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Asian Pacific Journal of Cancer... Jun 2024Lung cancer is the most common malignancy and among the leading cause of cancer death worldwide. Therefore, there is an important need for biomarkers that can be used in...
OBJECTIVE
Lung cancer is the most common malignancy and among the leading cause of cancer death worldwide. Therefore, there is an important need for biomarkers that can be used in the early diagnosis of the disease and in the follow-up of treatment. Circular RNAs (circRNAs) have a covalently closed circular structure that lacks 3' and 5' polar ends and is resistant to RNAase enzymes. Due to these properties, they can be stably found in body fluids. Therefore, they can serve as potential biomarkers in the diagnosis, monitoring of therapeutic response and prognosis of cancer. In our study, we aimed to investigate the expression levels of circRNA molecules in the treatment of lung cancer and to determine those that have the potential to be biomarkers.
METHODS
In this in vitro study, expression levels of 163 circRNAs were investigated in A549 cells, a non-small cell lung cancer cell line, before and after treatment with carboplatin and pemetrexed. Total RNA isolation and cDNA synthesis were performed after treatments. Expression levels of circRNA genes were determined by RT-qPCR method with the designed divergent primer sequences.
RESULTS
The study revealed the characterisation of differentially expressed circRNAs by treatment in lung cancer cells. Of them, hsa_circ_0001320 is not expressed in cancer cells, is expressed only after treatment, and increased the level of its expression in response to combination therapy.
CONCLUSION
As a result, while carboplatin, pemetrexed, and combined drug applications changed the expression levels of some circRNAs in lung cancer cells, some circRNAs were expressed only after treatment. In treatment follow-up and management, hsa_circ_0001320 has been identified as potential biomarker candidate.
Topics: Humans; RNA, Circular; Lung Neoplasms; Biomarkers, Tumor; Prognosis; Carcinoma, Non-Small-Cell Lung; Carboplatin; Pemetrexed; Gene Expression Regulation, Neoplastic; Tumor Cells, Cultured
PubMed: 38918678
DOI: 10.31557/APJCP.2024.25.6.2147 -
Poultry Science Jun 2024Goose creates important economic value depending on their enrich nutrients of meat. Our previous study investigates potential candidate genes associated with variations...
Goose creates important economic value depending on their enrich nutrients of meat. Our previous study investigates potential candidate genes associated with variations in meat quality between Xianghai Flying (XHF) Goose and Zi Goose through genomic and transcriptome integrated analysis. Screening of 5 differential expression candidate genes related to muscle development identified by the F XP-EHH and RNA-seq in breast muscle from various geese. Among them, C1QTNF1 (C1q and TNF related protein 1), a gene of unknown function in goose, which observed mutations in coding sequence regions in sequencing data. Its function was explored after overexpression and knockdown which designed depending on the genetic sequence of the goose, respectively. Results showed that over-expression of C1QTNF1 significantly enhances cell proliferation and viability. In addition, the expression levels of the fusion marker gene Myomaker and the differentiation marker gene MyoD are significantly upregulated in cells. Knock-down C1QTNF1 leads to down regulated Myomaker and MyoD which involved muscle formation. But, the expression level of muscle atrophy marker MuRF is not significantly changed among different transfection groups. Since protein structures and interactions are closely related to their functions, we further analyzed the C1QTNF1 for physicochemical properties, structural predictions, protein interactions and homology. It can be reasonably inferred that C1QTNF1 has a similar effect to collagen, which may affect muscle development. In summary, we first speculate that C1QTNF1 may play an important regulatory role in muscle growth and development and thereby contributes to the further understanding of the genetic mechanisms that underlie meat quality traits of goose.
PubMed: 38917607
DOI: 10.1016/j.psj.2024.103927 -
Microbiology Spectrum Jun 2024The discovery of antimicrobials with novel mechanisms of action is crucial to tackle the foreseen global health crisis due to antimicrobial resistance. Bacterial...
UNLABELLED
The discovery of antimicrobials with novel mechanisms of action is crucial to tackle the foreseen global health crisis due to antimicrobial resistance. Bacterial two-component signaling systems (TCSs) are attractive targets for the discovery of novel antibacterial agents. TCS-encoding genes are found in all bacterial genomes and typically consist of a sensor histidine kinase (HK) and a response regulator. Due to the conserved Bergerat fold in the ATP-binding domain of the TCS HK and the human chaperone Hsp90, there has been much interest in repurposing inhibitors of Hsp90 as antibacterial compounds. In this study, we explore the chemical space of the known Hsp90 inhibitor scaffold 3,4-diphenylpyrazole (DPP), building on previous literature to further understand their potential for HK inhibition. Six DPP analogs inhibited HK autophosphorylation and had good antimicrobial activity against Gram-positive bacteria. However, mechanistic studies showed that their antimicrobial activity was related to damage of bacterial membranes. In addition, DPP analogs were cytotoxic to human embryonic kidney cell lines and induced the cell arrest phenotype shown for other Hsp90 inhibitors. We conclude that these DPP structures can be further optimized as specific disruptors of bacterial membranes providing binding to Hsp90 and cytotoxicity are lowered. Moreover, the X-ray crystal structure of resorcinol, a substructure of the DPP derivatives, bound to the HK CheA represents a promising starting point for the fragment-based design of novel HK inhibitors.
IMPORTANCE
The discovery of novel antimicrobials is of paramount importance in tackling the imminent global health crisis of antimicrobial resistance. The discovery of novel antimicrobials with novel mechanisms of actions, e.g., targeting bacterial two-component signaling systems, is crucial to bypass existing resistance mechanisms and stimulate pharmaceutical innovations. Here, we explore the possible repurposing of compounds developed in cancer research as inhibitors of two-component systems and investigate their off-target effects such as bacterial membrane disruption and toxicity. These results highlight compounds that are promising for further development of novel bacterial membrane disruptors and two-component system inhibitors.
PubMed: 38917423
DOI: 10.1128/spectrum.00146-24 -
PloS One 2024Neutrophil proteinase 3 (PR3) is an important drug target for inflammatory lung diseases such as chronic obstructive pulmonary disease and cystic fibrosis. Drug...
Neutrophil proteinase 3 (PR3) is an important drug target for inflammatory lung diseases such as chronic obstructive pulmonary disease and cystic fibrosis. Drug discovery efforts targeting PR3 require active enzyme for in vitro characterization, such as inhibitor screening, enzymatic assays, and structural studies. Recombinant expression of active PR3 overcomes the need for enzyme supplies from human blood and in addition allows studies on the influence of mutations on enzyme activity and ligand binding. Here, we report the expression of recombinant PR3 (rPR3) using a baculovirus expression system. The purification and activation process described resulted in highly pure and active PR3. The activity of rPR3 in the presence of commercially available inhibitors was compared with human PR3 by using a fluorescence-based enzymatic assay. Purified rPR3 had comparable activity to the native human enzyme, thus being a suitable alternative for enzymatic studies in vitro. Further, we established a surface plasmon resonance-based assay to determine binding affinities and kinetics of PR3 ligands. These methods provide valuable tools for early drug discovery aiming towards treatment of lung inflammation.
Topics: Humans; Myeloblastin; Ligands; Recombinant Proteins; Animals; Sf9 Cells; Surface Plasmon Resonance; Protein Binding; Baculoviridae; Kinetics; Gene Expression; Spodoptera
PubMed: 38917138
DOI: 10.1371/journal.pone.0294827 -
PloS One 2024Understanding the genetic diversity of existing genetic resources at the DNA level is an effective approach for germplasm conservation and utilization in breeding...
Understanding the genetic diversity of existing genetic resources at the DNA level is an effective approach for germplasm conservation and utilization in breeding programs. However, the patterns of genetic diversity and population structure remain poorly characterized, making germplasm conservation and breeding efforts difficult to succeed. Thus, this study is aimed to evaluate the genetic diversity and population structure of 49 barley accessions collected from different geographic origins in Ethiopia. Twelve SSR markers were used to analyze all accessions and a total of 61 alleles were found, with a mean of 5.08 alleles per locus. The analysis pointed out the existence of moderate to high values of polymorphic information content ranging from 0.39 to 0.91 and the mean Shannon diversity index(I) was 1.25, indicating that they were highly informative markers. The highest Euclidean distance (1.32) was computed between accession 9950 and two accessions (247011 and 9949), while the lowest Euclidean distance (0.00) was estimated between accessions 243191 and 243192. The result of molecular variance analysis revealed that the highest variation was found among accessions (47) relative to within accessions (44) and among geographic origins (9). Cluster analysis grouped the 49 barley accessions into three major clusters regardless of their geographic origin which could be due to the presence of considerable gene flow (2.72). The result of the STRUCTURE analysis was consistent with neighbor-joining clustering and principal coordinate analysis. Generally, this study concluded that the variation among accessions was more important than the difference in geographical regions to develop an appropriate conservation strategy and for parental selection to use in breeding programs. This information will be helpful for barley conservation and breeding, and it may speed up the development of new competing barley varieties.
Topics: Hordeum; Ethiopia; Genetic Variation; Microsatellite Repeats; Phylogeny; Alleles; Genetic Markers; Polymorphism, Genetic; Cluster Analysis; Genetics, Population
PubMed: 38917122
DOI: 10.1371/journal.pone.0305945 -
PloS One 2024Bellamya purificata is an important medicinal value and economically farmed species in China. However, because little is known about the genetic characteristics of this...
Bellamya purificata is an important medicinal value and economically farmed species in China. However, because little is known about the genetic characteristics of this species, the utilization of high-quality germplasm resources is hindered. The study examined the genetic differentiation between, and the structure of 12 B. purificata populations in Guangxi using 7 microsatellite DNA markers. High genetic diversity occurred in each population, with mean observed heterozygosity 0.655 and a mean expected heterozygosity 0.832. Analysis of molecular variance reveals genetic diversity to be greater within (95.2%) than among populations (4.8%). Genetic differentiation between populations is weak (Fst = 0.048, P < 0.001), with mixing of genetic clusters prevalent at the level of the individual. Genetic flow exists between populations (Nm = 3.084-11.778), with Longshui and Guilin populations exchanging frequently. A Mantel test reveals a low correlation between geographic and genetic distances (r = 0.2482, P < 0.071), suggesting that dispersal between neighboring populations facilitates population exchange. No significant heterozygosity excess was observed for any population (P > 0.05), indicating a lack of recent genetic bottlenecks. The results provide important genetic information for B. purificata, and data for potential germplasm discovery and aquaculture development.
Topics: China; Genetic Variation; Microsatellite Repeats; Genetics, Population; Gene Flow; Phylogeny
PubMed: 38917086
DOI: 10.1371/journal.pone.0305197 -
Microbiology Spectrum Jun 2024Acetic acid bacteria are used in many industrial processes such as the production of vinegar, vitamin C, the antidiabetic drug miglitol, and various artificial...
Acetic acid bacteria are used in many industrial processes such as the production of vinegar, vitamin C, the antidiabetic drug miglitol, and various artificial flavorings. These industrially important reactions are primarily carried out by an arsenal of periplasmic-facing membrane-bound dehydrogenases that incompletely oxidize their substrates and shuttle electrons directly into the respiratory chain. Among these dehydrogenases, GOX in was predicted to be a pyrroloquinoline quinone-dependent dehydrogenase of unknown function. However, after multiple analysis by a number of labs, no dehydrogenase activity has been detected. Reanalysis of GOX1969 sequence and structure reveals similarities to BamB, which functions as a subunit of the β-barrel assembly machinery complex that is responsible for the assembly of β-barrel outer membrane proteins in Gram-negative bacteria. To test if the physiological function of GOX1969 is similar to BamB in , we introduced the gene into an ∆ mutant. Growth deficiencies in the ∆ mutant were restored when was expressed on the plasmid pGox1969. Furthermore, increased membrane permeability conferred by deletion was restored upon expression, which suggests a direct link between GOX1969 and a role in maintaining outer membrane stability. Together, this evidence strongly suggests that GOX1969 is functionally acting as a BamB in . As such, functional information on uncharacterized genes will provide new insights that will allow for more accurate modeling of acetic acid bacterial metabolism and further efforts to design rational strains for industrial use.IMPORTANCE is an industrially important member of the acetic acid bacteria. Experimental characterization of putative genes is necessary to identify targets for further engineering of rational acetic acid bacteria strains that can be used in the production of vitamin C, antidiabetic compounds, artificial flavorings, or novel compounds. In this study, we have identified an undefined dehydrogenase GOX1969 with no known substrate and defined structural similarities to outer membrane biogenesis protein BamB in K12. Furthermore, we demonstrate that GOX1969 is capable of complementing knockout phenotypes in K12. Taken together, these findings enhance our understanding of physiology and expand the list of potential targets for future industrial strain design.
PubMed: 38916353
DOI: 10.1128/spectrum.01060-24 -
MBio Jun 2024The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we...
The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from . Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the -cAMP-mediated allosteric transition. Moreover, the second -cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of .IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from , DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.
PubMed: 38916345
DOI: 10.1128/mbio.01144-24 -
Microbiology Spectrum Jun 2024Gut bacteria belonging to the family play a pivotal role in regulating host energy balance and metabolic homeostasis. As a commensal bacterium, has been implicated in...
UNLABELLED
Gut bacteria belonging to the family play a pivotal role in regulating host energy balance and metabolic homeostasis. As a commensal bacterium, has been implicated in modulating host energy homeostasis, albeit the underlying mechanism remains elusive. Therefore, this study aimed to investigate the impact of supplementation on various physiological parameters, intestinal morphology, particularly adipose tissue accumulation, and glucolipid metabolism in mice. The findings reveal that mice supplemented with for 6 weeks exhibited a notable increase in body weight, fat mass, adipocyte size, and serum triglyceride (TG) levels. Notably, the increased fat accumulation is observed despite consistent feed intake in treated mice. Mechanistically, supplementation significantly improved the structure integrity of intestinal villi and enhanced energy absorption efficiency while reducing excretion of carbohydrates and fatty acids in feces. This was accompanied by upregulation of glucose and fatty acid transporter expression. Furthermore, supplementation with promoted adipogenesis in both liver and adipose tissues, as evidenced by increased levels of hepatic pyruvate, acetyl-CoA, and TG, along with elevated expression levels of genes associated with lipid synthesis. Regarding the microbiological aspect, supplementation correlated with an increased abundance of genus bacteria and enhanced carbohydrate enzyme activity. In summary, supplementation significantly promotes fat accumulation in mice by augmenting energy absorption and adipogenesis, possibly mediated by the expansion of bacteria population with robust glycolipid metabolic ability.
IMPORTANCE
The clusters have been implicated in energy metabolism, the specific species and underlying mechanisms remain unclear. This present study is the first to report is able to affect fat accumulation and glycolipid metabolism. We indicated that gavage of promoted the adipogenesis and fat accumulation in mice by not only increasing the abundance of bacteria but by also enhancing the metabolic absorption of carbohydrates and fatty acids significantly. Obviously, changes of gut microbiota caused by the , especially the significant increase of bacteria, contributed to the fat accumulation of mice. In addition, the enhancement of genus bacteria remarkably improved the synthesis of hepatic pyruvate, acetyl-CoA, and triglyceride levels, as well as reduced the excretion of fecal carbohydrates, short-chain fatty acids, and free fatty acids remarkably. These findings will help us to understand the relationship of specific bacteria and host energy homeostasis.
PubMed: 38916334
DOI: 10.1128/spectrum.04116-23 -
Frontiers in Plant Science 2024, an aerial green alga, exhibits remarkable adaptability to the extreme conditions of Antarctica by forming layered colonies capable of utilizing far-red light for...
, an aerial green alga, exhibits remarkable adaptability to the extreme conditions of Antarctica by forming layered colonies capable of utilizing far-red light for photosynthesis. Despite a recent report on the structure of 's unique light-harvesting chlorophyll (Chl)-binding protein complex (Pc-frLHC), which facilitates far-red light absorption and uphill excitation energy transfer to photosystem II, the specific genes encoding the subunits of Pc-frLHC have not yet been identified. Here, we report a draft genome sequence of strain 4113, originally isolated from soil samples on Ongul Island, Antarctica. We obtained a 92 Mbp sequence distributed in 1,045 scaffolds comprising 10,244 genes, reflecting 87.1% of the core eukaryotic gene set. Notably, 26 genes associated with the light-harvesting Chl / binding complex (LHC) were identified, including four Pc-frLHC genes, with similarity to a noncanonical Lhca gene with four transmembrane helices, such as Ot_Lhca6 in and Cr_LHCA2 in . A comparative analysis revealed that Pc-frLHC shares homology with certain Lhca genes found in and species. This similarity indicates that Pc-frLHC has evolved from an ancestral Lhca gene with four transmembrane helices and branched out within the Trebouxiaceae family. Furthermore, RNA-seq analysis conducted during the initiation of Pc-frLHC gene induction under red light illumination indicated that Pc-frLHC genes were induced independently from other genes associated with photosystems or LHCs. Instead, the genes of transcription factors, helicases, chaperones, heat shock proteins, and components of blue light receptors were identified to coexpress with Pc-frLHC. Those kinds of information could provide insights into the expression mechanisms of Pc-frLHC and its evolutional development.
PubMed: 38916036
DOI: 10.3389/fpls.2024.1409116