Discovery of antiphage systems in the lactococcal plasmidome.

Until the late 2000s, lactococci substantially contributed to the discovery of various plasmid-borne phage defence systems, rendering these bacteria an excellent antiphage discovery resource. Recently, there has been a resurgence of interest in identifying novel antiphage systems in lactic acid bacteria owing to recent reports of so-called 'defence islands' in diverse bacterial genera. Here, 321 plasmid sequences from 53 lactococcal strains were scrutinized for the presence of antiphage systems. Systematic evaluation of 198 candidates facilitated the discovery of seven not previously described antiphage systems, as well as five systems, of which homologues had been described in other bacteria. All described systems confer resistance against the most prevalent lactococcal phages, and act post phage DNA injection, while all except one behave like abortive infection systems. Structure and domain predictions provided insights into their mechanism of action and allow grouping of several genetically distinct systems. Although rare within our plasmid collection, homologues of the seven novel systems appear to be widespread among bacteria. This study highlights plasmids as a rich repository of as yet undiscovered antiphage systems.

Topic Clusters of Successful Aging Studies: Results of a Topic Modeling Approach.

BACKGROUND AND OBJECTIVES: Literature regarding successful aging reflects a wide variety of fields and perspectives. Given the range of definitions and approaches found in published literature, it is important to investigate clusters of topics studied over time. This study aimed to show the change of topic clusters within successful aging studies. RESEARCH DESIGN AND METHODS: The study used topic modeling methodology to analyze vast amounts of abstract data. Among publications collected from Scopus (4,458) and Web of Science (5,187), 5,610 publications were analyzed. Topic clusters were analyzed in two ways: by a) division of time (1960s - 1990s, 2000s, 2010s, 2020s) and b) all years combined. RESULTS: In the 1960s - 1990s, 11 topic clusters ranging from health to emotional well-being emerged without any dominant domain. In the 2000s, two clusters related to social support and health appeared as major clusters. In the 2010s, one topic cluster that included words related to health and social participation was the biggest. In the 2020s, emotional health and social participation appeared again as one of the major clusters and health-related topics started to diverge into subgroups like physical health and mental health. In all years of publications combined, the major cluster involved words that are related to either health or social domains. DISCUSSION AND IMPLICATIONS: Results revealed that successful aging has been studied in many fields using multidimensional perspectives. The dominant categories were health and social domains. These findings suggest interprofessional practice, an interdisciplinary approach in research, and multi-sector involvement in policy.

Embedding Biomimetic Vascular Networks via Coaxial Sacrificial Writing into Functional Tissue.

Printing human tissues and organs replete with biomimetic vascular networks is of growing interest. While it is possible to embed perfusable channels within acellular and densely cellular matrices, they do not currently possess the biomimetic architectures found in native vessels. Here, coaxial sacrificial writing into functional tissues (co-SWIFT) is developed, an embedded bioprinting method capable of generating hierarchically branching, multilayered vascular networks within both granular hydrogel and densely cellular matrices. Coaxial printheads are designed with an extended core-shell configuration to facilitate robust core-core and shell-shell interconnections between printed branching vessels during embedded bioprinting. Using optimized core-shell ink combinations, biomimetic vessels composed of a smooth muscle cell-laden shell that surrounds perfusable lumens are coaxially printed into granular matrices composed of: 1) transparent alginate microparticles, 2) sacrificial microparticle-laden collagen, or 3) cardiac spheroids derived from human induced pluripotent stem cells. Biomimetic blood vessels that exhibit good barrier function are produced by seeding these interconnected lumens with a confluent layer of endothelial cells. Importantly, it is found that co-SWIFT cardiac tissues mature under perfusion, beat synchronously, and exhibit a cardio-effective drug response in vitro. This advance opens new avenues for the scalable biomanufacturing of vascularized organ-specific tissues for drug testing, disease modeling, and therapeutic use.

Functional and practical insights into three lactococcal antiphage systems.

The persistent challenge of phages in dairy fermentations requires the development of starter cultures with enhanced phage resistance. Recently, three plasmid-encoded lactococcal antiphage systems, named Rhea, Aristaios, and Kamadhenu, were discovered. These systems were found to confer high levels of resistance against various Skunavirus members. In the present study, their effectiveness against phage infection was confirmed in milk-based medium, thus validating their potential to ensure reliable dairy fermentations. We furthermore demonstrated that Rhea and Kamadhenu do not directly hinder phage genome replication, transcription, or associated translation. Conversely, Aristaios was found to interfere with phage transcription. Two of the antiphage systems are encoded on pMRC01-like conjugative plasmids, and the Kamadhenu-encoding plasmid was successfully transferred by conjugation to three lactococcal strains, each of which acquired substantially enhanced phage resistance against Skunavirus members. Such advances in our knowledge of the lactococcal phage resistome and the possibility of mobilizing these protective functions to bolster phage protection in sensitive strains provide practical solutions to the ongoing phage problem in industrial food fermentations.IMPORTANCEIn the current study, we characterized and evaluated the mechanistic diversity of three recently described, plasmid-encoded lactococcal antiphage systems. These systems were found to confer high resistance against many members of the most prevalent and problematic lactococcal phage genus, rendering them of particular interest to the dairy industry, where persistent phage challenge requires the development of starter cultures with enhanced phage resistance characteristics. Our acquired knowledge highlights that enhanced understanding of lactococcal phage resistance systems and their encoding plasmids can provide rational and effective solutions to the enduring issue of phage infections in dairy fermentation facilities.

Promoting safety of underground machinery operators through participatory ergonomics and fuzzy model analysis to foster sustainable mining practices.

One of the most vital parameters to achieve sustainability in any field is encompassing the Occupational Health and Safety (OHS) of the workers. In mining industry where heavy earth moving machineries are largely employed, ergonomic hazards turn out to be significant OHS hazards causing Musculoskeletal Disorders (MSDs) in the operators. Nevertheless, the Indian mining industry lacks a comprehensive technique of OHS risk assessment, especially for ergonomic hazards that cause MSDs. This research appraises ergonomic hazards and develops Fuzzy Musculoskeletal-disorders Index (FMI) model to evaluate ergonomic-related MSDs. Work process and work tool ergonomic risk factors were identified through literature review and directives recommended by experts. Work posture was evaluated using RULA. The data-collecting approach was implemented using participatory ergonomic and design science principles. The FMI results show average MSDs score of 3.69, indicating high to extremely high risk. Surface plots show that combined work tool and work process was the most sensitive factors to MSDs risk compared to other two combinations. A two-sample t-test validated the FMI. The findings should help safety experts and managers develop effective OHS management plans and programmes for the sustainability of Indian mining industry.

Machine learning-assisted high-throughput screening for Anti-MRSA compounds.

BACKGROUND: Antimicrobial resistance is a major public health threat, and new agents are needed. Computational approaches have been proposed to reduce the cost and time needed for compound screening. AIMS: A machine learning (ML) model was developed for the in silico screening of low molecular weight molecules. METHODS: We used the results of a high-throughput Caenorhabditis elegans methicillin-resistant Staphylococcus aureus (MRSA) liquid infection assay to develop ML models for compound prioritization and quality control. RESULTS: The compound prioritization model achieved an AUC of 0.795 with a sensitivity of 81% and a specificity of 70%. When applied to a validation set of 22,768 compounds, the model identified 81% of the active compounds identified by high-throughput screening (HTS) among only 30.6% of the total 22,768 compounds, resulting in a 2.67-fold increase in hit rate. When we retrained the model on all the compounds of the HTS dataset, it further identified 45 discordant molecules classified as non-hits by the HTS, with 42/45 (93%) having known antimicrobial activity. CONCLUSION: Our ML approach can be used to increase HTS efficiency by reducing the number of compounds that need to be physically screened and identifying potential missed hits, making HTS more accessible and reducing barriers to entry.

Genome-Wide Analysis of the SRPP/REF Gene Family in Taraxacum kok-saghyz Provides Insights into Its Expression Patterns in Response to Ethylene and Methyl Jasmonate Treatments.

Taraxacum kok-saghyz (TKS) is a model plant and a potential rubber-producing crop for the study of natural rubber (NR) biosynthesis. The precise analysis of the NR biosynthesis mechanism is an important theoretical basis for improving rubber yield. The small rubber particle protein (SRPP) and rubber elongation factor (REF) are located in the membrane of rubber particles and play crucial roles in rubber biosynthesis. However, the specific functions of the SRPP/REF gene family in the rubber biosynthesis mechanism have not been fully resolved. In this study, we performed a genome-wide identification of the 10 TkSRPP and 2 TkREF genes' family members of Russian dandelion and a comprehensive investigation on the evolution of the ethylene/methyl jasmonate-induced expression of the SRPP/REF gene family in TKS. Based on phylogenetic analysis, 12 TkSRPP/REFs proteins were divided into five subclades. Our study revealed one functional domain and 10 motifs in these proteins. The SRPP/REF protein sequences all contain typical REF structural domains and belong to the same superfamily. Members of this family are most closely related to the orthologous species T. mongolicum and share the same distribution pattern of SRPP/REF genes in T. mongolicum and L. sativa, both of which belong to the family Asteraceae. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the TkSRPP/REFs gene family. The expression levels of most TkSRPP/REF members were significantly increased in different tissues of T. kok-saghyz after induction with ethylene and methyl jasmonate. These results will provide a theoretical basis for the selection of candidate genes for the molecular breeding of T. kok-saghyz and the precise resolution of the mechanism of natural rubber production.

Smooth muscle expression of RNA editing enzyme ADAR1 controls vascular integrity and progression of atherosclerosis.

Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 ( IFIH1 ) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background, and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.

Correction: Convergent synthesis of thiodiazole dioxides from simple ketones and amines through an unusual nitrogen-migration mechanism.

[This corrects the article DOI: 10.1039/D3SC04478E.].

Evaluating Molecular Mechanism of Viral Inhibition of Aerosolized Smart Nano-Enabled Antiviral Therapeutic (SNAT) on SARS-CoV-2-Infected Hamsters.

Smart Nano-enabled Antiviral Therapeutic (SNAT) is a promising nanodrug that previously demonstrated efficacy in preclinical studies to alleviate SARS-CoV-2 pathology in hamsters. SNAT comprises taxoid (Tx)-decorated amino (NH2)-functionalized near-atomic size positively charged silver nanoparticles (Tx-[NH2-AgNPs]). Herein, we aimed to elucidate the molecular mechanism of the viral inhibition and safety of aerosolized SNAT treatment in SARS-CoV-2-infected golden Syrian hamsters. High-resolution transmission electron microscopy (HR-TEM) coupled with energy dispersive spectroscopy (EDS) and ELISAs showed SNAT binds directly to the SARS-CoV-2 virus by interacting with intact spike (S) protein, specifically to S2 subunit. SNAT (≥1 µg/mL) treatment significantly lowered SARS-CoV-2 infections of Calu-3 cells. Extraction-free whole transcriptome assay was used to detect changes in circulatory micronome in hamsters treated intranasally with SNAT (two doses of 10 µg/mL of 2 mL each administered 24 h apart). Uninfected hamsters treated with SNAT had altered circulatory concentrations of 18 microRNAs (8 miRNAs upregulated, 10 downregulated) on day 3 post-treatment compared to uninfected controls. SNAT-induced downregulation of miR-141-3p and miR-200b-3p may reduce viral replication and inflammation by targeting Ythdf2 and Slit2, respectively. Further, SNAT treatment significantly lowered IL-6 expression in infected hamster lungs compared to untreated infected hamsters. Taken together, we demonstrate that SNAT binds directly to SARS-CoV-2 via the S protein to prevent viral entry and propose a model by which SNAT alters the cellular miRNA-directed milieu to promote antiviral cellular processes and neutralize infection. Our results provide insights into the use of low-dose intranasally delivered SNAT in treating SARS-CoV-2 infections in a hamster model.

Total Synthesis of (±)-Baphicacanthcusine A Enabled by Sequential Ring Contractions.

Reported herein is the first total synthesis of the poly-pseudoindoxyl natural product baphicacanthcusine A. The synthesis leverages the oxidative rearrangement of indoles to pseudoindoxyls to install vicinal pseudoindoxyl heterocycles in a diastereoselective manner. Key steps include an acid-mediated cyclization/indole transposition, two diastereoselective oxidative ring contractions, and a site-selective C--H oxygenation. The synthesis of the oxidation precursors was guided by recognition of an element of hidden symmetry. This work provides a foundation for the chemical synthesis of other poly-pseudoindoxyl alkaloids.

Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season.

The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion. In this investigation, we used high-throughput 16S rDNA sequencing and bioinformatics to analyze the S. purpurea phytotelm bacteriome as it changes through the growing season (May-September) in plants from the north-central region of the species' native range. Additionally, we used molecular techniques to detect and quantify bacterial nitrogenase genes (nifH) in all phytotelm samples to explore the hypothesis that diazotrophy is an additional mechanism of supplying biologically available nitrogen to S. purpurea. The results of this study indicate that while prokaryote diversity remains relatively stable in plants at different locations within our region, diversity changes significantly as the growing season progresses. Furthermore, nifH genes were detected at biologically significant concentrations in one hundred percent of samples, suggesting that nitrogen fixation may be an important contributor to the S. purpurea nutrient budget.

Low-Power Analog Integrated Architecture of the Voting Classification Algorithm for Diabetes Disease Prediction.

A low-power (∼ 600nW), fully analog integrated architecture for a voting classification algorithm is introduced. It can effectively handle multiple-input features, maintaining exceptional levels of accuracy and with very low power consumption. The proposed architecture is based on a versatile Voting algorithm that selectively incorporates one of three key classification models: Bayes or Centroid, or, the Learning Vector Quantization model; all of which are implemented using Gaussian-likelihood and Euclidean distance function circuits, as well as a current comparison circuit. To evaluate the proposed architecture, a comprehensive comparison with popular analog classifiers is performed, using real-life diabetes dataset. All model architectures were trained using Python and compared with the software-based classifiers. The circuit implementations were performed using the TSMC 90 nm CMOS process technology and the Cadence IC Suite was utilized for the design, schematic and post-layout simulations. The proposed classifiers achieved sensitivity of ≥ 96.7% and specificity of ≥ 89.7%.

Machine Learning Based Prediction of Post-operative Infrarenal Endograft Apposition for Abdominal Aortic Aneurysms.

OBJECTIVE: Challenging infrarenal aortic neck characteristics have been associated with an increased risk of type Ia endoleak after endovascular aneurysm repair (EVAR). Short apposition (< 10 mm circumferential shortest apposition length [SAL]) on the first post-operative computed tomography angiography (CTA) has been associated with type Ia endoleak. Therefore, this study aimed to develop a model to predict post-operative SAL in patients with an abdominal aortic aneurysm based on the pre-operative shape. METHODS: A statistical shape model was developed to obtain principal component scores. The dataset comprised patients treated by standard EVAR without complications (n = 93) enriched with patients with a late type Ia endoleak (n = 54). The infrarenal SAL was obtained from the first post-operative CTA and subsequently binarised (< 10 mm and ≥ 10 mm). The principal component scores that were statistically different between the SAL groups were used as input for five classification models, and evaluated by means of leave one out cross validation. Area under the receiver operating characteristic curves (AUC), accuracy, sensitivity, and specificity were determined for each classification model. RESULTS: Of the 147 patients, 24 patients had an infrarenal SAL < 10 mm and 123 patients had a SAL ≥ 10 mm. The gradient boosting model resulted in the highest AUC of 0.77. Using this model, 114 patients (77.6%) were correctly classified; sensitivity (< 10 mm apposition was correctly predicted) and specificity (≥ 10 mm apposition was correctly predicted) were 0.70 and 0.79 based on a threshold of 0.21, respectively. CONCLUSION: A model was developed to predict which patients undergoing EVAR will achieve sufficient graft apposition (≥ 10 mm) in the infrarenal aortic neck based on a statistical shape model of pre-operative CTA data. This model can help vascular specialists during the planning phase to accurately identify patients who are unlikely to achieve sufficient apposition after standard EVAR.

Tissue perfusion in DIEP flaps using Indocyanine Green Fluorescence Angiography, Hyperspectral imaging, and Thermal imaging.

Flap necrosis continues to occur in skin free flap autologous breast reconstruction. Therefore, we investigated the benefits of indocyanine green angiography (ICGA) using quantitative parameters for the objective, perioperative evaluation of flap perfusion. In addition, we investigated the feasibility of hyperspectral (HSI) and thermal imaging (TI) for postoperative flap monitoring. A single-center, prospective observational study was performed on 15 patients who underwent deep inferior epigastric perforator (DIEP) flap breast reconstruction (n=21). DIEP-flap perfusion was evaluated using ICGA, HSI, and TI using a standardized imaging protocol. The ICGA perfusion curves and derived parameters, HSI extracted oxyhemoglobin (oxyHb) and deoxyhemoglobin (deoxyHb) values, and flap temperatures from TI were analyzed and correlated to the clinical outcomes. Post-hoc quantitative analysis of intraoperatively collected data of ICGA application accurately distinguished between adequately and insufficiently perfused DIEP flaps. ICG perfusion curves identified the lack of arterial inflow (n=2) and occlusion of the venous outflow (n=1). In addition, a postoperatively detected partial flap epidermolysis could have been predicted based on intraoperative quantitative ICGA data. During postoperative monitoring, HSI was used to identify impaired perfusion areas within the DIEP flap based on deoxyHb levels. The results of this study showed a limited added value of TI. Quantitative, post-hoc analysis of ICGA data produced objective and reproducible parameters that enabled the intraoperative detection of arterial and venous congested DIEP flaps. HSI appeared to be a promising technique for postoperative flap perfusion assessment. A diagnostic accuracy study is needed to investigate ICGA and HSI parameters in real-time and demonstrate their clinical benefit.

Bacterial esterases reverse lipopolysaccharide ubiquitylation to block host immunity.

Aspects of how Burkholderia escape the host's intrinsic immune response to replicate in the cell cytosol remain enigmatic. Here, we show that Burkholderia has evolved two mechanisms to block the activity of Ring finger protein 213 (RNF213)-mediated non-canonical ubiquitylation of bacterial lipopolysaccharide (LPS), thereby preventing the initiation of antibacterial autophagy. First, Burkholderia's polysaccharide capsule blocks RNF213 association with bacteria and second, the Burkholderia deubiquitylase (DUB), TssM, directly reverses the activity of RNF213 through a previously unrecognized esterase activity. Structural analysis provides insight into the molecular basis of TssM esterase activity, allowing it to be uncoupled from its isopeptidase function. Furthermore, a putative TssM homolog also displays esterase activity and removes ubiquitin from LPS, establishing this as a virulence mechanism. Of note, we also find that additional immune-evasion mechanisms exist, revealing that overcoming this arm of the host's immune response is critical to the pathogen.

Health Care Use for Eye Pain.

Importance: National estimates regarding the frequency of presentations and patterns of care for eye pain are unknown. This information could guide research and clinical efforts to optimize outcomes. Objective: To estimate eye pain visits in the US in the outpatient and emergency department (ED) settings. Design, Setting, and Participants: This retrospective cross-sectional study of National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey data (2008-2019) analyzed a population-based sample of visits to outpatient clinics and EDs. The sample consisted of patients presenting with eye pain. Data were analyzed from September 2023 to April 2024. Main Outcomes and Measures: Weighted sample data estimated outpatient and ED eye pain presentations including patient and clinician characteristics, diagnoses (International Statistical Classification of Diseases and Related Health Problems, Tenth Revision [ICD-10]), and disposition. Results: From 2008 through 2019, 4.6 million (95% CI, 3.9 million to 5.3 million) outpatient and 1.0 million (95% CI, 0.8 million to 1.1 million) ED eye pain visits occurred annually. Patients were predominantly women (63.2% [95% CI, 59.4%-67.0%]) and older than 60 years (46.6% [95% CI, 42.4%-51.0%]) in the outpatient setting. Patients presenting to the ED were more often men (51.8% [95% CI, 48.7%-55.0%]) and aged younger than 45 years (aged <15 years: 16.4% [95% CI, 13.9%-18.8%]; 15-24 years: 19.2% [95% CI, 16.6%-21.7%]; and 25-44 years: 35.6% [95% CI, 32.7%-38.5%]). In nearly half of outpatient eye pain visits, the major problem was classified as nonacute (2.0 million [95% CI, 1.6 million to 2.3 million]). Eye pain was the primary reason for the visit (RFV) in 42.0% (95% CI, 37.8%-46.2%) of outpatient visits and 66.9% (95% CI, 62.9%-70.9%) of ED eye pain visits. It was the only RFV in 18.3% (95% CI, 15.0%-21.7%) of outpatient and 32.7% (95% CI, 29.0%-36.4%) of ED eye pain encounters. Ophthalmologists evaluated the largest number of outpatient visits (45.3% [95% CI, 38.8%-51.7%). The primary diagnosis was non-vision threatening for most outpatient (78.5% [95% CI, 56.8%-100%]) and ED (69.9% [95% CI, 62.1%-77.7%]) visits when eye pain was the primary RFV. Additional follow-up was scheduled in 89.4% (95% CI, 86.2%-92.6%) of visits. Conclusions and Relevance: More than 5 million eye pain visits occur annually; the largest percentage are outpatient with ophthalmologists. Most diagnoses were non-vision threatening in both the outpatient and ED setting and resulted in additional care. Expanding therapeutic approaches to treat the causes of eye pain may reduce the burden on the health care system and optimize outcomes.