An essential and highly selective protein import pathway encoded by nucleus-forming phage

Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here, we identify two components of this protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together, our results allow us to propose a multistep model for the Protein Import Chimallivirus pathway, where proteins are targeted to PicA by amino acids on their surface and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts.

Enhancing Raw Bovine Milk Quality using Ultraviolet-C (UV-C) Irradiation: A Microbial and Lipid Peroxidation Study

This study investigated the efficacy of ultraviolet-C (UV-C) irradiation in enhancing the quality of raw bovine milk by targeting microbial populations and lipid peroxidation, both of which are key factors in milk spoilage. We categorized the raw milk samples into three groups based on initial bacterial load: low (<3 Log 10 CFU/mL), medium (3-4 Log 10 CFU/mL), and high (>4 Log 10 CFU/mL). Using a 144 W thin-film UV-C reactor, we treated the milk with a flow rate of 3 L/min. We measured the bacterial count including standard plate count, coliform count, coagulase-negative staphylococci count, and lactic acid bacteria count and lipid peroxidation (via thiobarbituric acid reactive substances assay) pre- and post-treatment. Our results show that UV-C treatment significantly reduced bacterial counts, with the most notable reductions observed in high and medium initial load samples (>4 and 3-4 Log 10 CFU/mL, respectively). The treatment was particularly effective against coliforms, showing higher reduction efficiency compared to coagulase-negative staphylococci and lactic acid bacteria. Notably, lipid peroxidation in UV-C treated milk was significantly lower than in pasteurized or untreated milk, even after 72 hours. These findings demonstrate the potential of UV-C irradiation as a pre-treatment method for raw milk, offering substantial reduction in microbial content and prevention of lipid peroxidation, thereby enhancing milk quality.

Effect of chemical and electrochemical decontamination protocols on single and multiple-used healing abutments: A comparative analysis of contact surface area, micro-gap, micro-leakage, and surface topography

INTRODUCTION

Although the combined use of chemical and electrochemical decontamination protocols can completely remove contaminants from the surfaces of one-time used healing abutments (HAs), their effectiveness in multiple-used HAs remains unknown. We aimed to investigate the effect of reused HAs frequency on the implant-HA contact surface area, micro-gap, microleakage, and surface topography following chemical and combined chemical and electrochemical decontamination protocols.

METHODS

Ninety bone level titanium implants were assembled with 90 bone level HAs, in which 80 contaminated HA samples were collected from human participants. The retrieved HAs were randomly divided into two groups according to the cleaning protocol: ultrasonication with 5.25% NaOCl solution for 15 min and steam autoclaving (group I); ultrasonication with 5.25% NaOCl solution for 15 min, followed by electrochemical cleaning and steam autoclaving (group II). The control group (group III) comprised 10 new unused HAs. The cleaning protocol was applied after each insertion as follows: (a) single-use and cleaning, (b) double-use and double cleaning cycles, (c) triple-use and triple cleaning cycles, and (d) more than triple-use and more than triple cleaning cycles. The contact surface area and micro-gap were assessed with micro-computed tomography scanning technique, microleakage test using 2% methylene blue staining, surface morphology with scanning electron microscopy, and surface elemental composition with energy-dispersive X-ray spectroscopy analysis.

RESULTS

Group Id exhibited the smallest contact surface area. The values of the micro-gap volumes and microleakage were significantly different (p < 0.001) in the descending order of Id > Ic > Ib > IId > Ia, IIa, and III. Morphological evaluation of Groups IIa, IIb, and IIc revealed that residual biological debris was optimally removed without altering their surface properties.

CONCLUSIONS

Chemical and electrochemical decontamination protocols are more effective than NaOCl cleaning methods, particularly for multiple consecutive uses with better decontamination levels, which decreases micro-gap volume and microleakage without surface alterations. Although the use of combined decontamination protocols for the contact surface area at the implant-HA interface showed comparable results with the control, change in the contact surface area was observed following the NaOCl cleaning methods. Therefore, titanium HA reuse can be considered in multiple times, if they are cleaned and sterilized using combined chemical and electrochemical decontamination protocols.

Die hard: cell death mechanisms and their implications in nanotoxicology

Cell death is a fundamental biological process, and its fine-tuned regulation is required for life. However, the complexity of regulated cell death is often reduced to a matter of live-dead discrimination. Here, we provide a perspective on programmed or regulated cell death, focusing on apoptosis, pyroptosis, necroptosis, and ferroptosis (the latter three cell death modalities are examples of regulated necrosis). We also touch on other, recently described manifestations of (pathological) cell death including cuproptosis. Furthermore, we address how engineered nanomaterials impact on regulated cell death. We posit that an improved understanding of nanomaterial-induced perturbations of cell death may allow for a better prediction of the consequences of human exposure and could also yield novel approaches by which to mitigate these effects. Finally, we provide examples of the harnessing of nanomaterials to achieve cancer cell killing through the induction of regulated cell death.

Reverse transcriptase droplet digital PCR vs reverse transcriptase quantitative real-time PCR for serum HBV RNA quantification

Serum hepatitis B virus (HBV) RNA is a novel marker reflecting the activity of covalently closed circular DNA. However, the methodology for detecting HBV RNA has been a technical challenge. In this study, the performance of reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) for quantifying HBV RNA was compared with that of reverse transcription quantitative real-time PCR (RT-qPCR) in serum samples collected from treatment-naïve patients with different phases of chronic hepatitis B (CHB). A total of 417 serum samples, including 136 HBeAg-positive CHB and 281 HBeAg-negative CHB were examined. HBV RNA levels measured by RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. The limit of detections of RT-ddPCR and RT-qPCR assays were 102 and 103 copies/mL, respectively. Our results also demonstrated that RT-ddPCR was superior to RT-qPCR in terms of its consistency for quantifying HBV RNA across all concentrations. In the HBeAg-positive group, serum HBV RNA levels based on RT-ddPCR were moderately correlated with HBV DNA (r = 0.591, P < .001) and HBsAg (r = 0.502, P < .001). Among patients with HBeAg-negative CHB, serum HBV RNA levels were moderately correlated with HBV DNA (r = 0.603, P < .001) but had weak correlation with HBsAg (r = 0.203, P = .001). In summary, RT-ddPCR could enhance the sensitivity of serum HBV RNA detection, particularly among the HBeAg-negative group with low viral loads. Thus, RT-ddPCR could serve as an optimal method for HBV RNA quantification in clinical practice.

Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7

β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B_2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred ⁴H₃/⁴E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a ⁴H₃/⁴E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B_2,5 conformation rapidly relaxed to a E₃/⁴H₃ conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B_2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.