Search Results (69)

Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism. Full article

Background/Objectives: Understanding beef cattle farmers’ knowledge, attitudes, and practices on infectious disease prevention, antimicrobial use, and antimicrobial resistance (AMR) is important to developing stewardship programs. Methods: A cross-sectional stratified mail or phone survey of beef cattle producers in Illinois was conducted between June and August 2022. Ordinal logistic regression models assessed the impact of having a biosecurity plan on beef cattle farmers’ familiarity with cattle diseases. Logistic regression models evaluated associations between antimicrobial treatment practices and the type of cattle operations. Results: A total of 514 producers responded to all or some of the questions. Only 45% of producers were familiar with AMR, and 11% were concerned about cattle infections with antibiotic-resistant bacteria. Producers agreed or strongly agreed (64%) that inappropriate AMU contributes to the development of AMR. Most producers (70%) thought that antimicrobials were as effective in treating infectious diseases as 5 years ago. Only 50% of farms were visited by a veterinarian in the previous year and 35% had their biosecurity evaluated. Producers were more familiar with infectious diseases if their farm biosecurity was assessed. Treating respiratory infections was the most common reason for antimicrobial use. Compared to cow–calf farmers, whole-cycle farmers had a higher probability of having their farm’s biosecurity evaluated (OR = 1.66) and having a veterinarian visit in the previous year (OR = 2.16). Whole-cycle (OR = 3.92) and stocker/backgrounder (OR = 2.18) farmers had a higher probability of treating their cattle with antibiotics than cow–calf farmers. Conclusions: Antimicrobial stewardship and farm biosecurity programs are needed to raise awareness of disease prevention, AMU, and AMR among Illinois beef cattle producers. Full article

Carl Woese’s thesis of cellular evolution emphasized that the last universal common/cellular ancestor (LUCA) must have evolved by drawing from “global inventions”. Yet, existing theories regarding the origin(s) of LUCA have mostly centered upon scenarios that LUCA had evolved mostly independently. In an earlier paper, we advanced a new theory regarding the origin(s) of LUCA that extends Woese’s original insights. Our theory centers upon the possibility that different vesicles and protocells can merge with and acquire each other as a form of variation, selection, and retention, driven by wet-and-dry cycles and other similar cyclical processes. In this paper, we use computer simulation to show that under a variety of simulated conditions, LUCA can indeed be produced by our proposed processes. We hope that our study can stimulate laboratory testing of some key hypotheses that vesicles’ absorption, acquisition, and merger has indeed been a central force in driving the evolution of LUCA. Full article

Idiopathic pulmonary fibrosis (IPF) is a progressive, often fatal lung disease characterized by tissue scarring and declining lung function. The MUC5B promoter polymorphism rs35705950, a significant genetic predisposition for IPF, paradoxically associates with better survival and slower disease progression than other IPF genotypes. This study investigates the potential paradoxical protective effects of this MUC5B variant in lung fibrosis. For this purpose, we developed a transgenic mouse model overexpressing the human MUC5B rs35705950 variant in the proximal large airways. Lung fibrosis was induced through subcutaneous injection of bleomycin. Results demonstrated significantly reduced lung fibrosis severity in transgenic mice compared to wild-type mice, assessed by trichrome staining, Ashcroft scoring, and hydroxyproline levels. Additionally, transgenic mice showed significantly lower levels of inflammatory cells and cytokines (TNFα, IL-6, IFNγ) and growth factors (PDGF, CTGF, IL-13) in the bronchoalveolar lavage fluid and lung tissues. There was also a significant decrease in mRNA expressions of fibrosis-related markers (periostin, fibronectin, Col1a1). In summary, this study reveals that mucin overexpression related to the MUC5B rs35705950 variant in the large airways significantly attenuates lung fibrosis and inflammatory responses in transgenic mice. These findings suggest that the rs35705950 variant modulates inflammatory and fibrotic responses in the proximal airways, which may contribute to the slower disease progression observed in IPF patients carrying this variant. Our study offers a possible explanation for the paradoxical beneficial effects of the MUC5B variant despite its role as a significant predisposing factor for IPF. Full article

The careful arrangement of nanomaterials (NMs) holds promise for revolutionizing various fields, from electronics and biosensing to medicine and optics. This review delves into the intricacies of nano-assembly (NA) techniques, focusing on oriented-assembly methodologies and stimuli-dependent approaches. The introduction provides a comprehensive overview of the significance and potential applications of NA, setting the stage for review. The oriented-assembly section elucidates methodologies for the precise alignment and organization of NMs, crucial for achieving desired functionalities. The subsequent section delves into stimuli-dependent techniques, categorizing them into chemical and physical stimuli-based approaches. Chemical stimuli-based self-assembly methods, including solvent, acid–base, biomolecule, metal ion, and gas-induced assembly, are discussed in detail by presenting examples. Additionally, physical stimuli such as light, magnetic fields, electric fields, and temperature are examined for their role in driving self-assembly processes. Looking ahead, the review outlines futuristic scopes and perspectives in NA, highlighting emerging trends and potential breakthroughs. Finally, concluding remarks summarize key findings and underscore the significance of NA in shaping future technologies. This comprehensive review serves as a valuable resource for researchers and practitioners, offering insights into the diverse methodologies and potential applications of NA in interdisciplinary research fields. Full article

Open fractures and prosthetic joints are prone to bacterial infections, especially those involving biofilms, and are worsened by antibiotic inefficacy and resistance. This highlights the need for targeted treatments against orthopedic infections. LL-37, a human cathelicidin, is known for its antimicrobial properties. This study aimed to synthesize and evaluate LL-37-derived antimicrobial peptides (AMPs) for antibacterial efficacy and toxicity. Several truncated LL-37 analogues were created and tested against 18 bacterial strains, both ATCC and orthopedic clinical isolates, using MIC and MBC assays. Synergy with antibiotics and resistance development were also analyzed, alongside cytotoxicity on NIH-3T3 fibroblasts and hemolytic activity assessments. Six AMPs were synthesized, with FK-16 and GF-17 emerging as the most effective. The MIC values ranged from 4.69 to 18.75 µg/mL and 2.34 to 18.75 µg/mL, respectively, against S. epidermidis and S. aureus, with the MBC values matching the MIC values. Cytotoxicity tests showed no toxicity at concentrations below 75 µg/mL for GF-17 and 150 µg/mL for FK-16. Hemolytic activity was below 1% at 18.75 µg/mL for GF-17 and 75 µg/mL for FK-16. These AMPs showed no synergistic effects with antibiotics and no resistance development. FK-16 and GF-17 effectively removed biofilms, particularly against S. epidermidis. Incorporating these AMPs into surgical materials (hydrogels, cements, etc.) could enhance infection control in orthopedic procedures, warranting further in vivo studies. Full article

Light detection and ranging (lidar) scanning tools are available that can make rapid digital estimations of biomass. Voxelization and convex hull are two algorithms used to calculate the volume of the scanned plant canopy, which is correlated with biomass, often the primary trait of interest. Voxelization splits the scans into regular-sized cubes, or voxels, whereas the convex hull algorithm creates a polygon mesh around the outermost points of the point cloud and calculates the volume within that mesh. In this study, digital estimates of biomass were correlated against hand-harvested biomass for field-grown corn, broom corn, and energy sorghum. Voxelization (r = 0.92) and convex hull (r = 0.95) both correlated well with plant dry biomass. Lidar data were also collected in a large breeding trial with nearly 900 genotypes of energy sorghum. In contrast to the manual harvest studies, digital biomass estimations correlated poorly with yield collected from a forage harvester for both voxel count (r = 0.32) and convex hull volume (r = 0.39). However, further analysis showed that the coefficient of variation (CV, a measure of variability) for harvester-based estimates of biomass was greater than the CV of the voxel and convex-hull-based biomass estimates, indicating that poor correlation was due to harvester imprecision, not digital estimations. Overall, results indicate that the lidar-based digital biomass estimates presented here are comparable or more precise than current approaches. Full article

The potential effects of poly- and perfluoroalkyl substances (PFAS) are a recently emergent human and environmental health concern. There is a consistent link between PFAS exposure and cancer, but the mechanisms are poorly understood. Although epidemiological evidence supporting PFAS exposure and cancer in general is conflicting, there is relatively strong evidence linking PFAS and testicular germ cell tumors (TGCTs). However, no mechanistic studies have been performed to date concerning PFAS and TGCTs. In this report, the effects of the legacy PFAS perfluorooctanesulfonic acid (PFOS) and the newer “clean energy” PFAS lithium bis(trifluoromethylsulfonyl)imide (LiTFSi, called HQ-115), on the tumorigenicity of TGCTs in mice, TGCT cell survival, and metabolite production, as well as gene regulation were investigated. In vitro, the proliferation and survival of both chemo-sensitive and -resistant TGCT cells were minimally affected by a wide range of PFOS and HQ-115 concentrations. However, both chemicals promoted the growth of TGCT cells in mouse xenografts at doses consistent with human exposure but induced minimal acute toxicity, as assessed by total body, kidney, and testis weight. PFOS, but not HQ-115, increased liver weight. Transcriptomic alterations of PFOS-exposed normal mouse testes were dominated by cancer-related pathways and gene expression alterations associated with the H3K27me3 polycomb pathway and DNA methylation, epigenetic pathways that were previously showed to be critical for the survival of TGCT cells after cisplatin-based chemotherapy. Similar patterns of PFOS-mediated gene expression occurred in PFOS-exposed cells in vitro. Metabolomic studies revealed that PFOS also altered metabolites associated with steroid biosynthesis and fatty acid metabolism in TGCT cells, consistent with the proposed ability of PFAS to mimic fatty acid-based ligands controlling lipid metabolism and the proposed role of PFAS as endocrine disrupters. Our data, is the first cell and animal based study on PFAS in TGCTs, support a pro-tumorigenic effect of PFAS on TGCT biology and suggests epigenetic, metabolic, and endocrine disruption as potential mechanisms of action that are consistent with the non-mutagenic nature of the PFAS class. Full article

Point-of-care (POC) diagnostic platforms are globally employed in modern smart technologies to detect events or changes in the analyte concentration and provide qualitative and quantitative information in biosensing. Surface plasmon-coupled emission (SPCE) technology has emerged as an effective POC diagnostic tool for developing robust biosensing frameworks. The simplicity, robustness and relevance of the technology has attracted researchers in physical, chemical and biological milieu on account of its unique attributes such as high specificity, sensitivity, low background noise, highly polarized, sharply directional, excellent spectral resolution capabilities. In the past decade, numerous nano-fabrication methods have been developed for augmenting the performance of the conventional SPCE technology. Among them the utility of plasmonic gold nanoparticles (AuNPs) has enabled the demonstration of plethora of reliable biosensing platforms. Here, we review the nano-engineering and biosensing applications of AuNPs based on the shape, hollow morphology, metal–dielectric, nano-assembly and heterometallic nanohybrids under optical as well as biosensing competencies. The current review emphasizes the recent past and evaluates the latest advancements in the field to comprehend the futuristic scope and perspectives of exploiting Au nano-antennas for plasmonic hotspot generation in SPCE technology. Full article

Lung and breast cancers rank as two of the most common and lethal tumors, accounting for a substantial number of cancer-related deaths worldwide. While the past two decades have witnessed promising progress in tumor therapy, developing targeted tumor therapies continues to pose a significant challenge. NAD(P)H quinone oxidoreductase 1 (NQO1), a two-electron reductase, has been reported as a promising therapeutic target across various solid tumors. β-Lapachone (β-Lap) and deoxynyboquinone (DNQ) are two NQO1 bioactivatable drugs that have demonstrated potent antitumor effects. However, their curative efficacy has been constrained by adverse effects and moderate lethality. To enhance the curative potential of NQO1 bioactivatable drugs, we developed a novel DNQ derivative termed isopentyl-deoxynyboquinone (IP-DNQ). Our study revealed that IP-DNQ treatment significantly increased reactive oxygen species generation, leading to double-strand break (DSB) formation, PARP1 hyperactivation, and catastrophic energy loss. Notably, we discovered that this novel drug induced both apoptosis and programmed necrosis events, which makes it entirely distinct from other NQO1 bioactivatable drugs. Furthermore, IP-DNQ monotherapy demonstrated significant antitumor efficacy and extended mice survival in A549 orthotopic xenograft models. Lastly, we identified that in mice IP-DNQ levels were significantly elevated in the plasma and tumor compared with IB-DNQ levels. This study provides novel preclinical evidence supporting IP-DNQ efficacy in NQO1⁺ NSCLC and breast cancer cells. Full article

Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices. Full article

Microglia are found pathologically at all stages of multiple sclerosis (MS) lesion development and are hypothesized to contribute to both inflammatory injury and neuroprotection in the MS brain. Transient receptor potential vanilloid 4 (TRPV4) channels are widely expressed, play an important role as environmental sensors, and are involved in calcium homeostasis for a variety of cells. TRPV4 modulates myeloid cell phagocytosis in the periphery and microglial motility in the central nervous system. We hypothesized that TRPV4 deletion would alter microglia phagocytosis in vitro and lessen disease activity and demyelination in experimental autoimmune encephalitis (EAE) and cuprizone-induced demyelination. We found that genetic deletion of TRPV4 led to increased microglial phagocytosis in vitro but did not alter the degree of demyelination or remyelination in the cuprizone mouse model of MS. We also found no difference in disease in EAE following global or microglia-specific deletion of Trpv4. Additionally, lesioned and normal appearing white matter from MS brains exhibited similar TRPV4 expression compared to healthy brain tissue. Taken together, these findings indicate that TRPV4 modulates microglial activity but does not impact disease activity in mouse models of MS, suggesting a muted and/or redundant role in MS pathogenesis. Full article

Influenza A virus (IAV) populations harbor large subpopulations of defective-interfering particles characterized by internally deleted viral genomes. These internally deleted genomes have demonstrated the ability to suppress infectivity and boost innate immunity, rendering them promising for therapeutic and immunogenic applications. In this study, we aimed to investigate the diversity and complexity of the internally deleted IAV genomes within a panel of plaque-purified avian influenza viruses selected for their enhanced interferon-inducing phenotypes. Our findings unveiled that the abundance and diversity of internally deleted viral genomes were contingent upon the viral subculture and plaque purification processes. We observed a heightened occurrence of internally deleted genomes with distinct junctions in viral clones exhibiting enhanced interferon-inducing phenotypes, accompanied by additional truncation in the nonstructural 1 protein linker region (NS1Δ76-86). Computational analyses suggest the internally deleted IAV genomes can encode a broad range of carboxy-terminally truncated and intrinsically disordered proteins with variable lengths and amino acid composition. Further research is imperative to unravel the underlying mechanisms driving the increased diversity of internal deletions within the genomes of viral clones exhibiting enhanced interferon-inducing capacities and to explore their potential for modulating cellular processes and immunity. Full article

Agrivoltaic systems, which combine the cultivation of crops with solar panel installations, offer a novel solution to the dual challenges of energy production and agricultural productivity. This research verifies the impact of agrivoltaic (APV) conditions on the growth and quality of garlic and kimchi cabbage over two consecutive years in Naju-si, Jeollanam Province, Republic of Korea. In the 2019–2020 cultivation season, both kimchi cabbage and garlic grown under APV conditions experienced weight reductions of 18% and 15%, respectively, when compared to those grown in conventional settings. Intriguingly, despite the altered light conditions of APV leading to microenvironmental changes (mainly 41% light reduction), the quality of these crops, particularly in terms of their sulfur compound concentrations, remained consistent. This suggests that there was no discernible difference in the sensory quality of APV-grown kimchi cabbage and garlic compared to their traditionally grown counterparts. These findings highlight the potential of APV systems in promoting sustainable agriculture by balancing both crop yield and quality. Based on these results, the study suggests three innovative cultivation techniques to enhance crop growth in APV environments. Full article

Trichomoniasis, caused by Trichomonas vaginalis (TV), is the most common non-viral sexually transmitted infection (STI) worldwide, affecting over 174 million people annually and is frequently associated with reproductive co-morbidities. However, its detection can be time-consuming, subjective, and expensive for large cohort studies. This case–control study, conducted at the Mount Sinai Adolescent Health Center in New York City, involved 36 women with prevalent TV infections and 36 controls. The objective was to examine Internal Transcribed Spacer region-1 (ITS1) amplicon-derived communities for the detection of prevalent TV infections with the same precision as clinical microscopy and the independent amplification of the TV-specific TVK3/7 gene. DNA was isolated from clinician-collected cervicovaginal samples and amplified using ITS1 primers in a research laboratory. Results were compared to microscopic wet-mount TV detection of concurrently collected cervicovaginal samples and confirmed against TV-specific TVK3/7 gene PCR. The area under the receiver operating characteristics curve (AUC) for diagnosing TV using ITS1 communities was 0.92. ITS1 amplicons displayed an intra-class correlation coefficient (ICC) of 0.96 (95% CI: 0.93–0.98) compared to TVK3/7 PCR fragment testing. TV cases showed an increased risk of bacterial vaginosis (BV) compared to the TV-negative controls (OR = 8.67, 95% CI: 2.24–48.54, p-value = 0.0011), with no significant differences regarding genital yeast or chlamydia infections. This study presents a bioinformatics approach to ITS1 amplicon next-generation sequencing that is capable of detecting prevalent TV infections. This approach enables high-throughput testing for TV in stored DNA from large-scale epidemiological studies. Full article