bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinctive mechanism of LHCSR3 expression and function under osmotic stress inChlamydomonas reinhardtii
Authors: Madireddi Sai Kiran , Yadav Ranay Mohan , Bag Pushan , Zamal Mohammad Yusuf , Subramanyam Rajagopal 
Published: May 2023

AbstractLight-harvesting complex stress-related protein 3 (LHCSR3) expression is observed in various protoxidizing conditions like high light and nutrient starvation. LHCSR3 expression is essential for energy-dependent quenching (qE), whereas its role under nutrient starvation is elusive. It is also unclear how nutrient starvation can induce LHCSR3 expression under subsaturating light intensities. To study the role of LHCSR3 under nutrient starvation, theC. reinhardtiicells are grown under osmotic stress that would prevent water uptake; therefore same holds true for soluble nutrients in the medium. In this work, we have shown that LHCSR3 expression can occur under osmotic stress and subsaturating light intensities, whereas it does not elicit qE. Further examination of thylakoid membrane architecture from wild-type andnpq4mutant grown under nutrient starvation revealed that LHCSR3 expression affects the interaction between the PSII core with its peripheral LHCII antenna and possibly can prevent excitation energy transfer. Thylakoid lumen acidification is essential for the expression and function of LHCSR3. Under saturating light intensities, this is achieved by the increased rate of photosynthetic electron flow coupled with proton translocation into the thylakoid lumen. Whereas, under nutrient starvation, the reports of LHCSR3 expression also showed reduced photosynthetic electron flow. Therefore, an alternative mechanism should exist for developing the proton gradient. We observed the downregulation of chloroplast (cp) ATP synthase activity and its abundance under osmotic stress, suggesting the role of (cp) ATP synthase in thylakoid lumen acidification under reduced photosynthetic electron flow. This observation is supported by the expression of LHCSR3 in (cp) ATP-synthase mutantatpFupon exposure to moderate light intensity. This study proposes that the mechanism of LHCSR3 expression and its functionality can vary with the type of photooxidizing stress.
Diffusion MRI Harmonization via Personalized Template Mapping
Authors: Xia Yihao , Shi Yonggang 
Published: May 2023

AbstractOne fundamental challenge in diffusion MRI (dMRI) harmonization is to disentangle the contributions of scanner-related effects from the variable brain anatomy for the observed imaging signals. Conventional harmonization methods rely on establishing an atlas space to resolve anatomical variability and generate a unified inter-site mapping function. However, this approach is limited in accounting for the misalignment of neuroanatomy that still widely persists even after registration, especially in regions close to cortical boundaries. To overcome this challenge, we propose a personalized framework in this paper to more effectively address the confounding from the misalignment of neuroanatomy in dMRI harmonization. Instead of using a common template representing site-effects for all subjects, the main novelty of our method is the adaptive computation of personalized templates for both source and target scanning sites to estimate the inter-site mapping function. We integrate our method with the rotation invariant spherical harmonics (RISH) features to achieve the harmonization of dMRI signals between sites. In our experiments, the proposed approach is applied to harmonize the dMRI data acquired from two scanning platforms: Siemens Prisma and GE MR750 from the Adolescent Brain Cognitive Development (ABCD) dataset and compared with a state-of-the-art method based on RISH features. Our results indicate that the proposed harmonization framework achieves superior performance not only in reducing inter-site variations due to scanner differences but also in preserving sex-related biological variability in original cohorts. Moreover, we assess the impact of harmonization on the estimation of fiber orientation distributions (FOD) and show the robustness of the personalized harmonization procedure in preserving the fiber orientation of original dMRI signals.
A eukaryote-specific factor mediates an early step in the assembly of plant photosystem II
Authors: Keller Jakob-Maximilian , Frieboes Maureen Julia , Jödecke Ludwig , Kappel Sandrine , Wulff Natalia , Rindfleisch Tobias , Sandoval-Ibanez Omar , Gerlach Ines , Thiele Wolfram , Bock Ralph , Eirich Jürgen , Finkemeier Iris , Schünemann Danja , Zoschke Reimo , Schöttler Mark Aurel , Armbruster Ute 
Published: May 2023

ABSTRACTThe initial step of oxygenic photosynthesis is the thermodynamically challenging extraction of electrons from water and the release of molecular oxygen. This light-driven process, which is the basis of life on Earth, is catalyzed by the photosystem II (PSII) within the thylakoid membrane of photosynthetic organisms. The biogenesis of PSII requires a controlled step-wise assembly process of which the early steps are considered to be highly conserved between plants and their cyanobacterial progenitors. This assembly process involves auxiliary proteins, which are likewise conserved. In the present work, we show that in plants, the early assembly step, in which the PSII reaction center (RC) is associated with the intrinsic antenna protein CP47 to form the RC47 intermediate, is facilitated by a novel eukaryote-exclusive assembly factor. This factor, we named DEAP2 for DECREASED ELECTRON TRANSPORT AT PSII, works in concert with the conserved PAM68 assembly factor. Thedeap2andpam68mutants showed similar defects in PSII accumulation and assembly of the RC47 intermediate. The combined lack of both proteins results in a loss of functional PSII and the inability of plants to grow photoautotrophically on soil. While overexpression of DEAP2 partially rescued thepam68PSII accumulation phenotype, this effect was not reciprocal. DEAP2 accumulates at 20-fold higher levels than PAM68, together suggesting that both proteins have distinct functions. In summary, our results uncover eukaryotic adjustments to the PSII assembly process, which involve the addition of DEAP2 for the rapid progression from RC to RC47.
Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marinaandZostera pacifica) beds in different geographic settings in Southern California
Authors: Waters Tanner , Gold Zachary , Obaza Adam , Ambrose Richard F. , Eagle Robert A. 
Published: May 2023

AbstractSeagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these changes are affecting biodiversity over time. This study evaluates the assemblages of fish found at fiveZosterabeds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.
Temporal control of Num1 contact site formation reveals a relationship between mitochondrial division and mitochondria-plasma membrane tethering
Authors: Harper Clare S. , Casler Jason C. , Lackner Laura L. 
Published: May 2023

ABSTRACTMitochondrial division is critical for maintenance of mitochondrial morphology and cellular homeostasis. Previous work has suggested that the mitochondria-ER-cortex anchor (MECA), a tripartite membrane contact site between mitochondria, the ER, and the plasma membrane, is involved in mitochondrial division. However, its role is poorly understood. We developed a system to control MECA formation and depletion, which allowed us to investigate the relationship between MECA-mediated contact sites and mitochondrial division. Num1 is the protein that mediates mitochondria-ER-plasma membrane tethering at MECA sites. Using both rapamycin-inducible dimerization and auxin-inducible degradation components coupled with Num1, we developed systems to temporally control the formation and depletion of the native contact site. Additionally, we designed a regulatable Num1-independant mitochondria-PM tether. We found that mitochondria-PM tethering alone is not sufficient to rescue mitochondrial division and that a specific feature of Num1-mediated tethering is required. This study demonstrates the utility of systems that regulate contact site formation and depletion in studying the biological functions of membrane contact sites.
Deep learning-driven characterization of single cell tuning in primate visual area V4 unveils topological organization
Authors: Willeke Konstantin F. , Restivo Kelli , Franke Katrin , Nix Arne F. , Cadena Santiago A. , Shinn Tori , Nealley Cate , Rodriguez Gabrielle , Patel Saumil , Ecker Alexander S. , Sinz Fabian H. , Tolias Andreas S. 
Published: May 2023

AbstractDeciphering the brain’s structure-function relationship is key to understanding the neuronal mechanisms underlying perception and cognition. The cortical column, a vertical organization of neurons with similar functions, is a classic example of primate neocortex structure-function organization. While columns have been identified in primary sensory areas using parametric stimuli, their prevalence across higher-level cortex is debated. A key hurdle in identifying columns is the difficulty of characterizing complex nonlinear neuronal tuning, especially with high-dimensional sensory inputs. Here, we asked whether area V4, a mid-level area of the macaque visual system, is organized into columns. We combined large-scale linear probe recordings with deep learning methods to systematically characterize the tuning of >1,200 V4 neurons usingin silicosynthesis of most exciting images (MEIs), followed byin vivoverification. We found that the MEIs of single V4 neurons exhibited complex features like textures, shapes, or even high-level attributes such as eye-like structures. Neurons recorded on the same silicon probe, inserted orthogonal to the cortical surface, were selective to similar spatial features, as expected from a columnar organization. We quantified this finding using human psychophysics and by measuring MEI similarity in a non-linear embedding space, learned with a contrastive loss. Moreover, the selectivity of the neuronal population was clustered, suggesting that V4 neurons form distinct functional groups of shared feature selectivity, reminiscent of cell types. These functional groups closely mirrored the feature maps of units in artificial vision systems, hinting at shared encoding principles between biological and artificial vision. Our findings provide evidence that columns and functional cell types may constitute universal organizing principles of the primate neocortex, simplifying the cortex’s complexity into simpler circuit motifs which perform canonical computations.
Towards Computing Attributions for Dimensionality Reduction Techniques
Authors: Scicluna Matthew , Grenier Jean-Christophe , Poujol Raphaël , Lemieux Sébastien , Hussin Julie G 
Published: May 2023

AbstractWe describe the problem of computing local feature attributions for dimensionality reduction methods. We use one such method that is well established within the context of supervised classification – using the gradients of target outputs with respect to the inputs – on the popular dimensionality reduction technique t-SNE, widely used in analyses of biological data. We provide an efficient implementation for the gradient computation for this dimensionality reduction technique. We show that our explanations identify significant features using novel validation methodology; using synthetic datasets and the popular MNIST benchmark dataset. We then demonstrate the practical utility of our algorithm by showing that it can produce explanations that agree with domain knowledge on a SARS-CoV-2 sequence dataset. Throughout, we provide a road map so that similar explanation methods could be applied to other dimensionality reduction techniques to rigorously analyze biological datasets.
Compression algorithm for colored de Bruijn graphs
Authors: Rahman Amatur , Dufresne Yoann , Medvedev Paul 
Published: May 2023

AbstractA colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead. The software is available athttp://github.com/medvedevgroup/ESSColor.
Recurrent Viral Capture of Cellular Phosphodiesterases that Antagonize OAS-RNase L
Authors: Goldstein Stephen A. , Elde Nels C. 
Published: May 2023

AbstractPhosphodiesterases (PDEs) encoded by viruses are putatively acquired by horizontal transfer of cellular PDE ancestor genes. Viral PDEs inhibit the OAS-RNase L antiviral pathway, a key effector component of the innate immune response. Although the function of these proteins is well-characterized, the origins of these gene acquisitions is less clear. Phylogenetic analysis revealed at least five independent PDE acquisition events by ancestral viruses. We found evidence that PDE-encoding genes were horizontally transferred between coronavirus genera. Three clades of viruses withinNidovirales: merbecoviruses (MERS-CoV), embecoviruses (OC43), and toroviruses encode independently acquired PDEs, and a clade of rodent alphacoronaviruses acquired an embecovirus PDE via recent horizontal transfer. Among rotaviruses, the PDE of Rotavirus A was acquired independently from Rotavirus B and G PDEs, which share a common ancestor. Conserved motif analysis suggests a link between all viral PDEs and a similar ancestor among the mammalian AKAP7 proteins despite low levels of sequence conservation. Additionally, we used ancestral sequence reconstruction and structural modeling to reveal that sequence and structural divergence are not well-correlated among these proteins. Specifically, merbecovirus PDEs are as structurally divergent from the ancestral protein and the solved structure of human AKAP7 PDE as they are from each other. In contrast, comparisons of Rotavirus B and G PDEs reveal virtually unchanged structures despite evidence for loss of function in one, suggesting impactful changes that lie outside conserved catalytic sites. These findings highlight the complex and volatile evolutionary history of viral PDEs and provide a framework to facilitate future studies.
Distributed Genetic Effects of the Corpus Callosum Subregions Suggest Links to Neuropsychiatric Disorders and Related Traits
Authors: Campbell Megan L. , Dalvie Shareefa , Shadrin Alexey , van der Meer Dennis , O’Connell Kevin , Frei Olekasander , Andreassen Ole A. , Stein Dan J. , Rokicki Jaroslav 
Published: May 2023

AbstractBackgroundThe corpus callosum (CC) is a brain structure with a high heritability and potential role in psychiatric disorders. However, the genetic architecture of the CC and the genetic link with psychiatric disorders remains largely unclear. We investigated the genetic architectures of the volume of the CC and its subregions, and the genetic overlap with psychiatric disorders.MethodsWe applied multivariate GWAS to genetic and T1-weighted MRI data of 40,894 individuals from the UK Biobank, aiming to boost genetic discovery and to assess the pleiotropic effects across volumes of the five subregions of the CC (posterior, mid posterior, central, mid anterior and anterior) obtained by FreeSurfer 7.1. Multivariate GWAS was run combining all subregions, co-varying for relevant variables. Gene-set enrichment analyses were performed using MAGMA. Linkage disequilibrium score regression (LDSC) was used to determine SNP-based heritability of total CC volume and volumes of its subregions as well as their genetic correlations with relevant psychiatric traits.ResultsWe identified 70 independent loci with distributed effects across the five subregions of the CC (p < 5 × 10−8). Additionally, we identified 33 significant loci in the anterior subregion, 23 in the mid anterior, 29 in the central, 7 in the mid posterior and 56 in the posterior subregion. Gene-set analysis revealed 156 significant genes contributing to volume of the CC subregions (p < 2.6 × 10−6). LDSC estimated the heritability of CC to (h2SNP=0.38, SE=0.03), and subregions ranging from 0.22 (SE=0.02) to 0.37 (SE=0.03). We found significant genetic correlations of total CC volume with bipolar disorder (BD, rg=-0.09, SE=0.03; p=5.9 × 10−3) and drinks consumed per week (rg=-0.09, SE=0.02; p=4.8 × 10−4), and volume of the mid anterior subregion with BD (rg=-0.12, SE=0.02; p=2.5 × 10−4), major depressive disorder (rg=-0.12, SE=0.04; p=3.6 × 10−3), drinks consumed per week (rg=-0.13, SE=0.04; p=1.8 × 10−3) and cannabis use (rg=-0.09, SE=0.03; p=8.4 × 10−3).ConclusionsOur results demonstrate that the CC has a polygenic architecture implicating multiple genes, and show that CC subregion volumes are heritable. We found distinct genetic factors are involved in the development of anterior and posterior subregions, consistent with their divergent functional specialization. Significant genetic correlation between volumes of the CC and bipolar disorder, drinks per week, major depressive disorder and cannabis consumption subregion volumes with psychiatric traits is noteworthy and deserving of further investigation.
Nutritional composition and metabolic analysis of the newly hatchedAnguilla japonicafrom embryo to preleptocephali obtained from artificial reproduction
Authors: Li Kang , Li Yuangu , Li Tiezhu , Cui Rongfeng , Liu Liping 
Published: May 2023

AbstractThe starter diet for Japanese eel (Anguilla japonica) has always been a difficult problem for the realization of total artificial reproduction. Therefore, this research analyzed the nutritional composition of artificially fertilized eggs, and transcriptome of samples from early hatchlings of fry to better understand nutrients requirements. The composition of crude lipid and crude protein in fertilized eggs was 7.24%±0.32% and 10.56%±0.41%, respectively. Seven kinds of essential amino acids (EAA) were detected but took a comparable lower content (3.19%) than other marine fish eggs. We randomly assembled 265.74 million clean reads and identified 1751 differentially expressed genes (DEGs) (P< 0.01) from pre-leptocephalus larvae. A total of 23 KEGG pathways related to the digestive and metabolic system were detected. Genes related to the secretion pathway of saliva, pancreatic juice and other digestive juices were significantly changed. The genes of carbohydrate metabolism, glycerolipid metabolism and glycerophospholipid metabolism were up-regulated significantly with the growth of the larvae (day 0 to 12). This study will facilitate future studies on the nutrition of eel larvae and other biological traits to reproductive research.
Multiplex PCR with Nanopore Sequencing for Sequence-Based Detection of Four Tilapia Pathogens
Authors: Delamare-Deboutteville Jérôme , Meemetta Watcharachai , Pimsannil Khaettareeya , Gan Han Ming , Khor Li Imm Laura , Mohan Chadag Vishnumurthy , Dong Ha Thanh , Senapin Saengchan 
Published: May 2023

AbstractBackgroundTilapia aquaculture faces significant threats posed by four prominent pathogens: tilapia lake virus (TiLV), infectious spleen and kidney necrosis virus (ISKNV),Francisella orientalis, andStreptococcus agalactiae. Currently, employed molecular diagnostic methods for these pathogens rely on multiple singleplex PCR reactions, which are time-consuming and expensive.MethodsIn this study, we present an approach utilizing a multiplex PCR (mPCR) assay, coupled with rapid Nanopore sequencing, enabling the one-tube simultaneous detection and one-reaction Nanopore sequencing-based validation of four pathogens.ResultsOur one-tube multiplex assay exhibits a detection limit of 1,000 copies per reaction for TiLV, ISKNV, andS. agalactiae, while forF. orientalis, the detection limit is 10,000 copies per reaction. This sensitivity is sufficient for diagnosing infections and co-infections in clinical samples from sick fish, enabling rapid confirmation of the presence of pathogens. Integrating multiplex PCR and Nanopore sequencing provides an alternative approach platform for fast and precise diagnostics of major tilapia pathogens in clinically sick animals, adding to the available toolbox for disease diagnostics.
Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga,Closterium peracerosum-strigosum-littoraleComplex
Authors: Kawaguchi Yawako W. , Tsuchikane Yuki , Tanaka Keisuke , Taji Teruaki , Suzuki Yutaka , Toyoda Atsushi , Ito Motomi , Watano Yasuyuki , Nishiyama Tomoaki , Sekimoto Hiroyuki , Tsuchimatsu Takashi 
Published: May 2023

AbstractGenome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than twofold heritable genome size variation among the unicellular Zygnematophycean alga,Closterium peracerosum-strigosum-littorale(C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1segregation analysis. Sixde novoassembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in theC. psl. complex, despite its possible detrimental effects.