The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes such as carotenoids, respiratory quinones and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for the saturation of the isoprene chains of phospholipids have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.

Cellular membranes are essential for compartmentalization, maintenance of membrane permeability and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically dialkyl glycerol diethers (DGDs) and glycerol dialkyl glycerol tetraethers (GDGTs). Terbinafine has been proposed as an inhibitor of GDGT biosynthesis in Archaea based on radiolabel incorporation studies. Here, we have studied the early cellular responses of the archaeon Sulfolobus acidocaldarius to terbinafine whose membrane is mostly composed of the membrane-spanning GDGTs. Depletion of GDGTs and an accompanying accumulation of DGDs upon treatment with terbinafine was growth phase and dose dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, resulting in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine primarily targets the respiratory complex along with genes involved in motility, fatty acid metabolism and GDGT cyclization. Combined, these findings suggest that respiratory stress is the preliminary response of S.acidocaldarius to terbinafine while targeting multiple proteins involved in isoprenoid biosynthesis and saturation.

Cancer cells exhibit aberrant extracellular matrix mechanosensing due to altered expression of mechanosensory cytoskeletal proteins. Aberrant mechanosensing of the tumor microenvironment (TME) by cancer cells has been shown to be associated with cancer development and progression. Recent studies show that altered mechanosensing changes the mechanobiological properties of cells, and, in turn, cells become susceptible to mechanical perturbations. Due to an increasing understanding of cell biomechanics and cellular machinery, several approaches have emerged to target the mechanobiological properties of cancer cells and cancer-associated cells to inhibit cancer growth and progression. In this review, we summarize the progress that happened in the development of mechano-based approaches to target cancer by interfering with the cellular mechanosensing machinery and overall TME.

Ketogenic diet (KD) is getting in the focus as auxiliary cancer therapy, since it provides sufficient energy supply for healthy cells, while impairing energy production in tumor cells underlying the Warburg effect. Thereby, it can assist in inhibiting tumor growth and simultaneously counteract cachexia, which is frequently observed in cancer patients under chemotherapy. In order to provide molecular evidence for the proposed synergistic inhibition of tumor growth, we applied untargeted quantitative metabolome analysis on a breast cancer xenograft mouse model. Healthy mice and such bearing breast cancer xenografts and receiving chemotherapy were compared after treatment with control diet and KD. Metabolomic profiling was performed on plasma samples, applying high-performance liquid chromatography coupled to tandem mass spectrometry. Statistical analysis revealed metabolic fingerprints comprising numerous significantly regulated features in the group of mice bearing breast cancer. This fingerprint disappeared after treatment with KD, resulting in recovery to the metabolic status observed in healthy mice receiving control diet. Moreover, amino acid metabolism as well as fatty acid transport were found to be affected by both, the tumor and the applied KD. Our results provide clear evidence of a significant molecular effect of KD in the context of tumor growth inhibition.

The immobilisation of bacteria on biochar has shown potential for enhanced remediation of petroleum hydrocarbon-contaminated soil. However, there is a lack of knowledge on the effect of bacterial immobilisation on biosolids-derived biochar for the remediation of diesel-contaminated soil. The aim of this current study was to assess the impact of the immobilisation on biosolids-derived biochar of an autochthonous hydrocarbonoclastic bacteria, Ochrobacterium sp. (BIB) on the remediation of diesel-contaminated soil using a laboratory based mesocosm study. Additionally, the effect of fertiliser application on the efficacy of the BIB treatment was investigated. Biochar (BC) application alone led to significantly higher hydrocarbon removal compared to the control treatment at all sampling times (4,887 – 11,589 mg/kg higher). When Ochrobacterium sp. was immobilised on biochar (BIB), the hydrocarbon removal was higher than BC by 5,533 mg/kg and 1,607 mg/kg at weeks 10 and 22, respectively. However, when BIB was co-applied with fertiliser (BIBF), the hydrocarbon removal was lower than BIB by 6,987 – 11,767 mg/kg. Quantitative PCR analysis revealed that the gene related to Ochrobacterium sp. was higher in BIB than in the BC treatment, which likely contributed to higher hydrocarbon removal in the BIB treatment. The findings of this study demonstrate that bacteria immobilisation on biosolids-derived biochar is a promising technique for the remediation of diesel-contaminated soil. Future studies should focus on optimising the immobilisation process for enhanced hydrocarbon removal.

The study examines malnutrition's triple burden, including anaemia, overweight, and stunting, among children aged 6-59 months. Using data from the National Family Health Survey-5 (2019-21), the study identifies risk factors and assesses the contribution at different levels to existing malnutrition burden. A random intercept multilevel logistic regression model and spatial analysis are employed to identify child, maternal, and household level risk factors for stunting, overweight, and anaemia. The study finds that 34% of children were stunted, 4% overweight, and 66% anaemic. Stunting and anaemia prevalence were higher in central and eastern regions, while overweight was more prevalent in the north-eastern and northern regions. At macro-level, the coexistence of stunting, overweight, and anaemia circumstantiates the triple burden of childhood malnutrition with substantial spatial variation (Moran’s I: stunting-0.53, overweight-0.41 and anaemia-0.53). Multilevel analysis reveals that child, maternal, and household variables play a substantial role in determining malnutrition burden in India. The nutritional health is significantly influenced by a wide range of determinants, necessitating multilevel treatments targeting households to address this diverse group of coexisting factors. Given the intra-country spatial heterogeneity, the treatment also needs to be tailor-made for various disaggregated levels.

Oxidative stress is an elevated intracellular level of free oxygen radicals that cause lipid peroxidation, protein denaturation, DNA hydroxylation, and apoptosis, ultimately negotiating cells viability. Antioxidants can scavenge such free radicals, thus reducing the oxidative stress and eventually prevent cellular damage. Medicinal plants, fruits, and spices remain the prioritized sources of antioxidants and antimicrobial properties since the time immemorial, but in contrast to plants, microorganisms can be grown at a faster rate under controlled conditions. They are non-toxic, non-carcinogenic, and biodegradable as compared to synthetic antioxidants. Microorganisms including actinomycetes, archaea, bacteria, protozoa, yeast, and fungi are auspicious source of vital bioactive compounds. The list comprises ample of bioactive components from microorganisms. One of them is bacteriocins, which are ribosomally synthesized antimicrobial peptides product of Eurotium sp., Streptomyces parvulus, S. thermophiles, Lactococcus lactis, etc. It has a great potential as next-generation antibiotics targeting the multiple-drug resistant pathogens. Pneumocandins are antifungal lipohexapeptides derived from the fungus Glarea lozoyensis, and inhibit 1,3-β-glucan synthase of the fungal cell wall and act as a precursor for the synthesis of caspofungin. It is widely used against invasive fungal infections and has been recently approved by the FDA. Taxol (paclitaxel), a chemotherapeutic drug derived from the bark of Taxus brevifolia can also be produced by endophytic fungi Taxomyces andreanae and Nodulisporium sylviforme. It is known to inhibit several fungi such as Pythium, Aphanomyces and Phytophthora. Hispidin and its derivate isolated from P. hispidus, reduce inducible nitric oxide synthase (iNOS) expression, obstruct the transcriptional activity of NF-κB, and also decrease the production of reactive oxygen species (ROS) in macrophages. Astaxanthin, known as an “aquatic” carotenoid produced by H. pluvialis, also has excellent ROS quenching activity. This study mainly focuses on fascinating antioxidant and antimicrobial compounds that have been scarcely investigated in microorganisms and discuss the promise and challenges of microorganisms as providers of health benefits.

Microorganisms including actinomycetes, archaea, bacteria, fungi, yeast, and micro algae are the auspicious source of vital bioactive compounds. In this review, the existing state of the art re-garding antimicrobial molecules from microorganisms has been summarized. The potential an-timicrobial compounds from actinomycetes, particularly Streptomyces sp.; archaea; fungi including endophytic and marine-derived fungi, mushroom; yeast, and microalgae were briefly described. Furthermore, this review briefly summarized the activity and mode of action of bacteriocins, a ribosomally synthesized antimicrobial peptides product of Eurotium sp., Streptomyces parvulus, S. thermophiles, Lactococcus lactis, etc. Bacteriocins have inherent properties such as targeting multi-ple-drug resistant pathogens, which allows them to be considered next-generation antibiotics. Similarly, Glarea lozoyensis derived antifungal lipohexpeptides i.e., pneumocandins, inhibits 1,3-β-glucan synthase of the fungal cell wall and acts as a precursor for the synthesis of caspo-fungin, is also elaborated. In conclusion, this review highlights the possibility of using microor-ganisms as an antimicrobial resource for biotechnological, nutraceutical, and pharmaceutical ap-plications. However, more investigations are still required to separate, purify, and characterize these bioactive compounds and transfer these primary drugs into clinically approved antibiotics.

Enteroaggregative Escherichia coli (EAEC) are highly heterogeneous in virulence; we wanted to understand the pathogenic potential of EAEC isolated various clinical and non-clinical sources in an animal model. We infected male BALB/c mice in six mice/group with 50 EAEC isolates, isolated from clinical and non-clinical sources. We studied colonization, weight loss, stool shedding, inflammatory markers and its relationship with 21 virulence genes and phylogroups, EAEC organ burden and histopathological changes. We detected significantly more inflammatory changes and fecal lactoferrin and calprotectin levels in mice infected with EAEC isolated from symptomatic cases. In clinical EAEC isolates, the presence of chromosomal genes {(aap (46%), aaiC (23.3%), and SPATEs (pet (13.3%), sat (20%), sigA and pic (6.6%)}, adhesive variants {(agg4A (53.3%), aggA (53.3%), aafA (36.6%), agg3A (40%)} of EAEC, and master regulator gene aggR (66.6%) were associated with higher levels of lactoferrin and calprotectin. Also, 70% (9/13) of EAEC isolated from acute diarrheal cases bearing chuA (70%) in our study were assigned to group B2 (4 isolates) and D (5 isolates). Real-time PCR analysis revealed that colonization by EAEC strains from different clinical and non-clinical sources occurs up to 10-15 days of life. Even from non-diarrhoeal stools and non-clinical sources, had the potential to cause prolonged colonization, weight loss, and inflammation in the intestine though the degree varied. Moreover, better understanding of EAEC pathogenic pathways is desperately needed in different clinical scenarios.

Biosynthetic gene clusters are specific genomic regions in microorganisms, like bacteria and fungi, responsible for producing bioactive compounds. Identifying these clusters is complex due to their diverse nature. This research presents a comprehensive approach to effective BGC identification. The study focuses on five classes of Natural Products: PKS , NRPS, RiPP, Terpenes, and Hybrid PKS-NRPS. Data was gathered from the MiBIG database in GBK format. Protein sequences from each file were extracted, and sequences under the same BGC ID were combined. Physicochemical properties were calculated, and sequence embeddings were generated using NLP techniques like CountVec, TFIDF, and Word2Vec specific to each NP class. An integrated feature matrix was created by merging physicochemical properties and generated embeddings. This matrix was used for training and testing of nine ML models such SVM, RF and many more. The study explored data balancing techniques with and without SMOTE and employed Grid Search for parameter optimization. This led to six datasets and 54 models. The LR model, using TFIDF with SMOTE, emerged as the most effective, achieving an accuracy of 0.96, AUC of 0.9912, and other strong metrics. This method enhances BGC identification for drug development, offering a broader understanding of their applications in medicine and biotechnology.

Background: Increase of collagen I (COL I)/COL III ratio enhances vessel wall stiffness and renders vessels less resistant to blood flow and pressure changes. We hypothesized that COL I/COL III ratio is increased in the brain arteriovenous malformations (bAVMs), which is associated with bAVM hemorrhage. Method: Surgically resected human bAVM samples and mouse bAVMs induced in three transgenic mouse lines with activin receptor-like kinase 1 or endoglin deletion in the endothelial cells or in the brain focally. Colony-stimulating factor receptor inhibitor was used to transiently deplete microglia. COL I and COL III levels, hemorrhage, and gene expression in bAVMs were analyzed. Results: The COL I and COL III levels and the COL I/COL III ratio were higher on human and mouse bAVMs than controls, which was associated with bAVM hemorrhage. Col I and Col III mRNAs were also increased in mouse bAVMs. The degree of microhemorrhage in mouse bAVMs was positively correlated with Col I/Col III ratios. Transient depletion of microglia reduced Col I/Col III ratio and microhemorrhage in mouse bAVMs. Conclusion: COL I/COL III ratio are increased in bAVM vessels, which is associated with bAVM hemorrhage. Depletion of microglia reduces Col I/Col III ratio and hemorrhage in mice bAVMs.

Hereditary Hemorrhagic Telangiectasia (HHT), also known as Osler-Weber-Rendu syndrome, is a rare and inherited vascular disorder, characterized by the development of arteriovenous malformations (AVMs) in various organs and telangiectasia (small AVM) in the mucocutaneous. The majority of HHT patients have haploinsufficiency of genes involved in the transforming growth factor-beta (TGFβ) signaling pathway, including endoglin (ENG), activin receptor-like kinase 1 (ALK1, also known as ACVRL1), or SMAD4. Active angiogenesis is also required for telangiectasia and AVM development. Anti-angiogenic strategies have been tested in patients and animal models extensively. However, the exact mechanisms for telangiectasia and AVM development remain unclear. In this review, we discuss recent advances in identifying disease mechanisms, and potential therapeutic targets.

Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Optical genome mapping (OGM) is an emerging technology that enables genome-wide detection of all classes of SVs at a high resolution and sensitivity. Identification of cryptic SVs leading to gene disruption or predicted novel gene fusions could be important drivers for cancer development and/or portend a prognostic relevance, which could be used to modify the treatment plan. A cohort of 106 consented cases that had a successful OGM analysis performed were included in the study. Demographic, clinical, laboratory and treatment data were collected. Routine diagnostic and prognostic testing were done on the peripheral blood and bone marrow aspirate as indicated. Additional samples of peripheral blood and/or bone marrow were sent for OGM testing. OGM led to a change in risk stratification in 17/66 (25.75%) of patients with hematological malignancies, the majority of these patients (15/66, 22.72%), having their risk stratification upgraded with a resulting change in treatment of 14 patients. This study highlights the ability of OGM to detect rare, cryptic and clinically relevant variants that potentially impact disease diagnosis, risk stratification and actionable treatment targets.

Abstract: Endoglin (ENG) is a causative gene of type 1 hereditary hemorrhagic telangiectasia (HHT1). HHT1 patients have arteriovenous malformations (AVMs) in multiple organs, including the brain. In mice, Eng deletion induced by R26RCreER or SM22aCre leads to AVM development in the brain and other organs. We have reported that the severity of brain AVM in mice with activin receptor-like kinase 1 (Alk1, an HHT2 causative gene) mutation is correlated with the number of Alk1 negative endothelial cells (ECs). We hypothesized that increase of Eng negative ECs will enhance AVM severity. To increase EC Eng deletion, we used a codon improved cre (icre), which is more potent in recombination of floxed alleles than the wild type (WT) cre. R26RCreER;Eng^f/f mice that have Rosa promoter driving and tamoxifen (TM) inducible WT cre expression globally and PdgfbiCreER;Eng^f/f that have Pdgfb promoter driving and TM inducible icre expression in ECs were treated with 3 intra-peritoneal injections of TM (2.5 mg/25g of body weight) to delete Eng globally or in the ECs. AAV-VEGF was stereotactically injected into the brain to induce brain focal angiogenesis and brain AVM. We found that iCre caused more Eng deletion in the brain indicated by lower level of Eng proteins (p<0.001) and fewer Eng positive ECs (p=0.01) than mice with WT cre. Mice with iCre mediated Eng deletion have more abnormal vessels (p=0.02), CD68⁺ macrophages (p=0.002), and hemorrhage (p=0.04), and less vascular pericyte and smooth muscle coverage than mice with WT cre. In addition, arteriovenous shunts were detected in the intestines of icre mice, a phenotype that have not been detected in WT cre mice before. RNAseq analysis showed that 8 out of the 10 top upregulated pathways identified by Gene Ontology (GO) analysis are related to the inflammation. Therefore, increase of Eng deletion in ECs exacerbates AVM severity, which is associated with enhanced inflammation. Strategies that can reduce Eng negative ECs could be used to develop new therapies to reduce AVM severity for HHT1 patients.