bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artemisia extracts Differ from Artemisinin Effects on Human Hepatic CYP450s 2B6 and 3A4 in vitro
Authors: Kane Ndeye F. , Kiani Bushra H. , Desrosiers Matthew R. , Towler Melissa J. , Weathers Pamela J. 
Published: June 2022

AbstractEthnopharmacological relevanceThe Chinese medicinal herb, Artemisia annua L., has been used for >2,000 yr as traditional tea infusions to treat a variety of infectious diseases including malaria, and its use is spreading globally (along with A. afra Jacq. ex Willd.) mainly through grassroots efforts.Aim of the studyArtemisinin is more bioavailable delivered from the plant, Artemisia annua L. than the pure drug, but little is known about how delivery via a hot water infusion (tea) alters induction of hepatic CYP2B6 and CYP3A4 that metabolize artemisinin.Materials and MethodsHepaRG cells were treated with 10 μM artemisinin or rifampicin (positive control), and teas (10 g/L) of A. annua SAM, and A. afra SEN and MAL with 1.6, 0.05 and 0 mg/gDW artemisinin in the leaves, respectively; qPCR, and Western blots, were used to measure CYP2B6 and CYP3A4 responses. Enzymatic activity of these P450s was measured using liver microsomes and P450-Glo assays.ResultsAll teas inhibited activity of CYP2B6 and CYP3A4. Artemisinin and the high artemisinin-containing tea infusion (SAM) induced CYP2B6 and CYP3A4 transcription, but artemisinin-deficient teas, MAL and SEN, did not. Artemisinin increased CYP2B6 and CYP3A4 protein levels, but none of the three teas did, indicating a post-transcription inhibition by all three teas.ConclusionsThis study showed that Artemisia teas inhibit activity and artemisinin autoinduction of CYP2B6 and CYP3A4 post transcription, a response likely the effect of other phytochemicals in these teas. Results are important for understanding Artemisia tea posology.
A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction
Authors: Dharni Jaspinder Singh , Dhatt Balpreet Kaur , Paul Puneet , Gao Tian , Awada Tala , Staswick Paul , Hupp Jason , Yu Hongfeng , Walia Harkamal 
Published: June 2022

SummaryOur understanding of the physiological response of rice inflorescence (panicle) to environmental stresses is limited by the challenge of accurately determining panicle photosynthetic parameters and their impact on grain yield. This is primarily due to lack of a suitable gas exchange methodology for panicles, as well as non-destructive methods to accurately determine panicle surface area. To address these challenges, we have developed a custom panicle gas exchange cylinder compatible with the LiCor 6800 Infra-red Gas Analyzer. Accurate surface area measurements were determined with a 3D panicle imaging platform to normalize the panicle-level photosynthetic measurements. We observed differential responses in both panicle and flag leaf for two temperate Japonica rice genotypes (accessions, TEJ-1 and TEJ-2) exposed to heat stress during early grain filling. There was a notable divergence in relative photosynthetic contribution of flag leaf and panicles for the genotype tolerant to heat stress (TEJ-2) compared to the less tolerant accession. The novelty of this approach is that it is non-destructive and more accurately determines panicle area and photosynthetic parameters, enabling researchers to monitor temporal changes in panicle physiology during the reproductive development. The method is useful for panicle-level measurements under diverse environmental stresses, and for evaluating genotypic variation for panicle physiology and architecture in other cereals with compact inflorescences.
Three Novel Methods for Determining Motor Threshold with Transcranial Magnetic Stimulation Outperform Conventional Procedures
Authors: Wang Boshuo , Peterchev Angel V. , Goetz Stefan M. 
Published: June 2022

AbstractObjectiveThresholding of neural responses is central to many applications of transcranial magnetic stimulation (TMS), but the stochastic aspect of neuronal activity and motor evoked potentials (MEPs) challenges thresholding methods. We analyzed existing methods for obtaining TMS motor threshold and their variations, introduced new methods from other fields, and compared their accuracy and speed.ApproachIn addition to existing relative-frequency methods, such as the five-out-of-ten method, we examined adaptive methods based on a probabilistic motor threshold model using maximum-likelihood (ML) or maximuma- posteriori(MAP) estimation. To improve the performance of these adaptive estimation methods, we explored variations in the estimation procedure and inclusion of population-level prior information. We adapted a Bayesian estimation method which iteratively incorporated information of the TMS responses into the probability density function. A family of non-parametric stochastic root-finding methods with different convergence criteria and stepping rules were explored as well. The performance of the thresholding methods was evaluated with an independent stochastic MEP model.Main ResultsThe conventional relative-frequency methods required a large number of stimuli, were inherently biased on the population level, and had wide error distributions for individual subjects. The parametric estimation methods obtained the thresholds much faster and their accuracy depended on the estimation method, with performance significantly improved when population-level prior information was included. Stochastic root-finding methods were comparable to adaptive estimation methods but were much simpler to implement and did not rely on a potentially inaccurate underlying estimation model.SignificanceTwo-parameter MAP estimation, Bayesian estimation, and stochastic root-finding methods have better error convergence compared to conventional single-parameter ML estimation, and they all require significantly fewer TMS pulses for accurate estimation than conventional relative-frequency methods. Stochastic root finding appears particularly attractive due to the low computational requirements, simplicity of the algorithmic implementation, and independence from potential model flaws in the parametric estimators.
MenDEL: PCR Primer Design as Constrained Optimization Process
Authors: German Sergei , Mitchell Leslie A. , Vela Gartner Antonio , Fenyö David , Boeke Jef D. 
Published: June 2022

AbstractMotivationThe synthesis of large DNA assemblies has applications in biotechnology, and can help us better understand genome biology. These large DNA assemblies are often constructed from many smaller DNA segments, and it is critical to assess that they are correctly assembled. One low cost and rapid method to ensure that the connection between each segment is correct is to use PCR with primer pairs that span assembly junctions. However, the design of PCR primers for large assemblies consisting of multiple segments, and therefore containing multiple assembly junctions, is a challenging process. Rule-based automation of the process often results in finding primers that satisfy general criteria, but are not necessarily the best fit for every particular junction.ResultsWe have developed MenDEL – a web-based DNA design application, that provides a primer pair computation tool for multiple assembly junctions in such a way that for each junction we automatically pick the optimal pair of primers based on user specified constraints.Availability and ImplementationThe MenDEL application is available at https://mendel-isg.nyumc.org to registered users, and the code base for computing junction primers is available at https://github.com/MendelProject/PrimerOptimization.
Position representations of moving objects align with real-time position in the early visual response
Authors: Johnson Philippa A. , Blom Tessel , van Gaal Simon , Feuerriegel Daniel , Bode Stefan , Hogendoorn Hinze 
Published: June 2022

AbstractWhen localising a moving object, the brain receives outdated sensory information about its position, due to the time required for neural transmission and processing. The brain may overcome these fundamental delays through predictively encoding the position of moving objects using information from their past trajectories. In the present study, we evaluated this proposition using multivariate analysis of high temporal resolution electroencephalographic data. We tracked neural position representations of moving objects at different stages of visual processing, relative to the real-time position of the object. During early stimulus-evoked activity, position representations of moving objects were activated substantially earlier than the equivalent activity evoked by unpredictable flashes, aligning the earliest representations of moving stimuli with their real-time positions. These findings indicate that the predictability of straight trajectories enables full compensation for the neural delays accumulated early in stimulus processing, but that delays still accumulate across later stages of cortical processing.
Neuronal Population Encoding of Identity in Primate Prefrontal Cortex
Authors: Sharma KK , Diltz MA , Lincoln T , Albuquerque ER , Romanski LM 
Published: June 2022

AbstractThe ventrolateral prefrontal cortex (VLPFC) shows robust activation during the perception of faces and voices. However, little is known about what categorical features of social stimuli drive neural activity in this region. Since perception of identity and expression are critical social functions, we examined whether neural responses to naturalistic stimuli were driven by these two categorial features in the prefrontal cortex. We recorded single neurons in the VLPFC, while two macaques viewed short audiovisual videos of unfamiliar conspecifics making expressions of aggressive, affiliative, and neutral valence. Of the 285 neurons responsive to the audiovisual stimuli, 111 neurons had a main effect (two-way ANOVA) of identity, expression or their interaction in their stimulus related firing rates; however, decoding of expression and identity using single unit firing rates rendered poor accuracy. Interestingly, when decoding from pseudopopulations of recorded neurons, the accuracy for both expression and identity increased with population size, suggesting that the population transmitted information relevant to both variables. Principal components analysis of mean population activity across time revealed that population responses to the same identity followed similar trajectories in the response space, facilitating segregation from other identities. Our results suggest that identity is a critical feature of social stimuli that dictates the structure of population activity in the VLPFC, during the perception of vocalizations and their corresponding facial expressions. These findings enhance our understanding of social behavior beyond the temporal lobe in macaques and humans.Significance StatementPrimates are unique in their ability to process and utilize complex, multisensory social information. The brain networks that support this are distributed across the temporal and frontal lobes. In this study, we characterize how social variables like identity and expression are encoded in the neural activity of the ventrolateral prefrontal cortex (VLPFC), a prefrontal region of the macaque brain. We found that single neurons do not appear to encode these variables, but populations of neurons display similar activity patterns that are primarily differentiated by the identity of the conspecific that a macaque is attending to. Furthermore, by employing dynamic, multisensory stimuli, our experiment better approximates real world conditions, making our findings more generalizable.
Superior colliculus visual neural sensitivity at the lower limit of natural self-induced image displacements
Authors: Hafed Ziad M. , Chen Chih-Yang , Khademi Fatemeh 
Published: June 2022

AbstractVisual pattern analysis relies on computations from neurons possessing spatially confined receptive fields. Often, such receptive fields are orders of magnitude larger than the visual pattern components being processed, as well as these components’ minute displacements on the retina, whether due to small object or self motions. Yet, perception effortlessly handles such visual conditions. Here, we show that in the primate superior colliculus, a brain structure long associated with oculomotor control, neurons with relatively large receptive fields are still sensitive to visual pattern displacements as small as 1 min arc. We used real-time gaze-contingent retinal image stabilization to control the instantaneous spatio-temporal luminance modulation of detailed patterns experienced by neurons, probing sensitivity to the lower limit of natural self-induced image displacements. Despite a large difference between pattern displacement amplitudes and receptive field sizes, collicular neurons were strongly sensitive to the visual pattern consequences of the smallest possible image-shifting eye movements.
Vti1a/b support distinct aspects of TGN and cis-/medial Golgi organization
Authors: van Bommel Danique M , Toonen Ruud F , Verhage Matthijs 
Published: June 2022

AbstractRetrograde trafficking towards the trans-Golgi network (TGN) is important for dense core vesicle (DCV) biogenesis. Here, we used Vti1a/b deficient neurons to study the impact of disturbed retrograde trafficking on Golgi organization and cargo sorting. In Vti1a/b deficient neurons, staining intensity of cis-/medial Golgi proteins (e.g., GM130 and giantin) was increased, while intensity of TGN-resident proteins (e.g., TGN38 and TMEM87A) was decreased. Levels and localization of DCV cargo markers and LAMP1 were altered. This phenotype was not caused by reduced Golgi membrane availability or absence of the TGN compartment. The phenotype was partially phenocopied by disturbing sphingolipid homeostasis, but was not rescued by overexpression of sphingomyelin synthases or the sphingolipid synthesis inhibitor myriocin. We conclude that Vti1a/b are important for distinct aspects of TGN and cis-/medial Golgi organization. Our data underline the importance of retrograde trafficking for Golgi organization, DCV cargo sorting and the distribution of proteins of the regulated secretory pathway.
Model of inverse bleb growth explains giant vacuole dynamics during cell mechanoadaptation
Authors: Cairoli Andrea , Spenlehauer Alice , Overby Darryl R , Lee Chiu Fan 
Published: June 2022

AbstractCells can withstand hostile environmental conditions manifest as large mechanical forces such as pressure gradients and/or shear stresses by dynamically changing their shape. Such conditions are realized in the Schlemm’s canal of the eye where endothelial cells that cover the inner vessel wall are subjected to the hydrodynamic pressure gradients exerted by the aqueous humor outflow. These cells form fluid-filled dynamic outpouchings of their basal membrane calledgiant vacuoles. The inverse of giant vacuoles are reminiscent of cellular blebs, extracellular cytoplasmic protrusions triggered by local temporary disruption of the contractile actomyosin cortex. Inverse blebbing has been first observed experimentally during sprouting angiogenesis, but its underlying physical mechanisms are poorly understood. Here, we identify giant vacuole formation as inverse blebbing and formulate a biophysical model of this process. Our model elucidates how cell membrane mechanical properties affect the morphology and dynamics of giant vacuoles and predicts coarsening akin to Ostwald ripening between multiple invaginating vacuoles. Our results are in qualitative agreement with observations from the formation of giant vacuoles during perfusion experiments. Our model not only elucidates the biophysical mechanisms driving inverse blebbing and giant vacuole dynamics, but also identifies universal features of the cellular response to pressure loads that are relevant to many experimental contexts.Significance statementHuman Schlemm’s canal endothelial cells in physiological conditions are subjected to a pressure gradient caused by the flow of aqueous humor in the basal-to-apical direction across the endothelium leading to the formation of cellular outpouchings called giant vacuoles. The physical mechanisms regulating giant vacuole formation are unknown. By describing giant vacuoles as inward blebs, we formulate a model of their growth and collapse that captures the characteristic features observed experimentally. Our theory reveals that the abrupt increase in surface tension caused by membrane stretching, which is required to accommodate the large areal strains locally induced by inward blebbing, limits giant vacuole growth. The model also predicts a competition between multiple invaginating vacuoles in which big vacuoles win over small vacuoles.
Chromosomal assembly of the flat oyster (Ostrea edulisL.) genome as a new genetic ressource for aquaculture
Authors: Boutet Isabelle , Alves Monteiro Homère J. , Baudry Lyam , Takeuchi Takeshi , Bonnivard Eric , Billoud Bernard , Farhat Sarah , Gonzales-Haraya Ricardo , Salaun Benoit , Andersen Ann , Toullec Jean-Yves , Lallier François , Flot Jean-François , Guiglielmoni Nadège , Guo Ximing , Cui Li , Allam Bassem , Pales-Espinoza Emmanuelle , Hemmer-Hansen Jakob , Marbouty Martial , Koszul Romain , Tanguy Arnaud 
Published: June 2022

AbstractThe European flat oyster (Ostrea edulisL.) is the endemic species of the European coasts. Its exploitation has been reduced during the last decades, because of the appearance of two parasites that have led to the collapse of the stocks and the strong decline of the natural oyster beds.O. edulishas been the subject of numerous studies and programs in population genetics and on the presence of the parasitesBonamia ostreaeandMarteilia refringens. These studies investigated the effects of these parasites mainly on immunity at the molecular and cellular levels. Several genetic selection programs especially related to resistance to the parasite have been initiated. Within the framework of a European project (PERLE 2) which aims to produce genetic lines ofO. eduliswith hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species on the foreshore, obtaining a reference genome has proved to be essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio technology, Illumina, 10X linked and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudo-chromosomes. Annotation of the genome revealed the presence of 35962 protein-coding genes. We analyzed in details the transposable elements (TE) diversity in the flat oyster genome, highlight some specificities in tRNA and miRNA composition and provide first insights in the molecular response ofO. edulistoM. refringens. This genome will serve as a reference for genomic studies onO. edulisto better understand its basic physiology or developing genetic markers in breeding projects for aquaculture or natural reef restoration.
A moonlighting function of a chitin polysaccharide monooxygenase, CWR-1, in allorecognition in Neurospora crassa
Authors: Detomasi Tyler C. , Rico-Ramírez Adriana M. , Sayler Richard I. , Gonçalves A. Pedro , Marletta Michael A. , Glass N. Louise 
Published: June 2022

AbstractOrganisms require the ability to differentiate themselves from organisms of different or even the same species. Allorecognition processes in filamentous fungi are essential to ensure identity of an interconnected syncytial colony to protect it from exploitation and disease. Neurospora crassa has three cell fusion checkpoints controlling formation of an interconnected mycelial network. The locus that controls the second checkpoint, which allows for cell wall dissolution and subsequent fusion between cells/hyphae, cwr, encodes two linked genes, cwr-1 and cwr-2. Previously, it was shown that cwr-1 and cwr-2 show severe linkage disequilibrium with six different haplogroups present in N. crassa populations. Isolates from an identical cwr haplogroup show robust fusion, while somatic cell fusion between isolates of different haplogroups is significantly blocked in cell wall dissolution. The cwr-1 gene encodes a putative polysaccharide monooxygenase (PMO). Herein we confirm that CWR-1 is a C1-oxidizing chitin PMO. We show that the PMO domain of CWR-1 was sufficient for checkpoint function and cell fusion blockage; however, through analysis of active-site, histidine-brace mutants, the catalytic activity of CWR-1 was ruled out as a major factor for allorecognition. Swapping a portion of the PMO domain (V86 to T130) did not switch cwr haplogroup specificity, but rather cells containing this chimera exhibited a novel haplogroup specificity. Allorecognition to mediate cell fusion blockage is likely occurring through a protein-protein interaction between CWR-1 with CWR-2. These data highlight a moonlighting role in allorecognition of the CWR1 PMO domain.
Six-Dimensional Single-Molecule Imaging with Isotropic Resolution using a Multi-View Reflector Microscope
Authors: Zhang Oumeng , Guo Zijian , He Yuanyuan , Wu Tingting , Vahey Michael D. , Lew Matthew D. 
Published: June 2022

AbstractWe report a radially and azimuthally polarized multi-view reflector (raMVR) microscope for precise imaging of the 3D positions and 3D orientations of single molecules (SMs, 10.9 nm and 2.0° precisions using 5000 photons). These precisions are ∼1.5 times better than those of existing methods for SM orientation-localization microscopy. The raMVR microscope achieves 6D super-resolution imaging of Nile red (NR) molecules transiently bound to 150 nm, 350 nm, and 1 µm-diameter lipid-coated spheres, accurately resolving their spherical morphology despite refractive-index mismatch. Simply by observing the rotational dynamics o raMVR images also resolve the infiltration of lipid membranes by amyloid-beta oligomers without covalent labeling. Finally, we demonstrate 6D imaging of HEK-293T cell membranes, where the orientations of merocyanine 540 molecules reveal heterogeneities in membrane fluidity. With its ∼2 µm depth range, nearly isotropic 3D spatial resolution, and superior orientation measurement precision, we expect the raMVR microscope to enable 6D imaging of molecular dynamics within biological and chemical systems with unprecedented detail.