bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Fusarium solani Associated with Tobacco (Nicotiana tabacum) Root Rot in Henan, China
Authors: Qiu Rui , Li Caihong , Zhang Yingying , Li Xiaojie , Li Chengjun , Liu Chang , Zhang Mengdan , Bai Jingke , Chen Yuguo , Li Fangfang , Li Shujun
Published: March 2024

The aim of this study was to characterize the Fusarium solani species complex (FSSC) population obtained from tobacco roots with root rot symptoms by morphological characteristics, molecular tests, and assessment of pathogenicity. Cultures isolated from roots were white to cream with sparse mycelium on potato dextrose agar, with colony growth of 21.5 ± 0.5 to 29.5 ± 0.5 mm after 3 days. Sporodochia were cream on carnation leaf agar (CLA) and Spezieller Nährstoffarmer agar (SNA), and macroconidia formed in sporodochia were 3 to 6 septate and straight to slightly curved, with wide central cells, a slightly short blunt apical cell, and a straight to almost cylindrical basal cell with a distinct foot shape, ranging in size from 20.92 to 64.37 × 3.91 to 6.57 μm. Microconidia formed on CLA were reniform and fusiform, with 0 or 1 to occasionally 2 septa, that formed on long monophialidic conidiogenous cells, with a size range of 5.99 to 32.32 × 1.76 to 5.84 μm. Globose to oval chlamydospores were smooth- to rough-walled, 6.5 to 13.3 ± 0.37 μm in diameter, and terminal or intercalary and occurred singly, in pairs, or occasionally in short chains on SNA. Molecular tests consisted of sequencing and phylogenetic analysis of the translation elongation factor-1 alpha (EF-1α), RNA polymerase II largest subunit, and second largest subunit regions. All the obtained sequences revealed 98.14 to 100% identity to F. solani in both Fusarium ID and Fusarium MLST databases. Phylogenetic trees of the EF-1α gene and concatenated three-locus data showed that isolates from tobacco in Henan grouped in the proposed group 5, which is nested within FSSC clade 3 (FSSC 5). Twenty-seven of the 28 isolates caused root rot in artificially inoculated tobacco seedlings, with a disease severity index ranging from 15.00 ± 1.67 to 91.11 ± 2.22. Cross-pathogenicity tests showed that three representative isolates were virulent to six species of Solanaceae and two species of Poaceae, with disease severity indexes ranging from 6.12 ± 0.56 to 84.44 ± 0.00, indicating that these isolates have a wide host range. The results may inform the control of tobacco root rot through improved crop rotations.
Molecular and Biological Characteristics of a Peach Latent Mosaic Viroid PC Isolate in Peach from China: Base Mutations in Hairpin Stems and Implications for Symptomatology
Authors: Lu Meiguang , Zhang Zimeng , Huang Wen , Zhou Jun , Zhang Zhixiang , Li Shifang
Published: March 2024

Peach latent mosaic viroid (PLMVd) infects peach trees in China and induces a conspicuous albino phenotype (peach calico, PC) that is closely associated with variants containing a 12-to-14 nucleotide hairpin insertion capped by a U-rich loop. Initially, PC disease distribution was limited to parts of Italy, and it was first detected in the field in China in 2019. To explore the molecular and biological characteristics of PLMVd PC isolates in peach in China, we conducted a comprehensive analysis of disease phenotype development and investigated the data-associated pathogenicity and in vivo dynamics of the Chinese isolate PC-A2 using slash-inoculation into GF-305 peach seedlings. Inoculated seedlings displayed PC symptoms much earlier following topping treatment, and PLMVd infectivity was further assessed using bioassay and semiquantitative RT-PCR experiments. Evolutionary analysis showed that the PC isolate and its progeny variants clustered into a single phylogroup distinct from reference PC-C40 isolates from Italy and PC-K1 and PC-K2 from South Korea. Some PC-A2 progeny variants from green leaves of PC-expressing seedlings showed unbalanced point mutations in hairpin stems compared with the PC-C40 reference sequence and constituted a new stem insertion type. The results reveal associations between the recessive phenotypes of peach albino symptoms and base variation in hairpin stem insertions relative to the PC-C40/chloroplastic heat shock protein 90 reference sequence.
DNA hypomethylation of Syk induces oxidative stress and apoptosis via the PKCβ/P66shc signaling pathway in diabetic kidney disease
Authors: Zhang Rui , Qin Chunmei , Zhang Junlin , HonghongRen  , Wang Yiting , Wu Yucheng , Zhao Lijun , Wang Jiali , Zhang Jie , Liu Fang
Published: March 2024

Epigenetic alterations, especially DNA methylation, have been shown to play a role in the pathogenesis of diabetes mellitus (DM) and its complications, including diabetic kidney disease (DKD). Spleen tyrosine kinase (Syk) is known to be involved in immune and inflammatory disorders. We, therefore, investigated the possible involvement of Syk promoter methylation in DKD, and the mechanisms underlying this process. Kidney tissues were obtained from renal biopsies of patients with early and advanced DKD. A diabetic mouse model (ApoE−/− DM) was generated from ApoE knockout (ApoE−/−) mice using a high‐fat and high‐glucose diet combined with low‐dose streptozocin intraperitoneal injection. We also established an in vitro model using HK2 cells. A marked elevation in the expression levels of Syk, PKCβ, and P66shc in renal tubules was observed in patients with DKD. In ApoE−/− DM mice, Syk expression and the binding of Sp1 to the Syk gene promoter were both increased in the kidney. In addition, the promoter region of the Syk gene exhibited hypomethylation. Syk inhibitor (R788) intervention improved renal function and alleviated pathologic changes in ApoE−/− DM mice. Moreover, R788 intervention alleviated oxidative stress and apoptosis and downregulated the expression of PKCβ/P66shc signaling pathway proteins. In HK2 cells, oxLDL combined with high‐glucose stimulation upregulated Sp1 expression in the nucleus (compared with control and oxLDL groups), and this was accompanied by an increase in the binding of Sp1 to the Syk gene promoter. SP1 silencing downregulated the expression of Syk and inhibited the production of reactive oxygen species and cell apoptosis. Finally, PKC agonist intervention reversed the oxidative stress and apoptosis induced by Syk inhibitor (R406). In DKD, hypomethylation at the Syk gene promoter was accompanied by an increase in Sp1 binding at the promoter. As a consequence of this enhanced Sp1 binding, Syk gene expression was upregulated. Syk inhibitors could attenuate DKD‐associated oxidative stress and apoptosis via downregulation of PKCβ/P66shc signaling pathway proteins. Together, our results identify Syk as a promising target for intervention in DKD.
A Comparative Study on the Superiority of AOS DP3-7 Over 5-ALA in Facilitating Pigment Change in Peppers
Authors: Chen Xingqiang , Chen Haidong , Shang Zheng
Published: March 2024

This study investigates the impact of Alginate Oligosaccharides (AOS) and 5-Aminolevulinic Acid (5-ALA) on the maturation process of red peppers, focusing on color transformation, weight gain, seed density, and skin thickness. Treatments included foliar applications of 100 ppm solutions of AOS and 5-ALA, compared with a control group, over a period of two weeks in a controlled environment. Results indicated that AOS and 5-ALA treatments accelerated the ripening process, as evidenced by increased uniformity in color transformation and significant weight gain in treated groups. Further examination revealed notable differences in seed distribution and skin thickness, with AOS and 5-ALA peppers exhibiting a denser seed population and variations in skin thickness. Biochemical pathway analysis suggested that these biostimulants could modulate ethylene signaling and other ripening-related processes, influencing both external fruit characteristics and internal development. This comprehensive study offers valuable insights into the complex mechanisms of fruit ripening and the application of biostimulants to enhance crop quality and market value.
A candidate reference method for the quantification of α-synuclein in cerebrospinal fluid using an SI traceable primary calibrator and multiple reaction monitoring
Authors: Zhang Leran , Illes-Toth Eva , Cryar Adam , Drinkwater Giles , Di Vagno Lucia , Pons Marie-Laure , Mateyka Julia , McCullough Bryan , Achtar Eli , Clarkson Cailean , Göschel Laura , Körtvélyessy Peter , Mussell Chris , Hopley Christopher J. , Flöel Agnes , Hirtz Christophe , Lehmann Sylvain , Quaglia Milena
Published: March 2024

Objectives

α-synuclein aggregation is an indicator of neurodegenerative diseases such as Parkinson’s disease (PD) and recent advances have suggested that this protein could serve as a potential biomarker. It has been indicated that soluble and oligomeric α-synuclein in biological fluids could have diagnostic applications for PD. Clinical laboratories currently rely on antibody-based assays to detect α-synuclein. These assays have limited specificity, low sensitivity and poor inter-lab reproducibility, which prevents the validation of α-synuclein as a biomarkers. This study aims to fill the unmet need for the standardisation of clinical measurements for α-synuclein.

Methods

We report the first candidate reference method for α-synuclein, using an SI traceable primary calibrator for α-synuclein and isotope dilution mass spectrometry. The primary calibrator was traceably quantified utilising a combination of amino acid analysis and nuclear magnetic resonance. A targeted sample clean-up procedure involving a non-denaturing Lys-C digestion and solid-phase extraction allowed for the sensitive detection of multiple proteotypic α-synuclein peptides in cerebrospinal fluid (CSF) samples.

Results

The candidate reference method procedure showed linearity across three orders of magnitude, covering the physiological levels of α-synuclein in CSF (LOQ = 0.1 ng/g). The method was used to quantify a cohort of CSF samples and the measurements were correlated with immunoassay-based quantifications.

Conclusions

The SI traceable quantification of α-synuclein in complex biological matrices means that the role of this protein can be further elucidated in synucleinopathies. This candidate reference method would lead to the harmonisation of α-synuclein measurements, which may allow for development of high throughput clinical tests.
Searching Post-translational Modifications in Cross-linking Mass Spectrometry Data
Authors: Zhou Chen , Lai Shengzhi , Dai Shuaijian , Zhao Peize , Li Ning , Yu Weichuan
Published: March 2024

Cross-linking mass spectrometry (XL-MS) is a technique for investigating protein-protein interactions (PPIs) and protein structures. In the realm of biology, post-translational modifications (PTMs) play a critical role in regulating PPIs and reshaping protein structures. However, the identification of PTMs in XL-MS data poses a great computational challenge and thus remains unexplored. In this study, we introduce SeaPIC, the first XL-MS tool that enables biologists to investigate PTMs in PPIs and protein structures. Our experiments demonstrate the successful identification of PTMs within cross-linked peptides, which were previously undiscovered.
Physics-informed machine learning for automatic model reduction in chemical reaction networks
Authors: Pateras Joseph , Zhang Colin , Majumdar Shriya , Pal Ayush , Ghosh Preetam
Published: March 2024

Physics-informed machine learning emerges as a transformative approach, bridging the gap between the high fidelity of mechanistic models and the adaptive, data-driven insights afforded by artificial intelligence and machine learning. In the realm of chemical reaction network modeling, this synergy is particularly valuable. It offers a solution to the pro-hibitive computational costs associated with detailed mechanistic models, while also capitalizing on the predictive power and flexibility of machine learning algorithms. This study exemplifies this innovative fusion by applying it to the critical biomedical challenge of Aβfibril aggregation, shedding light on the mechanisms underlying Alzheimer’s disease. A corner-stone of this research is the introduction of an automatic reaction order model reduction framework, tailored to optimize the scale of reduced order kinetic models. This framework is not merely a technical enhancement; it represents a paradigm shift in how models are constructed and refined. By automatically determining the most appropriate level of detail for modeling reaction networks, our proposed approach significantly enhances the efficiency and accuracy of simulations. This is particularly crucial for systems like Aβaggregation, where the precise characterization of nucleation and growth kinetics can provide insights into potential therapeutic targets. The potential generalizability of this automatic model reduction technique to other network models is a key highlight of this study. The methodology developed here has far-reaching implications, offering a scalable and adaptable tool for a wide range of applications beyond biomedical research. The ability to dynamically adjust model complexity in response to the specific demands of the system under study is a powerful asset. This flexibility ensures that the models remain both computationally feasible and scientifically relevant, capable of accommodating new data and evolving understandings of complex phenomena.
Cathodoluminescent and Characteristic X-ray-emissive Rare-Earth-doped Core/Shell Immunolabels for Spectromicroscopic Analysis of Cell Surface Receptors
Authors: Habermann Sebastian , Gerken Lukas R. H. , Kociak Mathieu , Monachon Christian , Kissling Vera M. , Gogos Alexander , Herrmann Inge K.
Published: March 2024

Understanding the localization and the interactions of biomolecules at the nanoscale and in the cellular context remains challenging. Electron microscopy (EM) as a non-Abbe limited technique gives access to the cellular ultra-structure yet results in grey-scale images and averts unambiguous (co-)localization of biomolecules. Multimodal nanoparticle-based immunolabels for correlative cathodoluminescence electron microscopy (CCLEM) and energy-dispersive X-ray spectromicroscopy (EDX-SM) are presented. The single-particle STEM-cathodoluminescence (CL) and characteristic X-ray emissivity of sub-20 nm lanthanide-doped nanoparticles were exploited as unique spectral fingerprints for precise localization and label identification. To maximize the nanoparticle brightness, lanthanides were incorporated in a low-phonon host lattice and separated from the environment using a passivating shell. The core/shell nanoparticles were then functionalized with either folic (terbium-doped) or caffeic acid (europium-doped). Their potential for immunolabeling was successfully demonstrated using HeLa cells expressing different surface receptors that bind to folic or caffeic acid, respectively. Both particle populations showed single-particle CL emission along with a distinctive energy-dispersive X-ray signal, with the latter enabling colour-based localization of receptors within swift imaging times well below 2 mins per µm2while offering high resolution with a pixel size of 2.78 nm. Taken together, these results open a route to color immunolabelling based on electron spectromicroscopy.

Table of Contents

Small (sub-20 nm) lanthanide-doped nanoparticles were successfully utilized in electron microscopy to label biological structures and contextualize them in the cell’s ultrastructure. Leveraging unique energy-dispersive X-ray signatures, the nanoparticles’ location and doping-identity was easily and fast retrieved, demonstrating the methods’ potential to (co)-localize labels while supplying a holistic impression of the underlying processes, as entire cells could be mapped.
Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes
Authors: Kosir Tjasa , Das Hirak , Pedersen Marc Pilegaard , Anteghini Marco , Oeljeklaus Silke , Martins dos Santos Vitor , van der Klei Ida J. , Warscheid Bettina
Published: March 2024

Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namelySaccharomyces cerevisiaewild-type andpex3cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal β-oxidation genes and the corresponding proteins were enhanced inpex3cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology.

Omics comparison of wild-type and peroxisome-deficient (pex3) yeast cells uncovered processes that are affected by loss of peroxisomes. β-oxidation enzymes were upregulated, whereas most peroxins were decreased. Also, several non-peroxisomal transcripts/proteins were significantly altered. Our data represent a rich source of candidate genes connected to peroxisome biology.
Chaperone-Mediated Autophagy in Fish: A Key Function Amid a Changing Environment
Authors: Schnebert Simon , Vélez Emilio J , Goguet Maxime , Dias Karine , Véron Vincent , García-Pérez Isabel , Radler Lisa M , Cardona Emilie , Fontagné-Dicharry Stéphanie , Van Delft Pierre , Dittrich-Domergue Franziska , Bernard Amélie , Beaumatin Florian , Herpin Amaury , Cleveland Beth , Seiliez Iban
Published: March 2024

Chaperone-Mediated Autophagy (CMA) is a major pathway of lysosomal proteolysis critical for cellular homeostasis and metabolism. While extensively studied in mammals, CMA’s existence in fish has only been confirmed recently, offering exciting insights into its role in species facing environmental stress. Here, we shed light on the existence of 2 genes encoding the CMA-limiting factor Lamp2A (lysosomal associated membrane protein 2A) in rainbow trout (RT,Oncorhynchus mykiss), revealing distinct expression patterns across various tissues. Notably, RT lacking the most expressed Lamp2A exhibit profound hepatic proteome disturbances during acute nutritional stress, underscoring its pivotal role as a guardian of hepatic proteostasis. Building upon these findings, we introduce and validate the CMA activation score as a reliable indicator of CMA status, providing a valuable tool for detecting cellular stress in fish under environmental threats. Overall, our study offers new perspectives into understanding CMA from evolutionary and environmental contexts.

Abstract Figure
Measuring X inactivation skew for retinal diseases with adaptive nanopore sequencing
Authors: Gocuk Sena A , Lancaster James , Su Shian , Jolly Jasleen K , Edwards Thomas L , Hickey Doron G , Ritchie Matthew E , Blewitt Marnie E , Ayton Lauren N , Gouil Quentin
Published: March 2024

X-linked genetic disorders typically affect females less severely than males due to the presence of a second X chromosome not carrying the deleterious variant. However, the phenotypic expression in females is highly variable, which may be explained by an allelic skew in X chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions.

We propose a novel approach using nanopore sequencing to quantify skewed X inactivation accurately. By phasing sequence variants and methylation patterns, this single assay reveals the disease variant, X inactivation skew, its directionality, and is applicable to all patients and X-linked variants. Enrichment of X-chromosome reads through adaptive sampling enhances cost-efficiency. Our study includes a cohort of 16 X-linked variant carrier females affected by two X-linked inherited retinal diseases: choroideremia andRPGR-associated retinitis pigmen-tosa. As retinal DNA cannot be readily obtained, we instead determine the skew from peripheral samples (blood, saliva and buccal mucosa), and correlate it to phenotypic outcomes. This revealed a strong correlation between X inactivation skew and disease presentation, confirming the value in performing this assay and its potential as a way to prioritise patients for early intervention, such as gene therapy currently in clinical trials for these conditions.

Our method of assessing skewed X inactivation is applicable to all long-read genomic datasets, providing insights into disease risk and severity and aiding in the development of individualised strategies for X-linked variant carrier females.
Single cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy
Authors: Shin Gyeong-Jin , Choi Byung-Han , Eum Hye Hyeon , Jo Areum , Kim Nayoung , Kang Huiram , Hong Dongwan , Jang Jiyoung Joan , Lee Hwi-Ho , Lee Yeon-Su , Lee Yong Sun , Lee Hae-Ock
Published: March 2024

Single cell RNA sequencing (scRNA-seq) has emerged as a versatile tool in biology, enabling comprehensive genomic-level characterization of individual cells. Currently, most scRNA-seq methods generate barcoded cDNAs by capturing polyA tails of mRNAs, which excludes many non-coding RNAs (ncRNAs), especially those transcribed by RNA polymerase III (Pol III). Although previously thought to be expressed constitutively, Pol III-transcribed ncRNAs are expressed variably in healthy and disease states and play important roles therein, necessitating their profiling at the single cell level. In this study, we have developed a measurement protocol for nc886 as a model case, as an initial step for scRNA-seq for Pol III-transcribed ncRNAs. Specifically, we spiked in an oligo-tagged nc886-specific primer during the polyA tail capture process for the 5’-reading in scRNA-seq. We then produced sequencing libraries for standard 5’ gene expression and oligo-tagged nc886 separately, to accommodate different cDNA sizes and ensure undisturbed transcriptome analysis. We applied this protocol in three cell lines which express high, low, and zero levels of nc886, respectively. Our results show that the identification of oligo tags exhibited limited target specificity, and sequencing reads of nc886 enabled the correction of non-specific priming. These findings suggest that gene-specific primers (GSPs) can be employed to capture RNAs lacking a polyA tail, with subsequent sequence verification ensuring accurate gene expression counting. Moreover, we embarked on an analysis of differentially expressed genes in cell line sub-clusters with differential nc886 expression, demonstrating variations in gene expression phenotypes. Collectively, the primer spike-in strategy allows us for a combined analysis of ncRNAs and gene expression phenotype.
Antigenic drift expands viral escape pathways from imprinted host humoral immunity
Authors: Maurer Daniel P. , Vu Mya , Schmidt Aaron G.
Published: March 2024

An initial virus exposure can imprint antibodies such that future responses to antigenically drifted strains are dependent on the identity of the imprinting strain. Subsequent exposure to antigenically distinct strains followed by affinity maturation can guide immune responses toward generation of cross-reactive antibodies. How viruses evolve in turn to escape these imprinted broad antibody responses is unclear. Here, we used clonal antibody lineages from two human donors recognizing conserved influenza virus hemagglutinin (HA) epitopes to assess viral escape potential using deep mutational scanning. We show that even though antibody affinity maturation does restrict the number of potential escape routes in the imprinting strain through repositioning the antibody variable domains, escape is still readily observed in drifted strains and attributed to epistatic networks within HA. These data explain how influenza virus continues to evolve in the human population by escaping even broad antibody responses.
scDTL: single-cell RNA-seq imputation based on deep transfer learning using bulk cell information
Authors: Zhao Liuyang , Tian Jun , Xie Yufeng , Jiang Landu , Huang Jianhao , Xie Haoran , Zhang Dian
Published: March 2024

Motivation

The growing amount of single-cell RNA sequencing (scRNA-seq) data allows researchers to investigate cellular heterogeneity and gene expression profiles, providing a high-resolution view of transcriptome at the single-cell level. However, dropout events, which are often present in scRNA-seq data, remain challenges for downstream analysis. Although a number of studies have been developed to recover single-cell expression profiles, their performance is sometimes limited by not fully utilizing the inherent relations between genes.

Results

To address the issue, we propose a deep transfer learning based approach called scDTL for scRNA-seq data imputation by exploring the bulk RNA-sequencing information. scDTL firstly trains an imputation model for bulk RNA-seq data using a denoising autoencoder (DAE). We then apply a domain adaptation architecture that builds a mapping between bulk gene and single-cell gene domains, which transfers the knowledge learned by the bulk imputation model to scRNA-seq learning task. In addition, scDTL employs a parallel operation with a 1D U-Net denoising model to provide gene representations of varying granularity, capturing both coarse and fine features of the scRNA-seq data. At the final step, we use the cross-channel attention mechanism to fuse the features learned from the transferred bulk imputer and U-Net model. In the evaluation, we conduct extensive experiments to demonstrate that scDTL based approach could outperform other state-of-the-art methods in the quantitative comparison and downstream analyses.

Contact

zhangd@szu.edu.cnortianj@sustech.edu.cn
Seasonal genotypic and phenotypic differentiation of a cosmopolitan freshwater diatom
Authors: Cristini Domiziana , Kelly Joseph B. , Mahler Pia , Becks Lutz
Published: March 2024

Most ecosystems are characterized by seasonality, which, through biotic and abiotic changes, influences species biomass dynamics. Recent studies have shown that ecologically important traits can evolve rapidly in response to environmental changes, resulting in eco-evolutionary dynamics with consequences for population and community dynamics. Evidence for seasonal effects on intraspecific variation is still scarce and understanding eco-evolutionary dynamics in the presence of seasonal fluctuations remains a major challenge. Following the phytoplankton spring bloom in Lake Constance, we investigated how seasonal changes influence the intraspecific diversity ofAsterionella formosaboth at genotypic and phenotypic levels. We found a high degree of genetic and phenotypic differentiation characterizingAsterionellapopulation, explained by a clustering of the isolates into early and late spring according to lake thermal stratification. Yet, most traits related to environmental parameters as well as fitness in different seasonal environments did not show a clear response to seasonality (i.e., temperature and nutrients), indicating that seasonal changes in biotic interactions (i.e., parasitic chytrids) were the major drivers of the observed seasonal shift inAsterionellagenotypes. Our results highlight the importance of studying eco-evolutionary processes for understanding variations in population and community dynamics in response to seasonal environmental fluctuations.
EXPLANA: A user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies
Authors: Fouquier Jennifer , Stanislawski Maggie , O’Connor John , Scadden Ashley , Lozupone Catherine
Published: March 2024

Motivation

Longitudinal microbiome studies (LMS) are increasingly common but have analytic challenges including non-independent data requiring mixed-effects models and large amounts of data that motivate exploratory analysis to identify factors related to outcome variables. Although change analysis (i.e. calculating deltas between values at different timepoints) can be powerful, how to best conduct these analyses is not always clear. For example, observational LMS measurements show natural fluctuations, so baseline might not be a reference of primary interest; whereas, for interventional LMS, baseline is a key reference point, often indicating the start of treatment.

Results

To address these challenges, we developed a feature selection workflow for cross-sectional and LMS that supports numerical and categorical data called EXPLANA (EXPLoratory ANAlysis). Machine-learning methods were combined with different types of change calculations and downstream interpretation methods to identify statistically meaningful variables and explain their relationship to outcomes. EXPLANA generates an interactive report that textually and graphically summarizes methods and results. EXPLANA had good performance on simulated data, with an average area under the curve (AUC) of 0.91 (range: 0.79-1.0, SD = 0.05), outperformed an existing tool (AUC: 0.95 vs. 0.56), and identified novel order-dependent categorical feature changes. EXPLANA is broadly applicable and simplifies analytics for identifying features related to outcomes of interest.
Development of a high-throughput, quantitative platform using human cerebral organoids to study virus-induced neuroinflammation in Alzheimer’s disease
Authors: Olson Meagan N. , Dawes Pepper , Murray Liam F. , Barton Nathaniel J. , Sundstrom Jonathan , Orszulak Adrian R. , Chigas Samantha M. , Tran Khanh , Aylward Aimee J. , Caliandro Michele F. , Riechers Sean-Patrick H. , Afshari Khashayar , Wang Qi , Garber Manuel , Humphries Fiachra , Orzalli Megan H. , Golenbock Douglas T. , Heneka Michael T. , Oh Hyung Suk , Church George M. , Young-Pearse Tracy L. , Knipe David M. , Readhead Benjamin , Chan Yingleong , Lim Elaine T.
Published: March 2024

Neuroinflammation is a central process in the pathogenesis of several neurodegenerative diseases such as Alzheimer’s disease (AD), and there are active efforts to target pathways involved in neuroinflammation for molecular biomarker discovery and therapeutic development in neurodegenerative diseases. It was also proposed that there may be an infectious etiology in AD that is associated with viruses such as herpes simplex virus (HSV-1) and influenza A virus (IAV), leading to neuroinflammation-induced AD pathogenesis or disease progression. We sought to develop high-throughput, quantitative molecular biomarker assays using dissociated cells from human cerebral organoids (dcOrgs), that can used for screening compounds to reverse AD-associated neuroinflammation. We found that HSV-1 infection, but not IAV infection, in dcOrgs led to increased intracellular Aβ42 and phosphorylated Tau-Thr212 (pTau-212) expression, lower ratios of secreted Aβ42/40, as well as neuronal loss, and increased proportions of astrocytes and microglia, which are hallmarks of AD. Among the glia cell-type markers, Iba1 (microglia) and GFAP (astrocyte) expression were most strongly correlated with HSV-1 expression, which further supported that these biomarkers are perturbed by glia-mediated neuroinflammation. By performing large-scale RNA sequencing, we observed that differentially expressed transcripts in HSV-1 infected dcOrgs were specifically enriched for AD-associated GWAS genes, but not for genes associated with other common neurodegenerative, neuropsychiatric or autoimmune diseases. Immediate treatment of HSV-1 infected dcOrgs with anti-herpetic drug acyclovir (ACV) rescued most of the cellular and transcriptomic biomarkers in a dosage-dependent manner, indicating that it is possible to use our high-throughput platform to identify compounds or target genes that can reverse these neuroinflammation-induced biomarkers associated with AD.
Constant companions: Wild zebra finch pairs display extreme spatial cohesion
Authors: Tyson Chris , Loning Hugo , Griffith Simon C. , Naguib Marc
Published: March 2024

Many animals maintain long-term monogamous partnerships, but the extent to which partners associate varies substantially and has implications for the scope of cooperation between pair members. Zebra finches (Taeniopygia castanosis) are monogamously paired for life and maintain continuous partnerships, raising questions as to if and how they maintain pair cohesion despite being nonterritorial and having only short-range acoustic signals. While zebra finches are the best studied songbird in captivity, their social and spatial behaviour in the wild is poorly understood. Determining pair cohesion in songbirds to date has almost exclusively been studied at specific locations where pairs would be expected to meet, such as nesting or feeding sites, without quantifying broader movements. Here, we used solar-powered automated tracking to simultaneously monitor the movements of radio-tagged zebra finch pairs during periods with breeding activity. We reveal extremely high spatial cohesion with pairs using nearly identical home ranges and maintaining close spatial proximity across large areas. This characterisation of extremely high spatio-temporal coordination of zebra finch pairs provides important insights into the operation and benefits of monogamous relationships in highly mobile taxa, such as birds.
Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploidLudwigia grandiflorasubsp.hexapetalain western Europe
Authors: Stoeckel Solenn , Becheler Ronan , Portillo-Lemus Luis , Harang Marilyne , Besnard Anne-Laure , Lassalle Gilles , Causse-Védrines Romain , Michon-Coudouel Sophie , Park Daniel J. , Pope Bernard J. , Petit Eric J. , Barloy Dominique
Published: March 2024

Reproductive mode,i.e.,the proportion of individuals produced by clonality, selfing and outcrossing in populations, determines how hereditary material is transmitted through generations. It shapes genetic diversity and its structure over time and space, which can be used to infer reproductive modes.

Ludwigia grandiflorasubsp.hexapetala(Lgh) is a partially clonal, polyploid, hermaphroditic, and heteromorphic plant that recently colonized multiple countries worldwide. In western Europe, individuals are either self-incompatible caused by a late-acting self-incompatibility (LSI) system developing long-styled flowers, or self-compatible (SC), with short-styled flowers.

In this study, we genotyped 53 long- and short-styled populations newly colonizing France and northern Spain using SNPs to estimate rates of clonality, selfing and outcrossing. We found that populations reproduced mainly clonally but with a high diversity of genotypes along with rates of sexuality ranging from 10% up to 40%. We also found evidence for local admixture between long- and short-styled populations in a background of genetic structure between floral morphs that was twice the level found within morphs. Long- and short-styled populations showed similar rates of clonality but short-styled populations presented significantly higher rates of selfing, as expected considering their breeding system, and despite the small rates of failure of the LSI system. Within the 53 studied populations, the 13 short-styled populations had fewer effective alleles, lower observed heterozygosity, and higher inbreeding coefficients, linkage disequilibrium and estimates of selfing than what was found in long-styled populations. These results emphasize the necessity to consider the variation of reproductive modes when managing invasive plant species. The overall maintenance of higher genetic diversity with the possibility of maintaining populations clonally in the absence of compatible partners may explain why long-styled individuals seem to be more prevalent in all newly expanding populations worldwide. BeyondLgh, our methodological approach may inspire future studies to assess the reproductive modes in other autopolyploid populations.
Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches
Authors: Ammar Amro , Singh Vaidhvi , Ilic Sanja , Samiksha Fnu , Marsh Antoinette , Rodriguez-Palacios Alex
Published: March 2024

In medicine, parasitic cysts or cysticerci (fluid-filled cysts, larval stage of tapeworms) are believed to be sterile (no bacteria), and therein, the treatment of cysticerci infestations of deep extra-intestinal tissues (e.g., brain) relies almost exclusively on the use of antiparasitic medications, and rarely antibiotics. To date, however, it is unclear why common post-treatment complications include abscessation. This study quantified the microbial composition of parasitic cyst contents in a higher-order rodent host, using multi-kingdom shotgun metagenomics, to improve our understanding of gut microbial translocation and adaptation strategies in wild environments. Analysis was conducted on DNA from two hepatic parasitic cysts (Hydatigera (Taeenia) taeniaeformis) in an adult vole mouse (Microtus arvalis), and from feces, liver, and peritoneal fluid of three other vole family members living in a vegetable garden in Ohio, USA. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, includingParabacteroides distasonis, Klebsiella variicola, Enterococcus faecium, andLactobacillus acidophilus, inhabiting the cysts.Parabacteroides distasonisand other species were also present outside the cyst in the peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, but unexpectedly, it detected an insect-origin virus from the army moth (Pseudaletia/Mythimna unipuncta) known as Mythimna unipuncta granulovirus A (MyunGV-A) in both cysts, and in one fecal and one peritoneal sample from two different voles, indicating survival of the insect virus and adaption in voles. Metagenomics also revealed a significantly lower probability of fungal detection in the cysts compared to other samples (peritoneal fluid, p<0.05; and feces p<0.05), with single taxon detection in each cyst forMalasseziaandPseudophaeomoniella oleicola. The samples with a higher probability of fungi were the peritoneal fluid. In conclusion, commensal/pathobiont bacterial species can inhabit parasitic tapeworm cysts, which needs to be considered during therapeutic decisions of cysticerci or other chronic disease scenarios where immune privileged and spatially restricted ecosystems with limited nutrients and minimal presence of immune cells could facilitate microbial adaptation, such as within gut wall cavitating micropathologies in Crohn’s disease.
Alzheimer’s disease induced neurons bearingPSEN1mutations exhibit reduced excitability
Authors: Maksour Simon , Finol-Urdaneta Rocio K. , Hulme Amy J. , Cabral-da-Silva Mauricio Castro , Dias Anastacio Helena Targa , Balez Rachelle , Berg Tracey , Turner Calista , Sanz Muñoz Sonia , Engel Martin , Kalajdzic Predrag , Lisowski Leszek , Sidhu Kuldip , Sachdev Perminder S. , Dottori Mirella , Ooi Lezanne
Published: March 2024

Alzheimer’s disease (AD) is a devastating neurodegenerative condition that affects memory and cognition, characterized by neuronal loss and currently lacking a cure. Mutations inPSEN1(Presenilin 1) are among the most common causes of early-onset familial AD (fAD). While changes in neuronal excitability are believed to be early indicators of AD progression, the link betweenPSEN1mutations and neuronal excitability remains to be fully elucidated. This study examined induced pluripotent stem cell (iPSC)-derived NGN2 induced neurons (iNs) from fAD patients withPSEN1mutations S290C or A246E, alongside CRISPR-corrected isogenic cell lines, to investigate early changes in excitability. Electrophysiological profiling revealed reduced excitability in bothPSEN1mutant iNs compared to their isogenic controls. Neurons bearing S290C and A246E mutations exhibited divergent passive membrane properties compared to isogenic controls, suggesting distinct effects ofPSEN1mutations on neuronal excitability. Additionally, bothPSEN1backgrounds exhibited higher current density of voltage-gated potassium (Kv) channels relative to their isogenic iNs, while displaying comparable voltage-gated sodium (Nav) channel current density. This suggests that the Nav/Kv imbalance contributes to impaired neuronal firing in fAD iNs. Deciphering these early cellular and molecular changes in AD is crucial for understanding the disease pathogenesis.
A computational model for bacteriophageϕX174 gene expression
Authors: Hill Alexis M. , Ingle Tanvi A. , Wilke Claus O.
Published: March 2024

BacteriophageϕX174 has been widely used as a model organism to study fundamental processes in molecular biology. However, several aspects ofϕX174 gene regulation are not fully resolved. Here we construct a computational model forϕX174 and use the model to study gene regulation during the phage infection cycle. We estimate the relative strengths of transcription regulatory elements (promoters and terminators) by fitting the model to transcriptomics data. We show that the specific arrangement of a promoter followed immediately by a terminator, which occurs naturally in theϕX174 genome, poses a parameter identifiability problem for the model, since the activity of one element can be partially compensated for by the other. We also simulateϕX174 gene expression with two additional, putative transcription regulatory elements that have been proposed in prior studies. We find that the activities of these putative elements are estimated to be weak, and that variation inϕX174 transcript abundances can be adequately explained without them. Overall, our work demonstrates thatϕX174 gene regulation is well described by the canonical set of promoters and terminators widely used in the literature.
Neural networks built from enzymatic reactions can operate as linear and nonlinear classifiers
Authors: Samaniego Christian Cuba , Wallace Emily , Blanchini Franco , Franco Elisa , Giordano Giulia
Published: March 2024

The engineering of molecular programs capable of processing patterns of multi-input biomarkers holds great potential in applications ranging from in vitro diagnostics (e.g., viral detection, including COVID-19) to therapeutic interventions (e.g., discriminating cancer cells from normal cells). For this reason, mechanisms to design molecular networks for pattern recognition are highly sought after. In this work, we explore how enzymatic networks can be used for both linear and nonlinear classification tasks. By leveraging steady-state analysis and showing global stability, we demonstrate that these networks can function as molecular perceptrons, fundamental units of artificial neural networks—capable of processing multiple inputs associated with positive and negative weights to achieve linear classification. Furthermore, by composing orthogonal enzymatic reactions, we show that multi-layer networks can be constructed to achieve nonlinear classification.
Students' help-seeking mediates the relationship between happiness and self-strength: a comparative study on Chinese and Pakistani adolescents
Authors: Tabassum Umaira , Qiang Xing , Abbas Jaffar , Amjad Amjad Islam , Al-Sulaiti Khalid Ibrahim
Published: March 2024

Purpose

Positive psychology helps us understand the knowledge required to contribute to adolescents' societal development and adjustability. Adolescence is the crucial stage to work on for a balanced personality. The present study concerned adolescents' self-strength, happiness, and help-seeking behaviour. The authors aimed to explore the relationship between adolescents' self-strength and happiness and investigate the mediational effect of adolescents' help-seeking behaviour on their self-strength and happiness.

Design/methodology/approach

The research design of the current quantitative study was correlational, and 809 adolescents from China and Pakistan participated in the present study. Data were personally collected from participants through self-developed scales.

Findings

We deployed Pearson correlation and simple mediation using SPSS software and found a linear, positive, strong (r = 0.654, n = 809, p = 0.000 < 0.01) and statistically significant correlation between adolescents' self-strength and happiness. The authors also found a significant indirect effect of help-seeking on adolescents' self-strength and happiness at (β = 0.373, t(907) = 7.01).

Research limitations/implications

Using self-reported scales to gather information was one of the study's limitations. Adolescents may have misunderstood the notion or construct narrated in words or responded biasedly despite the bilingual scales.

Practical implications

This study offers social and practical implications for educators, parents, and school administrators to address the development of adolescents' personalities using a positive psychology lens.

Originality/value

The findings are of significant importance for teachers working in the elementary schools. They may work on adolescents' self-strength, happiness, and help-seeking to develop balanced personalities.
Development of an atrial transseptal puncture procedure in horses to access the left heart: An ultrasound‐guided jugular vein and transhepatic approach
Authors: Vernemmen Ingrid , Van Steenkiste Glenn , Buschmann Eva , Cornelis Kristoff , Schauvliege Stijn , Ibrahim Lara , Decloedt Annelies , van Loon Gunther
Published: March 2024

Background

Radiofrequency ablation has been successfully applied to treat right atrial arrhythmias in horses. Ablation of left‐sided arrhythmias requires a retrograde transarterial approach which is complicated. In human medicine, the left atrium is accessed through transseptal puncture (TSP) of the fossa ovalis (FO) using a caudal approach via the femoral vein.

Objectives

To develop a zero fluoroscopy TSP technique for horses using a jugular vein (cranial) and transhepatic (caudal) approach.

Study design

In vivo experimental study.

Methods

Transseptal puncture was performed in 18 horses admitted for euthanasia and donated for scientific research under general anaesthesia: using a jugular vein approach (10 horses), a transhepatic approach (2 horses) or both (6 horses). Radiofrequency energy was applied on a guidewire to perforate the FO and allow sheath advancement under intracardiac and transthoracic echocardiographic guidance. Puncture lesions were inspected post‐mortem.

Results

Transseptal puncture was successful in 17/18 horses, of which 15/16 jugular vein approaches and 5/8 transhepatic approaches. Failure was due to technical malfunction, inability to advance the guidewire toward the heart and inability to advance the sheath through the FO. Intracardiac echocardiography was essential to safely guide the puncture process. Atrial arrhythmias caused by the TSP occurred in 13/18 horses. Puncture lesions were found in the right atrium in the FO region, and left atrium ventral to pulmonary vein ostium III.

Main limitations

Because in several horses two approaches were tested consecutively, it cannot be excluded that the second TSP was performed at the previous puncture site. Due to the developmental nature of the study the approaches were not randomised and did not allow comparison.

Conclusion

Transseptal puncture is feasible in horses using ultrasound guidance and allows for electrophysiological exploration of the left heart. Further studies are needed to evaluate post‐operative follow‐up.