bluuebunny/crossref_metadata_2025_split huggingface dataset:
α-Synuclein strains that cause distinct pathologies differentially inhibit proteasome
Authors: Suzuki Genjiro , Imura Sei , Hosokawa Masato , Katsumata Ryu , Nonaka Takashi , Hisanaga Shin-Ichi , Saeki Yasushi , Hasegawa Masato 
Published: March 2020

AbstractAbnormal α-synuclein aggregation has been implicated in several diseases and is known to spread in a prion-like manner. There is a relationship between protein aggregate structure (strain) and clinical phenotype in prion diseases, however, whether differences in the strains of α-synuclein aggregates account for the different pathologies remained unclear. Here, we generated two types of α-synuclein fibrils from identical monomer and investigated their seeding and propagation ability in mice and primary-cultured neurons. One α-synuclein fibril induced marked accumulation of phosphorylated α-synuclein and ubiquitinated protein aggregates, while the other did not, indicating the formation of α-synuclein two strains. Notably, the former α-synuclein strain inhibited proteasome activity and co-precipitated with 26S proteasome complex. Further examination indicated that structural differences in the C-terminal region of α-synuclein strains lead to different effects on proteasome activity. These results provide a possible molecular mechanism to account for the different pathologies induced by different α-synuclein strains.
Generation and biobanking of patient-derived glioblastoma organoids and their application in CAR-T cell testing
Authors: Jacob Fadi , Ming Guo-li , Song Hongjun 
Published: March 2020

AbstractGlioblastoma tumors exhibit extensive inter- and intra-tumoral heterogeneity, which has contributed to poor outcomes of numerous clinical trials and continues to complicate the development of effective therapeutic strategies. Currentin vitromodels do not preserve the cellular and mutational diversity of parent tumors and often require a lengthy generation time with variable efficiency. Here, we describe detailed procedures for generating glioblastoma organoids (GBOs) from surgically resected patient tumor tissue using a chemically defined medium without cell dissociation. By preserving cell-cell interactions and minimizing clonal selection, GBOs maintain the cellular heterogeneity of parent tumors. We include methods for passaging and cryopreserving GBOs for continued use, biobanking, and long-term recovery. We further describe procedures for investigating patient-specific responses to immunotherapies by co-culturing GBOs with chimeric antigen receptor (CAR) T cells. This protocol takes approximately 2-4 weeks to generate GBOs and 5-7 days to perform CAR-T cell co-culture. Competence with human cell culture, tissue processing, immunohistology, and microscopy is required for optimal results.Short SummaryDetailed procedures for generating and biobanking glioblastoma organoids from resected patient tumor tissue and testing CAR-T cell efficacy by co-culture. Additional procedures for tissue processing, immunohistology, and detecting hypoxia gradients and actively proliferating cells.Associated Link Box for Key ReferenceJacob, F. et al. A Patient-derived glioblastoma organoid model and biobank recapitulates inter- and intra-tumoral heterogeneity. Cell 180, 188-204 e122, doi:10.1016/j.cell.2019.11.036 (2020).
Unclusterable, underdispersed arrangement of insect-pollinated plants in pollinator niche space
Authors: Herrera Carlos M. 
Published: March 2020

AbstractPollinators can mediate facilitative or competitive relationships between plant species, but the comparative importance of these two conflicting phenomena in shaping community-wide pollinator resource use remains unexplored. This paper examines the idea that the arrangement in pollinator niche space of plant species samples comprising complete or nearly complete regional or local plant communities can help to evaluate the relative importance of facilitation and competition as drivers of community-wide pollinator resource use. Pollinator composition data for insect-pollinated plants from the Sierra de Cazorla mountains (southeastern Spain), comprising 85% of families and ~95% of widely distributed insect-pollinated species, were used to address the following questions at regional (45 sites, 221 plant species) and local (one site, 73 plant species) spatial scales: (1) Do objectively identifiable plant species clusters occur in pollinator niche space ? Four different pollinator niche spaces were considered whose axes were defined by insect orders, families, genera and species; and (2) If all plant species form a single, indivisible cluster in pollinator niche space, Are they overdispersed or underdispersed relative to a random arrangement ? “Clusterability” tests failed to reject the null hypothesis that there was only one pollinator-defined plant species cluster in pollinator niche space, irrespective of spatial scale, pollinator niche space or pollinator importance measurement (proportions of pollinator individuals or flowers visited by each pollinator type). Observed means of pairwise interspecific dissimilarity in pollinator composition were smaller than randomly simulated values in the order-, family- and genus-defined pollinator niche spaces at both spatial scales, thus revealing significantly non-random, underdispersed arrangement of plant species within the single cluster existing in each of these pollinator niche spaces. In the undisturbed montane habitats studied, arrangement of insect-pollinated plant species in pollinator niche space did not support a major role for interspecific competition as a force shaping community-wide pollinator resource use by plants, but rather suggested a situation closer to the facilitation-dominated extreme in a hypothetical competition-facilitation gradient. Results also highlight the importance of investigations on complete or nearly complete insect-pollinated plant communities for addressing novel hypotheses on the ecology and evolution of plant-pollinator systems.
A Novel Small Animal Model of Norovirus Diarrhea
Authors: Roth Alexa N. , Helm Emily W. , Mirabelli Carmen , Kirsche Erin , Smith Jonathan C. , Eurell Laura B. , Ghosh Sourish , Altan-Bonnet Nihal , Wobus Christiane E. , Karst Stephanie M. 
Published: March 2020

ABSTRACTHuman noroviruses are the leading cause of severe childhood diarrhea worldwide yet we know very little about their pathogenic mechanisms. Murine noroviruses cause diarrhea in interferon-deficient adult mice but these hosts also develop systemic pathology and lethality, reducing confidence in the translatability of findings to human norovirus disease. Herein we report that a murine norovirus causes self-resolving diarrhea in the absence of systemic disease in wild-type neonatal mice, thus mirroring the key features of human norovirus disease and representing a robust norovirus small animal disease model. Intriguingly, lymphocytes are critical for controlling acute norovirus replication while simultaneously contributing to disease severity, likely reflecting their dual role as targets of viral infection and key components of the host response.
Systemic hypoxia inhibits T cell response by limiting mitobiogenesis via matrix substrate-level phosphorylation arrest
Authors: Saragovi Amijai , Abramovitch Ifat , Omar Ibrahim , Arbib Eliran , Toker Ori , Gottlieb Eyal , Berger Michael 
Published: March 2020

SUMMARYSystemic oxygen restriction (SOR) is prevalent in numerous clinical conditions including chronic obstructive pulmonary disease (COPD). However, the influence of SOR on T cell protective immunity remains uncharacterized. Here we show the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells. We find that low oxygen diminishes CD8+ T cell viral responsein vivo. Using genetic and pharmacological models, we demonstrate that respiratory restriction inhibits ATP dependent matrix processes, all critical for mitochondrial biogenesis. The effect mediated by respiratory restriction could be rescued by TCA cycle re-stimulation, which led to increased mitochondrial matrix localized ATP via substrate-level phosphorylation. Finally, we demonstrate that short exposure to atmospheric oxygen pressure rescues the CD8+ viral response under systemic oxygen restrictionin vivo. Our findings reveal the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells and provide a new approach for reducing viral infections in COPD.HighlightsSystemic chronic hypoxia compromises CD8+ T cell activationShortly upon activation, T cells’ cytoplasmic activity becomes independent of mitochondrial ATP outfluxRespiratory-blockade arrests mitochondrial remodeling due to energy depletionUncoupler-based TCA stimulation rescues respiratory-restricted activated CD8+ T cells by stimulating matrix localized substrate-level phosphorylationCD8+ T cell arrest due to hypoxiain vivocan be rescued by short exposure to atmospheric oxygen pressure.
Calcium activates purified human TRPA1 with and without its N-terminal ankyrin repeat domain in the absence of calmodulin
Authors: Moparthi Lavanya , Moparthi Satish Babu , Wenger Jérôme , Zygmunt Peter M. 
Published: March 2020

AbstractExtracellular influx of calcium or release of calcium from intracellular stores have been shown to activate mammalian TRPA1 as well as to sensitize and desensitize TRPA1 electrophilic activation. Calcium binding sites on both intracellular N- and C-termini have been proposed. Here, we demonstrate based on fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET) and bilayer patch-clamp studies, a direct calmodulin-independent action of calcium on the purified human TRPA1 (hTRPA1), causing structural changes and activation of hTRPA1 with and without its N-terminal ankyrin repeat domain (N-ARD). Thus, calcium can activate hTRPA1 by direct interaction with binding sites outside the N-ARD.
Embryogenesis, polyembryony, and settlement in the gorgonianPlexaura homomalla
Authors: Wells Christopher D. , Tonra Kaitlyn J. , Lasker Howard R. 
Published: March 2020

ABSTRACTUnderstanding the ontogeny and reproductive biology of reef-building organisms can shed light on patterns of population biology and community structure. This knowledge is particularly important for Caribbean octocorals, which seem to be more resilient to long-term environmental change than scleractinian corals and provide some of the same ecological services. We monitored the development of the black sea rodPlexaura homomalla, a common, widely distributed octocoral on shallow Caribbean reefs, from eggs to 3-polyp colonies over the course of 73 days. In aquaria on St John, U.S. Virgin Islands, gametes were released in spawning events three to six days after the July full moon. Cleavage started 3 hours after fertilization and was holoblastic, equal, and radial. Embryos were positively buoyant until becoming planulae. Planulae were competent after 4 days. Symbiodiniaceae began infecting polyps at around 8 days post fertilization. Development was typical for Caribbean octocorals, except for the occurrence of a novel form of asexual reproduction in octocorals: polyembryony. Fragmentation of embryos during development may represent a temporally varied tradeoff between number and size of propagules, in which large eggs have higher fertilization rates followed by polyembryony, which maximizes the number of surviving recruits by generating more, albeit smaller, larvae. Polyembryony may contribute to the success of some gorgonians on Caribbean reefs as other anthozoans are in decline.
Development and optimization of a germination assay and long-term storage forCannabis sativapollen
Authors: Gaudet Daniel , Yadav Narendra Singh , Sorokin Aleksei , Bilichak Andrii , Kovalchuk Igor 
Published: March 2020

AbstractPollen viability and storage is of great interest to cannabis breeders and researchers to maintain desirable germplasm for future use in breeding or for biotechnological and gene editing applications. Here, we report a simple and efficient cryopreservation method for long-term storage ofCannabis sativapollen. Additionally, we have deciphered the bicellular nature of cannabis pollen using DAPI staining. We have also standardized a pollen germination assay to assess the viability of cannabis pollen, and found pollen collected from different principal growth stages exhibits different longevity. Finally, we developed a long-term storage method which includes pollen combination with baked whole wheat flower and desiccation under vacuum for cryopreservation. By using this method, we were able to maintain germination viability in liquid nitrogen after 4 months, suggesting potentially indefinite preservation of cannabis pollen.
Gatekeeper transcription factors regulate switch between lineage preservation and cell plasticity
Authors: Ray Tania , Shah Anit , Bulla Gary A. , Ray Partha S. 
Published: March 2020

SummaryReprogramming somatic cells to pluripotency by repressing lineage-instructive transcription factors (TFs) alone has not been pursued because lineage specification is thought to be regulated by transcriptional regulatory networks (TRNs) comprising of multiple TFs rather than by single pivotal “gatekeeper” TFs. Utilizing an intra-species somatic cell hybrid model, we identified Snai2 and Prrx1 as the most critical determinants of mesenchymal commitment in rat embryonic fibroblasts (REFs) and demonstrate that siRNA-mediated knockdown of either of these master regulators is adequate to convert REFs into functional adipocytes, chondrocytes or osteocytes without requiring exogenous TFs or small molecule cocktails. Furthermore, knockdown of Snai2 alone proved sufficient to transform REFs to dedifferentiated pluripotent stem-like cells (dPSCs) that formed embryoid bodies capable of triple germ-layer differentiation. These findings suggest that inhibition of a single gatekeeper TF in a lineage committed cell is adequate for acquisition of cell plasticity and reprogramming without requiring permanent genetic modification.Graphical AbstractSchematic diagram depicting transdifferentiation of REFs into adipocytes, osteocytes, chondrocytes and dedifferentiation into MSCs on individual treatment with siSnai2 or siPrrx1. dPSCs were generated only in the siSnai2 group.
Population structure in Arctic marine forests is shaped by diverse recolonisation pathways and far northern glacial refugia
Authors: Bringloe Trevor T. , Verbruggen Heroen , Saunders Gary W. 
Published: March 2020

AbstractThe Arctic is experiencing a rapid shift towards warmer regimes, calling for a need to understand levels of biodiversity and ecosystem responses to climate cycles. This study examines marine refugial locations during the Last Glacial Maximum in order to link recolonization pathways to patterns of genetic diversity in Arctic marine forests. We present genetic data for 109 species of seaweed to infer community-level patterns, and hindcast species distributions during the Last Glacial Maximum to further pinpoint likely refugial locations. Sequence data revealed contiguous populations extending from the Bering Sea to the Northwest Atlantic, with high levels of genetic diversity in the East Canadian Arctic. One fifth of the species sampled appeared restricted to Arctic waters. Hindcasted species distributions highlighted refugia in the Bering Sea, Northwest Atlantic, South Greenland, and Europe. We hypothesize that Arctic coastal systems were recolonized from many geographically disparate refugia leading to enriched diversity levels in the East Canadian Arctic, with important contributions stemming from northerly refugia likely centered along Southern Greenland. Moreover, we hypothesize these northerly refugia likely played a key role in promoting polar endemic diversity, as reflected by abundant unique population haplotypes and endemic species in the East Arctic.Significance StatementOur work challenges the existing paradigm that marine Arctic ecosystems are depauperate extensions of southerly (temperate) communities established in the wake of recent glaciation, fundamentally changing how these systems should be viewed and interpreted. We forward novel hypotheses regarding the recent history of Arctic marine systems, particularly with regards to endemism being an integral feature of Arctic biomes, and present a firm framework for future evolutionary research in this system typically viewed as “ecologically immature.”
Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit
Authors: Lin Li , Van de Velde Jan , Nguyen Na , Meyer Rick , An Yong-qiang Charles , Song Li , Valliyodan Babu , Prince Silvas , Wan Jinrong , Murphy Mackensie C , Kim Eiru , Lee Insuk , Pentecost Genevieve , Zhu Chengsong , Kushwaha Garima , Joshi Trupti , Chen Wei , Patil Gunvant , Mutava Raymond , Xu Dong , Vandepoele Klaas , Nguyen Henry T. 
Published: March 2020

ABSTRACTSome crops inhibit shoot growth but maintain root growth under water-deficit conditions. Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants remains a major challenge. We developed an efficient platform for identifying core transcription factors (TFs) that collectively regulate each other and/or themselves in response to water stress, and exploring their interconnected regulatory circuitry involved in root growth maintenance under water deficit in soybean. We performed multi-species phylogenetic footprinting combined with spatial-temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to identify conserved motifs that function in the water-stress response. Using these functional conserved cis-motifs, we applied a new approach to trace back motifs-associated core TFs ingroup as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We integrated a co-functional TF–TF network and conserved motif-centered TF–DNA networks to construct a core TF network defined by mutual cross-regulation among core TFs. We found that core TF ARG (Abscisic acid response element binding factor-like Root Growth regulator) represses BRG (Brassinosteroid enhanced expression-like Root Growth regulator) expression through binding to its promoter at a conserved binding site. ARG and BRG antagonistically regulate Phytochrome-interacting factor-like Root Growth regulator (PRG) and combinatorially regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light and multiple hormone signaling pathways and maintain root growth in response to varying degrees of water stress. Our study provides valuable information to unravel the complicated mechanisms of molecular networks involved in the regulation of root growth under water deficit.
Hormonal regulation of the BRC1-dependent strigolactone transcriptome involved in shoot branching responses
Authors: Kerr Stephanie C. , de Saint Germain Alexandre , Dissanayanke Indeewari M. , Mason Michael G. , Dun Elizabeth A. , Beveridge Christine A. , Tanurdzic Milos 
Published: March 2020

ABSTRACTThe plant hormone strigolactone (SL) inhibits shoot branching by suppressing the growth of axillary buds. This is thought to occur largely via regulation of the transcription factor BRANCHED1 (BRC1). Here, we clarify the central role of BRC1 and identify additional transcriptional responses by which SL might regulate axillary bud outgrowth in garden pea (Pisum sativum). We used a transcriptomic approach to identify differentially expressed transcripts in pea axillary buds in response to a synthetic SL,rac-GR24. Changes in transcript abundance were confirmed by measuring their response to GR245DS. BRC1 was required for the regulation of over half of the fourteen GR245DS-regulated genes, confirming its role as a mediator of SL transcriptional responses in axillary buds. All, but one, of the BRC1-dependent GR245DS-regulated genes were also regulated by branch-promoting treatments cytokinin (CK) and/or decapitation in an opposing manner to SL. This suggests that SL, CK, and decapitation regulate shoot branching via a common pathway. We used correlational analyses of gene co-expression data to infer a gene regulatory network consisting of nine key co-expression modules correlated withrac-GR24 treatment. Enrichment of GO terms such as cell proliferation, carbohydrate responses, and abscisic acid and jasmonic acid hormone pathways suggest a role for these in SL-mediated inhibition of shoot branching. In summary, we have shown that BRC1 is indeed a key transcriptional regulator of the SL signalling pathway in pea buds as well as a focal point of the SL, CK and decapitation signalling pathways to coordinate shoot branching in pea buds.One Sentence SummaryIdentification of genes that are strigolactone-responsive and BRC1-dependent in pea buds reveals a high degree of overlap among strigolactone, cytokinin and decapitation response pathways.
Multiplexed photo-activation of mRNA with single-cell resolution
Authors: Zhang Dongyang , Jin Shuaijiang , Piao Xijun , Devaraj Neal K. 
Published: March 2020

ABSTRACTWe demonstrate sequential optical activation of two types of mRNAs in the same mammalian cell through the sequential photocleavage of small molecule caging groups (‘photo-cages’) tethered to the 5′ untranslated region (5′-UTR) of an mRNA. Synthetic ‘photo-cages’ were conjugated onto target mRNA using RNA-TAG, an enzymatic site-specific RNA modification technique. Translation of mRNA was severely reduced upon conjugation of the ‘photo-cages’ onto the 5′-UTR. However, subsequent photo-release of the ‘cages’ from the mRNA transcript triggered activation of translation with single-cell spatiotemporal resolution. To achieve sequential photo-activation of two mRNAs in the same cell, we synthesized a pair of ‘photo-cages’ which can be selectively cleaved from mRNA upon photo-irradiation with different wavelengths of light. Sequential photo-activation of two mRNAs enabled precise optical control of translation of two unique transcripts. We believe that this modular approach to precisely and rapidly control gene expression will serve as a powerful tool in future biological studies that require controlling translation of multiple transcripts with high spatiotemporal resolution.