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After the ejection of viral DNA into the host cytoplasm, the temperate bacteriophage (phage) lambda integrates a cascade of expressions from various regulatory genes, coupled with DNA replication, to commit to a decision between lysis and lysogeny. Higher multiplicity of infection (MOI) greatly shifts the decision toward the lysogenic pathway. However, how the phage separates the MOI from replicated viral DNA during lysis-lysogeny decision-making is unclear. To quantitatively understand the role of viral DNA replication, we constructed a reporter system facilitating the visualization of individual copies of phage DNA throughout the phage life cycle, along with the lysis-lysogeny reporters. We showed that intracellular viral DNA diverges between the lytic and lysogenic pathways from the early phase of the infection cycle, mostly due to the synchronization and success of DNA injection, as well as the competition for replication resources, rather than the replication rate. Strikingly, we observed two distinct replication patterns during lysogenization and surprisingly heterogeneous integration kinetics, which advances our understanding of temperate phage life cycles. We revealed that the weak repression function of Cro is critical for an optimal replication rate and plays a crucial role in establishing stable lysogens., Importance: Temperate bacteriophages, such as lambda, incorporate environmental cues including host abundance and nutrient conditions to make optimal decisions between propagation and dormancy. A higher phage-to-host ratio or multiplicity of infection (MOI) during λ infection strongly biases toward lysogeny. However, a comprehensive understanding of this decision-making process and the impact of phage replication prior to the decision is yet to be achieved. Here, we used fluorescence microscopy to quantitatively track the spatiotemporal progression of viral DNA replication in individual cells with different cell fates. The implementation of this fluorescent reporter system and quantitative analysis workflow opens a new avenue for future studies to delve deeper into various types of virus-host interactions at a high resolution.

Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus., Competing Interests: Declaration of interests J.B.-D. is a scientific advisory board member of SNIPR Biome and Excision Biotherapeutics, a consultant to LeapFrog Bio and BiomX, and a scientific advisory board member and co-founder of Acrigen Biosciences. The Bondy-Denomy lab received research support from Felix Biotechnology. D.L.S. has financially compensated consulting agreements with Maze Therapeutics and Rezo Therapeutics., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The limited availability of effective agents for removing actinides from the lungs significantly restricts the effectiveness of medical treatments for nuclear emergencies. Inhalation is the primary route of internal contamination in 44.3% of actinide-related accidents, leading to the accumulation of radionuclides in the lungs and resulting in infections and potential tumor formation (tumorigenesis). This study focuses on the synthesis of a nanometal-organic framework (nMOF) material called ZIF-71-COOH, which is achieved by post-synthetic carboxyl functionalization of ZIF-71. The material demonstrates high and selective adsorption of uranyl, while also exhibiting increased particle size (≈2100 nm) when it aggregates in the blood, enabling passive targeting of the lungs through mechanical filtration. This unique property facilitates the rapid enrichment and selective recognition of uranyl, making nano ZIF-71-COOH highly effective in removing uranyl from the lungs. The findings of this study highlight the potential of self-aggregated nMOFs as a promising drug delivery system for targeted uranium decorporation in the lungs., (© 2023 Wiley-VCH GmbH.)

225 Ac is considered as one of the most promising radioisotopes for alpha-therapy because its emitted high-energy α-particles can efficiently damage tumor cells. However, it also represents a significant threat to healthy tissues owing to extremely high radiotoxicity if targeted therapy fails. This calls for a pressing requirement of monitoring the biodistribution of 225 Ac in vivo during the treatment of tumors. However, the lack of imageable photons or positrons from therapeutic doses of 225 Ac makes this task currently quite challenging. We report here a nanoscale luminescent europium-organic framework (EuMOF) that allows for fast, simple, and efficient labeling of 225 Ac in its crystal structure with sufficient 225 Ac-retention stability based on similar coordination behaviors between Ac 3+ and Eu 3+ . After labeling, the short distance between 225 Ac and Eu 3+ in the structure leads to exceedingly efficient energy transduction from 225 Ac-emitted α-particles to surrounding Eu 3+ ions, which emits red luminescence through a scintillation process and produces sufficient photons for clearcut imaging. The in vivo intensity distribution of radioluminescence signal originating from the 225 Ac-labeled EuMOF is consistent with the dose of 225 Ac dispersed among the various organs determined by the radioanalytical measurement ex vivo , certifying the feasibility of in vivo directly monitoring 225 Ac using optical imaging for the first time. In addition, 225 Ac-labeled EuMOF displays notable efficiency in treating the tumor. These results provide a general design principle for fabricating 225 Ac-labeled radiopharmaceuticals with imaging photons and propose a simple way to in vivo track radionuclides with no imaging photons, including but not limited to 225 Ac.

The chemical toxicity and the oxidative stress induced by the internal exposure of uranium is responsible for the long-term adverse effect of in vivo contamination of uranium. An agent with simultaneous removal capability of uranium and excess reactive oxygen species (ROS) is highly desired. Herein, the lacunary Keggin-type polyoxometalate (POM) is demonstrated to selectively bind with uranyl ions in the presence of excess essential divalent ions and exhibits a compelling ROS scavenging efficiency of 78.8%. In vivo uranium decorporation assays illustrate the uranium sequestration efficiencies of 74.0%, 49.4%, and 37.1% from kidneys by prophylactic, prompt, and delayed administration of lacunary POM solution, respectively. The superior ROS quenching and uranium removal performance in comparison with all reported bifunctional agents endow lacunary polyoxometalates as novel agents to effectively protect people from injuries caused by the internal exposure of actinides.

Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

With the extensive usage of gadolinium-based contrast agents (GBCAs) in magnetic resonance imaging (MRI), gadolinium deposition has been observed in the brain, kidneys, liver, etc ., and this is also closely related to the development of nephrogenic systemic fibrosis (NSF) in patients with renal dysfunction. Chelation, thereby promoting the elimination of deposited Gd(III), seems to be promising for alleviating these problems. Despite many ligands suitable for chelation therapy having been studied, the decorporation of transition metals ( e.g. iron, copper, lead, etc .) and actinides ( e.g. uranium, plutonium, etc .) has long been a primary concern, whereas the study of Gd(III) has been extremely limited. Due to their excellent metal binding abilities in vivo and therapeutic effects toward neurodegenerative diseases, bidentate hydroxypyridinone ligands are expected to be able to remove Gd(III) from the brain, kidneys, bones, and liver. Herein, the Gd(III) decorporation efficacy of a bidentate hydroxypyridinone ligand (Me-3,2-HOPO) has been evaluated. The complexation behavior between Me-3,2-HOPO and Gd(III) in solution and solid states was characterized with the assistance of potentiometric titration and X-ray diffraction techniques, respectively. Solution-based thermodynamic studies illustrate that the dominant species of complex between Gd(III) and Me-3,2-HOPO (HL) is GdL 2 + (log  β 120 = 11.8 (3)) at pH 7.4. The structure of the Gd-Me-3,2-HOPO crystal obtained from a room temperature reaction reveals the formation of a Gd(III) dimer that is chelated by four ligands as a result of metal ion hydration and ligand complexation. Cellular Gd(III) removal assays illustrate that Me-3,2-HOPO could effectively reduce final amounts of gadolinium by 77.6% and 66.1% from rat renal proximal tubular epithelial (NRK-52E) cells and alpha mouse liver 12 (AML-12) cells, respectively. Our current results suggest the potential of bidentate HOPO ligands as an effective approach to treat patients suffering from Gd(III) toxicity.

Despite the critical role actinide decorporation agents play in the emergency treatment of people in nuclear accidents and other scenarios that may cause internal contamination of actinides, new ligands have seldom been reported in recent decades because the current inventory has been limited to only a handful of functional groups. Therefore, new functional groups are always being urgently sought for the introduction of advanced actinide decorporation agents. Herein, a tropolone derivative, 2-hydroxy-6-(propan-2-yl)cyclohepta-2,4,6-trien-1-one (Hinokitiol or Hino), is proposed to be a promising candidate for this purpose by virtue of its well-demonstrated high membrane permeability and high affinity for metal ions. The coordination stoichiometry of Hino with uranyl is demonstrated to be 3:1 both in an aqueous solution (pH 7.4) and in the solid state. The results of a liquid-liquid extraction experiment further show that Hino exhibits strong chelating ability and selectivity toward uranyl over biological essential metal ions (i.e., Mn 2+ , Zn 2+ , Co 2+ , and Ni 2+ ) with an extraction efficiency of >90.0%. The in vivo uranyl removal efficacies of Hino in kidneys and bone of mice are demonstrated to be 67.0% and 32.3%, respectively. On the basis of the observations described above, it is highly possible that further modification of Hino will lead to a large family of multidentate agents with enhanced uranyl decorporation ability.

Phage P1 is a temperate phage which makes the lytic or lysogenic decision upon infecting bacteria. During the lytic cycle, progeny phages are produced and the cell lyses, and in the lysogenic cycle, P1 DNA exists as a low-copy-number plasmid and replicates autonomously. Previous studies at the bulk level showed that P1 lysogenization was independent of m ultiplicity o f i nfection (MOI; the number of phages infecting a cell), whereas lysogenization probability of the paradigmatic phage λ increases with MOI. However, the mechanism underlying the P1 behavior is unclear. In this work, using a fluorescent reporter system, we demonstrated this P1 MOI-independent lysogenic response at the single-cell level. We further observed that the activity of the major repressor of lytic functions (C1) is a determining factor for the final cell fate. Specifically, the repression activity of P1, which arises from a combination of C1, the anti-repressor Coi, and the corepressor Lxc, remains constant for different MOI, which results in the MOI-independent lysogenic response. Additionally, by increasing the distance between phages that infect a single cell, we were able to engineer a λ-like, MOI-dependent lysogenization upon P1 infection. This suggests that the large separation of coinfecting phages attenuates the effective communication between them, allowing them to make decisions independently of each other. Our work establishes a highly quantitative framework to describe P1 lysogeny establishment. This system plays an important role in disseminating antibiotic resistance by P1-like plasmids and provides an alternative to the lifestyle of phage λ. IMPORTANCE Phage P1 has been shown potentially to play an important role in disseminating antibiotic resistance among bacteria during lysogenization, as evidenced by the prevalence of P1 phage-like elements in animal and human pathogens. In contrast to phage λ, a cell fate decision-making paradigm, P1 lysogenization was shown to be independent of MOI. In this work, we built a simple genetic model to elucidate this MOI independency based on the gene-regulatory circuitry of P1. We also proposed that the effective communication between coinfecting phages contributes to the lysis-lysogeny decision-making of P1 and highlighted the significance of spatial organization in the process of cell fate determination in a single-cell environment. Finally, our work provides new insights into different strategies acquired by viruses to interact with their bacterial hosts in different scenarios for their optimal survival.

An agent for actinide sequestration with fast uranium uptake kinetics and efficient in vivo uranium removal using a nanoscale metal-organic framework (nano-MOF) is proposed. UiO-66 nanoparticles post-synthetically functionalized with carboxyl groups, UiO-66-(COOH) 4 -180, exhibit the fastest uranium uptake kinetics reported with more than 65 % of uranyl in fetal bovine serum (FBS) removed within 5 min. Moreover, the in vivo bio-distribution studies show that the material partially accumulates in kidneys and femurs where uranium mainly deposits facilitating the in vivo sequestration of uranium. The results of the in vivo uranium decorporation assays with mice show that UiO-66-(COOH) 4 -180 could successfully reduce the amounts of uranyl deposited in kidneys and femurs by up to 55.4 % and 36.5 %, respectively, and is significantly more efficient than the commercial actinide decorporation agent, ZnNa 3 -DTPA., (© 2020 Wiley-VCH GmbH.)

Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy., (Copyright © 2020 Guan and Bondy-Denomy.)

Spatial organization of biological processes allows for variability in molecular outcomes and coordinated development. Here, we investigate how organization underpins phage lambda development and decision-making by characterizing viral components and processes in subcellular space. We use live-cell and in situ fluorescence imaging at the single-molecule level to examine lambda DNA replication, transcription, virion assembly, and resource recruitment in single-cell infections, uniting key processes of the infection cycle into a coherent model of phage development encompassing space and time. We find that different viral DNAs establish separate subcellular compartments within cells, which sustains heterogeneous viral development in single cells. These individual phage compartments are physically separated by the E. coli nucleoid. Our results provide mechanistic details describing how separate viruses develop heterogeneously to resemble single-cell phenotypes.

Objective: To study the expression of pyroptosis signaling pathway related proteins in breast cancer tissues and paracancer tissues, analyze their relationship with breast cancer clinicopathologic features, and explore their relationship to prognosis., Methods: Immunohistochemistry ElivisionTM plus was used to detect the expression of caspase-1, IL-1β and Gasdermin-D (GSDMD) in 108 cases of breast cancer and 23 cases of benign lesions adjacent to breast cancer., Results: Using 108 cases of breast cancer and 23 cases of para-cancerous benign tissues, the pyroptosis signaling pathway effector proteins caspase-1, IL-1β, and GSDMD were positively correlated with each other. The higher the expression level, the lower the histophologic grade of breast cancer, the smaller the tumor size, the lower the clinical stage, the lower the possibility of lymph node metastasis, the lower the risk of death, and the better the prognosis., Conclusions: Pyroptosis signaling pathway effectors caspase-1, IL-1β and GSDMD expression may play an important role in the invasion, metastasis, and prognosis of breast cancer., Competing Interests: None., (IJCEP Copyright © 2020.)

Two three-dimensional uranyl framework compounds consisting of 1,2,4-benzenetricarboxylic ligands and uranyl units have been synthesized under mild solvothermal conditions. Compound 1 adopts an open framework structure built from uranyl pentamers, which is a rare topology for uranyl structures. Compound 2 is constructed from UO 8 and UO 7 bipyramids that are connected by the ligand to form a three-dimensional framework. As a consequence, compound 1 exhibits an unusual photoluminescence spectrum of one broad peak at 545 nm with a significant red shift compared to the typical uranyl emissive peaks as shown in the spectra of uranyl nitrate and compound 2. In addition, since compound 1 crystallizes in the noncentrosymmetric space group Cc, its secondary-harmonic generation property was measured under 1064 nm laser radiation, showing a moderate SHG signal response of 0.91 × KDP.

Background: Macroalgae and microalgae, as feedstocks for third-generation biofuel, possess competitive strengths in terms of cost, technology and economics. The most important compound in brown macroalgae is alginate, and the synergistic effect of endolytic and exolytic alginate lyases plays a crucial role in the saccharification process of transforming alginate into biofuel. However, there are few studies on the synergistic effect of endolytic and exolytic alginate lyases, especially those from the same bacterial strain., Results: In this study, the endolytic alginate lyase AlyPB1 and exolytic alginate lyase AlyPB2 were identified from the marine bacterium Photobacterium sp. FC615. These two enzymes showed quite different and novel enzymatic properties whereas behaved a strong synergistic effect on the saccharification of alginate. Compared to that when AlyPB2 was used alone, the conversion rate of alginate polysaccharides to unsaturated monosaccharides when AlyPB1 and AlyPB2 acted on alginate together was dramatically increased approximately sevenfold. Furthermore, we found that AlyPB1 and AlyPB2 acted the synergistic effect basing on the complementarity of their substrate degradation patterns, particularly due to their M-/G-preference and substrate-size dependence. In addition, a novel method for sequencing alginate oligosaccharides was developed for the first time by combining the 1 H NMR spectroscopy and the enzymatic digestion with the exo-lyase AlyPB2, and this method is much simpler than traditional methods based on one- and two-dimensional NMR spectroscopy. Using this strategy, the sequences of the final tetrasaccharide and pentasaccharide product fractions produced by AlyPB1 were easily determined: the tetrasaccharide fractions contained two structures, ΔGMM and ΔMMM, at a molar ratio of 1:3.2, and the pentasaccharide fractions contained four structures, ΔMMMM, ΔMGMM, ΔGMMM, and ΔGGMM, at a molar ratio of ~ 1:1.5:3.5:5.25., Conclusions: The identification of these two novel alginate lyases provides not only excellent candidate tool-type enzymes for oligosaccharide preparation but also a good model for studying the synergistic digestion and saccharification of alginate in biofuel production. The novel method for oligosaccharide sequencing described in this study will offer a very useful approach for structural and functional studies on alginate., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2019.)

Chondroitin sulfate/dermatan sulfate (CS/DS) sulfatases are potential tools for structural and functional studies of CD/DS chains. In our previous study, a CS/DS 4- O -endosulfatase (endoVB4SF) was identified from a marine bacterium (Wang et al., 2015). Herein, another CS/DS 4- O -sulfatase (exoPB4SF) was identified from a Photobacterium sp. ExoPB4SF shares an 83% identity with endoVB4SF but showed strict exolytic activity. Comparative studies were performed for both enzymes on the basis of biochemical features, substrate-degrading patterns and three-dimensional structures. exoPB4SF exhibited a wider temperature and pH adaptability and better thermostability than endoVB4SF. Furthermore, exoPB4SF is a strict exolytic sulfatase that only releases the sulfate group from the GalNAc residue located at the reducing end, whereas endoVB4SF preferentially removed sulfate esters from the reducing end toward the non-reducing end though its directional degradation property was not strict. In addition, the structure of endoVB4SF was determined by X-ray crystallography at 1.95 Å. It adopts a globular conformation with two monomers per asymmetric unit. The exoPB4SF structure was constructed by homology modeling. Molecular docking results showed that although the residues around the catalytic center are conserved, the residues at the active site of endoVB4SF adopted a more favorable conformation for the binding of long CS/DS chains than those of exoPB4SF, which may explain why the two highly homogenous sulfatases possessed different action patterns. The results of this study provide insight into the structure-function relationship of CS/DS endo- and exosulfatases for the first time.

Glycosaminoglycan (GAG) sulfatases, which catalyze the hydrolysis of sulfate esters from GAGs, belong to a large and conserved sulfatase family. Bacterial GAG sulfatases are essential in the process of sulfur cycling and are useful for the structural analysis of GAGs. Only a few GAG-specific sulfatases have been studied in detail and reported to date. Herein, the GAG-degrading Photobacterium sp. FC615 was isolated from marine sediment, and a novel Δ 4,5 hexuronate-2- O -sulfatase (PB2SF) was identified from this bacterium. PB2SF specifically removed 2- O -sulfate from the unsaturated hexuronate residue located at the non-reducing end of GAG oligosaccharides produced by GAG lyases. A structural model of PB2SF was constructed through a homology-modeling method. Six conserved amino acids around the active site were chosen for further analysis using site-directed mutagenesis. N113A, K141A, K141H, H143A, H143K, H205A, and H205K mutants exhibited only feeble activity, while the H310A, H310K, and D52A mutants were totally inactive, indicating that these conserved residues, particularly Asp52 and His310, were essential in the catalytic mechanism. Furthermore, bioinformatic analysis revealed that GAG sulfatases with specific degradative properties clustered together in the neighbor-joining phylogenetic tree. Based on this finding, 60 Δ 4,5 hexuronate-2- O -sulfatases were predicted in the NCBI protein database, and one with relatively low identity to PB2SF was characterized to confirm our prediction. Moreover, the signature sequences of bacterial Δ 4,5 hexuronate-2- O -sulfatases were identified. With the reported signature motifs, the sulfatase sequence of the Δ 4,5 hexuronate-2- O -sulfatase family could be simply identified before cloning. Taken together, the results of this study should aid in the identification and further application of novel GAG sulfatases.

Uranium poses a threat for severe renal and bone damage in vivo. With the rapid development of nuclear industry, it is more urgent than ever to search for potential in vivo uranium chelators. In this work, 3-hydroxy-2-pyrrolidinone (HPD) is investigated as a new potential uranium decorporation ligand. The potentiometric titration measurements were carried out, and the stability constants were determined to be log β 110 = 10.5(7), log β 120 = 20.7(9), and log β 130 = 28.2(4). The species distribution diagram shows that nearly all uranyl is complexed by HPD at pH 7.4 under the defined condition. A single crystal of uranyl and HPD complexes, [(UO 2 ) 3 O(H 2 O) 3 (C 4 H 6 NO 2 ) 3 ]·NO 3 ·12H 2 O (uranyl-HPD), was obtained via an evaporation method. The overall structure of uranyl-HPD is a trimer that consists of three uranyl units and three HPD ligands. The uranyl unit is equatorially coordinated by three oxygen atoms from two HPD agents, one coordinated water molecule, and one μ 3 -O atom that is shared by three uranyl units. The results of the cytotoxicity assay indicate that the ligand is less toxic than the chelators used clinically (i.e., DTPA-ZnNa 3 and 3-hydroxy-1,2-dimethyl-4(1 H)-pyridone (DFP)). The results of the uranium removal assay using the NRK-52E cell show that it could reduce as much as 58% of the uranium content at the cellular level. Furthermore, the in vivo uranium decorporation assays demonstrate that HPD can remove 52% of uranium deposited in the kidney but shows poor uranium removal efficacy in the bone.

Bacteriophage λ has served as an important model for molecular biology and different cellular processes over the past few decades. In 1992, the phage strain used in most laboratories around the world, thought of as λ wild type, was discovered to carry a mutation in the stf gene which encodes four side tail fibers. Up to now, the role of the side tail fibers during the infection cycle, especially at the single-cell level, remains largely unknown. Here we utilized fluorescent reporter systems to characterize the effect of the side tail fibers on phage infection. We found that the side tail fibers interfere with phage DNA ejection process, most likely through the binding with their receptors, OmpC, leading to a more frequent failed infection. However, the side tail fibers do not seem to affect the lysis-lysogeny decision-making or lysis time., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Cellular decision-making arises from the expression of genes along a regulatory cascade, which leads to a choice between distinct phenotypic states. DNA dosage variations, often introduced by replication, can significantly affect gene expression to ultimately bias decision outcomes. The bacteriophage lambda system has long served as a paradigm for cell-fate determination, yet the effect of DNA replication remains largely unknown. Here, through single-cell studies and mathematical modeling we show that DNA replication drastically boosts cI expression to allow lysogenic commitment by providing more templates. Conversely, expression of CII, the upstream regulator of cI, is surprisingly robust to DNA replication due to the negative autoregulation of the Cro repressor. Our study exemplifies how living organisms can not only utilize DNA replication for gene expression control but also implement mechanisms such as negative feedback to allow the expression of certain genes to be robust to dosage changes resulting from DNA replication., (Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: The CRISPR-Cas system is a widespread prokaryotic defense system which targets and cleaves invasive nucleic acids, such as plasmids or viruses. So far, a great number of studies have focused on the components and mechanisms of this system, however, a direct visualization of CRISPR-Cas degrading invading DNA in real-time has not yet been studied at the single-cell level., Methods: In this study, we fluorescently label phage lambda DNA in vivo , and track the labeled DNA over time to characterize DNA degradation at the single-cell level., Results: At the bulk level, the lysogenization frequency of cells harboring CRISPR plasmids decreases significantly compared to cells with a non-CRISPR control. At the single-cell level, host cells with CRISPR activity are unperturbed by phage infection, maintaining normal growth like uninfected cells, where the efficiency of our anti-lambda CRISPR system is around 26%. During the course of time-lapse movies, the average fluorescence of invasive phage DNA in cells with CRISPR activity, decays more rapidly compared to cells without, and phage DNA is fully degraded by around 44 minutes on average. Moreover, the degradation appears to be independent of cell size or the phage DNA ejection site suggesting that Cas proteins are dispersed in sufficient quantities throughout the cell., Conclusions: With the CRISPR-Cas visualization system we developed, we are able to examine and characterize how a CRISPR system degrades invading phage DNA at the single-cell level. This work provides direct evidence and improves the current understanding on how CRISPR breaks down invading DNA.

Boron nitride nanotubes (BNNTs) exhibit a range of properties that hold great potential for many fields of science and technology; however, they have inherently low chemical reactivity, making functionalization for specific applications difficult. Here we propose that covalent functionalization of BNNTs via reduction chemistry could be a highly promising and viable strategy. Through density functional theory calculations of the electron affinity of BNNTs and their binding energies with various radicals, we reveal that their chemical reactivity can be significantly enhanced via reducing the nanotubes (i.e., negatively charging). For example, a 5.5-fold enhancement in reactivity of reduced BNNTs toward NH2 radicals was predicted relative to their neutral counterparts. The localization characteristics of the BNNT π electron system lead the excess electrons to fill the empty p orbitals of boron sites, which promote covalent bond formation with an unpaired electron from a radical molecule. In support of our theoretical findings, we also experimentally investigated the covalent alkylation of BNNTs via reduction chemistry using 1-bromohexane. The thermogravimetric measurements showed a considerable weight loss (12-14%) only for samples alkylated using reduced BNNTs, suggesting their significantly improved reactivity over neutral BNNTs. This finding will provide an insight in developing an effective route to chemical functionalization of BNNTs.

Citrobacter freundii is a Gram-negative opportunistic pathogen that is associated with urinary tract infections. Bacteriophages infecting C. freundii can be used as an effective treatment to fight these infections. Here, we announce the complete genome sequence of the C. freundii Felix O1-like myophage Mordin and describe its features., (Copyright © 2015 Guan et al.)

While production of engineered carbon nanotubes (CNTs) has escalated in recent years, knowledge of risk associated with exposure to these materials remains unclear. We report on the cytotoxicity of four CNT variants in human lung epithelial cells (A549) and murine macrophages (J774). Morphology, metal content, aggregation/agglomeration state, pore volume, surface area and modifications were determined for the pristine and oxidized single-walled (SW) and multi-walled (MW) CNTs. Cytotoxicity was evaluated by cellular ATP content, BrdU incorporation, lactate dehydrogenase (LDH) release, and CellTiter-Blue (CTB) reduction assays. All CNTs were more cytotoxic than respirable TiO2 and SiO2 reference particles. Oxidation of CNTs removed most metallic impurities but introduced surface polar functionalities. Although slopes of fold changes for cytotoxicity endpoints were steeper with J774 compared to A549 cells, CNT cytotoxicity ranking in both cell types was assay-dependent. Based on CTB reduction and BrdU incorporation, the cytotoxicity of the polar oxidized CNTs was higher compared to the pristine CNTs. In contrast, pristine CNTs were more cytotoxic than oxidized CNTs when assessed for cellular ATP and LDH. Correlation analyses between CNTs' physico-chemical properties and average relative potency revealed the impact of metal content and surface area on the potency values estimated using ATP and LDH assays, while surface polarity affected the potency values estimated from CTB and BrdU assays. We show that in order to reliably estimate the risk posed by these materials, in vitro toxicity assessment of CNTs should be conducted with well characterized materials, in multiple cellular models using several cytotoxicity assays that report on distinct cellular processes.

Boron nitride nanotubes (BNNTs) exhibit a range of properties that are as compelling as those of carbon nanotubes (CNTs); however, very low production volumes have prevented the science and technology of BNNTs from evolving at even a fraction of the pace of CNTs. Here we report the high-yield production of small-diameter BNNTs from pure hexagonal boron nitride powder in an induction thermal plasma process. Few-walled, highly crystalline small-diameter BNNTs (∼5 nm) are produced exclusively and at an unprecedentedly high rate approaching 20 g/h, without the need for metal catalysts. An exceptionally high cooling rate (∼10(5) K/s) in the induction plasma provides a strong driving force for the abundant nucleation of small-sized B droplets, which are known as effective precursors for small-diameter BNNTs. It is also found that the addition of hydrogen to the reactant gases is crucial for achieving such high-quality, high-yield growth of BNNTs. In the plasma process, hydrogen inhibits the formation of N2 from N radicals and promotes the creation of B-N-H intermediate species, which provide faster chemical pathways to the re-formation of a h-BN-like phase in comparison to nitridation from N2. We also demonstrate the fabrication of macroscopic BNNT assemblies such as yarns, sheets, buckypapers, and transparent thin films at large scales. These findings represent a seminal milestone toward the exploitation of BNNTs in real-world applications.

Numerous studies have described the altered expression and the causal role of microRNAs (miRNAs) in human cancer. However, to date, efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here we find that nucleolin (NCL), a major nucleolar protein, posttranscriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, that are causally involved in breast cancer initiation, progression, and drug resistance. We also show that NCL is commonly overexpressed in human breast tumors and that its expression correlates with that of NCL-dependent miRNAs. Finally, inhibition of NCL using guanosine-rich aptamers reduces the levels of NCL-dependent miRNAs and their target genes, thus reducing breast cancer cell aggressiveness both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.

Reduced single-walled carbon nanotubes (r-SWCNT) are shown to react readily at room temperature under inert atmosphere conditions with epoxide moieties, such as those in triglycidyl p-amino phenol (TGAP), to produce a soft covalently bonded interface around the SWCNT. The soft interface is compatible with the SWCNT-free cross-linked cured matrix and acts as a toughener for the composite. Incorporation of 0.2 wt % r-SWCNT enhances the ultimate tensile strength, toughness and fracture toughness by 32, 118, and 40%, respectively, without change in modulus. A toughening rate (dK(IC)/dwt(f)) of 200 MPa m(0.5) is obtained. The toughening mechanism is elucidated through dynamic mechanical analyses, Raman spectroscopy and imaging, and stress-strain curve analyses. The method is scalable and applicable to epoxy resins and systems used commercially.

Single-walled carbon nanotube films are promising candidates for applications requiring transparent conductors due to their low sheet resistance and high transparency in the visible region. Vacuum filtration is a common and easy to implement technique to produce such films but it is complicated by the need to transfer the films to desired substrates. Here we report conditions under which single-walled carbon nanotube films produced by vacuum filtration detach from the filter membrane upon submersion into water, providing a facile method to transfer filtration-produced nanotube films to desired substrates. Sheet resistance and transparency measurements show that these films are competitive with other high conductivity films made through more cumbersome procedures. Films post-treated with nitric acid or made with acid pre-treated nanotubes have superior performance to those made with high-purity nanotubes without any acid treatment. Thermal imaging by scanning thermal microscopy indicates that heat dissipation by the film is comparable to that of a glass substrate.

The C 1s X-ray absorption spectra of several isolated bundles of single-walled carbon nanotubes (SWCNT) have been measured using scanning transmission X-ray microscopy. First the C 1s and O 1s spectra of a purified but unfunctionalized SWCNT were measured. The C 1s --> pi* transition at 285 eV exhibited almost as strong a dichroic effect (spectral dependence on orientation) as that found in multiwalled carbon nanotubes (Najafi; et al. Small 2008, 7, 2279-2285). Second, purified SWCNT were functionalized with dodecyl and then investigated by STXM. Spectral evidence for the dodecyl functionalization is presented and discussed in comparison to the X-ray absorption spectra of aliphatic hydrocarbons. Both orientation and functionalization mapping of an individual SWCNT bundle is demonstrated.

We have successfully applied coupled thermogravimetry, mass spectrometry, and infrared spectroscopy to the quantification of surface functional groups on single-walled carbon nanotubes. A high-purity single-walled carbon nanotube sample was subjected to a rapid functionalization reaction that attached butyric acid moieties to the nanotube sidewalls. This sample was then subjected to thermal analysis under inert desorption conditions. Resultant infrared and mass spectrometric data were easily utilized to identify the desorption of the butyric acid groups across a narrow temperature range and we were able to calculate the degree of substitution of the attached acid groups within the nanotube backbone as 1.7 carbon atoms per hundred, in very good agreement with independent analytical measurements made by inductively coupled plasma optical emission spectrometry (ICP-OES). The thermal analysis technique was also able to discern the presence of secondary functional moieties on the nanotube samples that were not accessible by ICP-OES. This work demonstrates the potential of this technique for assessing the presence of multiple and diverse functional addends on the nanotube sidewalls, beyond just the principal groups targeted by the specific functionalization reaction.

Single-walled carbon nanotubes (SWCNT) have been reduced with sodium naphthalide in THF. The reduced SWCNT are not only soluble in dimethylsulfoxide (DMSO) to form a stable solution/suspension, but also react spontaneously at room temperature with DMSO to evolve hydrocarbon gases and are converted into functionalized SWCNT. The degree of functionalization is about 2C% and the addends are mainly methyl and small oxygen-containing hydrocarbons. The functionalized SWCNT are apparently more soluble and stable in DMSO solution. It may open a new era for further processing and applications.

We report a rapid and efficient procedure to functionalize SWNT where free radicals generated at room temperature by a redox reaction between reduced SWNT and diacyl peroxide derivatives were covalently attached to the SWNT wall.

A novel method combining wet chemistry for synthesis of an Fe core, 532 nm laser irradiation of Fe nanoparticles and Au powder in liquid medium for deposition of an Au shell, and sequential magnetic extraction/acid washing for purification has been developed to fabricate oxidation-resistant Fe@Au magnetic core-shell nanoparticles. The nanoparticles have been extensively characterized at various stages during and up to several months after completion of the synthesis by a suite of electron microscopy techniques (HRTEM, HAADF STEM, EDX), X-ray diffraction (XRD), UV-vis spectroscopy, inductively coupled plasma atomic emission spectroscopy, and magnetometry. The surface plasmon resonance of the Fe@Au nanoparticles is red shifted and much broadened as compared with that of pure colloidal nano-gold, which is explained to be predominantly a shell-thickness effect. The Au shell consists of partially fused approximately 3-nm-diameter fcc Au nanoparticles (lattice interplanar distance, d = 2.36 A). The 18-nm-diameter magnetic core is bcc Fe single domain (d = 2.03 A). The nanoparticles are superparamagnetic at room temperature (300 K) with a blocking temperature, T(b), of approximately 170 K. After 4 months of shelf storage in normal laboratory conditions, their mass magnetization per Fe content was measured to be 210 emu/g, approximately 96% of the Fe bulk value.