bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensory and motor electrophysiological mapping of the cerebellum in humans
Authors: Ashida Reiko , Walsh Peter , Brooks Jonathan C.W. , Edwards Richard J. , Cerminara Nadia L. , Apps Richard 
Published: April 2020

AbstractDamage to the cerebellum during posterior fossa surgery can lead to ataxia and in paediatric cases, the risk of cerebellar mutism syndrome. Animal electrophysiological and human imaging studies have shown compartmentalisation of sensorimotor and cognitive functions within the cerebellum. In the present study, electrophysiological monitoring of sensory and motor pathways was carried out to assess the location of limb sensorimotor representation within the human cerebellum, as a potential approach for real time assessment of neurophysiological integrity to reduce the incidence of cerebellar surgical morbidities.Thirteen adult and paediatric patients undergoing posterior fossa surgery were recruited. For sensory mapping (n=8), electrical stimulation was applied to the median nerves, the posterior tibial nerves, or proximal and distal limb muscles and evoked field potential responses were sought on the cerebellar surface. For motor mapping (n=5), electrical stimulation was applied to the surface of the cerebellum and evoked EMG responses were sought in facial and limb muscles.Evoked potentials on the cerebellar surface were found in two patients (25% of cases). In one patient, the evoked response was located on the surface of the right inferior posterior cerebellum in response to stimulation of the right leg. In the second patient, stimulation of the extensor digitorum muscle in the left forearm evoked a response on the surface of the left inferior posterior lobe. In the motor mapping cases no evoked EMG responses could be found.Intraoperative electrophysiological mapping, therefore, indicates it is possible to record evoked potentials on the surface of the human cerebellum in response to peripheral stimulation.
Time course of changes in the long latency feedback response parallels the fast process of short term motor adaptation
Authors: Coltman Susan K. , Gribble Paul L. 
Published: April 2020

AbstractAdapting to novel dynamics involves modifying both feedforward and feedback control. We investigated whether the motor system alters feedback responses during adaptation to a novel force field in a manner similar to adjustments in feedforward control. We simultaneously tracked the time course of both feedforward and feedback systems via independent probes during a force field adaptation task. Participants (n=35) grasped the handle of a robotic manipulandum and performed reaches to a visual target while the hand and arm were occluded. We introduced an abrupt counter-clockwise velocity-dependent force field during a block of reaching trials. We measured movement kinematics and shoulder and elbow muscle activity with surface EMG electrodes. We tracked the feedback stretch response throughout the task. Using force channel trials we measured overall learning, which was later decomposed into a fast and slow process. We found that the long-latency feedback response (LLFR) was upregulated in the early stages of learning and was correlated with the fast component of feedforward adaptation. The change in feedback response was specific to the long-latency epoch (50-100 ms after muscle stretch) and was observed only in the triceps muscle, which was the muscle required to counter the force field during adaptation. The similarity in time course for the LLFR and the estimated time course of the fast process suggests both are supported by common neural circuits. While some propose that the fast process reflects an explicit strategy, we argue instead that it may be a proxy for the feedback controller.New & NoteworthyWe investigated whether changes in the feedback stretch response were related to the proposed fast and slow processes of motor adaptation. We found that the long latency component of the feedback stretch response was upregulated in the early stages of learning, and the time course was correlated with the fast process. While some propose that the fast process reflects an explicit strategy, we argue instead that it may be a proxy for the feedback controller.
Ultra-sparse connectivity within the lateral hypothalamus
Authors: Burdakov Denis , Karnani Mahesh M. 
Published: April 2020

AbstractThe lateral hypothalamus (LH) contains neuronal populations which generate fundamental behavioural actions such as feeding, sleep, movement, attack and evasion. Their activity is also correlated with various appetitive and consummatory behaviours as well as reward seeking. It is unknown how neural activity within and among these populations is coordinated. One hypothesis postulates that they communicate using inhibitory and excitatory synapses, forming local microcircuits. We inspected this hypothesis using quadruple whole cell recordings and optogenetics to screen thousands of potential connections in brain slices. In contrast to the neocortex, we found near zero connectivity within the LH. In line with its ultra-sparse intrinsic connectivity, we found that the LH does not generate local beta and gamma oscillations. This suggests that LH neurons integrate incoming input within individual neurons rather than through local network interactions, and that input from other brain structures is decisive for selecting active populations in LH.
Perivascular Secretome Influences Hematopoietic Stem Cell Maintenance in a Gelatin Hydrogel
Authors: Barnhouse Victoria , Petrikas Nathan , Crosby Cody , Zoldan Janet , Harley Brendan 
Published: April 2020

ABSTRACTAdult hematopoietic stem cells (HSCs) produce the body’s full complement of blood and immune cells. They reside in specialized microenvironments, or niches, within the bone marrow. The perivascular niche near blood vessels is believed to help maintain primitive HSCs in an undifferentiated state but demonstration of this effect is difficult.In vivostudies make it challenging to determine the direct effect of the endosteal and perivascular niches as they can be in close proximity, and two-dimensionalin vitrocultures often lack an instructive extracellular matrix environment. We describe a tissue engineering approach to develop and characterize a three-dimensional perivascular tissue model to investigate the influence of the perivascular secretome on HSC behavior. We generate 3D endothelial networks in methacrylamide-functionalized gelatin hydrogels using human umbilical vein endothelial cells (HUVECs) and mesenchymal stromal cells (MSCs). We identify a subset of secreted factors important for HSC function, and examine the response of primary murine HSCs in hydrogels to the perivascular secretome. Within 4 days of culture, perivascular conditioned media promoted maintenance of a greater fraction of hematopoietic stem and progenitor cells. This work represents an important first-generation perivascular model to investigate the role of niche secreted factors on the maintenance of primary HSCs.
Lineage-specific diversification in the usage of D-glutamate and D-aspartate in early-branching metazoans
Authors: Moroz Leonid L. , Sohn Dosung , Romanova Daria Y. , Kohn Andrea B. 
Published: April 2020

AbstractD-amino acids are unique and essential signaling molecules in neural, hormonal, and immune systems. However, the presence of D-amino acids and their recruitment in early animals is mostly unknown due to limited information about prebilaterian metazoans. Here, we performed the comparative survey of L-/D-aspartate and L-/D-glutamate in representatives of four phyla of basal Metazoa: cnidarians (Aglantha); placozoans (Trichoplax), sponges (Sycon) and ctenophores (Pleurobrachia, Mnemiopsis, Bolinopsis, andBeroe), which are descendants of ancestral animal lineages distinct from Bilateria. Specifically, we used high-performance capillary electrophoresis for microchemical assays and quantification of the enantiomers. L-glutamate and L-aspartate were abundant analytes in all species studied. However, we showed that the placozoans, cnidarians, and sponges had high micromolar concentrations of D-aspartate, whereas D-glutamate was not detectable. In contrast, we found that in ctenophores, D-glutamate was the dominant enantiomer with no or trace amounts of D-aspartate. This situation illuminates prominent lineage-specific diversifications in the recruitment of D-amino acids and suggests distinct signaling functions of these molecules early in the animal evolution. We also hypothesize that a deep ancestry of such recruitment events might provide some constraints underlying the evolution of neural and other signaling systems in Metazoa.HighlightsD-amino acids are essential for intercellular signaling and evolutionEnantiomers have been quantified in early-branching animalsLineage-specific recruitment of D-glutamate could occur in ctenophoresD-aspartate is one of the primary enantiomers in other metazoansDeep ancestry of such events could provide constraints in the evolution of signalingGraphical AbstractD-amino acids are essential for intercellular signaling. Direct microchemical quantification of enantiomers in representatives of early-branching animals suggests lineage-specific recruitments of D-glutamate and D-aspartate. Deep ancestry of such events might provide some constraints underlying the evolution of neural and other signaling systems in Metazoa.
What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data
Authors: Richelle Anne , Kellman Benjamin P. , Wenzel Alexander T. , Chiang Austin W.T. , Reagan Tyler , Gutierrez Jahir M. , Joshi Chintan , Li Shangzhong , Liu Joanne K. , Masson Helen , Lee Jooyong , Li Zerong , Heirendt Laurent , Trefois Christophe , Juarez Edwin F. , Bath Tyler , Borland David , Mesirov Jill P. , Robasky Kimberly , Lewis Nathan E. 
Published: April 2020

AbstractLarge-scale omics experiments have become standard in biological studies, leading to a deluge of data. However, researchers still face the challenge of connecting changes in the omics data to changes in cell functions, due to the complex interdependencies between genes, proteins and metabolites. Here we present a novel framework that begins to overcome this problem by allowing users to infer how metabolic functions change, based on omics data. To enable this, we curated and standardized lists of metabolic tasks that mammalian cells can accomplish. We then used genome-scale metabolic networks to define gene modules responsible for each specific metabolic task. We further developed a framework to overlay omics data on these modules to predict pathway usage for each metabolic task. The proposed approach allows one to directly predict how changes in omics experiments change cell or tissue function. We further demonstrated how this new approach can be used to leverage the metabolic functions of biological entities from the single cell to their organization in tissues and organs using multiple transcriptomic datasets (human and mouse). Finally, we created a web-based CellFie module that has been integrated into the list of tools available in GenePattern (www.genepattern.org) to enable adoption of the approach.
Allelic differences of clustered terpene synthases contribute to correlated intra-specific variation of floral and herbivory-induced volatiles in a wild tobacco
Authors: Xu Shuqing , Kreitzer Christoph , McGale Erica , Lackus Nathalie D. , Guo Han , Köllner Tobias G. , Schuman Meredith C. , Baldwin Ian T. , Zhou Wenwu 
Published: April 2020

SummaryPlant volatile emissions can recruit predators of herbivores for indirect defence and attract pollinators to aid in pollination. Although volatiles involved in defence and pollinator attraction are primarily emitted from leaves and flowers, respectively, they will co-evolve if their underlying genetic basis is intrinsically linked, either due to pleiotropy or genetic linkage. However, direct evidence of co-evolving defence and floral traits is scarce.We characterized intra-specific variation of herbivory-induced plant volatiles (HIPVs), the key components of indirect defence against herbivores, and floral volatiles in the wild tobaccoNicotiana attenuata.We found that variation of (E)-β-ocimene and (E)-α-bergamotene contributed to the correlated changes in HIPVs and floral volatiles amongN. attenuatanatural accessions. Intra-specific variations of (E)-β-ocimene and (E)-α-bergamotene emissions resulted from allelic variation of two genetically co-localized terpene synthase genes,NaTPS25andNaTPS38respectively.Analyzing haplotypes ofNaTPS25andNaTPS38revealed that allelic variations ofNaTPS25andNaTPS38resulted in correlated changes of (E)-β-ocimene and (E)-α-bergamotene emission in HIPVs and floral volatiles inN. attenuata.Together, these results provide evidence that pleiotropy and genetic linkage result in correlated changes in defences and floral signals in natural populations, and the evolution of plant volatiles is likely under diffuse selection.
Phylogenetic analysis of Michigan’s freshwater sponges (Porifera, Spongillidae) using extended COI mtDNA sequences
Authors: Kolomyjec Stephen H. , Willford Roger A. ,   THE FALL 2019 GENETICS CLASS
Published: April 2020

AbstractKolomyjecet al.(2020). Phylogenetic analysis of Michigan’s freshwater sponges (Porifera, Spongillidae) using extended COI mtDNA sequences. –Zoologica Scripta, 00, 000-000. The phylogenetic relationships of eight species of freshwater sponges sampled throughout the State of Michigan in the North American Great Lakes region were examined as part of a Course-based Undergraduate Research Experience (CURE). An extended version of the standard cytochrome oxidase subunit I (COI) metazoan DNA was used for sequencing and Bayesian phylogenetic inference. The extended gene region (COI-ext) produces a 1,200 bp amplicon instead of the standard 640 bp fragment which compensates for the standard amplicon’s low informatics value in Phylum Porifera. The species examined clustered into strongly supported monophyletic species groups within the familySpongillidae. This study represents the first look at the phylogenetic relationships of freshwater sponges in the Great Lakes Region.Per Kolomyjec, College of Science and the Environment, Lake Superior State University, 650 W Easterday Ave., Sault Sainte Marie, MI 49783, USA. E-mailskolomyjec@lssu.edu
Serotonin depletion impairs both Pavlovian and instrumental reversal learning in healthy humans
Authors: Kanen Jonathan W. , Apergis-Schoute Annemieke M. , Yellowlees Robyn , Arntz Frederique E. , van der Flier Febe E. , Price Annabel , Cardinal Rudolf N. , Christmas David M. , Clark Luke , Sahakian Barbara J. , Crockett Molly J. , Robbins Trevor W. 
Published: April 2020

AbstractSerotonin is implicated in aversive processing and updating responses to changing environmental circumstances. Optimising behaviour to maximise reward and minimise punishment may require shifting strategies upon encountering new situations. Likewise, emotional reactions to threats are critical for survival yet must be modified as danger shifts from one source to another. Whilst numerous psychiatric disorders are characterised by behavioural and emotional inflexibility, few studies have examined the contribution of serotonin in humans. We modelled both processes in two independent experiments (N = 97), using instrumental and aversive Pavlovian reversal learning paradigms, respectively. Upon depleting the serotonin precursor tryptophan – in a double-blind randomised placebo-controlled design – healthy volunteers showed impairments in updating both behaviour and emotion to reflect changing contingencies. Reversal deficits in each domain, furthermore, were correlated with the extent of tryptophan depletion. These results translate findings in experimental animals to humans and have implications for the neurochemical basis of cognitive inflexibility.
Genomes of Animal Mitochondria have not Evolved According to Common Models of Substitution Probabilities
Authors: Cavender James 
Published: April 2020

AbstractCommon probabilistic models of substitutions of bases (Jukes-Cantor, Kimura 2-parameter, Tamura-Nei, F84, HKY, and the 6-parameter models used in linear invariants methods) must be rejected, at least for mitochondrial genomes of animals. They are rejected by a new test that is simple and lenient.
A C++ library for protein sub-structure search
Authors: Zhou Jianfu , Grigoryan Gevorg 
Published: April 2020

AbstractSummaryMASTER is a previously published algorithm for protein sub-structure search. Given a database of protein structures and a query structural motif, composed of multiple disjoint segments, it finds all sub-structures from the database that align onto the query to within a pre-specified backbone root-mean-square deviation. Here, we present an improved version of the algorithm, MASTER v.2, in the form of an open-source C++ Application Program Interface library, thereby providing programmatic access to structure search functionality. An entirely reorganized approach to database representation now enables large structural databases to be stored in memory, further simplifying development of automated search-based methods. Given the increasingly important role of structure-based data mining, our improved implementation should find ample uses in structural biology applications.AvailabilityMASTER is available athttps://grigoryanlab.org/master/master-v2.php.Contactgevorg.grigoryan@dartmouth.edu
Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome
Authors: Rychel Kevin , Sastry Anand V. , Palsson Bernhard O. 
Published: April 2020

AbstractThe transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression, and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover novel or recently discovered roles for at least 5 regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states, revealing a putative anaerobic metabolism role for SigG. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis.
Effects of optogenetic stimulation of basal forebrain parvalbumin neurons on Alzheimer’s disease pathology
Authors: Wilson Caroline A , Fouda Sarah , Sakata Shuzo 
Published: April 2020

AbstractNeuronal activity can modify Alzheimer’s disease pathology. Although overexcitation of neurons can facilitate disease progression, the induction of cortical gamma oscillations can reduce amyloid load and improve cognitive functions in mouse models. These beneficial effects of gamma oscillations can be caused by either optogenetic activation of cortical parvalbumin-positive (PV+) neurons or 40 Hz repetitive sensory stimuli. However, given the fact that cortical gamma oscillations can be induced by multiple mechanisms, it is still unclear whether other approaches to induce gamma oscillations can also be beneficial. Here we show that optogenetic activation of PV+ neurons in the basal forebrain (BF) increases amyloid burden, rather than reducing it. We applied 40 Hz optical stimulation in the BF of 5xFAD mice by expressing channelrhodopsin-2 (ChR2) in PV+ neurons. After one-hour induction of cortical gamma oscillations over three days, we observed the increase in the concentration of amyloid-β42 in the frontal cortical region, but not amyloid-β40. The density of amyloid plaques also increased in the medial prefrontal cortex and the septal nuclei, both of which are targets of BF PV+ neurons. These results suggest that effects of cortical gamma oscillations on Alzheimer’s disease pathology can be bidirectional depending on their induction mechanisms.Significance StatementAlzheimer’s disease (AD) is the most common cause of dementia. Although numerous molecular targets have been identified, the development of treatment is still a challenge. Accumulating evidence shows that artificial control of neuronal activity can modify AD pathology. In particular, the induction of cortical gamma (~40 Hz) oscillations can ameliorate AD pathology and improve cognitive functions. Here we show that optogenetic activation of parvalbumin-positive (PV+) neurons in the basal forebrain (BF) has opposite effects. By expressing channelrhodopsin-2 (ChR2) in PV+ neurons of an AD mouse model and optically stimulating BF PV+ neurons, we induced gamma oscillations and found increased amyloid burden. These results imply that AD pathology can be modified bidirectionally depending on induction mechanisms of gamma oscillations.
BD5: an open HDF5-based data format to represent quantitative biological dynamics data
Authors: Kyoda Koji , Ho Kenneth H. L. , Tohsato Yukako , Itoga Hiroya , Onami Shuichi 
Published: April 2020

AbstractBD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML(Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML- based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics.
Coronavirus, as a source of pandemic pathogens
Authors: Konishi T. 
Published: April 2020

AbstractThe coronavirus and the influenza virus have similarities and differences. In order to comprehensively compare them, their genome sequencing data were examined by principal component analysis. Variations in coronavirus were smaller than those in a subclass of the influenza virus. In addition, differences among coronaviruses in a variety of hosts were small. These characteristics may have facilitated the infection of different hosts. Although many of the coronaviruses were more conservative, those repeatedly found among humans showed annual changes. If SARS-CoV-2 changes its genome like the Influenza H type, it will repeatedly spread every few years. In addition, the coronavirus family has many other candidates for subsequent pandemics.One Sentence SummaryThe genome data of coronavirus were compared to influenza virus, to investigate its spreading mechanism and future status. Coronavirus would repeatedly spread every few years. In addition, the coronavirus family has many other candidates for subsequent pandemics.