bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytokinin response regulatorARR16regulates seed coat permeability in Arabidopsis natural accessions
Authors: Sano Naoto , Domergue Frédéric , North Helen M. 
Published: February 2023

AbstractThe seed coat that encases the embryo is constituted from multiple specialized-cell layers and their permeability significantly influences seed quality traits that have major agronomic impact. The regulatory mechanisms that modulate seed coat permeability are, however, not well understood. Here, we identified a novel regulatory gene for seed permeability through a genome wide association study (GWAS) in Arabidopsis based on image analysis of tetrazolium staining.Type-A ARABIDOPSIS RESPONSE REGULATOR 16(ARR16) is a component of the signal transduction pathway for the plant hormone cytokinins (CKs), and in addition to less permeable seed coats,arr16mutant seeds were larger, had a longer lifespan, and more suberin phenolics, the hydrophobic lipid biopolyester components of cell walls that act as a water-repellant. Moreover, double mutants in CK receptorARABIDOPSIS HISTIDINE KINASEgenes, notablyahk2 ahk4andahk3 ahk4, showed similar seed phenotypes to those ofarr16. Based on naturally-occurring variation in theARR16gene, eight haplotypes were detected and associated with permeable or impermeable phenotypes. Permeable haplotypes had significantly lower suberin autofluorescence compared to impermeable haplotypes. RT-qPCR analysis demonstrated thatARR16transcripts were highly abundant in developing seeds of representative accessions having permeable haplotypes but not in those of having impermeable haplotypes, indicating that these haplotypes were causal forARR16transcript abundance and thereby regulate seed coat permeability in natural accessions. Our findings demonstrate a new role for CKs signaling in seed coat differentiation and that this underlies natural variation for seed permeability through the modulation of suberin accumulation.Significance StatementSeed coat permeability affects key traits that impact seed quality, such as dormancy, longevity, and germination tolerance to abiotic stress. Little is currently known about how seed coat permeability is modulated. Here, we developed an original method for quantification of seed coat permeability through imaging and used this in a genome-wide association study with Arabidopsis accessions. The CKs response regulatorARR16was identified as a causal gene thereby establishing a novel function for this phytohormone in seed coat differentiation. Moreover, this was linked to the modulation of suberin accumulation byARR16and for the first time implicates CKs signal transduction in the control of suberin deposition in seeds.
Boldine modulates glial transcription and functional recovery in a murine model of contusion spinal cord injury
Authors: Toro Carlos A. , Johnson Kaitlin , Hansen Jens , Siddiq Mustafa M. , Vásquez Walter , Zhao Wei , Graham Zachary A. , Sáez Juan C. , Iyengar Ravi , Cardozo Christopher P. 
Published: February 2023

AbstractMembrane channels such as connexins (Cx), pannexins (Panx) and P2X7receptors (P2X7R) are permeable to calcium ions and other small molecules such as ATP and glutamate. Release of ATP and glutamate through these channels is a key mechanism driving tissue response to traumas such as spinal cord injury (SCI). Boldine, an alkaloid isolated from the Chilean boldo tree, blocks both Cx hemichannels (HC) and Panx. To test if boldine could improve function after SCI, boldine or vehicle was administered to treat mice with a moderate severity contusion-induced SCI. Boldine led to greater spared white matter and increased locomotor function as determined by the Basso Mouse Scale and horizontal ladder rung walk tests. Boldine treatment reduced immunostaining for markers of activated microglia (Iba1) and astrocytic (GFAP) markers while increasing that for axon growth and neuroplasticity (GAP-43). Cell culture studies demonstrated that boldine blocked glial HC, specifically Cx26 and Cx30, in cultured astrocytes and blocked calcium entry through activated P2X7R. RT-qPCR studies showed that boldine treatment reduced expression of the chemokine Ccl2, cytokine IL-6 and microglial gene CD68, while increasing expression of the neurotransmission genes Snap25 and Grin2b, and Gap-43. Bulk RNA sequencing (of the spinal cord revealed that boldine modulated a large number of genes involved in neurotransmission in in spinal cord tissue just below the lesion epicenter at 14 days after SCI. Numbers of genes regulated by boldine was much lower at 28 days after injury. These results indicate that boldine treatment ameliorates injury and spares tissue to increase locomotor function.
Flow augmentation from off-channel storage improves salmonid habitat and survival
Authors: Rossi Gabriel J. , Obedzinski Mariska , Pneh Shelley , Pierce Sarah Nossaman , Boucher William T. , Slaughter Weston M. , Flynn Keane M. , Grantham Theodore E. 
Published: February 2023

[A]AbstractIn the Western United States, juvenile salmon and steelhead are especially vulnerable to streamflow depletion in the dry season. Releasing water from off-channel storage is a method of streamflow augmentation increasingly used to offset impacts of anthropogenic flow alteration. However, to date, no studies have evaluated the effects of these small-scale flow augmentations on salmonids. Here we quantify the effects of one such augmentation project on habitat connectivity, water quality, invertebrate drift, juvenile salmonid movement and survival. Our study took place in a Northern California stream and included an unusually wet summer (2019) and a more typical dry summer (2020). We found that differences in ambient streamflows between the two years mediated the physical and ecological effects of a 13.9 L/s augmentation treatment. In the dry year, flow augmentation significantly improved dissolved oxygen and habitat connectivity at sites > 1.5 km downstream from the point of augmentation and had a marginal warming effect on stream temperature. During the wet year, both dissolved oxygen and water temperature effects were negligible. In both years, augmentation had a small but positive effect on invertebrate drift. Inter-pool movement of juvenile steelhead (Oncorhynchus mykiss) and stocked Coho Salmon (O. kisutch) increased due to augmentation during the dry summer. Flow augmentation also increased the survival probability for salmonids, with a larger effect during the dry summer (24% higher survival for Coho and 20% higher for steelhead), than during the wet summer (when no effect was observed for steelhead survival and Coho Salmon survival increased by 11%). This study indicates that appropriately designed and timed flow augmentations can improve conditions for rearing salmonids in small streams, particularly during dry years. More broadly it provides empirical evidence that efforts to restore summer streamflow in small, salmon-bearing streams can yield significant ecological benefits.
Coupled Biomechanical and Ionic Excitability in Developing Neural Cell Networks
Authors: Gates Sylvester J. , Alvarez Phillip , Cao Kan , O’Neill Kate , Losert Wolfgang 
Published: February 2023

AbstractWaves and oscillations play a key role in the flow and processing of information in the brain. Recent work has demonstrated that in addition to electrical activity, biomechanical signaling can also be excitable and thus capable of self-sustaining oscillations and waves. Here we measured the biomechanical dynamics of actin polymerization in neural precursor cells throughout their differentiation into populations of neurons and astrocytes. Fluorescence-based live-cell imaging allowed us to analyze the dynamics of actin in conjunction with the dynamics of calcium signals. Actin dynamics throughout differentiation showed a rhythmic character, localized mostly in processes, with changes in scale associated with differentiation. Furthermore, actin dynamics impact ionic dynamics, with an increase in the frequency of calcium bursts accompanied by a decrease in cell-cell correlations when actin dynamics is inhibited. This impact of cytoskeletal dynamics on cell-cell coupling and ionic neural cell signaling suggests that information flow in the brain may be able to harness both biomechanical and electrical/ionic excitability.
CBD can be combined with additional cannabinoids for optimal seizure reduction and requires GPR55 for its anticonvulsant effects
Authors: Kollipara Roshni , Langille Evan , Tobin Cameron , French Curtis R. 
Published: February 2023

AbstractBackgroundCannabis has demonstrated anticonvulsant properties, and cannabis-based medicines are approved to treat pediatric patients with severe pediatric epilepsies that are particularly refractive to approved anti-epileptic drugs (AEDs). About thirty percent of epileptic patients do not have satisfactory seizure management with AEDs and could potentially benefit from cannabis-based intervention. Here we report the use of single and combined cannabinoids to treat Pentylenetetrazol (PTZ) induced convulsions in a zebrafish model, their effect on gene expression, and a simple assay for assessing their uptake in zebrafish tissues. These data provide novel insights as to the potential of treating epilepsy with cannabinoids.MethodsZebrafish larvae were treated with cannabinoids and their seizures measured through an optimized behaviour tracking method. Cannabinoid uptake was measured with a novel HPLC-UV method. Gene expression changes were assessed using quantitative PCR (qPCR), and chemical inhibitors of potential cannabinoid receptors were used to block activity.ResultsTreatment with cannabinol (CBN), cannabichromene (CBC) and cannabigerol (CBG) decreased seizure intensity at lower doses than CBD when accounting for the amount of cannabinoid recovered from exposed larvae. Δ9-tetrahydrocannabinol (Δ9-THC), Δ8-tetrahydrocannabinol (Δ8-THC) were effective at higher doses. Synergistic effects were observed between CBD and other cannabinoids such as Δ9-THC, Δ8-THC, and CBG. The reduction of PTZ induced seizures via CBD is partially mediated by the G-protein coupled receptor GPR55, as pharmacological inhibition of the receptor reduced the therapeutic action of CBD. Changes in expression of endocannabinoid system (napepld, gde1, faah, ptgs2a) and neural (fosab, pyya) genes in response to phytocannabinoid treatment were observed and highlight novel mechanisms of phytocannabinoid action.ConclusionsCBD can be combined with additional cannabinoids for optimal reduction of seizure activity and requires the activity of GPR55. Changes infosabregulation of gene expression and endocannabinoid signalling may influence the anticonvulsant effects of cannabis, however further investigation is required.
Spatio-temporal coherence of circadian clocks and gating of differentiation inAnabaenafilaments
Authors: Arbel-Goren Rinat , Dassa Bareket , Zhitnitsky Anna , Valladares Ana , Herrero Antonia , Flores Enrique , Stavans Joel 
Published: February 2023

AbstractCircadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacteriumAnabaenasp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle; that gene expression in different vegetative intervals along a developed filament was discoordinated; and that the circadian clock was active in individual heterocysts. Furthermore,Anabaenamutants lacking thekaiABCgenes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs inAnabaena, the gating of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen deficient conditions, the functional unit inAnabaenais reduced from a full filament under nitrogen-rich conditions, to the vegetative cell interval between heterocysts.
The thermostability of a Vaccine Delivery system X-Protein (VADEX-Pro) based protein nanoparticle
Authors: Liou Gunn-Guang , Kan Ming-Chung 
Published: February 2023

AbstractWe have adapted split GFP technology into the protein nanoparticle platform, Vaccine Delivery system X (VADEX), created in previous study. To evaluate the capability of this new platform, a model protein, maltose binding protein (MBP), was fused to the β-strand 11 of sfGFP and co-expressed with VADEX-10 which was composed of LYRRLE peptide and N-terminal part up to β-strand 10 of sfGFP. When these two fusion proteins were expressed in a cell, they were assembled into PNP spontaneously with a dynamic light scattering (DLS) particle size of 26 nm. This nanoparticle platform was renamed as VADEX-Pro for its capacity of expressing large protein on PNP. The thermostability of the assembled PNP was verified by both SDS-PAGE and DLS analysis following treatment. This PNP was stable at 25 °C and at temperatures as high as 40 °C for at least two months. Mutations that replaced cysteine residue of the LYRRLE peptide with serine or alanine destabilized and induced degradation of the VADEX-based PNP. The results in this study showed that the non-covalent complementation of split sfGFP became irreversible when reconstituted sfGFP was assembled in a VADEX-Pro PNP. This platform may be applied in developing thermostable vaccines.
Water hardness variously influences tissue physiology of freshwater fish -Cyprinus carpiovarkoi: A report on glucose, oxidative stress and antioxidant biomarkers
Authors: Dasgupta Proteek 
Published: February 2023

AbstractFishes endemic to freshwater habitat are strongly influenced by water hardness with physiological consequences. The present study aimed to understand the effects of four-fold sequential increase from soft to hard waters, on selected tissues of Koi carp, a popular ornamental freshwater fish. Secondary stress markers - Glucose, Oxidative stress (Malondialdehyde – Lipid Peroxidation damage) and Antioxidants (Catalase, Glutathione-S-Transferase and Glutathione) were quantified in gills and white muscle after 14 days of exposure to hardness of 75 (Soft - TS), 150 (Moderate - TM), 225 (Hard - TH) to 300 (Very Hard - TV) mg CaCO3/L. Both the examined tissues were distinctly affected by soft and moderate waters. Glucose in gills (p< 0.05) was proportional to the rise in hardness concentration. Soft, moderate and very hard waters (75, 150 and 300 mg CaCO3/L) affected gills and muscle due to elevated MDA concentrations (p< 0.05). CAT and GST provided antioxidative protection to the tissues. The study results showed tissue-specific differential responses and more importantly, concentrations below 225 mg CaCO3/L elicited strong oxidative impairment in both gill and muscle.
Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox
Authors: Middelkamp Sjors , Manders Freek , Peci Flavia , van Roosmalen Markus J. , González Diego Montiel , Bertrums Eline J.M. , van der Werf Inge , Derks Lucca L.M. , Groenen Niels M. , Verheul Mark , Trabut Laurianne , Brandsma Arianne M. , Antoniou Evangelia , Reinhardt Dirk , Bierings Marc , Belderbos Mirjam E. , van Boxtel Ruben 
Published: February 2023

AbstractDetection of somatic mutations in single cells has been severely hampered by technical limitations of whole genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole genome sequencing (WGS), but still generate hundreds of artefacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolkit (PTATO), to accurately detect single base substitutions, small insertions and deletions (indels) and structural variants in PTA-based WGS data. PTATO includes a machine learning approach to distinguish PTA-artefacts from true mutations with high sensitivity (up to 90% for base substitution and 95% for indels), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that many hematopoietic stem and progenitor cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS technologies, have normal somatic single base substitution burdens, but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
Pervasive, conserved secondary structure in highly charged protein regions
Authors: Triandafillou Catherine G. , Pan Rosalind Wenshan , Dinner Aaron R. , Drummond D. Allan 
Published: February 2023

AbstractUnderstanding how protein sequences confer function remains a defining challenge in molecular biology. Two approaches have yielded enormous insight yet are often pursued separately: structure-based, where sequence-encoded structures mediate function, and disorder-based, where sequences dictate physicochemical and dynamical properties which determine function in the absence of stable structure. Here we study highly charged protein regions (>40% charged residues), which are routinely presumed to be disordered. Using recent advances in structure prediction and experimental structures, we show that roughly 40% of these regions form well-structured helices. Features often used to predict disorder—high charge density, low hydrophobicity, low sequence complexity, and evolutionarily varying length—are also compatible with solvated, variable-length helices. We show that a simple composition classifier predicts the existence of structure far better than well-established heuristics based on charge and hydropathy. We show that helical structure is more prevalent than previously appreciated in highly charged regions of diverse proteomes and characterize the conservation of highly charged regions. Our results underscore the importance of integrating, rather than choosing between, structure- and disorder-based approaches.
Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly
Authors: Adamson Roslin J , Payne N Connor , Bartual Sergio G. , Mazitschek Ralph , Bullock Alex N 
Published: February 2023

AbstractKEAP1 promotes the ubiquitin-dependent degradation of NRF2 by assembling into a CUL3-dependent ubiquitin ligase complex. Oxidative and electrophilic stress inhibit KEAP1 allowing NRF2 to accumulate for transactivation of stress response genes. To date there are no structures of the KEAP1-CUL3 interaction nor binding data to show the contributions of different domains to their binding affinity. We determined a crystal structure of the BTB and 3-box domains of human KEAP1 in complex with the CUL3 N-terminal domain that showed a heterotetrameric assembly with 2:2 stoichiometry. To support the structural data, we developed a versatile TR-FRET-based assay system to profile the binding of BTB-domain-containing proteins to CUL3 and determine the contribution of distinct protein features, revealing the importance of the CUL3 N-terminal extension for high affinity binding. We further provide direct evidence that the investigational drug CDDO does not disrupt the KEAP1-CUL3 interaction, even at high concentrations, but reduces the affinity of KEAP1-CUL3 binding. The TR-FRET-based assay system offers a generalizable platform for profiling this protein class and may form a suitable screening platform for ligands that disrupt these interactions by targeting the BTB or 3-box domains to block E3 ligase function.Graphical abstractHighlightsA new crystal structure defines KEAP1 BTB and 3-box domain interactions with CUL3KEAP1 and CUL3 form a heteromeric 2:2 complex with aKDvalue of 0.2 µMA generalizable TR-FRET platform enables multimodal profiling of BTB proteinsThe investigational drug CDDO is a partial antagonist of the KEAP1-CUL3 interaction
Characterization of microsatellite markers for the duckweedSpirodela polyrhizaandLemna minortested on samples from Europe or the United States of America
Authors: Kerstetter Jae E. , Reid Andrea L. , Armstrong Joshua T. , Zallek Taylor A. , Hobble Trapper T. , Turcotte Martin M. 
Published: February 2023

AbstractMicrosatellite primers are a valuable tool to use for both observational and experimental studies in numerous taxa. Here, we develop 18 and 16 microsatellite markers for the widespread duckweedsLemna minorandSpirodela polyrhiza, respectively. All 18L. minorprimers and 12 of the 16S. polyrhizaprimers amplified polymorphic loci when tested on samples from Europe or Western Pennsylvania, USA.
Loss of the benthic life stage in Medusozoa and colonization of the open ocean
Authors: Boosten Manon , Sant Camille , Da Silva Ophélie , Chaffron Samuel , Guidi Lionel , Leclère Lucas 
Published: February 2023

AbstractIn marine environments, life cycle strategies strongly impact species dispersal and their ability to colonize new habitats. Pelagic medusozoans (jellyfish and siphonophores) exhibit various reproductive strategies, variations of meroplanktonic and holoplanktonic life cycles. In the ancestral meroplanktonic life cycle, a benthic polyp stage alternates with a pelagic medusa stage. During the course of evolution, some medusozoans lost their benthic stage, leading to a holoplanktonic life cycle. The ecological consequences of these losses have not been addressed at global scale. Here, integrating metabarcoding and environmental data fromTara Oceansinto a phylogenetic framework, we show that each convergent transition toward a holoplanktonic life cycle is associated with a more offshore distribution compared to meroplanktonic medusozoans. Our analyses showed that holoplanktonic medusozoans are more globally distributed and relatively more abundant than meroplanktonic medusozoans, although they are less diversified and occupy a more peripheral position in a global plankton community interactome. This suggests that holoplanktonic medusozoans have acquired a greater tolerance to biotic and abiotic conditions. Overall, our results demonstrate the relationship between medusozoan life cycles, distribution, and biotic interactions, suggesting that the loss of the benthic stage promoted colonization of the open ocean.
Amygdala AVPR1A mediates susceptibility to chronic social isolation in females
Authors: François Marie , Delgado Isabella Canal , Lafond Alexandre , Lewis Eastman M. , Kuromaru Mia , Hassouna Rim , Deng Shuliang , Thaker Vidhu V. , Dölen Gül , Zeltser Lori M. 
Published: February 2023

SummaryFemales are more sensitive to social exclusion, which could contribute to their heightened susceptibility to anxiety disorders. Chronic social isolation stress (CSIS) for at least 7 weeks after puberty induces anxiety-related behavioral adaptations in female mice. Here, we show thatArginine vasopressin receptor 1a(Avpr1a)-expressing neurons in the central nucleus of the amygdala (CeA) mediate these sex-specific effects, in part, via projections to the caudate putamen. Loss of function studies demonstrate that AVPR1A signaling in the CeA is required for effects of CSIS on anxiety-related behaviors in females but has no effect in males or group housed females. This sex-specificity is mediated by AVP produced by a subpopulation of neurons in the posterodorsal medial nucleus of the amygdala that project to the CeA. Estrogen receptor alpha signaling in these neurons also contributes to preferential sensitivity of females to CSIS. These data support new therapeutic applications for AVPR1A antagonists in women.