bluuebunny/crossref_metadata_2025 huggingface dataset:
DeSide: A unified deep learning approach for cellular decomposition of bulk tumors based on limited scRNA-seq data
Authors: Xiong Xin , Liu Yerong , Pu Dandan , Yang Zhu , Bi Zedong , Tian Liang , Li Xuefei
Published: May 2023

Cellular decomposition employing bulk RNA-sequencing (RNA-seq) has been consistently under investigation due to its high fidelity, ease of use, and cost-effectiveness compared to single cell RNA-sequencing (scRNA-seq). However, the intricate nature of the tumor microenvironment, and the significant heterogeneity among patients and cells have made it challenging to precisely evaluate the cellular composition of solid tumors using a unified model. In this work, we developed DeSide, a deep learning and single-cell decomposition method for solid tumors, to estimate proportions of cell types presented in tumor samples. Our new deep neural network (DNN) architecture considers only non-cancerous cells during the training process, indirectly calculating the proportion of cancerous cells. This approach avoids directly handling the often more variable heterogeneity of cancerous cells, and instead leverages scRNA-seq data from three different cancer types to empower the DNN model with a robust generalization capability across diverse cancers. Additionally, we used a new sampling method and filtering strategies to simulate the gene expression profiles (GEPs) of solid tumors, creating a carefully controlled training set that could be compared to the bulk RNA-seq data from The Cancer Genome Atlas (TCGA), a database of bulk RNA-seq data collected from cancer patients. Relying on limited yet diverse scRNA-seq data, our approach outperformed current methods in accurately predicting the celluar composition of samples from TCGA and an additional validation set. Furthermore, we demonstrated that the predicted cellular composition can be utilized to stratify cancer patients into different groups with varying overall survival rates. With increased availability of scRNA-seq data for various types of tumors, DeSide holds the potential for a more precise cellular decomposition model using bulk RNA-seq.
NRF2 activation in the heart induces glucose metabolic reprogramming and mediates cardioprotection via upregulation of the pentose phosphate pathway
Authors: Zoccarato Anna , Smyrnias Ioannis , Reumiller Christina M , Hafstad Anne D , Chong Mei , Richards Daniel A , Santos Celio XC , Visnagri Asjad , Bromage Daniel I , Zhang Xiaohong , Sawyer Greta , Thompson Richard , Shah Ajay M
Published: May 2023

Rationale

The transcription factor NRF2 is well recognized as a master regulator of antioxidant responses and cytoprotective genes. Previous studies showed that NRF2 protects mouse hearts during chronic hemodynamic overload at least in part by reducing oxidative stress. Evidence from other tissues suggests that NRF2 may modulate glucose intermediary metabolism but whether NRF2 has such effects in the heart is unclear.

Objective

To investigate the role of NRF2 in regulating glucose intermediary metabolism and cardiac function during disease stress.

Methods and Results

Cardiomyocyte-specific Keap1 knockout (csKeap1KO) mice, deficient in the endogenous inhibitor of NRF2, were used as a novel model of constitutively active NRF2 signaling. Targeted metabolomics and isotopomer analysis were employed in studies with13C6-glucose in csKeap1KO and wild-type (WT) mice. Pharmacological and genetic approaches were utilized in neonatal rat ventricular cardiomyocytes (NRVM) to explore molecular mechanisms. We found that cardiac-specific activation of NRF2 upregulated key enzymes of the Pentose Phosphate Pathway (PPP), redirected glucose metabolism towards the PPP and protected the heart against pressure overload-induced cardiac dysfunction.In vitro, knockdown of Keap1 upregulated PPP enzymes and reduced cell death in NRVM subjected to chronic neurohumoral stimulation. These pro-survival effects were abolished by pharmacological inhibition of the PPP or silencing of the PPP rate-limiting enzyme glucose-6-phosphate dehydrogenase (G6PD). Knockdown of NRF2 in NRVM increased stress-induced DNA damage which was rescued by supplementing the cells with either NADPH or nucleosides, the two main products of the PPP. Activation of NRF2 also protected the heart against myocardial infarction-induced DNA damage, dysfunction, and adverse remodeling.

Conclusions

These results indicate that NRF2 regulates cardiac metabolic reprogramming by stimulating the diversion of glucose into the PPP, thereby providing cardiac protection during stress by generating NADPH and providing nucleotides to prevent stress-induced DNA damage.
Phototaxis is a state-dependent behavioral sequence inHydra vulgaris
Authors: Kim Soonyoung , Robinson Jacob T.
Published: May 2023

Understanding how internal states like satiety are connected to animal behavior is a fundamental question in neuroscience.Hydra vulgaris, a freshwater cnidarian with only eleven neuronal cell types, serves as a tractable model system for studying state-dependent behaviors. We find that starvedHydraconsistently moves toward light, while fedHydrado not. By modeling this behavior as a set of three sequences - head orientation, jump distance, and jump rate -we demonstrate that the satiety state only affects the rate of the animal jumping to a new position, while the orientation and jump distance are unaffected. These findings yield insights into how internal states in a simple organism,Hydra, affect specific elements of a behavior, and offer general principles for studying the relationship between state-dependent behaviors and their underlying molecular mechanisms.
Resolving the unsolved: Comprehensive assessment of tandem repeats at scale
Authors: Dolzhenko Egor , English Adam , Dashnow Harriet , De Sena Brandine Guilherme , Mokveld Tom , Rowell William J. , Karniski Caitlin , Kronenberg Zev , Danzi Matt C. , Cheung Warren , Bi Chengpeng , Farrow Emily , Wenger Aaron , Martínez-Cerdeño Verónica , Bartley Trevor D , Jin Peng , Nelson David , Zuchner Stephan , Pastinen Tomi , Quinlan Aaron R. , Sedlazeck Fritz J. , Eberle Michael A
Published: May 2023

Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare monogenic diseases. Recent advances in sequencing have enabled accurate, long reads that can characterize the full-length sequence and methylation profile of TRs. However, despite these advances in sequencing technology, computational methods to fully profile tandem repeats across the genome do not exist. To address this gap, we introduce tools for tandem repeat genotyping (TRGT), visualization and an accompanying TR database. TRGT accurately resolves the length and sequence composition of TR regions in the human genome. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 99.56%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all repeat expansions while also identifying methylation signals, mosaicism, and providing finer resolution of repeat length. Additionally, we release a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
Spatial connectivity increases ecosystem resilience towards an ongoing regime shift
Authors: Olin Agnes B. , Bergström Ulf , Bodin Örjan , Sundblad Göran , Eriksson Britas Klemens , Erlandsson Mårten , Fredriksson Ronny , Eklöf Johan S.
Published: May 2023

Ecosystem regime shifts can have severe ecological and economic consequences, making it a top priority to understand how to make systems more resilient. Theory predicts that spatial connectivity and the local environment interact to shape resilience, but empirical studies are scarce. Here, we use >7000 fish samplings from the Baltic Sea coast to test this prediction in an ongoing, spatially propagating shift in dominance from predatory fish to an opportunistic mesopredator, with cascading effects throughout the food web. After controlling for the influence of the driver (increasing mesopredator densities), we find that predatory fish habitat connectivity increases resilience towards the shift, but only when densities of fish-eating top predators (seals, cormorants) are low. Resilience also increases with temperature, likely through boosted predatory fish growth and recruitment. These findings confirm theoretical predictions that spatial connectivity and the local environment can act together to shape resilience towards regime shifts.
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

Light-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

One 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

ABSTRACT

The 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

Seagrass 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

Mitochondrial 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

Deciphering 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

We 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

A 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

Phosphodiesterases (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

Background

The 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.

Methods

We 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.

Results

We 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).

Conclusions

Our 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

The 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

Background

Tilapia 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.

Methods

In 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.

Results

Our 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

Genome 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.
Comparative evaluation of synthetic cytokines for enhancing production and performance of NK92 cell-based therapies
Authors: Deol Simrita , Donahue Patrick S. , Mitrut Roxanna E. , Hammitt-Kess Iva J. , Ahn Jihae , Zhang Bin , Leonard Joshua N.
Published: May 2023

Autologous immune cell therapies are potentially curative, but cost and manufacturing complexity limit access. Off-the-shelf therapies may address these gaps, but further development is needed. The NK92 cell line has a natural killer-like phenotype, has efficacy in cancer clinical trials, and is safe after irradiation. However, NK92 lose activity post-injection, limiting efficacy. This may be addressed by engineering NK92 to express stimulatory factors, for which comparative analysis is needed. Thus, we systematically explored expression of synthetic cytokines for enhancing NK92 production and performance. All synthetic cytokines evaluated (membrane-bound IL2 and IL15, and engineered versions of Neoleukin-2/15, IL15, IL12, and decoy resistant IL18) enhanced NK92 cytotoxicity. Genetically modified cells preferentially expanded by expressing membrane-bound but not soluble synthetic cytokines, and all engineered cells remained sensitive to irradiation. Interestingly, some membrane-bound cytokines conferred cell-contact independent paracrine activity partly attributable to extracellular vesicles. Finally, we characterized interactions within consortia of differently engineered NK92.
The role of structuralvscellular remodeling in arrhythmogenesis: personalized computer models of atrial fibrillation
Authors: Pikunov Andrey V. , Syunyaev Roman A. , Ali Rheeda , Prakosa Adityo , Boyle Patrick M. , Steckmeister Vanessa , Kutschka Ingo , Rytkin Eric , Voigt Niels , Trayanova Natalia , Efimov Igor R.
Published: May 2023

Atrial fibrillation (AF) is a progressive disease involving both structural and functional remodeling. To investigate the contribution of cell-scale functional remodeling to AF pathogenesis, we combined personalized 3D anatomical models with pathology-specific ionic models. The latter were developed using recordings in myocytes isolated from patients in sinus rhythm, paroxysmal, postoperative, and persistent AF. To quantify AF dynamics, we developed a novel algorithm for locating RDs by backtracking the conduction velocity field from the wavebreak regions. We demonstrate that our novel algorithm is at least 700 times faster than the traditional phase singularity analysis. The inducibility of simulated AF was not pathology-dependent, but pathological models demonstrate a more extensive arrhythmogenic substrate compared to the sinus rhythm. AF driver locations depend on electrophysiological remodeling; differences between pathology-specific models are explained by differences in wavebreak patterns. Specifically, RDs tend to dwell in the regions with the highest wavebreak probability.
Unrestricted Versus Regulated Open Data Governance: A Bibliometric Comparison of SARS-CoV-2 Nucleotide Sequence Databases
Authors: Sheehan Nathanael , Botta Federico , Leonelli Sabina
Published: May 2023

Two distinct modes of data governance have emerged in accessing and reusing viral data pertaining to COVID-19: an unrestricted model, espoused by data repositories part of the International Nucleotide Sequence Database Collaboration and a regulated model promoted by the Global Initiative on Sharing All Influenza data. In this paper, we focus on publications mentioning either infrastructure in the period between January 2020 and January 2023, thus capturing a period of acute response to the COVID-19 pandemic. Through a variety of bibliometric and network science methods, we compare the extent to which either data infrastructure facilitated collaboration from different countries around the globe to understand how data reuse can enhance forms of diversity between institutions, countries, and funding groups. Our findings reveal disparities in representation and usage between the two data infrastructures. We conclude that both approaches offer useful lessons, with the unrestricted model providing insights into complex data linkage and the regulated model demonstrating the importance of global representation.
Dual roles of crustacean female sex hormone during juvenile stage in the kuruma prawnMarsupenaeus japonicus
Authors: Toyota Kenji , Matsushima Hanako , Osanai Rei , Okutsu Tomoyuki , Yamane Fumihiro , Ohira Tsuyoshi
Published: May 2023

The crustacean female sex hormone (CFSH) has been identified as a female-specific hormone that plays a crucial role in female phenotype developments in the blue crabCallinectes sapidus. To date, its homologous genes have been reported in various decapod species. Additionally, unlike the blue crab, several species have two different CFSH subtypes. The kuruma prawnMarsupenaeus japonicusis a representative example species of this phenomenon, having two CFSH subtypes identified from the eyestalk (MajCFSH) and ovary (MajCFSH-ov). Eyestalk-type MajCFSH is expressed predominantly in the eyestalk at the same level in both sexes, indicating no female-specificity. Here, we conducted gene knockdown analysis of eyestalk-type MajCFSH using sexually immature juveniles of kuruma prawn (average body length: ∼10 mm) to elucidate its physiological functions. As a result, MajCFSH-knockdown did not affect the development of sex-specific characteristics such as external reproductive organs, while it induced apparent growth suppression in male juveniles, implying that MajCFSH may play a male-specific juvenile growth role. Moreover, MajCFSH-knockdown female and male juveniles changed their body color to become brighter, indicating that MajCFSH has the ability to change body color by dispersing the pigment granules in the chromatophore. Overall, our present study improved our understanding of the physiological roles of CFSH using kuruma prawn.

Highlights

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MajCFSH-knockdown was conducted using sexually immature juveniles of kuruma prawn.

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MajCFSH-knockdown male juveniles showed significant growth suppression.

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MajCFSH-knockdown female and male juveniles changed their body color to become brighter.
Cul3 substrate adaptor SPOP targets Nup153 for degradation
Authors: Ong Joseph Y. , Torres Jorge Z.
Published: May 2023

SPOP is a Cul3 substrate adaptor responsible for degradation of many proteins related to cell growth and proliferation. Because mutation or misregulation of SPOP drives cancer progression, understanding the suite of SPOP substrates is important to understanding regulation of cell proliferation. Here, we identify Nup153, a component of the nuclear basket of the nuclear pore complex, as a novel substrate of SPOP. SPOP and Nup153 bind to each other and colocalize at the nuclear envelope and some nuclear foci in cells. The binding interaction between SPOP and Nup153 is complex and multivalent. Nup153 is ubiquitylated and degraded upon expression of SPOPWTbut not its substrate binding-deficient mutant SPOPF102C. Depletion of SPOP via RNAi leads to Nup153 stabilization. Upon loss of SPOP, the nuclear envelope localization of spindle assembly checkpoint protein Mad1, which is tethered to the nuclear envelope by Nup153, is stronger. Altogether, our results demonstrate SPOP regulates Nup153 levels and expands our understanding of the role of SPOP in protein and cellular homeostasis.
Patterns of early neocortical amyloid beta accumulation: a positron emission tomography population-based study
Authors: Lecy Emily E. , Min Hoon-Ki , Apgar Christopher J. , Maltais Daniela D. , Lundt Emily S. , Albertson Sabrina M. , Senjem Matthew L. , Schwarz Christopher G. , Botha Hugo , Graff-Radford Jonathan , Jones David T. , Vemuri Prashanthi , Kantarci Kejal , Knopman David S. , Petersen Ronald C. , Jack Clifford R. , Lee Jeyeon , Lowe Val J.
Published: May 2023

Introduction

The widespread deposition of amyloid beta (Aβ) plaques in late-stage Alzheimer’s disease (AD) is well defined and confirmed byin vivopositron emission tomography (PET). However, there are discrepancies between which regions contribute to the earliest topographical Aβ deposition within the neocortex.

Methods

This study investigated Aβ signals in the peri-threshold SUVr range using Pittsburgh compound B (PiB) PET in a population-based study cross-sectionally and longitudinally. PiB-PET scans from 1,088 participants were assessed to determine the early patterns of PiB loading in the neocortex.

Results

Early-stage Aβ loading is seen first in the temporal, cingulate, and occipital regions. Regional early deposition patterns are similar in both Apolipoprotein ε4 (APOE) carriers and non-carriers. Hierarchical clustering analysis shows groups with different patterns of early amyloid deposition.

Discussion

These finding of initial Aβ deposition patterns may be of significance for diagnostics and understanding the development of different AD phenotypes.
Research Paradigm of the International Classification of Functioning, Disability and Health (ICF) with Item Response Theory: Clarification, Classification, and Challenge
Authors: Feng Chun , Liu Shou-Guo , Lin Feng
Published: May 2023

Objectives

The purpose of this literature review was to clarify the sufficiency and efficiency needs, as well as the stratification and the assignment scoring principles of the International Classification of Functioning, Disability and Health (ICF) core set, in conjunction with the Item Response Theory (IRT)-derived functioning outcome measures.

Methods

A literature search has been done on the PubMed database. We included studies involving the IRT-derived ICF evaluation tool. Our main outcome was the assignment and stratification scoring principle of IRT-derived ICF-based functioning outcome measures.

Results

46 relative articles met the eligibility criteria of our review. On this basis, this review was undertaken to track the research progress of the ICF-based and IRT-modeling measurement tools and screen the final core set. This review included a classification of IRT modeling for ICF studies and a summary of existing research paradigms of IRT-derived ICF outcome measures. Moreover, this review identified blind spots related to scoring assignment principles and “difficulty parameter” in current ICF-based IRT studies.

Conclusion

The ICF is the worldwide terminology system for functioning categories, while ICF-based evaluation in clinical practice and scientific research has elicited the underlying challenges. However, the algorithm of the ICF-based IRT modeling may advance the understanding of ICF clinical application and enable a new paradigm for the design of IRT-derived ICF questionnaires, namely the parsimonious core set of ICF. Additionally, the Wright map has the potential to facilitate an understanding of the rehabilitation process and tailor rehabilitation goals.
Global substrate identification and high throughputin vitrodephosphorylation reactions uncover PP1 and PP2A-B55 specificity principles
Authors: Hein Jamin B. , Nguyen Hieu T. , Garvanska Dimitriya H. , Nasa Isha , Feng Yinnian , Mendez Blanca Lopez , Davey Norman , Kettenbach Arminja N , Fordyce Polly M. , Nilsson Jakob
Published: May 2023

Phosphoprotein phosphatases (PPPs) dephosphorylate Serine (Ser)/Threonine (Thr) residues to regulate major signaling pathways and cellular transitions. Despite the central role of PPPs the substrates in most cellular processes and the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here we develop a novelin vitroassay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A- B55, which reveals common and unique preferences for the two phosphatases. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with quantitative phosphoproteomics to identify more than 2000 regulated phosphorylation sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with the MRBLE:Dephos results. We use these insights to specifically alter INCENP dephosphorylation kinetics at mitotic exit, resulting in defective cytokinesis thus underscoring the biological relevance of our determined specificity principles. Finally, we provide a comprehensive characterization of PP1 binding motifs and demostrate how binding of phosphatases to substrates shapes dephosphorylation specificity. Collectively, we develop novel approaches to advance our ability to investigate protein phosphatases and use these to provide a framework for understanding mitotic exit regulation by dephosphorylation.
Mitochondrial CISD1/Cisd accumulation blocks mitophagy and genetic or pharmacological inhibition rescues neurodegenerative phenotypes inPink1/parkinmodels
Authors: Martinez Aitor , Sanchez-Martinez Alvaro , Pickering Jake T. , Twyning Madeleine J. , Terriente-Felix Ana , Chen Po-Lin , Chen Chun-Hong , Whitworth Alexander J.
Published: May 2023

Background

Mitochondrial dysfunction and toxic protein aggregates have been shown to be key features in the pathogenesis of neurodegenerative diseases, such as Parkinson’s disease (PD). Functional analysis of genes linked to PD have revealed that the E3 ligase Parkin and the mitochondrial kinase PINK1 are important factors for mitochondrial quality control. PINK1 phosphorylates and activates Parkin, which in turn ubiquitinates mitochondrial proteins priming them and the mitochondrion itself for degradation. However, it is unclear whether dysregulated mitochondrial degradation or the toxic build-up of certain Parkin ubiquitin substrates is the driving pathophysiological mechanism leading to PD. The iron-sulphur cluster containing proteins CISD1 and CISD2 have been identified as major targets of Parkin in various proteomic studies.

Methods

We employedin vivo Drosophilaand human cell culture models to study the role of CISD proteins in cell and tissue viability as well as aged-related neurodegeneration, specifically analysing aspects of mitophagy and autophagy using orthogonal assays.

Results

We discovered that theDrosophilahomolog Cisd accumulates during aging, as well as inPink1andparkinmutant flies. We observed that build-up of Cisd is particularly toxic in neurons, resulting in mitochondrial defects and Ser65-phospho-Ubiquitin accumulation. Age-related increase of Cisd blocks mitophagy and impairs autophagy flux. Importantly, reduction of Cisd levels upregulates mitophagyin vitroandin vivo, and ameliorates pathological phenotypes in locomotion, lifespan and neurodegeneration inPink1/parkinmutant flies. In addition, we show that pharmacological inhibition of CISD1/2 by rosiglitazone and NL-1 induces mitophagy in human cells and rescues the defective phenotypes ofPink1/parkinmutants.

Conclusion

Altogether, our studies indicate that Cisd accumulation during aging and inPink1/parkinmutants is a key driver of pathology by blocking mitophagy, and genetically and pharmacologically inhibiting CISD proteins may offer a potential target for therapeutic intervention.