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Abstract Viral infections can cause cellular dysregulation of metabolic reactions. Viruses alter host metabolism to meet their replication needs. The impact of viruses on specific metabolic pathways is not well understood, even in well‐studied viruses, such as human adenovirus. Adenoviral infection is known to influence cellular glycolysis and respiration; however, global effects on overall cellular metabolism in response to infection are unclear. Furthermore, few studies have employed an untargeted approach, combining emphasis on viral dosage and infection. To address this, we employed untargeted metabolomics to quantify the dynamic metabolic shifts in fibroblasts infected with human adenovirus serotype 5 (HAdV‐5) at three dosages (0.5, 1.0, and 2.0 multiplicity of infection [MOI]) and across 4 time points (6‐, 12‐, 24‐, and 36‐h post‐infection [HPI]). The greatest differences in individual metabolites were observed at 6‐ and 12‐h post‐infection, correlating with the early phase of the HAdV‐5 infection cycle. In addition to its effects on glycolysis and respiration, adenoviral infection downregulates cysteine and unsaturated fatty acid metabolism while upregulating aspects of purine metabolism. These results reveal specific metabolic pathways dysregulated by adenoviral infection and the associated dynamic shifts in metabolism, suggesting that viral infections alter energetics via profound changes in lipid, nucleic acid, and protein metabolism. The results revealed previously unconsidered metabolic pathways disrupted by HAdV‐5 that can alter cellular metabolism, thereby prompting further investigation into HAdV mechanisms and antiviral targeting. 

AbstractRecently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacteriumIocasia fonsfrigidaestrain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-d-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (K_M = 0.27 mM;k_cat = 0.36 s⁻¹;k_cat/K_M = 1.34 mM⁻¹s⁻¹) compared to the enzymatic hydrolysis of barley b-d-glucan (K_M: 0.04 mM,k_cat: 0.51 s⁻¹,k_cat/K_M = 0.08 mM⁻¹s⁻¹). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid–pretreated cellulosic feedstock. Key points•IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance•IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass•IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis 

Standardized protocols for absolute quantification of potato virus Y (PVY) from potato tissue is critical for host-virus dynamic studies. Here, we developed a standardized protocol using a cloned viral sequence as standards to detect and quantify PVY. Starting with total RNA, concentrated via column-based kit, this protocol is able to detect approximately 50 viral copies/reaction from multiple PVY strains. Validation of this protocol confirmed linearity across 8 orders of magnitude with high repeatability, reproducibility and statistical robustness across three independent runs. This protocol offers reliable PVY quantification to manage potato crop health and enables comparative studies with other viral systems. 

The use of true potato seed (TPS) is fundamental to potato breeding and research, but can be hindered by poor germination and seed dormancy. TPS germination studies had focused mainly on seed treatment methods after seed extraction and not in combination with the seed extraction methods used. In potato, TPS extraction using water, using yeast fermentation or using sodium bicarbonate are common, but TPS extraction using dilute aqueous hydrochloric acid (HCl) followed by bleach treatment (3% sodium hypochlorite) had never been tested in potato even though this is standard practice for tomato seeds. Therefore, three seed extraction methods (water, 0.1 M HCl, and 0.8% yeast fermentation) in combination with three seed treatment methods (water, 1500 ppm GA3, and 3% sodium hypochlorite) were tested on diploid TPS at 1 week and 1 month after seed extraction. TPS treated with GA3 improved germination for both 1 week- and 1 month-old seeds, while TPS treated with 3% sodium hypochlorite only improved germination for 1 month-old seeds. This study shows that TPS extraction using water, yeast or HCl had no effect on germination, but supports the use of GA3 or bleach to promote TPS germination. 

Due to theoretical and practical applications in biomedical, environmental, and industrial microbiology, robust metrics for quantifying the virulence of pathogens is vital. For many virus–host systems, multiple virus strains propagate through host populations. Each strain may exhibit a different virulence level. Likewise, different hosts may manifest different levels of host resilience to infection by a given virus. Recent publications have assessed metrics for quantifying virulence (VR) from growth curve data. Regardless of the metric used, a feature that most methods have in common is focus on the exponential growth phase of virus–host interactions. Often ignored is mortality phase. Following a report introducing the Stacy–Ceballos Inhibition Index (ISC), a robust metric to quantify relative virulence (VR) between viruses, we have turned attention to quantifying relative resilience (RR) between hosts in single-virus/single-host (SVSH) experimental infections. Although resilience during viral infection impacts the entire host growth curve, RR has particular biological significance during the mortality phase. In this report, we argue that calculating RR using a modified ISC provides a robust metric for comparisons between SVSH infections. Wet lab data from fusellovirus infections in Sulfolobales, bacteriophage infections in Mycobacteriales, and simulated infected-host growth profiles form the basis for developing this metric, RR, for quantifying resilience. 

Archaeal group II chaperonins, also known as heat shock proteins (HSPs), are abundantly expressed in Sulfolobales. HSPα and HSPβ gene expression is upregulated during thermal shock. HSPs form large 18-mer complexes that assist in folding nascent proteins and protecting resident proteins during thermal stress. Engineered HSPs have been designed for industrial applications. Since temperature flux in the geothermal habitats of Sulfolobales impacts intracellular temperature, it follows that HSPs have developed thermotolerance. However, despite the low pH (i.e., pH < 4) typical for these habitats, intracellular pH in Sulfolobales is maintained at ~6.5. Therefore, it is not presumed that HSPs have evolved acid-tolerance. To test tolerance to low pH, HSPs were studied at various pH and temperature values. Both circular dichroism and intrinsic fluorescence indicate that HSPα and HSPβ retain structural integrity at neutral pH over a wide range of temperatures. Structural integrity is compromised for all HSPs at ultra-low pH (e.g., pH 2). Secondary structures in HSPs are resilient under mildly acidic conditions (pH 4) but Anilino naphthalene 8-sulfonate binding shows shifts in tertiary structure at lower pH. Trypsin digestion shows that the HSPβ-coh backbone is the most flexible and HSPβ is the most resilient. Overall, results suggest that HSPα and HSPβ exhibit greater thermostability than HSPβ-coh and that there are limits to HSP acid-tolerance. Molecular dynamics (MD) simulations complement the wet lab data. Specifically, MD suggests that the HSPβ secondary structure is the most stable. Also, despite similarities in pH- and temperature-dependent behavior, there are clear differences in how each HSP subtype is perturbed. 

In his seminal work, Chatterjee (Citation2021) introduced a novel correlation measure that is distribution-free, asymptotically normal, and consistent against all alternatives. In this article, we study the probabilistic relationships between Chatterjee’s correlation and the widely used Spearman’s correlation. We show that, under independence, the two sample-based correlations are asymptotically joint normal and asymptotically independent. Under dependence, the magnitudes of two correlations can be substantially different. We establish some extreme cases featuring large differences between these two correlations. Motivated by these findings, a new independence test is proposed by combining Chatterjee’s and Spearman’s correlations into a maximal strength measure of variable association. Our simulation study and real-data application show the good sensitivity of the new test to different correlation patterns. 

Infection with hepatitis B virus (HBV) is a main risk factor for hepatocellular carcinoma (HCC). Extracellular vesicles, such as exosomes, play an important role in tumor development and metastasis, including regulation of HBV-related HCC. In this study, we have characterized exosome microRNA and proteins released in vitro from hepatitis B virus (HBV)-related HCC cell lines SNU-423 and SNU-182 and immortalized normal hepatocyte cell lines (THLE2 and THLE3) using microRNA sequencing and mass spectrometry. Bioinformatics, including functional enrichment and network analysis, combined with survival analysis using data related to HCC in The Cancer Genome Atlas (TCGA) database, were applied to examine the prognostic significance of the results. More than 40 microRNAs and 200 proteins were significantly dysregulated (p < 0.05) in the exosomes released from HCC cells in comparison with the normal liver cells. The functional analysis of the differentially expressed exosomal miRNAs (i.e., mir-483, mir-133a, mir-34a, mir-155, mir-183, mir-182), their predicted targets, and exosomal differentially expressed proteins (i.e., POSTN, STAM, EXOC8, SNX9, COL1A2, IDH1, FN1) showed correlation with pathways associated with HBV, virus activity and invasion, exosome formation and adhesion, and exogenous protein binding. The results from this study may help in our understanding of the role of HBV infection in the development of HCC and in the development of new targets for treatment or non-invasive predictive biomarkers of HCC. 

ABSTRACT Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage. 

In his seminal work, Chatterjee (2021) introduced a novel correlation measure which is distribution-free, asymptotically normal, and consistent against all alternatives. In this paper, we study the probabilistic relationships between Chatterjee's correlation and the widely used Spearman's correlation. We show that, under independence, the two sample-based correlations are asymptotically joint normal and asymptotically independent. Under dependence, the magnitudes of two correlations can be substantially different. We establish some extremal cases featuring large differences between these two correlations. Motivated by these findings, a new independence test is proposed by combining Chatterjee's and Spearman's correlations into a maximal strength measure of variable association. Our simulation study and real data application show the good sensitivity of the new test to different correlation patterns.