bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an amplicon-based high throughput sequencing method for genotypic characterisation of norovirus in oysters
Authors: Fitzpatrick Amy H , Rupnik Agnieszka , O’Shea Helen , Crispie Fiona , Cotter Paul D. , Keaveney Sinéad 
Published: December 2022

AbstractNorovirus is a highly diverse RNA virus often implicated in food-borne outbreaks, particularly shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbour various pathogens, including human pathogenic viruses. The application of Sanger or amplicon-based High Throughput Sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges i) distinguishing multiple genotypes/variants in a single sample and ii) low concentrations of norovirus RNA. Here we have assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerase and Reverse Transcriptase (RT) enzymes were compared, and performance was evaluated based on i) the number of reads passing quality filters per sample, ii) the number of correct genotypes identified, and iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterise norovirus populations in naturally contaminated oysters.ImportanceWhile foodborne outbreaks account for approximately 14% of norovirus cases (Verhoef L, Hewitt J, Barclay L, Ahmed S, Lake R, Hall AJ, Lopman B, Kroneman A, Vennema H, Vinjé J, Koopmans M. 2015. 1999-2012. Emerg Infect Dis 21:592–599), we do not have standardised high-throughput sequencing methods for genotypic characterisation in foodstuffs. Here we present an optimised amplicon high- throughput sequencing method for the genotypic characterisation of norovirus in oysters. This method can accurately detect and characterise norovirus at concentrations typically detected in oysters. It will permit the investigation of norovirus genetic diversity in complex matrices and contribute to ongoing surveillance of norovirus in the environment.
Individual Astrocyte Morphology in the Collagenous Lamina Cribrosa Revealed by Multicolor DiOlistic Labeling
Authors: Waxman Susannah , Quinn Marissa , Donahue Cara , Falo Louis D. , Sun Daniel , Jakobs Tatjana C. , Sigal Ian A. 
Published: December 2022

AbstractAstrocytes in the lamina region of the optic nerve head play vital roles in supporting retinal ganglion cell axon health. In glaucoma, these astrocytes are implicated as early responders to stressors, undergoing characteristic changes in cell function as well as cell morphology. Much of what is currently known about individual lamina astrocyte morphology has been learned from rodent models which lack a defining feature of the human optic nerve head, the collagenous lamina cribrosa (LC). Current methods available for evaluation of collagenous LC astrocyte morphology have significant shortcomings. We aimed to evaluate Multicolor DiOlistic labeling (MuDi) as an approach to reveal individual astrocyte morphologies across the collagenous LC.Gold microcarriers were coated with all combinations of three fluorescent cell membrane dyes, DiI, DiD, and DiO, for a total of seven dye combinations. Microcarriers were delivered to 150μm-thick coronal vibratome slices through the LC of pig, sheep, goat, and monkey eyes via MuDi. Labeled tissues were imaged with confocal and second harmonic generation microscopy to visualize dyed cells and LC collagenous beams, respectively. GFAP labeling of DiOlistically-labeled cells with astrocyte morphologies was used to investigate cell identity. 3D models of astrocytes were created from confocal image stacks for quantification of morphological features.DiOlistic labeling revealed fine details of LC astrocyte morphologies including somas, primary branches, higher-order branches, and end-feet. Labeled cells with astrocyte morphologies were GFAP+. Astrocytes were visible across seven distinct color channels, allowing high labeling density while still distinguishing individual cells from their neighbors. MuDi was capable of revealing tens to hundreds of collagenous LC astrocytes, in situ, with a single application. 3D astrocyte models allowed automated quantification of morphological features including branch number, length, thickness, hierarchy, and straightness as well as Sholl analysis.MuDi labeling provides an opportunity to investigate morphologies of collagenous LC astrocytes, providing both qualitative and quantitative detail, in healthy tissues. This approach may open doors for research of glaucoma, where astrocyte morphological alterations are thought to coincide with key functional changes related to disease progression.
Reach corrections toward moving objects are faster than reach corrections toward jumping targets
Authors: Reschechtko Sasha , Gnanaseelan Cynthiya , Pruszynski J. Andrew 
Published: December 2022

AbstractVisually guided reaching is a common motor behavior that engages subcortical circuits to mediate rapid corrections. These circuits help us successfully grasp objects we see, even if those objects move during the reach. Although these neural mechanisms have evolved for interaction with the physical world, they are almost always studied in the context of reaching toward virtual targets displayed on a computer or projection screen. Virtual targets are unrealistic both because they cannot be physically grasped and because they generally move by “jumping” from one place to another instantaneously. Recent work has indicated that various aspects of “real” visual stimuli, including proximity and graspability, elicit distinct neural activity. In this study, we instructed participants to perform rapid reaches to physical objects. On some trials, these objects either moved realistically (continuously from one position to another) or unrealistically (jumping instantaneously to an equivalent position). Participants were consistently faster in correcting their reach trajectories when the object moved continuously.
Mapping whole brain effects of infrared neural stimulation with positron emission tomography
Authors: Meneghetti Marcello , Gudmundsen Frederik , Jessen Naja S. , Sui Kunyang , Baun Christina , Palner Mikael , Markos Christos 
Published: December 2022

AbstractThe combination of neuroimaging and targeted neuromodulation is a crucial tool to gain a deeper understanding of neural networks at a circuit level. Infrared neurostimulation (INS) is a promising optical modality that allows to evoke neuronal activity with high spatial resolution without need for the introduction of exogenous substances in the brain. Here, we report the use of whole-brain functional [18F]fluorodeoxyglucose positron emission tomography (FDG-PET) imaging during INS in the dorsal striatum, performed using a multifunctional soft neural probe. We demonstrate the possibility to identify multi-circuit connection patterns in both cortical and subcortical brain regions within a single scan. By using a bolus plus infusion FDG-PET scanning protocol, we were able to observe the metabolic rate evolution in these regions during the experiments and correlate its variation with the onset of the INS stimulus. Due to the focality of INS and the large amount of viable molecular targets for PET, this novel approach to simultaneous imaging and stimulation is highly versatile. This pilot study can pave the way to further understand the brain connectivity on a global scale.
Significant SAR11 removal by a hard-bottom community
Authors: Dadon-Pilosof Ayelet , Conley Keats , Suzuki Marcelino T. 
Published: December 2022

AbstractMicroorganisms are a key component of the marine food webs through the microbial loop. In previous work, we have shown that some bacteria, including CandidatusPelagibacterspp (SAR11)—the most abundant bacterium in the ocean—can evade filtration by benthic and planktonic tunicates. Here we tested whether differential removal of microbial taxa by benthic filter-feeders can be observed in the distribution and abundance of microbial taxa from hard-bottom subtidal communities, a common coastal habitat in the Eastern Mediterranean Sea towards the open sea. The abundance of microbial groups along crosss-hore transects was measured based on combined flow cytometry and SSU rRNA gene metabarcoding. Our results show that most groups were depleted (up to 50%) over the hard-bottom compared to the open sea, but unexpectedly we did not observe a clear differential removal of different taxa, SAR 11 notably. This study indicates a strong top-down control of the abundance of pelagic microorganisms over shallow hard-bottom where suspension feeders are common.
Recurrent evolution of small body size and loss of the sword ornament in Northern Swordtail fish
Authors: Preising Gabriel A. , Gunn Theresa , Baczenas John J. , Pollock Alexa , Powell Daniel L. , Dodge Tristram O. , Machin Kairuz Jose Angel , Savage Markita , Lu Yuan , Fitschen-Brown Meredith , Cummings Molly , Thakur Sunishka , Tobler Michael , Ríos-Cardenas Oscar , Morris Molly , Schumer Molly 
Published: December 2022

AbstractAcross the tree of life, species have repeatedly evolved similar phenotypes. While well-studied for ecological traits, there is also evidence for convergent evolution of sexually selected traits. Swordtail fish (Xiphophorus) are a classic model system for studying sexual selection, and femaleXiphophorusexhibit strong mate preferences for large male body size and a range of sexually dimorphic ornaments. However, sexually selected traits have been lost multiple times in the genus. Phylogenetic relationships between species in this group have historically been controversial, likely as a result of prevalent gene flow, resulting in uncertainty over the number of losses of ornamentation and large body size. Here, we use whole-genome sequencing approaches to re-examine phylogenetic relationships within aXiphophorusclade that varies in the presence and absence of sexually selected traits. Using wild-caught individuals, we determine the phylogenetic placement of a small, unornamented species,X. continens, confirming an additional loss of ornamentation and large body size in the clade. With these revised phylogenetic relationships, we analyze evidence for coevolution between body size and other sexually selected traits using a phylogenetically independent contrasts approach. These results provide insights into the evolutionary pressures driving the recurrent loss of suites of sexually selected traits.
Adaptation of the binding domain ofLactobacillus acidophilusS-layer protein as a molecular tag for affinity chromatography development
Authors: Muruaga Emanuel J. , Uriza Paula J. , Eckert Gonzalo A. K. , Pepe María V. , Duarte Cecilia M. , Roset Mara S. , Briones Gabriel 
Published: December 2022

AbstractThe SLAPTAGis a novel molecular TAG derived from a protein domain present in the sequence ofLactobacillus acidophilusSlpA (SlpA284–444). Proteins from different biological sources, with different molecular weights or biochemical functions, can be fused in frame to the SLAPTAGand efficiently purified by the specific binding to a bacterial-derived chromatographic matrix named here Bio-Matrix (BM). Different binding and elution conditions were evaluated to set an optimized protocol for the SLAPTAG-based affinity chromatography (SAC). The binding equilibrium between SLAPTAGand BM was reached after a few minutes at 4°C, being the apparent dissociation constant (KD) of 4.3 µM, a value which is similar to different Kd determined for other S-layer proteins and their respective bacterial cell walls. A reporter protein was generated (H6-GFP-SLAPTAG) to compare the efficiency of the SAC against a commercial system based on a Ni2+-charged agarose matrix, observing no differences in the H6-GFP-SLAPTAGpurification performance. The stability and reusability of the BM were evaluated, and it was determined that the matrix was stable for more than a year, being possible to reuse it five times without a significant loss in the efficiency for protein purification. Alternatively, we explored the recovery of bound SLAP-tagged proteins by proteolysis using the SLAPASE(a SLAP-tagged version of the HRV-3c protease) that released a tag-less GFP (SLAPTAG-less). Additionally, iron nanoparticles were linked to the BM and the resulting BMmagwas successfully adapted for a magnetic SAC, a technique that can be potentially applied for high-throughput-out protein production and purification.
Rhythmic oscillations in the midbrain dopaminergic nuclei in mice
Authors: Oberto Virginie , Matsumoto Jumpei , Pompili Marco , Todorova Ralitsa , Papaleo Francesco , Nishijo Hisao , Venance Laurent , Vandecasteele Marie , Wiener Sidney 
Published: December 2022

AbstractDopamine release in the forebrain by midbrain ventral tegmental nucleus (VTA) and substantia nigra pars compacta (SNpc) neurons is implicated in reward processing, goal-directed learning, and decision-making. Rhythmic oscillations of neural excitability underlie coordination of network processing, and have been reported in these dopaminergic nuclei at several frequency bands. This paper provides a comparative characterization of several frequencies of oscillations of local field potential and single unit activity, highlighting some behavioral correlates. We recorded from optogenetically identified dopaminergic sites in mice training in operant olfactory and visual discrimination tasks. Rayleigh and Pairwise Phase Consistency (PPC) analyses revealed some VTA/SNc neurons phase-locked to each frequency range, with fast spiking interneurons (FSIs) prevalent at 1-2.5 Hz (slow) and 4 Hz bands, and dopaminergic neurons predominant in the theta band. More FSIs than dopaminergic neurons were phase-locked in the slow and 4 Hz bands during many task events. The highest incidence of phase-locking in neurons was in the slow and 4 Hz bands, and occurred during the delay between the operant choice and trial outcome (reward or punishment) signals. These data provide a basis for further examination of rhythmic coordination of activity of dopaminergic nuclei with other brain structures, and its impact for adaptive behavior.
Opioid receptor architecture for the modulation of brainstem functions
Authors: Hug Nicholas F. , Lindsay Nicole Mercer , McCallum William M. , Bryan Justin , Huang Karen , Ochandarena Nicole , Tassou Adrien , Scherrer Grégory 
Published: December 2022

AbstractOpioids produce profound and diverse effects on a range of behaviors, many driven by brainstem activity; however, the presence of opioid and opioid-like receptors at this level has been poorly studied outside of nociceptive structures and components of respiratory circuitry. While previous studies identified expression of µ, δ, κ, and nociceptin opioid and opioid-like receptors in the brainstem, patterns have not been fully delineated, and neither has receptor coexpression nor the behavioral implications of their expression in most structures. We aimed to elucidate expression patterns for all four receptors across somatosensory-motor, auditory, and respiratory brainstem circuits; identify recurring themes to provide insight into the mechanisms by which exogenous opioids affect broader brainstem circuits; and characterize the function of endogenous opioids in subcortical processing and behavior modulation. Using a fluorescent reporter mouse line for each receptor, we created a comprehensive atlas of brainstem receptor distribution and identified novel expression patterns in modality-specific circuits. Each receptor showed unique expression patterns across the brainstem with minimal correlation between receptors. Orofacial somatosensory-motor circuits expressed all four receptors, though generally in distinct regions, suggesting differential opiate modulation of afferent and efferent trigeminal signaling. Within the auditory circuits, receptors segregated along the vertical and horizontal processing pathways with minimal colocalization. Finally, the respiratory circuit strongly expressed the µ opioid receptor in multiple crucial structures with minimal presence of the other three receptors. We further assessed the functional significance of these expression patterns, using the respiratory circuitry as an example, by characterizing respiratory responses to selective opioid agonists, finding that each agonist caused unique alterations in breathing pattern and/or breath shape. Together, these results establish a comprehensive atlas of opioid and opioid-like receptor expression throughout the brainstem, laying the essential groundwork for further evaluation of opioid neuromodulation across the broad spectrum of behaviors.
Phenotypic plasticity during diel cycling hypoxia in Arctic char (Salvelinus alpinus)
Authors: Ducros Loïck , Touaibia Mohamed , Pichaud Nicolas , Lamarre Simon G. 
Published: December 2022

AbstractOxygen concentration naturally fluctuates in aquatic environments. Due to increased eutrophication caused by anthropic activities, this phenomenon could be amplified and result in a daily cycle of alternating normoxic and hypoxic conditions. At the metabolic level, lack of oxygen and reoxygenation can both have serious repercussions on fish due to fluctuations in ATP supply and demand and an elevated risk of oxidative burst. Thus, fish must adjust their phenotype to survive and equilibrate their energetic budget. However, their energy allocation strategy could imply a reduction in growth which could be deleterious for their fitness. Although the impact of cyclic hypoxia is a major issue for ecosystems and fisheries worldwide, our knowledge remains however limited. Our objective was to characterise the effects of cyclic hypoxia on growth and metabolism in fish. We monitored growth parameters (specific growth rate, condition factor), hepatosomatic and visceral indexes, relative heart mass and hematocrit of Arctic char (Salvelinus alpinus) exposed to thirty days of cyclic hypoxia. We also measured the hepatic protein synthesis rate, hepatic triglycerides as well as muscle glucose, glycogen and lactate, and quantified hepatic metabolites during this treatment. Arctic char appeared to acclimate well to oxygen fluctuations. The first days of cyclic hypoxia induced a profound metabolome reorganisation in the liver. However, fish rebalanced their metabolic activities and successfully maintained their growth and energetic reserves after one month of cyclic hypoxia. These results demonstrate the impressive ability of fish to cope with their changing environment.Summary statementThis study characterizes the metabolic adjustments performed by Arctic char when coping with one month of cyclic hypoxia. Fish reached a new phenotype by defending their growth and energy stores.
GWAS meta-analysis of resistance against Piscirickettsia salmonis in Atlantic salmon
Authors: Rodrigo Marín-Nahuelpi , Garcia Baltasar F. , Piña-Elgueda Agustin , Gallardo-Garrido Jousepth , López Paulina , Cichero Daniela , Moen Thomas , Ødegård Jørgen , Yáñez José M. 
Published: December 2022

ABSTRACTSalmonid rickettsial syndrome (SRS) remains as one of the most important pathogens for salmon farming. Genetic improvement has proven to be a viable alternative to reduce mortality in breeding stock. Understanding the genetic architecture of resistance has been a matter of ongoing research aimed at establishing the most appropriate method by which genomic information can be incorporated into breeding programs. However, the genetic architecture of complex traits such as SRS resistance may vary due to genetic and environmental background. In this work, we used the genotypes of a total of 5839 Atlantic salmon from 4 different experimental challenges againstPiscirickttsia salmonis, which were imputed high density (∼930K SNP) to perform within-population genomic-association analyses, followed by a meta-analysis of resistance to SRS defined as binary survival and day of death. The objectives of this study were to i) uncover the genomic regions associated with resistance to SRS among multiple populations; and ii) identify candidate genes associated with each trait definition. SNP-based meta-analysis revealed a clear QTL onSsa02for both traits while gene-based meta-analysis revealed 16 genes in common for both traits. Our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance toP. salmonisinSalmo salar.
Identification of Disease Modules Using Higher-Order Network Structure
Authors: Singh Pramesh , Kuder Hannah , Ritz Anna 
Published: December 2022

AbstractMotivationHigher-order interaction patterns among proteins have the potential to reveal mechanisms behind molecular processes and diseases. While clustering methods are used to identify functional groups within molecular interaction networks, these methods largely focus on edge density and do not explicitly take into consideration higher-order interactions. Disease genes in these networks have been shown to exhibit rich higher-order structure in their vicinity, and considering these higher-order interaction patterns in network clustering have the potential to reveal new disease-associated modules.ResultsWe propose a higher-order community detection method which identifies community structure in networks with respect to specific higher-order connectivity patterns beyond edges. Higher-order community detection on four different protein-protein interaction networks identifies biologically significant modules and disease modules that conventional edge-based clustering methods fail to discover. Higher-order clusters also identify disease modules from GWAS data, including new modules that were not discovered by top-performing approaches in a Disease Module DREAM Challenge. Our approach provides a more comprehensive view of community structure that enables us to predict new disease-gene associations.Availabilityhttps://github.com/Reed-CompBio/graphlet-clustering
DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis
Authors: Liu Yi , Yang Yun , Chen Wendong , Shen Feng , Xie Linhai , Zhang Yingying , Zhai Yuanjun , He Fuchu , Zhu Yunping , Chang Cheng 
Published: December 2022

AbstractRetention time (RT) alignment is one of the crucial steps in liquid chromatography-mass spectrometry (LC-MS)-based proteomic and metabolomic experiments, especially for large cohort studies, and it can be achieved using computational methods; the most popular methods are the warping function method and the direct matching method. However, the existing tools can hardly handle monotonic and non-monotonic RT shifts simultaneously. To overcome this, we developed a deep learning-based RT alignment tool, DeepRTAlign, for large cohort LC-MS data analysis. It first performs a coarse alignment by calculating the average time shift between any two samples and then uses RT and m/z as the main features to train its deep learning-based model. We demonstrate that DeepRTAlign has improved performances, especially when handling complex samples, by benchmarking it against current state-of-the-art approaches on 19 real-world proteomic and metabolomic datasets and the corresponding simulated datasets. Benchmarked on a dataset with known fold changes, the results showed that DeepRTAlign can improve the identification sensitivity of MS data without compromising the quantitative accuracy. Furthermore, using the MS features aligned by DeepRTAlign in a large cohort, we trained a classifier of 15 features to predict the early recurrence of hepatocellular carcinoma. The features were validated on an independent cohort using targeted proteomics with an AUC of 0.833. Being flexible and robust with four different feature extraction tools, DeepRTAlign provides an advanced solution to RT alignment in large cohort LC-MS data, which is currently one of the bottlenecks in proteomics and metabolomics research, especially for clinical applications.