Housekeeping U1 snRNA facilitates antiviral innate immunity by promoting TRIM25-mediated RIG-I activation

U1 small nuclear RNA (snRNA) is an abundant and evolutionarily conserved 164-nucleotide RNA species that functions in pre-mRNA splicing, and it is considered to be a housekeeping non-coding RNA. However, the role of U1 snRNA in regulating host antiviral immunity remains largely unexplored. Here, we find that RNVU1-18, a U1 pseudogene, is significantly upregulated in the host infected with RNA viruses, including influenza and respiratory syncytial virus. Overexpression of U1 snRNA protects cells against RNA viruses, while knockdown of U1 snRNA leads to more viral burden in vitro and in vivo. Knockout of RNVU1-18 is sufficient to impair the type I interferon-dependent antiviral innate immunity. U1 snRNA is required to fully activate the retinoic acid-inducible gene I (RIG-I)-dependent antiviral signaling, since it interacts with tripartite motif 25 (TRIM25) and enhances the RIG-I-TRIM25 interaction to trigger K63-linked ubiquitination of RIG-I. Our study reveals the important role of housekeeping U1 snRNA in regulating host antiviral innate immunity and restricting RNA virus infection.

Energy balance drives diurnal and nocturnal brain transcriptome rhythms

Plasticity in daily timing of activity has been observed in many species, yet the underlying mechanisms driving nocturnality and diurnality are unknown. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance and switch mice to be nocturnal or diurnal. Here, we present the rhythmic transcriptome of 21 tissues, including 17 brain regions, sampled every 4 h over a 24-h period from nocturnal and diurnal male CBA/CaJ mice. Rhythmic gene expression across tissues comprised different sets of genes with minimal overlap between nocturnal and diurnal mice. We show that non-clock genes in the suprachiasmatic nucleus (SCN) change, and the habenula was most affected. Our results indicate that adaptive flexibility in daily timing of behavior is supported by gene expression dynamics in many tissues and brain regions, especially in the habenula, which suggests a crucial role for the observed nocturnal-diurnal switch.

Isotype switching in human memory B cells sets intrinsic antigen-affinity thresholds that dictate antigen-driven fates

Memory B cells (MBCs) play a critical role in protection against homologous and variant pathogen challenge by either differentiating to plasma cells (PCs) or to germinal center (GC) B cells. The human MBC compartment contains both switched IgG+ and unswitched IgM+ MBCs; however, whether these MBC subpopulations are equivalent in their response to B cell receptor cross-linking and their resulting fates is incompletely understood. Here, we show that IgG+ and IgM+ MBCs can be distinguished based on their response to κ-specific monoclonal antibodies of differing affinities. IgG+ MBCs responded only to high-affinity anti-κ and differentiated almost exclusively toward PC fates. In contrast, IgM+ MBCs were eliminated by apoptosis by high-affinity anti-κ but responded to low-affinity anti-κ by differentiating toward GC B cell fates. These results suggest that IgG+ and IgM+ MBCs may play distinct yet complementary roles in response to pathogen challenge ensuring the immediate production of high-affinity antibodies to homologous and closely related challenges and the generation of variant-specific MBCs through GC reactions.

Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis

When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment-specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

Plasma growth factors maintain constitutive translation in platelets to regulate reactivity and thrombotic potential

ABSTRACT

Mechanisms of proteostasis in anucleate circulating platelets are unknown and may regulate platelet function. We investigated the hypothesis that plasma-borne growth factors/hormones (GFHs) maintain constitutive translation in circulating platelets to facilitate reactivity. Bio-orthogonal noncanonical amino acid tagging (BONCAT) coupled with liquid chromatography-tandem mass spectrometry analysis revealed constitutive translation of a broad-spectrum translatome in human platelets dependent upon plasma or GFH exposure, and in murine circulation. Freshly isolated platelets from plasma showed homeostatic activation of translation-initiation signaling pathways: phosphorylation of p38/ERK upstream kinases, essential intermediate MNK1/2, and effectors eIF4E/4E-BP1. Plasma starvation led to loss of pathway phosphorylation, but it was fully restored with 5-minute stimulation by plasma or GFHs. Cycloheximide or puromycin infusion suppressed ex vivo platelet GpIIb/IIIa activation and P-selectin exposure with low thrombin concentrations and low-to-saturating concentrations of adenosine 5'-diphosphate (ADP) or thromboxane analog but not convulxin. ADP-induced thromboxane generation was blunted by translation inhibition, and secondary-wave aggregation was inhibited in a thromboxane-dependent manner. Intravenously administered puromycin reduced injury-induced clot size in cremaster muscle arterioles, and delayed primary hemostasis after tail tip amputation but did not delay neither final hemostasis after subsequent rebleeds, nor final hemostasis after jugular vein puncture. In contrast, these mice were protected from injury-induced arterial thrombosis and thrombin-induced pulmonary thromboembolism (PE), and adoptive transfer of translation-inhibited platelets into untreated mice inhibited arterial thrombosis and PE. Thus, constitutive plasma GFH-driven translation regulates platelet G protein-coupled receptor reactivity to balance hemostasis and thrombotic potential.

De novo steroidogenesis in tumor cells drives bone metastasis and osteoclastogenesis

Osteoclasts play a central role in cancer-cell-induced osteolysis, but the molecular mechanisms of osteoclast activation during bone metastasis formation are incompletely understood. By performing RNA sequencing on a mouse breast carcinoma cell line with higher bone-metastatic potential, here we identify the enzyme CYP11A1 strongly upregulated in osteotropic tumor cells. Genetic deletion of Cyp11a1 in tumor cells leads to a decreased number of bone metastases but does not alter primary tumor growth and lung metastasis formation in mice. The product of CYP11A1 activity, pregnenolone, increases the number and function of mouse and human osteoclasts in vitro but does not alter osteoclast-specific gene expression. Instead, tumor-derived pregnenolone strongly enhances the fusion of pre-osteoclasts via prolyl 4-hydroxylase subunit beta (P4HB), identified as a potential interaction partner of pregnenolone. Taken together, our results demonstrate that Cyp11a1-expressing tumor cells produce pregnenolone, which is capable of promoting bone metastasis formation and osteoclast development via P4HB.

mSphere of Influence: Celebrating exceptions to the rule of lipid A essentiality

Kate Hummels works in the field of bacterial cell envelope biosynthesis and studies the regulation of the metabolic pathways needed to build the Gram-negative cell envelope. In this mSphere of Influence article, she reflects on how the papers "A penicillin-binding protein inhibits selection of colistin-resistant, lipopoligosaccharide-deficient Acinetobacter baumannii" by Boll et al. and "Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids" by Zik et al. made an impact on her by studying organisms that deviate from accepted norms to highlight the plethora of unanswered questions in cell envelope biology.

Expansion Kinetics of Flexible Polymers upon Release from a Disk-Shaped Confinement

A general theory is developed to explain the expansion kinetics of a polymer released from a confining cavity in a d-dimensional space. At beginning, the decompressed chain undergoes an explosive expansion while keeping the structure resembling a sphere. As the process continues, the chain transitions to a coil conformation, and the expansion significantly slows down. The kinetics are derived by applying Onsager's variational principle. Computer simulations are then conducted in a quasi-two-dimensional space to verify the theory. The average expansion of the chain size exhibits a distinctive sigmoidal variation on a logarithmic scale, characterized by two times and associated exponents that represent the fast and the slow dynamics, respectively. Through an analysis of the kinetic state diagrams, two important universal behaviors are discovered in the two expansion stages. The intersection of the expansion speed curves allows us to define the crossover point between the stages and study its properties. The scaling relations of the characteristic times and exponents are thoroughly investigated under different confining conditions, with the results strongly supporting the theory. Additional calculations conducted in a three-dimensional (3D) space demonstrate the robustness of the proposed theory in describing the kinetics of polymer expansion in both 2D and 3D spaces.

Nanogel-based composites for bacterial antibiofilm activity: advances, challenges, and prospects

Nano-based approaches, particularly nanogels, have recently emerged as a potential strategy for combating biofilm-related infections. Their exceptional characteristics including biocompatibility, biodegradability, stability, high water content, stimuli-responsiveness, and their nano size (which enables their penetration into biofilms) make nanogels a promising technology in the biomedical field. However, exploring nanogels for biofilm treatment remains in its early stages. This review examined the status of nanogels application for the treatment of bacterial biofilms. Recent investigations studied nanogels derived from natural polymers like chitosan (CS), hyaluronic acid (HA), and alginate, among others, for eliminating and inhibiting biofilms. These nanogels were utilized as carriers for diverse antibiofilm agents, encompassing antibiotics, antimicrobial peptides, natural extracts, and nanoparticles. Utilizing mechanisms like conventional antibody-mediated pathways, photodynamic therapy, photothermal therapy, chemodynamic therapy, and EPS degradation, these nanogels effectively administered antibiofilm drugs, exhibiting efficacy across several bacterial strains, notably Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Escherichia coli (E. coli), among others. Despite showing promise, nanogels remain relatively underexplored in biofilm treatment. This review concludes that research gaps are still present in biofilm treatment processes including (i) a better understanding of the stimuli-responsive behaviors of nanogels, (ii) active targeting strategies, and (iii) the narrow spectrum of antibiofilm agents loaded into nanogels. Hence, future studies could be directed towards the following elements: the exploration of multi-strain biofilms rather than single-strain biofilms, other endogenous and exogenous stimuli to trigger drug release, active targeting mechanisms, a broader range of antibiofilm agents when employing nanogels, and fostering more comprehensive and reliable biofilm treatment strategies. This review found that there are currently several research gaps as well in the use of nanogels for biofilm therapy, and these include: (i) very limited exogenous and endogenous stimuli were explored to trigger drug release from nanogels, (ii) the active targeting strategies were not explored, (iii) a very narrow spectrum of antibiofilm agents was loaded into nanogels, and (iv) only biofilms of single strains were investigated.

Switching Go̅-Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions

Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and β2-adrenergic receptor (β2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.

How the Orthodox Features of Orthopoxviruses Led to an Unorthodox Mpox Outbreak: What We've Learned, and What We Still Need to Understand

Orthopoxviruses have repeatedly confounded expectations in terms of the clinical illness they cause and their patterns of spread. Monkeypox virus (MPXV), originally characterized in the late 1950s during outbreaks among captive primates, has been recognized since the 1970s to cause human disease (mpox) in West and Central Africa, where interhuman transmission has largely been associated with nonsexual, close physical contact. In May 2022, a focus of MPXV transmission was detected, spreading among international networks of gay, bisexual, and other men who have sex with men. The outbreak grew in both size and geographic scope, testing the strength of preparedness tools and public health science alike. In this article we consider what was known about mpox before the 2022 outbreak, what we learned about mpox during the outbreak, and what continued research is needed to ensure that the global public health community can detect, and halt further spread of this disease threat.

Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens

BACKGROUND

The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing.

METHODS

Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences.

RESULTS

MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations.

CONCLUSIONS

We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.

Combining a Commercial Mixer with a Wall-Tube Electrode Allows the Arbitrary Control of Concentrations in Protein Film Electrochemistry

Protein film electrochemistry is a technique in which an enzyme is immobilized on an electrode in a configuration that allows following the changes in turnover frequency as a response to changes in the experimental conditions. Insights into the reactivity of the enzyme can be obtained by quantitatively modeling such responses. As a consequence, the more the technique allows flexibility in changing conditions, the more useful it becomes. The most commonly used setup, based on the rotating disc electrode, allows easy stepwise increases in the concentration of nongaseous substrates, or exposure to constant concentration of dissolved gas, but does not permit to easily decrease the concentration of nongaseous substrates, or to change the concentration of dissolved gas in a stepwise fashion. To overcome the limitation by mass transport of the substrate toward the electrode when working with fast enzymes, we have designed another kind of electrochemical cell based on the wall-tube electrode (WTE). We demonstrate here that by using a system combining two syringe pumps, a commercial mixer, and the WTE, it is possible to change the concentration of species in a stepwise fashion in all directions, opening new possibilities to study redox enzymes. As a proof of concept, this device was applied to the study of the electrochemical response of the cytochrome c nitrite reductase of Desulfovibrio desulfuricans.

Microplastics in the Water Column of the Rhine River Near Basel: 22 Months of Sampling

Measured microplastic concentrations in river surface waters fluctuate greatly. This variability is affected by season and is codriven by factors, such as sampling methodologies, sampling site, or sampling position within site. Unfortunately, most studies comprise single-instance measurements, whereas extended sampling periods are better suited to assessing the relevance of such factors. Moreover, microplastic concentrations in riverine water column remain underexplored. Similar to the oceans, however, this compartment likely holds significant amounts of microplastics. By representatively sampling the entire Rhine River cross-section near Basel through five sampling points over 22 months, we found a median microplastic (50-3000 μm) concentration of 4.48 n m-3, and estimated a widely ranging load between 4.04 × 102 n s-1 and 3.57 × 105 n s-1. We also show that the microplastic concentration in the water column was not well explained by river discharge. This suggests that although high discharge events as observed here can over short time periods lead to peak microplastic concentrations (e.g., 1.23 × 102 n m-3), microplastic load variance was not dominated by discharge in the study area.

DOTAD: A Database of Therapeutic Antibody Developability

The development of therapeutic antibodies is an important aspect of new drug discovery pipelines. The assessment of an antibody's developability-its suitability for large-scale production and therapeutic use-is a particularly important step in this process. Given that experimental assays to assess antibody developability in large scale are expensive and time-consuming, computational methods have been a more efficient alternative. However, the antibody research community faces significant challenges due to the scarcity of readily accessible data on antibody developability, which is essential for training and validating computational models. To address this gap, DOTAD (Database Of Therapeutic Antibody Developability) has been built as the first database dedicated exclusively to the curation of therapeutic antibody developability information. DOTAD aggregates all available therapeutic antibody sequence data along with various developability metrics from the scientific literature, offering researchers a robust platform for data storage, retrieval, exploration, and downloading. In addition to serving as a comprehensive repository, DOTAD enhances its utility by integrating a web-based interface that features state-of-the-art tools for the assessment of antibody developability. This ensures that users not only have access to critical data but also have the convenience of analyzing and interpreting this information. The DOTAD database represents a valuable resource for the scientific community, facilitating the advancement of therapeutic antibody research. It is freely accessible at http://i.uestc.edu.cn/DOTAD/ , providing an open data platform that supports the continuous growth and evolution of computational methods in the field of antibody development.

PDGFRA K385 mutants in myxoid glioneuronal tumors promote receptor dimerization and oncogenic signaling

Myxoid glioneuronal tumors (MGNT) are low-grade glioneuronal neoplasms composed of oligodendrocyte-like cells in a mucin-rich stroma. These tumors feature a unique dinucleotide change at codon 385 in the platelet-derived growth factor receptor α (encoded by the PDGFRA gene), resulting in the substitution of lysine 385 into leucine or isoleucine. The functional consequences of these mutations remain largely unexplored. Here, we demonstrated their oncogenic potential in fibroblast and Ba/F3 transformation assays. We showed that the K385I and K385L mutants activate STAT and AKT signaling in the absence of ligand. Co-immunoprecipitations and BRET experiments suggested that the mutations stabilized the active dimeric conformation of the receptor, pointing to a new mechanism of oncogenic PDGF receptor activation. Furthermore, we evaluated the sensitivity of these mutants to three FDA-approved tyrosine kinase inhibitors: imatinib, dasatinib, and avapritinib, which effectively suppressed the constitutive activity of the mutant receptors. Finally, K385 substitution into another hydrophobic amino acid also activated the receptor. Interestingly, K385M was reported in a few cases of brain tumors but not in MGNT. Our results provide valuable insights into the molecular mechanism underlying the activation of PDGFRα by the K385I/L mutations, highlighting their potential as actionable targets in the treatment of myxoid glioneuronal tumors.

More than double the fun with two-photon excitation microscopy

For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.

Scale-free bursting activity in shrinkage induced cracking

Based on computer simulations of a realistic discrete element model we demonstrate that shrinkage induced cracking of thin layers of heterogeneous materials, generating spectacular crack patterns, proceeds in bursts. These crackling pulses are characterized by scale free distributions of size and duration, however, with non-universal exponents depending on the system size and shrinking rate. On the contrary, local avalanches composed of micro-cracking events with temporal and spatial correlation are found to obey a universal power law statistics. Most notably, we demonstrate that the observed non-universality of the integrated signal is the consequence of the temporal superposition of the underlying local avalanches, which pop up in an uncorrelated way in homogeneous systems. Our results provide an explanation of recent acoustic emission measurements on drying induced shrinkage cracking and may have relevance for the acoustic monitoring of the electro-mechanical degradation of battery electrodes.

Immune system modulation & virus transmission during parasitism identified by multi-species transcriptomics of a declining insect biocontrol system

BACKGROUND

The Argentine stem weevil (ASW, Listronotus bonariensis) is a significant pasture pest in Aotearoa New Zealand, primarily controlled by the parasitoid biocontrol agent Microctonus hyperodae. Despite providing effective control of ASW soon after release, M. hyperodae parasitism rates have since declined significantly, with ASW hypothesised to have evolved resistance to its biocontrol agent. While the parasitism arsenal of M. hyperodae has previously been investigated, revealing many venom components and an exogenous novel DNA virus Microctonus hyperodae filamentous virus (MhFV), the effects of said arsenal on gene expression in ASW during parasitism have not been examined. In this study, we performed a multi-species transcriptomic analysis to investigate the biology of ASW parasitism by M. hyperodae, as well as the decline in efficacy of this biocontrol system.

RESULTS

The transcriptomic response of ASW to parasitism by M. hyperodae involves modulation of the weevil's innate immune system, flight muscle components, and lipid and glucose metabolism. The multispecies approach also revealed continued expression of venom components in parasitised ASW, as well as the transmission of MhFV to weevils during parasitism and some interrupted parasitism attempts. Transcriptomics did not detect a clear indication of parasitoid avoidance or other mechanisms to explain biocontrol decline.

CONCLUSIONS

This study has expanded our understanding of interactions between M. hyperodae and ASW in a biocontrol system of critical importance to Aotearoa-New Zealand's agricultural economy. Transmission of MhFV to ASW during successful and interrupted parasitism attempts may link to a premature mortality phenomenon in ASW, hypothesised to be a result of a toxin-antitoxin system. Further research into MhFV and its potential role in ASW premature mortality is required to explore whether manipulation of this viral infection has the potential to increase biocontrol efficacy in future.

Free PEG Suppresses Anaphylaxis to PEGylated Nanomedicine in Swine

Covalent conjugation of poly(ethylene glycol) (PEG) is frequently employed to enhance the pharmacokinetics and biodistribution of various protein and nanoparticle therapeutics. Unfortunately, some PEGylated drugs can induce elevated levels of antibodies that can bind PEG, i.e., anti-PEG antibodies (APA), in some patients. APA in turn can reduce the efficacy and increase the risks of allergic reactions, including anaphylaxis. There is currently no intervention available in the clinic that specifically mitigates allergic reactions to PEGylated drugs without the use of broad immunosuppression. We previously showed that infusion of high molecular weight free PEG could safely and effectively suppress the induction of APA in mice and restore prolonged circulation of various PEGylated therapeutics. Here, we explored the effectiveness of free PEG as a prophylaxis against anaphylaxis induced by PEG-specific allergic reactions in swine. Injection of PEG-liposomes (PL) resulted in anaphylactoid shock (pseudoanaphylaxis) within 1-3 min in both naïve and PL-sensitized swine. In contrast, repeated injection of free PEG alone did not result in allergic reactions, and injection of free PEG effectively suppressed allergic reactions to PL, including in previously PL-sensitized swine. These results strongly support the further investigation of free PEG for reducing APA and allergic responses to PEGylated therapeutics.

Particle-Based Artificial Antigen-Presenting Cell Systems for T Cell Activation in Adoptive T Cell Therapy

T cell-based adoptive cell therapy (ACT) has emerged as a promising treatment for various diseases, particularly cancers. Unlike other immunotherapy modalities, ACT involves directly transferring engineered T cells into patients to eradicate diseased cells; hence, it necessitates methods for effectively activating and expanding T cells in vitro. Artificial antigen-presenting cells (aAPCs) have been widely developed based on biomaterials, particularly micro- and nanoparticles, and functionalized with T cell stimulatory antibodies to closely mimic the natural T cell-APC interactions. Due to their vast clinical utility, aAPCs have been employed as an off-the-shelf technology for T cell activation in FDA-approved ACTs, and the development of aAPCs is constantly advancing with the emergence of aAPCs with more sophisticated designs and additional functionalities. Here, we review the recent advancements in particle-based aAPCs for T cell activation in ACTs. Following a brief introduction, we first describe the manufacturing processes of ACT products. Next, the design and synthetic strategies for micro- and nanoparticle-based aAPCs are discussed separately to emphasize their features, advantages, and limitations. Then, the impact of design parameters of aAPCs, such as size, shape, ligand density/mobility, and stiffness, on their functionality and biomedical performance is explored to provide deeper insights into the design concepts and principles for more efficient and safer aAPCs. The review concludes by discussing current challenges and proposing future perspectives for the development of more advanced aAPCs.

Tumor Microenvironment Activatable Nanoprodrug System for In Situ Fluorescence Imaging and Therapy of Liver Cancer

The development of new imaging and treatment nanoprodrug systems is highly demanded for diagnosis and therapy of liver cancer, a severe disease characterized by a high recurrence rate. Currently, available small molecule drugs are not possible for cancer diagnosis because of the fast diffusion of imaging agents and low efficacy in treatment due to poor water solubility and significant toxic side effects. In this study, we report the development of a tumor microenvironment activatable nanoprodrug system for the diagnosis and treatment of liver cancer. This nanoprodrug system can accumulate in the tumor site and be selectively activated by an excess of hydrogen peroxide (H2O2) in the tumor microenvironment, releasing near-infrared solid-state organic fluorescent probe (HPQCY-1) and phenylboronic acid-modified camptothecin (CPT) prodrug. Both HPQCY-1 and CPT prodrugs can be further activated in tumor sites for achieving more precise in situ near-infrared (NIR) fluorescence imaging and treatment while reducing the toxic effects of drugs on normal tissues. Additionally, the incorporation of hydrophilic multivalent chitosan as a carrier effectively improved the water solubility of the system. This research thus provides a practical new approach for the diagnosis and treatment of liver cancer.

Combined Experimental and Density Functional Theory Study on the Mechanism of the Selective Catalytic Reduction of NO with NH3 over Metal-Free Carbon-Based Catalysts

Metal-free carbon-based catalysts are attracting much attention in the low-temperature selective catalytic reduction of NOx with NH3 (NH3-SCR). However, the mechanism of the NH3-SCR reaction on carbon-based catalysts is still controversial, which severely limits the development of carbon-based SCR catalysts. Herein, we successfully reconstructed carbon-based catalysts through oxidation treatment with nitric acid, thereby enhancing their low-temperature activity in NH3-SCR. Combining experimental results and density functional theory (DFT) calculations, we proposed a previously unreported NH3-SCR reaction mechanism over carbon-based catalysts. We demonstrated that C-OH and C-O-C groups not only effectively activate NH3 but also remarkedly promote the decomposition of intermediate NH2NO. This study enhances the understanding of the NH3-SCR mechanism on carbon-based catalysts and paves the way to develop low-temperature metal-free SCR catalysts.

Impact of war on HIV-related healthcare services and health workers in eastern Ukraine: a qualitative study

The 2022 Russian invasion of Ukraine has caused serious challenges for healthcare workers (HCWs) and HIV-related healthcare services. This study assessed the effects of the invasion on HCWs wellbeing and on continuity of HIV services, using in-depth interviews with HCWs from facilities offering HIV antiretroviral therapy (ART) and pre-exposure prophylaxis (PrEP) services in the Donetsk region of Eastern Ukraine. A directed content analysis, with both inductive and deductive approaches, was conducted. Ten HCWs (6 [60%] doctors, 4 [40%] nurses; 9 [90%] female) were interviewed. Six respondents were displaced from their homes and worksites, and all described stress and threats to emotional wellbeing. HCWs used online consultations, encrypted mobile communication, and multi-month dispensing to support continuity of ART and PrEP services. They noted immediate needs for psychological and financial support, and access to laptop computers and mobile communications to ensure continuity of HIV services. Priorities for restoration of services include repair of health facilities, restoration of laboratory services and supply chains, and return of personnel and patients. HCWs made innovative, rapid adaptations to HIV services to keep ART and PrEP services running, demonstrating the resolve of Ukrainian HCWs to maintain continuity of HIV services despite the disruptions of war.

Platinum-group-metal quaternary alloys with lattice defects for enhanced oxygen electrocatalysis

We propose a facile coreduction method to synthesize a platinum-group-metal quaternary alloy anchored on nitrogen-doped hollow carbon spheres (PtPdRuIr/HCS) by using [MClx]y--1-butyl-3-methylimidazole (M = Pt, Pd, Ru, and Ir) ionic liquid. Owing to the steric hindrance of the imidazolium cations, Pt-group metal atoms of different sizes can be deposited at approximately the same pace for the growth of an alloy with lattice defects. The lattice-distorted PtPdRuIr/HCS exhibits enhanced activity toward oxygen electroreduction when benchmarked against Pt counterparts.

Zeta Potential and Size Analysis of Zeolitic Imidazolate Framework-8 Nanocrystals Prepared by Surfactant-Assisted Synthesis

The crystal nucleation and growth mechanism of monodispersed metal-organic framework nanoparticles were studied using time-resolved light dynamic, electrokinetic, and powder X-ray diffraction methods. We confirmed that zeolitic imidazolate framework-8 (ZIF-8) nanocrystals follow a nonclassical crystal growth pathway, where a fast nucleation occurs with dense liquid clusters or nanocrystals forming spontaneously when two precursors are mixed. We also explored the zeta potential and solvodynamic size changes of ZIF-8 prepared by a surfactant-assisted synthesis. Three modulators, including 1-methylimidazole (1-mIm), tris(hydroxymethyl)aminomethane (THAM), and (1-hexadecyl)trimethylammonium bromide (CTAB), were studied. We found that 1-mIm dramatically increases the rate of nucleation of ZIF-8. With an increasing amount of 1-mIm, which functions as a coordination modulator, the size increases, and the zeta potential of ZIF-8 decreases. Whereas THAM, as both a coordination and a deprotonation modulator, increases the size and zeta potential of ZIF-8 simultaneously, CTAB, as a long alkyl cationic surfactant, mainly adsorbs on the surface of ZIF-8, and the zeta potential of the formed ZIF-8 is controlled by the amount of CTAB in solution compared with its critical micelle concentration. Overall, we reveal that the modulator type and concentration can be used to control the size and zeta potential of the dispersed ZIF-8 nanocrystals in a colloid system. The experiments also enable identification of the nucleation and crystal growth processes of ZIF-8. The findings will be applicable to other nanocrystals in colloid systems, which are used for heterogeneous catalysis and guest molecular loadings.

Single Condensation Droplet Self-Ejection from Divergent Structures with Uniform Wettability

Coalescence-induced condensation droplet jumping has been extensively studied for anti-icing, condensation heat transfer, water harvesting, and self-cleaning. Another phenomenon that is gaining attention for potential enhancements is the self-ejection of individual droplets. However, the mechanism underlying this process remains elusive due to cases in which the abrupt detachment of an interface establishes an initial Laplace pressure difference. In this study, we investigate the self-ejection of individual droplets from uniformly hydrophobic microstructures with divergent geometries. We design, fabricate, and test arrays of truncated, nanostructured, and hydrophobic microcones arranged in a square pattern. High-speed microscopy reveals the dynamics of a single condensation droplet between four cones: after cycles of growth and stopped self-propulsion, the suspended droplet self-ejects without abrupt detachments. Through analytical modeling of the droplet in a conical pore as an approximation, we describe the slow isopressure growth phases and the rapid transients driven by surface energy release once a dynamic configuration is reached. Microcones with uniform wettability, in addition to being easier to fabricate, have the potential to enable the self-ejection of all nucleated droplets with a designed size, promising significant improvements in the aforementioned applications and others.

Controlling the Collision Type and Frequency of Single Pt Nanoparticles at Chemically Modified Gold Electrodes

Studying the electrochemical response of single nanoparticles at an electrode surface gives insight into the dynamic and stochastic processes that occur at the electrode interface. Herein, we investigated single platinum nanoparticle collision dynamics and type (elastic vs inelastic) at gold electrode surfaces modified with self-assembled monolayers (SAMs) of varying terminal chemistries. Collision events are measured via the faradaic current from catalytic reactions at the Pt surface. By changing the terminal, solution-facing group of a thiolate monolayer, we observed the effect of hydrophobicity at the solution-electrode interface on single-particle collisions by employing either a hydrophobic -CH3 terminal group (1-hexanethiol), a hydrophilic -OH terminal group (6-mercaptohexanol), or an equimolar mixture of the two. Changes in the terminal group lead to alterations in collision-induced current magnitude, collisional frequency, and the distinct shape of the collision event current transient. The effects of the terminal group of the SAM were probed by measuring quantitative differences in the events monitored through both the hydrogen evolution reaction (HER) and hydrazine oxidation. In both cases, a platinum nanoparticle (PtNP) favors adsorption to bare and hydrophilic surfaces but demonstrates elastic collision behavior when it collides with a hydrophobic surface. In the case of a mixed monolayer, distinct characteristics of hydrophobic and hydrophilic surfaces are observed. We report how single nanoparticle collisions can reveal nanoscale surface heterogeneity and can be used to manipulate the nature of single-particle interactions on an electrode surface by functionalized self-assembled monolayers.

USP3 promotes osteosarcoma progression via deubiquitinating EPHA2 and activating the PI3K/AKT signaling pathway

Ubiquitin-specific protease 3 (USP3) plays an important role in the progression of various tumors. However, the role of USP3 in osteosarcoma (OS) remains poorly understood. The aim of this study was to explore the biological function of USP3 in OS and the underlying molecular mechanism. We found that OS had higher USP3 expression compared with that of normal bone tissue, and high expression of USP3 was associated with poor prognosis in patients with OS. Overexpression of USP3 significantly increased OS cell proliferation, migration, and invasion. Mechanistically, USP3 led to the activation of the PI3K/AKT signaling pathway in OS by binding to EPHA2 and then reducing its protein degradation. Notably, the truncation mutant USP3-F2 (159-520) interacted with EPHA2, and amino acid 203 was found to play an important role in this process. And knockdown of EPHA2 expression reversed the pro-tumour effects of USP3-upregulating. Thus, our study indicates the USP3/EPHA2 axis may be a novel potential target for OS treatment.

Prognosis and chemotherapy drug sensitivity in liver hepatocellular carcinoma through a disulfidptosis-related lncRNA signature

Disulfidptosis, a new type of regulated cell death associated with the actin cytoskeleton, provides a new therapeutic tool for cancers. The direct relationship between disulfidptosis-related lncRNAs(DRLs) in liver hepatocellular carcinoma(HCC) remains unclear. We acquired transcriptomic data, corresponding clinical data, and tumor mutation data of HCC from the TCGA database. First of all, DRLs were determined through correlation analysis. Then, a prognostic model containing six DRLs was created by adopting univariate Cox regression, LASSO algorithm and multivariate Cox regression analysis. Based on the model, 424 HCC patients were divided into high- and low-risk groups. Next, we structured ROC curves and PCA through combining the model and clinical data. Enrichment analysis and immune infiltration analysis were adopted to further explore the relationship between the model and prognosis. In addition, we explored the relationship between the model and tumor mutation burden (TMB). There were significant differences between high- and low- risk groups, and patients in the high-risk group showed poor prognosis. Enrichment analysis suggested that metabolic progress was obviously different between the two groups. According to the analysis of immune infiltration, there were several differences in immune cells, function, and checkpoints. Patients with high-risk and high TMB demonstrated the least favorable prognosis. The two risk groups both manifested visiblly in chemotherapy drug sensitivity. To sum up, we set up a DRL-based signature and that may provide a predictable value for the prognosis and use of chemotherapy drugs for HCC patients.

Unveiling the anticancer effects of SGLT-2i: mechanisms and therapeutic potential

Cancer and diabetes are significant diseases that pose a threat to human health. Their interconnection is complex, particularly when they coexist, often necessitating multiple therapeutic approaches to attain remission. Sodium-glucose cotransporter protein two inhibitors (SGLT-2i) emerged as a treatment for hyperglycemia, but subsequently exhibited noteworthy extra-glycemic properties, such as being registered for the treatment of heart failure and chronic kidney disease, especially with co-existing albuminuria, prompting its assessment as a potential treatment for various non-metabolic diseases. Considering its overall tolerability and established use in diabetes management, SGLT-2i may be a promising candidate for cancer therapy and as a supplementary component to conventional treatments. This narrative review aimed to examine the potential roles and mechanisms of SGLT-2i in the management of diverse types of cancer. Future investigations should focus on elucidating the antitumor efficacy of individual SGLT-2i in different cancer types and exploring the underlying mechanisms. Additionally, clinical trials to evaluate the safety and feasibility of incorporating SGLT-2i into the treatment regimen of specific cancer patients and determining appropriate dosage combinations with established antitumor agents would be of significant interest.

Computational Characterization of Membrane Proteins as Anticancer Targets: Current Challenges and Opportunities

Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets.

The effects of visual skills training on cognitive and executive functions in stroke patients: a systematic review with meta-analysis

The visual system and associated skills are of particular importance in stroke rehabilitation. The process of neuroplasticity involved in restoring cognitive function during this period is mainly based on anatomical and physiological mechanisms. However, there is little evidence-based knowledge about the effects of visual skills training that could be used to improve therapeutic outcomes in cognitive rehabilitation. A computerized systematic literature search was conducted in the PubMed, Medline, and Web of Science databases from 1 January 1960 to 11 Febuary 2024. 1,787 articles were identified, of which 24 articles were used for the calculation of weighted standardized mean differences (SMD) after screening and eligibility verification. The findings revealed moderate effects for global cognitive function (SMD = 0.62) and activities of daily living (SMD = 0.55) as well as small effects for executive function (SMD = 0.20) - all in favor of the intervention group. The analyses indicate that the results may not be entirely robust, and should therefore be treated with caution when applied in practice. Visual skills training shows positive effects in improving cognitive and executive functions, especially in combination with high cognitive load and in an early phase of rehabilitation. An improvement in activities of daily living can also be observed with this type of intervention. The high heterogeneity of the studies and different treatment conditions require the identification of a relationship between certain visual skills and executive functions in future research.

A system for fluid pumping by liquid metal multi-droplets

The transportation and control of microfluidics have an important influence on the fields of biology, chemistry, and medicine. Pump systems based on the electrocapillary effect and room-temperature liquid metal droplets have attracted extensive attention. Flow rate is an important parameter that reflects the delivery performance of the pump systems. In the systems of previous studies, cylindrical structures are mostly used to constrain the droplet. The analysis and quantitative description of the influence of voltage frequency, alternating voltage, direct current voltage bias, and solution concentration on the flow rate are not yet comprehensive. Furthermore, the systems are driven by only one droplet, which limits the increase in flow rate. Therefore, a pump with a cuboid structure is designed and the droplet is bound by pillars, and the flow rate of the pump is increased by more than 200% compared with the cylindrical pump. For this structure, the mechanism of various factors on the flow rate is analyzed. To further enhance the flow rate, a pump system with multi-droplets is proposed. Moreover, the expression of flow velocity of the solution on the surface of each droplet and the relationship between the flow rate, alternating voltage, and the number of droplets are deduced. Finally, the potential of applying the multi-droplet cuboid pump system in drug delivery and analytical chemistry is demonstrated. Additionally, the core of the pump, the droplet area, is modularized, which breaks the overall structural limitations of the liquid metal pump and provides ideas for pump design.

Poverty and birth cohort effects of experiencing the 2007-2009 Great Recession during adolescence on major depressive episodes and mental health treatment of young adults in the United States

PURPOSE

Household economic adversity during adolescence is hypothesized to be a risk factor for poor mental health later in life. To test this hypothesis, we conducted a quasi-experimental analysis of an economic shock, the Great Recession of 2007-2009. We tested if going through adolescence during the Great Recession was associated with increased risk of major depressive episodes (MDE) and mental health treatment in young adulthood with potential moderation by household poverty to explore differences by economic adversity.

METHODS

We analyzed data on young adults age 18-29 years from the 2005-2019 National Survey on Drug Use and Health (N = 145,394). We compared participants who were adolescents during the recession to those followed-up prior to the recession. Regression analysis tested effect modification by household poverty status.

RESULTS

Adolescent exposure to the Great Recession was associated with higher likelihood of MDE during young adulthood (aOR = 1.30, 95% CI = 1.23, 1.37); there was no relationship with mental health treatment. Effects on MDE were stronger among those in households with higher incomes compared to those living in poverty.

CONCLUSION

Findings support the hypothesis that exposure to the Great Recession during adolescence may have increased risk for MDE, but raise questions about whether the mechanism of this association is economic distress.

Target isolation of diverse sesquiterpenoid from the stems of Daphne genkwa based on molecular networking

Guiding by LC-MS/MS analysis and the Global Natural Products Social (GNPS) Molecular Networking, three undescribed sesquiterpenoids, stedapgens A-C, and two known analogues were discovered in the barks of Daphne genkwa Sieb. et Zucc. The structures were determined by analysis of their spectroscopic data and quantum-chemical calculations. All the isolated novel compounds were tested for their acetylcholinesterase inhibitory activities with IC50 = 0.754 ± 0.059, 0.696 ± 0.026, and 0.337 ± 0.023 μg/ml. Among them, stedapgen A displayed promising inhibitory activities against AChE, and the binding sites were predicted by molecular docking.

2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons

Neural circuits are characterized by genetically and functionally diverse cell types. A mechanistic understanding of circuit function is predicated on linking the genetic and physiological properties of individual neurons. However, it remains highly challenging to map the functional properties of transcriptionally heterogeneous neuronal subtypes in mammalian cortical circuits in vivo. Here, we introduce a high-throughput two-photon nuclear phototagging (2P-NucTag) approach optimized for on-demand and indelible labeling of single neurons via a photoactivatable red fluorescent protein following in vivo functional characterization in behaving mice. We demonstrate the utility of this function-forward pipeline by selectively labeling and transcriptionally profiling previously inaccessible 'place' and 'silent' cells in the mouse hippocampus. Our results reveal unexpected differences in gene expression between these hippocampal pyramidal neurons with distinct spatial coding properties. Thus, 2P-NucTag opens a new way to uncover the molecular principles that govern the functional organization of neural circuits.

Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection

Poly(ADP-ribosyl)ation (PARylation), catalyzed mainly by poly(ADP-ribose) polymerase (PARP)1, is a key posttranslational modification involved in DNA replication and repair. Here, we report that TIMELESS (TIM), an essential scaffold of the replisome, is PARylated, which is linked to its proteolysis. TIM PARylation requires recognition of auto-modified PARP1 via two poly(ADP-ribose)-binding motifs, which primes TIM for proteasome-dependent degradation. Cells expressing the PARylation-refractory TIM mutant or under PARP inhibition accumulate TIM at DNA replication forks, causing replication stress and hyper-resection of stalled forks. Mechanistically, aberrant engagement of TIM with the replicative helicase impedes RAD51 loading and protection of reversed forks. Accordingly, defective TIM degradation hypersensitizes BRCA2-deficient cells to replication damage. Our study defines TIM as a substrate of PARP1 and elucidates how the control of replisome remodeling by PARylation is linked to stalled fork protection. Therefore, we propose a mechanism of PARP inhibition that impinges on the DNA replication fork instability caused by defective TIM turnover.

Mental Bandwidth is Associated with HIV and Viral Suppression Among Low-Income Women in Philadelphia

Behavioral economics research suggests poverty may influence behavior by reducing mental bandwidth, increasing future discounting, and increasing risk aversion. It is plausible that these decision-making processes are further impaired in the context of HIV or pregnancy. In this cross-sectional study of 86 low-income women in Philadelphia, multivariable models showed that HIV was associated with decreased mental bandwidth (one of two measures) and lower risk aversion. Pregnancy was not associated with any decision-making factors. Viral suppression was associated with greater mental bandwidth (one of two measures), and antenatal care engagement with lower future discounting. Anti-poverty interventions may be particularly beneficial to improve health behaviors in the context of HIV.

HemU and TonB1 contribute to hemin acquisition in Stenotrophomonas maltophilia

Introduction

The hemin acquisition system is composed of an outer membrane TonB-dependent transporter that internalizes hemin into the periplasm, periplasmic hemin-binding proteins to shuttle hemin, an inner membrane transporter that transports hemin into the cytoplasm, and cytoplasmic heme oxygenase to release iron. Fur and HemP are two known regulators involved in the regulation of hemin acquisition. The hemin acquisition system of Stenotrophomonas maltophilia is poorly understood, with the exception of HemA as a TonB-dependent transporter for hemin uptake.

Methods

Putative candidates responsible for hemin acquisition were selected via a homolog search and a whole-genome survey of S. maltophilia. Operon verification was performed by reverse transcription-polymerase chain reaction. The involvement of candidate genes in hemin acquisition was assessed using an in-frame deletion mutant construct and iron utilization assays. The transcript levels of candidate genes were determined using quantitative polymerase chain reaction.

Results

Smlt3896-hemU-exbB2-exbD2-tonB2 and tonB1-exbB1-exbD1a-exbD1b operons were selected as candidates for hemin acquisition. Compared with the parental strain, hemU and tonB1 mutants displayed a defect in their ability to use hemin as the sole iron source for growth. However, hemin utilization by the Smlt3896 and tonB2 mutants was comparable to that of the parental strain. HemA expression was repressed by Fur in iron-replete conditions and derepressed in iron-depleted conditions. HemP negatively regulated hemA expression. Like hemA, hemU was repressed by Fur in iron-replete conditions; however, hemU was moderately derepressed in response to iron-depleted stress and fully derepressed when hemin was present. Unlike hemA and hemU, the TonB1-exbB1-exbD1a-exbD1b operon was constitutively expressed, regardless of the iron level or the presence of hemin, and Fur and HemP had no influence on its expression.

Conclusion

HemA, HemU, and TonB1 contribute to hemin acquisition in S. maltophilia. Fur represses the expression of hemA and hemU in iron-replete conditions. HemA expression is regulated by low iron levels, and HemP acts as a negative regulator of this regulatory circuit. HemU expression is regulated by low iron and hemin levels in a hemP-dependent manner.

Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses

Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) genes encode a subfamily of receptor-like kinases (RLK) that regulate diverse processes during plant growth, development, and stress responses. The first CrRLK1L was identified from the Catharanthus roseus, commonly known as Madagascar periwinkle. Subsequently, CrRLK1L gene families have been characterized in many plants. The genome of T. aestivum encodes 15 CrRLK1L genes with 43 paralogous copies, with three homeologs each, except for -2-D and -7-A, which are absent. Chromosomal localization analysis revealed a markedly uneven distribution of CrRLK1L genes across seven different chromosomes, with chromosome 4 housing the highest number of genes, while chromosome 6 lacked any CrRLK1L genes. Tissue-specific gene expression analysis revealed distinct expression patterns among the gene family members, with certain members exhibiting increased expression in reproductive tissues. Gene expression analysis in response to various abiotic and biotic stress conditions unveiled differential regulation of gene family members. Cold stress induces CrRLK1Ls -4-B and -15-A while downregulating -3-A and -7B. Drought stress upregulates -9D, contrasting with the downregulation of -7D. CrRLK1L-15-B and -15-D were highly induced in response to 1 hr of heat, and combined drought and heat stress, whereas -10-B is downregulated. Similarly, in response to NaCl stress, only CrRLK1L1 homeologs were induced. Fusarium graminearum and Claviceps purpurea inoculation induces homeologs of CrRLK1L-6 and -7. The analysis of cis-acting elements in the promoter regions identified elements crucial for plant growth and developmental processes. This comprehensive genome-wide analysis and expression study provides valuable insights into the essential functions of CrRLK1L members in wheat.

Therapeutic potential of tyrosine-protein kinase MET in osteosarcoma

Osteosarcoma, the most prevalent primary bone tumor in children and young adults, can often be successfully treated with standard chemotherapy and surgery when diagnosed at an early stage. However, patients presenting with metastases face significant challenges in achieving a cure. Despite advancements in classical therapies over the past few decades, clinical outcomes for osteosarcoma have not substantially improved. Recently, there has been increased understanding of the biology of osteosarcoma, leading to the identification of new therapeutic targets. One such target is MET, a tyrosine kinase receptor for Hepatocyte Growth Factor (HGF) encoded by the MET gene. In vitro and in vivo studies have demonstrated that the HGF/MET pathway plays a crucial role in cancer growth, invasion, metastasis, and drug resistance across various cancers. Clinical trials targeting this pathway are already underway for lung cancer and hepatocellular carcinoma. Moreover, MET has also been implicated in promoting osteosarcoma progression. This review summarizes 3 decades' worth of research on MET's involvement in osteosarcoma and further explores its potential as a therapeutic target for patients with this disease.

DNA minicircles capable of forming a variety of non-canonical structural motifs

Although more than 10% of the human genome has the potential to fold into non-B DNA, the formation of non-canonical structural motifs as part of long dsDNA chains are usually considered as unfavorable from a thermodynamic point of view. However, recent experiments have confirmed that non-canonical motifs do exist and are non-randomly distributed in genomic DNA. This distribution is highly dependent not only on the DNA sequence but also on various other factors such as environmental conditions, DNA topology and the expression of specific cellular factors in different cell types. In this study, we describe a new strategy used in the preparation of DNA minicircles containing different non-canonical motifs which arise as a result of imperfect base pairing between complementary strands. The approach exploits the fact that imperfections in the pairing of complementary strands thermodynamically weaken the dsDNA structure at the expense of enhancing the formation of non-canonical motifs. In this study, a completely different concept of stable integration of a non-canonical motif into dsDNA is presented. Our approach allows the integration of various types of non-canonical motifs into the dsDNA structure such as hairpin, cruciform, G-quadruplex and i-motif forms but also combinations of these forms. Small DNA minicircles have recently become the subject of considerable interest in both fundamental research and in terms of their potential therapeutic applications.

Using rare genetic mutations to revisit structural brain asymmetry

Asymmetry between the left and right hemisphere is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variants, which typically exert small effects on brain-related phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We designed a pattern-learning approach to dissect the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior data fusion highlights the consequences of genetically controlled brain lateralization on uniquely human cognitive capacities.

Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers

The loss of E-cadherin (E-cad), an epithelial cell adhesion molecule, has been implicated in the epithelial-mesenchymal transition (EMT), promoting invasion and migration of cancer cells and, consequently, metastasis. However, recent studies have demonstrated that E-cad supports the survival and proliferation of metastatic cancer cells, suggesting that our understanding of E-cad in metastasis is far from comprehensive. Here, we report that E-cad upregulates the de novo serine synthesis pathway (SSP) in breast cancer cells. The SSP provides metabolic precursors for biosynthesis and resistance to oxidative stress, critically beneficial for E-cad-positive breast cancer cells to achieve faster tumor growth and more metastases. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, significantly and specifically hampered the proliferation of E-cad-positive breast cancer cells and rendered them vulnerable to oxidative stress, inhibiting their metastatic potential. Our findings reveal that E-cad adhesion molecule significantly reprograms cellular metabolism, promoting tumor growth and metastasis of breast cancers.

ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis

Gastrointestinal disease caused by Salmonella enterica is associated with the pathogen's ability to replicate within epithelial cells and macrophages. Upon host cell entry, the bacteria express a type-three secretion system encoded within Salmonella pathogenicity island 2, through which host-manipulating effector proteins are secreted to establish a stable intracellular niche. Transcription of this intracellular virulence program is activated by the PhoPQ two-component system that senses the low pH and the reduced magnesium concentration of host cell vacuoles. In addition to transcriptional control, Salmonella commonly employ RNA-binding proteins (RBPs) and small regulatory RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. ProQ is a globally acting RBP in Salmonella that promotes expression of the intracellular virulence program, but its RNA repertoire has previously been characterized only under standard laboratory growth conditions. Here, we provide a high-resolution ProQ interactome during conditions mimicking the environment of the Salmonella-containing vacuole (SCV), revealing hundreds of previously unknown ProQ binding sites in sRNAs and mRNA 3'UTRs. ProQ positively affected both the levels and the stability of many sRNA ligands, some of which were previously shown to associate with the well-studied and infection-relevant RBP Hfq. We further show that ProQ activates the expression of PhoP at the post-transcriptional level, which, in turn, leads to upregulation of the intracellular virulence program.

IMPORTANCE

Salmonella enterica is a major pathogen responsible for foodborne gastroenteritis, and a leading model organism for genetic and molecular studies of bacterial virulence mechanisms. One key trait of this pathogen is the ability to survive within infected host cells. During infection, the bacteria employ a type three secretion system that deliver effector proteins to target and manipulate host cell processes. The transcriptional regulation of this virulence program is well understood. By contrast, the factors and mechanisms operating at the post-transcriptional level to control virulence gene expression are less clear. In this study, we have charted the global RNA ligand repertoire of the RNA-binding protein ProQ during in vitro conditions mimicking the host cell environment. This identified hundreds of binding sites and revealed ProQ-dependent stabilization of intracellular-specific small RNAs. Importantly, we show that ProQ post-transcriptionally activates the expression of PhoP, a master transcriptional activator of intracellular virulence in Salmonella.

Neural correlates of model-based behavior in internet gaming disorder and alcohol use disorder

Background

An imbalance between model-based and model-free decision-making systems is a common feature in addictive disorders. However, little is known about whether similar decision-making deficits appear in internet gaming disorder (IGD). This study compared neurocognitive features associated with model-based and model-free systems in IGD and alcohol use disorder (AUD).

Method

Participants diagnosed with IGD (n = 22) and AUD (n = 22), and healthy controls (n = 30) performed the two-stage task inside the functional magnetic resonance imaging (fMRI) scanner. We used computational modeling and hierarchical Bayesian analysis to provide a mechanistic account of their choice behavior. Then, we performed a model-based fMRI analysis and functional connectivity analysis to identify neural correlates of the decision-making processes in each group.

Results

The computational modeling results showed similar levels of model-based behavior in the IGD and AUD groups. However, we observed distinct neural correlates of the model-based reward prediction error (RPE) between the two groups. The IGD group exhibited insula-specific activation associated with model-based RPE, while the AUD group showed prefrontal activation, particularly in the orbitofrontal cortex and superior frontal gyrus. Furthermore, individuals with IGD demonstrated hyper-connectivity between the insula and brain regions in the salience network in the context of model-based RPE.

Discussion and Conclusions

The findings suggest potential differences in the neurobiological mechanisms underlying model-based behavior in IGD and AUD, albeit shared cognitive features observed in computational modeling analysis. As the first neuroimaging study to compare IGD and AUD in terms of the model-based system, this study provides novel insights into distinct decision-making processes in IGD.

Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance

Elevated cancer metabolism releases lactic acid and CO2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are based explicitly on disrupting acid handling, signaling, or adaptations, possibly because the distinction between acid-sensitive and acid-resistant phenotypes is not clear. Here, we report pH-related phenotypes of sixty-eight colorectal cancer (CRC) cell lines by measuring i) extracellular acidification as a readout of acid production by fermentative metabolism and ii) growth of cell biomass over a range of extracellular pH (pHe) levels as a measure of the acid sensitivity of proliferation. Based on these measurements, CRC cell lines were grouped along two dimensions as "acid-sensitive"/"acid-resistant" versus "low metabolic acid production"/"high metabolic acid production." Strikingly, acid resistance was associated with the expression of CEACAM6 and CEACAM5 genes coding for two related cell-adhesion molecules, and among pH-regulating genes, of CA12. CEACAM5/6 protein levels were strongly induced by acidity, with a further induction under hypoxia in a subset of CRC lines. Lack of CEACAM6 (but not of CEACAM5) reduced cell growth and their ability to differentiate. Finally, CEACAM6 levels were strongly increased in human colorectal cancers from stage II and III patients, compared to matched samples from adjacent normal tissues. Thus, CEACAM6 is a marker of acid-resistant clones in colorectal cancer and a potential motif for targeting therapies to acidic regions within the tumors.

Abundant resources can trigger reduced consumption: Unveiling the paradox of excessive scrounging

In ecological contexts, it is conventionally expected that increased food availability would boost consumption, particularly when animals prioritize maximizing their food intake. This paper challenges this conventional wisdom by conducting an in-depth game-theoretic analysis of a basic foraging model, in which animals must choose between intensive food searching as producers or moderate searching while relying on group members as scroungers. Our study reveals that, under certain circumstances, increasing food availability can amplify the inclination to scrounge to such an extent that it leads to a reduction in animals' food consumption compared to scenarios with limited food availability. We further illustrate a similar phenomenon in a model capturing free-riding dynamics among workers in a company. We demonstrate that, under certain reward mechanisms, enhancing workers' production capacities can inadvertently trigger a surge in free-riding behavior, leading to both diminished group productivity and reduced individual payoffs. Our findings provide intriguing insights into the complex relationships between individual and group performances, as well as the intricate mechanisms underlying the emergence of free-riding behavior in competitive environments.