dependent Ca2+conductances, L- and T-type Ca2+channels. Removal of Ca2+from the external solution abolished CTCs. Ca2+release mechanisms reduced the duration and amplitude of Ca2+transients but did not block CTCs. These data reveal how colonic pacemaker ICC-SM exhibit complex Ca2+firing patterns and drive smooth muscle activity and overall colonic contractions.SynopsisHow Ca2+signaling in colonic submucosal pacemaker cells couples to smooth muscle responses is unknown. This study shows how ICC modulate colonic motility via complex Ca2+signaling and defines Ca2+transients’ sources using optogenetic techniques.
Genome-scale metabolic model of the diatomThalassiosira pseudonanahighlights the importance of nitrogen and sulfur metabolism in redox balance
Authors: van Tol Helena M. , Virginia Armbrust E. 
Published: October 2020

AbstractDiatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the character of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model ofThalassiosira pseudonanastrain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5-200 μmol photons m−2s−1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatomThalassiosira pseudonanaprovides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.
Characterization and structural prediction of the putative ORF10 protein in SARS-CoV-2
Authors: Schuster Noah A. 
Published: October 2020

AbstractUpstream of the 3’-untranslated region in the SARS-CoV-2 genome is ORF10 which has been proposed to encode for the ORF10 protein. Current research is still unclear on whether this protein is synthesized, but further investigations are still warranted. Herein, this study uses multiple bioinformatic tools to biochemically and functionally characterize the ORF10 protein, along with predicting its tertiary structure. Results indicate a highly ordered, hydrophobic, and thermally stable protein that contains at least one transmembrane region. This protein also possesses high residue protein-binding propensity, primarily in the N-terminal half. An assessment of forty-one missense mutations reveal slight changes in residue flexibility, mainly in the C-terminal half. However, these same mutations do not inflict significant changes on protein stability and other biochemical features. The predicted model suggests the ORF10 protein contains a β-α-β motif with a β-molecular recognition feature occurring in the first β-strand. Functionally, the ORF10 protein could be a membrane protein. A single pocket was identified in this protein but found to possess low druggability. The ORF10 itself consists of two distinct lineages: the SARS-CoV lineage and the SARS-CoV-2 lineage. Evidence of strong positive selection (dN/dS = 4.01) and purifying selection (dN/dS = 0.713) were found within the SARS-CoV-2 lineage and SARS-CoV lineage, respectively. Collectively, these results continue to assess the biological relevance of ORF10 and its putatively encoded protein, thereby aiding in diagnostic and possibly vaccine development.
Buprenorphine exposure alters the development and migration of interneurons in the cortex
Authors: Nieto-Estévez Vanesa , Donegan Jennifer J. , McMahon Courtney , Elam Hannah B. , Chavera Teresa A. , Varma Parul , Berg Kelly A. , Lodge Daniel J. , Hsieh Jenny 
Published: October 2020

ABSTRACTThe misuse of opioids has reached epidemic proportions over the last decade, with over 2.1 million people in the U.S. suffering from substance use disorders related to prescription opioid pain relievers. This increase in opioid misuse affects all demographics of society, including women of child-bearing age, which has led to a rise in opioid use during pregnancy. Opioid use during pregnancy has been associated with increased risk of obstetric complications and adverse neonatal outcomes, including neonatal abstinence syndrome. Currently, opioid use disorder in pregnant women is treated with long-acting opioid agonists, including buprenorphine. Although buprenorphine reduces illicit opioid use during pregnancy and improves infant outcomes at birth, few long-term studies of the neurodevelopmental consequences have been conducted. The goal of the current experiments was to examine the effects of buprenorphine on the development of the cortex using fetal brain tissue, 3D brain cultures, and rodent models. First, we demonstrated that we can grow cortical and subpallial spheroids, which model the cellular diversity, connectivity, and activity of the developing human brain. Next, we show that cells in the developing human cortex express the nociceptin opioid (NOP) receptor and that buprenorphine can signal through this receptor in cortical spheroids. Using subpallial spheroids to grow inhibitory interneurons, we show that buprenorphine can alter interneuron development and migration into the cortex. Finally, using a rodent model of prenatal buprenorphine exposure, we demonstrate that alterations in interneuron distribution can persist into adulthood. Together, these results suggest that more research is needed into the long-lasting consequences of buprenorphine exposure on the developing human brain.