bluuebunny/crossref_metadata_2025_split huggingface dataset:
DDIT3 (CHOP) contributes to retinal ganglion cell somal loss but not axonal degeneration in DBA/2J mice
Authors: Marola Olivia J. , Syc-Mazurek Stephanie B. , Libby Richard T. 
Published: July 2019

AbstractGlaucoma is an age-related neurodegenerative disease characterized by the progressive loss of retinal ganglion cells (RGCs). Chronic ocular hypertension, an important risk factor for glaucoma, leads to RGC axonal injury at the optic nerve head. This insult triggers molecularly distinct cascades governing RGC somal apoptosis and axonal degeneration. The molecular mechanisms activated by ocular hypertensive insult that drive both RGC somal apoptosis and axonal degeneration are incompletely understood. The cellular response to endoplasmic reticulum stress and induction of pro-apoptotic DNA damage inducible transcript 3 (DDIT3, also known as CHOP) has been implicated as a driver of neurodegeneration in many disease models, including glaucoma. RGCs express DDIT3 upon glaucoma-relevant insults, and importantly, DDIT3 has been shown to contribute to both RGC somal apoptosis and axonal degeneration after acute induction of ocular hypertension. However, the role of DDIT3 in RGC somal and axonal degeneration has not been critically tested in a model of age-related chronic ocular hypertension. Here, we investigated the role of DDIT3 in glaucomatous RGC death using an age-related, naturally occurring ocular hypertensive mouse model of glaucoma, DBA/2J mice (D2). To accomplish this, a null allele of Ddit3 was backcrossed onto the D2 background. Homozygous Ddit3 deletion did not alter gross retinal or optic nerve head morphology, nor did it change the ocular hypertensive profile of D2 mice. In D2 mice, Ddit3 deletion conferred mild protection to RGC somas but did not significantly prevent RGC axonal degeneration. Together, these data suggest that DDIT3 plays a minor role in perpetuating RGC somal apoptosis caused by chronic ocular hypertension-induced axonal injury, but does not significantly contribute to distal axonal degeneration.
17α-ethynylestradiol (EE2) limits the impact of ibuprofen upon respiration by streambed biofilms in a sub-urban stream
Authors: McClean Peter , Hunter William Ross 
Published: July 2019

AbstractPharmaceutical compounds such as the non-steroidal anti-inflammatory drug ibuprofen and the artificial estrogen 17α-ethynylestradiol (EE2) are contaminants of emerging concern in freshwater systems. Globally, human pharmaceutical use is growing by around ∼3 % per year, yet we know little about how interactions between different pharmaceuticals may affect aquatic ecosystems. Here we test how interactions between ibuprofen and EE2 affect the growth and respiration of streambed biofilms. We used contaminant exposure experiments to quantify how these compounds affected biofilm growth (biomass), respiration, net primary production (NPP) and gross primary production (GPP), both individually and in combination. We found no effects of either ibuprofen or EE2 on biofilm biomass (using ash free dry mass as a proxy) or gross primary production. Ibuprofen significantly reduced biofilm respiration and altered NPP. Concomitant exposure to EE2, however, counteracted the inhibitory effects of ibuprofen upon biofilm respiration. Our study, thus, demonstrates that interactions between pharmaceuticals in the environment may have complex effects upon microbial contributions to aquatic ecosystem functioning.
Calibrated feedback illumination for precise conventional fluorescence and PALM imaging applications
Authors: Mancebo A. , DeMars L. , Ertsgaard C. T. , Puchner E. M. 
Published: July 2019

AbstractSpatial light modulation using cost efficient digital mirror arrays (DMA) is finding broad applications in fluorescence microscopy due to the reduction of phototoxicity and bleaching and the ability to manipulate proteins in optogenetic experiments. However, the precise calibration of DMAs and their application to single-molecule localization microscopy (SMLM) remained a challenge because of non-linear distortions between the DMA and camera coordinate system caused by optical components. Here we develop a fast and easy to implement calibration procedure that determines these distortions by means of an optical feedback and matches the DMA and camera coordinate system with ~50 nm precision. As a result, a region from a fluorescence image can be selected with a higher precision for illumination compared to manual alignment of the DMA. We first demonstrate the application of our precisely calibrated light modulation by performing a proof-of concept fluorescence recovery after photobleaching experiment with the endoplasmic reticulum-localized protein IRE1 fused to GFP. Next, we develop a spatial feedback photoactivation approach for SMLM in which only regions of the cell are selected for photoactivation that contain photoactivatable fluorescent proteins. The reduced exposure of the cells to 405 nm light increases the possible imaging time by 44% until phototoxic effects cause a dominant fluorescence background and a change in the cell’s morphology. As a result, the mean number of reliable single molecule localizations is also significantly increased by 28%. Since the localization precision and the ability for single molecule tracking is not altered compared to traditional photoactivation of the entire field of view, spatial feedback photoactivation significantly improves the quality of SMLM images and the precision of single molecule tracking. Our calibration method therefore lays the foundation for improved SMLM with active feedback photoactivation far beyond the applications in this work.Statement of significanceActively patterned illumination in fluorescence microscopy can reduce bleaching and phototoxicity as well as actively manipulate proteins in optogenetic applications. Matching the coordinate system of the camera and the light patterning device such as digital mirror arrays (DMA) remains a challenge. We developed a fast and easy calibration procedure that determines and corrects for the transformation between the camera and DMA coordinate system with ~50 nm precision. Using this approach, we develop spatial feedback photoactivation for Single Molecule Localization Microscopy (SMLM) to photoswitch only intracellular regions containing photoswitchable fluorophores. Our results show a 44% improvement in the possible data acquisition time before phototoxic effects become detectable and a 28% increase in detected localizations. Spatial feedback photoactivation thus significantly improves SMLM experiments.
Increased presynaptic excitability in a migraine with aura mutation
Authors: Suryavanshi Pratyush , Sawant-Pokam Punam , Clair Sarah , Brennan KC 
Published: July 2019

AbstractMigraine is a common and disabling neurological disorder. The headache and sensory amplifications that characterize migraine are attributed to hyperexcitable sensory circuits, but a detailed understanding remains elusive. This is partly due to the paucity of genetic animal models associated with the common, less severe form of the disease. A mutation in casein kinase 1 delta (CK1δ) was identified in familial migraine with aura and advanced sleep phase syndrome. Spreading depolarization (SD), the phenomenon that underlies migraine aura, is facilitated in mice carrying one of the mutations (CK1δT44A). However, the mechanism of this susceptibility is not known. We used a combination of whole-cell electrophysiology and imaging,in vivoand inex vivobrain slices, to understand the cellular and synaptic underpinnings of this apparent circuit excitability. We found that despite normal synaptic activity and hyperpolarized neuronal membrane potentials at rest, CK1δT44Aneurons were more excitable upon repetitive stimulation compared to wild-type (WT) controls. This was due to reduced presynaptic adaptation to high-frequency stimuli at excitatory, but not inhibitory synapses. Reduced adaptation at glutamatergic CK1δT44Asynapses was mediated by a calcium-dependent enhancement of the size of the readily releasable pool of synaptic vesicles. This caused an increase in the cumulative amplitude of excitatory currents, and a higher excitation-to-inhibition ratio during sustained activity, bothin vivoand in brain slices. Fluorescence imaging revealed increased glutamate release in CK1δT44Acompared to WT brain slices, corroborating the presynaptic gain of function observed with electrophysiology. Action potential bursts elicited in individual CK1δT44Aneurons enhanced glutamatergic feedback excitation within local microcircuits, further amplifying firing frequencies. At a network levelin vivo, CK1δT44Amice showed increased duration of up state activity, which is dependent on recurrent excitation. Finally, we demonstrated that SD susceptibility of CK1δT44Abrain slices could be returned to WT levels with the same reductions in extracellular calcium that normalized presynaptic adaptation. Taken together, these findings show a stimulus-dependent presynaptic gain of function at glutamatergic synapses in a genetic model of migraine, that accounts for the increased SD susceptibility and may also explain the sensory amplifications that are associated with the disease.
Global profiling of myristoylation inToxoplasma gondiireveals key roles for lipidation in CDPK1 and MIC7 function
Authors: Broncel Malgorzata , Dominicus Caia , Hunt Alexander , Wallbank Bethan , Federico Stefania , Young Joanna , Treeck Moritz 
Published: July 2019

AbstractN-myristoylation is a ubiquitous class of protein lipidation across eukaryotes andN-myristoyl transferase has been proposed as an attractive drug target in several pathogens. Functionally the myristate often primes for subsequent palmitoylation and stable membrane attachment, however, growing evidence also suggests additional regulatory roles for myristoylation on proteins. Here we describe the first global chemoproteomic screening of protein myristoylation inToxoplasma gondii. Through quantitative mass spectrometry coupled with validated chemoproteomic tools, we identify 65 myristoylated proteins. We report functionally important myristoylation on the key signalling protein CDPK1 and, surprisingly, myristoylation of the microneme protein 7 (MIC7), a predicted type-I-transmembrane protein. We demonstrate that myristoylation of MIC7 is not important for the trafficking to micronemes, but appears to play a role in host cell invasion. This dataset represents a large fraction of the parasite’s myristoylated proteome and a prerequisite to investigate this modification inToxoplasma.
Comparison of Mortality and Viral Load in Rainbow Trout (Oncorhynchus mykiss) infected with Infectious Pancreatic Necrosis Virus (IPNV) Genogroups 1 and 5
Authors: Tapia David , Barría Agustín , Yáñez José M. 
Published: July 2019

ABSTRACTInfectious Pancreatic Necrosis Virus (IPNV) is the etiological agent of a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into eight genogroups, of which two are present in Chile, genogroups 1 and 5. Here we compare the mortality rate caused by isolates from both genogroups in rainbow trout (Oncorhynchus mykiss) fry to determine if there is an association between host susceptibility and phylogenetic characterization of IPNV. Fish were challenged by immersion with one of four isolates (two of each genogroup) and mortality curves were assessed after 30 days. Viral load was measured in all mortalities and in live fish sampled at 1, 7 and 20 days post-infection. Although mortality was low throughout the challenge, differences were found between fish infected with different isolates. Both isolates from genogroup 1, caused greater cumulative mortalities than either of the isolates from Genogroup 5. When combined, the overall mortality rate of fish challenged with genogroup 1 isolates was significantly higher than those infected with genogroup 5. However, viral load was lower on trout infected with genogroup 1 isolates. These results suggest that rainbow trout are more susceptible to IPNV isolates from genogroup 1 than genogroup 5.
Chromosome-level genome assembly of a butterflyfish,Chelmon rostratus
Authors: Huang Xiaoyun , Song Yue , Zhang Suyu , Yunga A , Zhang Mengqi , Chang Yue , Zhang He , Li Chang , Zhao Yong , Liu Meiru , Seim Inge , Fan Guangyi , Liu Xin , Liu Shanshan 
Published: July 2019

AbstractChelmon rostratus(Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish. As an ornamental fish, the genome information for this species might help understanding the genome evolution of Chaetodontidae and adaptation/evolution of coral reef fish.In this study, using the stLFR co-Barcode reads data, we assembled a genome of 638.70 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2.61 Mb, respectively. 94.40% of scaffold sequences were assigned to 24 chromosomes using Hi-C data and BUSCO analysis showed that 97.3% (2,579) of core genes were found in our assembly. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions.As the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.
Altered phosphorylation of the proteasome subunit Rpt6 has minimal impact on synaptic plasticity and learning
Authors: Scudder Samantha L. , Gonzales Frankie R. , Howell Kristin K. , Stein Ivar S. , Dozier Lara E. , Anagnostaras Stephan G. , Zito Karen , Patrick Gentry N. 
Published: July 2019

ABSTRACTDynamic control of protein degradation via the ubiquitin proteasome system is thought to play a crucial role in neuronal function and synaptic plasticity. The proteasome subunit Rpt6, an AAA ATPase subunit of the 19S regulatory particle, has emerged as an important site for regulation of 26S proteasome function in neurons. Phosphorylation of Rpt6 on serine 120 (S120) can stimulate the catalytic rate of substrate degradation by the 26S proteasome and this site is targeted by the plasticity-related kinase calcium/calmodulin-dependent kinase II (CaMKII), making it an attractive candidate for regulation of proteasome function in neurons. Several in vitro studies have shown that altered Rpt6 S120 phosphorylation can affect the structure and function of synapses. To evaluate the importance of Rpt6 S120 phosphorylation in vivo, we created two mouse models which feature mutations at S120 that block or mimic phosphorylation at this site. We find that peptidase and ATPase activities are upregulated in the phospho-mimetic mutant and downregulated in the phospho-dead mutant (S120 mutated to aspartic acid (S120D) or alanine (S120A), respectively). Surprisingly, these mutations had no effect on basal synaptic transmission, long-term potentiation, and dendritic spine dynamics and density in the hippocampus. Furthermore, these mutants displayed no deficits in cued and contextual fear memory. Thus, in a mouse model that blocks or mimics phosphorylation at this site, either compensatory mechanisms negate these effects, or small variations in proteasome activity are not enough to induce significant changes in synaptic structure, plasticity, or behavior.
Quantitative Cellular-Resolution Map of the Oxytocin Receptor in Postnatally Developing Mouse Brains
Authors: Newmaster Kyra T. , Nolan Zachary T. , Chon Uree , Vanselow Daniel J. , Weit Abigael R. , Tabbaa Manal , Hidema Shizu , Nishimori Katsuhiko , Hammock Elizabeth A.D. , Kim Yongsoo 
Published: July 2019

AbstractOxytocin receptor (OTR) plays critical roles in social behavior development. Despite its significance, brain-wide quantitative understanding of OTR expression remains limited in postnatally developing brains. Here, we validated and utilized fluorescent reporter mice (OTRvenus/+) to examine OTR cells across postnatal periods. We developed postnatal 3D template brains to register whole brain images with cellular resolution to systematically quantify OTR cell densities. We found that cortical regions showed temporally and spatially heterogeneous patterns with transient postnatal OTR expression without cell death. Cortical OTR cells were largely not GABAergic neurons with the exception of cells in layer 6b. Subcortical regions showed similar temporal regulation except the hypothalamus. Moreover, our unbiased approach identified two hypothalamic nuclei with sexually dimorphic OTR expression. Lastly, we created a website to easily share our imaging data. In summary, we provide comprehensive quantitative data to understand postnatal OTR expression in the mouse brain.
Identifying the fitness consequences of sex in complex natural environments
Authors: Rushworth Catherine A. , Brandvain Yaniv , Mitchell-Olds Tom 
Published: July 2019

AbstractIn the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. Here we use a large-scale transplant experiment of a North American wildflower to show that sex is associated with reduced lifetime fitness, despite lower herbivory. We separate the effects of sex from hybridity, finding that over-winter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped by complex natural environments, correlated traits, and the identity of mates, rather than sex itself.
Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities
Authors: Wang Yuliang , Ma Shuyi , Ruzzo Walter L. 
Published: July 2019

AbstractSpatial heterogeneity is a fundamental feature of the tumor microenvironment (TME), and tackling spatial heterogeneity in neoplastic metabolic aberrations is critical for tumor treatment. Genome-scale metabolic network models have been used successfully to simulate cancer metabolic networks. However, most models use bulk gene expression data of entire tumor biopsies, ignoring spatial heterogeneity in the TME. To account for spatial heterogeneity, we performed spatially-resolved metabolic network modeling of the prostate cancer microenvironment. We discovered novel malignant-cell-specific metabolic vulnerabilities targetable by small molecule compounds. We predicted that inhibiting the fatty acid desaturase SCD1 may selectively kill cancer cells based on our discovery of spatial separation of fatty acid synthesis and desaturation. We also uncovered higher prostaglandin metabolic gene expression in the tumor, relative to the surrounding tissue. Therefore, we predicted that inhibiting the prostaglandin transporter SLCO2A1 may selectively kill cancer cells. Importantly, SCD1 and SLCO2A1 have been previously shown to be potently and selectively inhibited by compounds such as CAY10566 and suramin, respectively. We also uncovered cancer-selective metabolic liabilities in central carbon, amino acid, and lipid metabolism. Our novel cancer-specific predictions provide new opportunities to develop selective drug targets for prostate cancer and other cancers where spatial transcriptomics datasets are available.
Strong population structure in Venezuelan populations ofCoccidioides posadasii
Authors: Teixeira Marcus M. , Alvarado Primavera , Roe Chandler , Thompson George R. , Patané José Salvatori , Sahl Jason W. , Keim Paul , Galgiani John N. , Litvintseva Ana , Matute Daniel R. , Barker Bridget M. 
Published: July 2019

ABSTRACTCoccidioides posadasiiis a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion ofC. posadasiiacross South America through southeastern Mexico, Honduras, Guatemala and Venezuela. Comparative phylogenomic analyses ofC. posadasiireveal that clinical strains from Venezuela are genetically distinct from the North American populations found in Arizona (AZ), Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations ofC. posadasiiin Central America. As expected, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck, and shows strong population structure. This analysis provides insight into potential forCoccidioidesspp. to invade new regions.
Genetic variation for root architectural traits in response to phosphorus deficiency in mungbean at the seedling stage
Authors: Reddy Venkata Ravi Prakash , Aski M. , Mishra G.P. , Dikshit H.K. , Singh Akanksha , Pandey Renu , Pal Madan , Gayacharan  , Ramtekey Vinita , Priti  , Rai Neha 
Published: July 2019

AbstractRoots enable the plant to survive in natural environment by providing anchorage and acquisition of water and nutrients. In this study, 153 mungbean genotypes were studied to compare root architectural traits under normal and low phosphorus conditions. Significant variations, medium to high heritability, near normal distribution and significant correlations were observed for studied root traits. Total root length (TRL) was positively correlated with total surface area (TSA), total root volume (TRV), total root tips (TRT) and root forks. The first two principal components explained the 79.19 % and 78.84% of the total variation under normal and low phosphorus conditions. TRL, TSA and TRV were major contributors of variation and can be utilized for screening of phosphorus uptake efficiency at seedling stage. Released Indian mungbean varieties were found to be superior for root traits than other genotypic groups. Based on comprehensive phosphorus efficiency measurement, IPM-288, TM 96-25, TM 96-2, M 1477, PUSA 1342 were found to be best five highly efficient genotypes whereas M 1131, PS-16, Pusa Vishal, M 831, IC 325828 were highly inefficient genotypes. These identified highly efficient lines are valuable genetic resources for phosphorus uptake efficiency that could be used in mungbean breeding programme.
A Curvature-Enhanced Random Walker Segmentation Method for Detailed Capture of 3D Cell Surface Membranes
Authors: Lutton E. Josiah , Collier Sharon , Bretschneider Till 
Published: July 2019

AbstractHigh-resolution 3D microscopy is a fast advancing field and requires new techniques in image analysis to handle these new datasets. In this work, we focus on detailed 3D segmentation ofDictyosteliumcells undergoing macropinocytosis captured on an iSPIM microscope. We propose a novel random walker-based method with a curvature-based enhancement term, with the aim of capturing fine protrusions, such as filopodia and deep invaginations, such as macropinocytotic cups, on the cell surface. We tested our method on both real and synthetic 3D image volumes, demonstrating that the inclusion of the curvature enhancement term can improve the segmentation of the aforementioned features. We show that our method performs better than other state of the art segmentation methods in 3D images ofDictyosteliumcells, and performs competitively against CNN-based methods in challenge datasets, demonstrating the ability to obtain accurate segmentations without the requirement of large training datasets. We also present an automated seeding method for microscopy data, which, combined with the curvature-enhanced random walker method, enables the segmentation of large time series with minimal input from the experimenter.