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Nucleus (Austin, Tex.) Dec 2024The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to... (Review)
Review
The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to identify and visualize individual pre-ribosomal particles on their way through the nuclear pore complex using both electron and light microscopy. In this review, we focused on the transport of pre-ribosomal particles in the nucleus on their way to and through the pores.
Topics: Cell Nucleolus; Nuclear Pore; Cytoplasm; Active Transport, Cell Nucleus; Humans; Animals; Ribosomes; Cell Nucleus
PubMed: 38940456
DOI: 10.1080/19491034.2024.2373052 -
Journal of Cell Science Jun 2024Some chemotherapy drugs modulate the formation of stress granules (SGs), which are RNA-containing cytoplasmic foci contributing to stress response pathways. How SGs...
Some chemotherapy drugs modulate the formation of stress granules (SGs), which are RNA-containing cytoplasmic foci contributing to stress response pathways. How SGs mechanistically contribute to pro-survival or pro-apoptotic functions must be better defined. The chemotherapy drug lomustine promotes SG formation by activating the stress-sensing eIF2α kinase HRI (encoded by the EIF2AK1 gene). Here, we applied a DNA microarray-based transcriptome analysis to determine the genes modulated by lomustine-induced stress and suggest roles for SGs in this process. We found that the expression of the pro-apoptotic EGR1 gene was specifically regulated in cells upon lomustine treatment. The appearance of EGR1-encoding mRNA in SGs correlated with a decrease in EGR1 mRNA translation. Specifically, EGR1 mRNA was sequestered to SGs upon lomustine treatment, probably preventing its ribosome translation and consequently limiting the degree of apoptosis. Our data support the model where SGs can selectively sequester specific mRNAs in a stress-specific manner, modulate their availability for translation, and thus determine the fate of a stressed cell.
Topics: Humans; RNA, Messenger; Early Growth Response Protein 1; Lomustine; Stress Granules; Apoptosis; Antineoplastic Agents, Alkylating
PubMed: 38940347
DOI: 10.1242/jcs.261825 -
Biomeditsinskaia Khimiia Jun 2024Renalase (RNLS) is a recently discovered protein that plays an important role in the regulation of blood pressure by acting inside and outside cells. Intracellular RNLS...
Renalase (RNLS) is a recently discovered protein that plays an important role in the regulation of blood pressure by acting inside and outside cells. Intracellular RNLS is a FAD-dependent oxidoreductase that oxidizes isomeric forms of β-NAD(P)H. Extracellular renalase lacking its N-terminal peptide and cofactor FAD exerts various protective effects via non-catalytic mechanisms. Certain experimental evidence exists in the literature that the RP220 peptide (a 20-mer peptide corresponding to the amino acid sequence RNLS 220-239) reproduces a number of non-catalytic effects of this protein, acting on receptor proteins of the plasma membrane. The possibility of interaction of this peptide with intracellular proteins has not been studied. Taking into consideration the known role of RNLS as a possible antihypertensive factor, the aim of this study was to perform proteomic profiling of the kidneys of normotensive and hypertensive rats using RP220 as an affinity ligand. Proteomic (semi-quantitative) identification revealed changes in the relative content of about 200 individual proteins in the kidneys of hypertensive rats bound to the affinity sorbent as compared to the kidneys of normotensive animals. Increased binding of SHR renal proteins to RP220 over the normotensive control was found for proteins involved in the development of cardiovascular pathology. Decreased binding of the kidney proteins from hypertensive animals to RP220 was noted for components of the ubiquitin-proteasome system, ribosomes, and cytoskeleton.
Topics: Animals; Rats; Kidney; Hypertension; Rats, Inbred SHR; Proteomics; Monoamine Oxidase; Male; Ligands; Peptides; Proteome
PubMed: 38940203
DOI: 10.18097/PBMC20247003145 -
Frontiers in Bioscience (Elite Edition) Jun 2024Due to the constant and improper use of chemicals, including pesticides, many substances, and their degradation products can accumulate in the soil and negatively affect...
BACKGROUND
Due to the constant and improper use of chemicals, including pesticides, many substances, and their degradation products can accumulate in the soil and negatively affect its organisms.
METHODS
In this study, morphological methods, Gram-staining, and Matrix-Assisted Laser Desorption/Ionzation Time of Flight Mass Spectrometry (MALDI-TOF MS) methods were used to isolate bacteria from agricultural soils, while genetic identification was conducted using 16S rRNA. The density of bacteria was determined using the spectrophotometric method, and the residual amount of cypermethrin was determined and analyzed using Gas chromatograohy-mass spectrometry (GC-MS) methods.
RESULTS
Nine isolates were obtained from various agricultural soils. Isolate No. 3 showed the greatest effectiveness against cypermethrin and was selected for further research. Isolate No. 3 was identified as the strain PDB-3 and was registered in the National Center for Biotechnology Information (NCBI) database (GenBank: OL587509.1). Using this strain, the influence of various external factors on the degradation of cypermethrin was studied. This bacterium demonstrated 100% degradation of cypermethrin in 20 days under optimal conditions (temperature: 30 °C; optical density (OD) = 0.2; cypermethrin concentration: 80 ± 0.02 mg/kg). In addition, PDB-3 changed the original structure of cypermethrin into various intermediate metabolites, such as 2-hydroxy-3-phenoxy benzeneacetonitrile, 3-phenoxybenzaldehyde, 3-phenoxybenzaldehyde, methyl stearate, anethol, citral, and phenol.
CONCLUSIONS
The results obtained using PDB-3 provide the basis for large-scale field trials on the bioremediation of cypermethrin-contaminated soils.
Topics: Pyrethrins; Ochrobactrum; Pesticides; Biodegradation, Environmental; Soil Microbiology; Gas Chromatography-Mass Spectrometry; RNA, Ribosomal, 16S; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 38939915
DOI: 10.31083/j.fbe1602020 -
Frontiers in Bioscience (Elite Edition) May 2024Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and...
BACKGROUND
Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and entomopathogens, lack effectiveness, necessitating alternative approaches.
METHODS
Gut-associated bacteria were isolated from the gut samples of fall armyworm and screened based on their chitinase and protease-producing ability before characterization through 16S rRNA gene sequence analysis. The efficient chitinase-producing FGE4 and FGE18 were chosen to test the biocontrol efficacy. As their respective cell suspensions and extracted crude chitinase enzyme, these two isolates were applied topically on the larvae, supplemented with their feed, and analyzed for their quantitative food use efficiency and survivability.
RESULTS
Twenty-one high chitinase and protease-producing bacterial isolates were chosen. Five genera were identified by 16S rRNA gene sequencing: , , , , and . In the biocontrol efficacy test, the consumption index and relative growth rate were lowered in larvae treated with FGE18 by topical application and feed supplementation. Similarly, topical treatment of FGE4 to larvae decreased consumption index, relative growth rate, conversion efficiency of ingested food, and digested food values.
CONCLUSION
The presence of gut bacteria with high chitinase activity negatively affects insect health. Utilizing gut-derived bacterial isolates with specific insecticidal traits offers a promising avenue to control fall armyworms. This research suggests a potential strategy for future pest management.
Topics: Animals; Spodoptera; Chitinases; RNA, Ribosomal, 16S; Bacteria; Bacillus licheniformis; Enterobacter cloacae; Larva; Pest Control, Biological; Gastrointestinal Tract
PubMed: 38939914
DOI: 10.31083/j.fbe1602015 -
Journal of Parasitology Research 2024Human toxocariasis (HT) is a zoonotic disease with a global expansion. Contaminated soil with spp. eggs is the main source of human infection, which may lead to severe...
BACKGROUND
Human toxocariasis (HT) is a zoonotic disease with a global expansion. Contaminated soil with spp. eggs is the main source of human infection, which may lead to severe complications depending on the organs invaded by migrating larvae.
AIM
This study is aimed at eliciting the prevalence of spp. eggs in public parks in Zahedan, southeast Iran, and providing new insight into the soil contamination rate in this area using microscopic and molecular methods.
METHODS
Based on five municipal districts, 240 soil samples were collected from public parks and playgrounds in Zahedan. The modified Sheather's flotation technique was employed to isolate spp. eggs from the soil, followed by microscopic assessment and molecular evaluation of internal transcribed spacer 1 and 2 ribosomal deoxyribonucleic acid (ITS1 and 2 rDNA) using nested polymerase chain reaction (nested PCR) to identify the presence of spp. eggs. The Sanger sequence was used to differentiate the species. Subsequently, all the sequenced data were blasted and compared with other sequences available in the GenBank.
RESULTS
Out of 240 soil samples collected, 7 (2.9%) samples were identified to contain spp. eggs using Sheather's flotation and microscopic techniques. Meanwhile, 19 (7.9%) samples were positive using nested PCR. According to the Sanger sequencing analysis findings, all positive samples were contaminated with .
CONCLUSION
As evidenced by the obtained results, only species were detected in public parks and playgrounds in Zahedan; therefore, control and prevention programs against this species should be considered in human and animal communities.
PubMed: 38939904
DOI: 10.1155/2024/2132696 -
Journal of Extracellular Biology Jan 2024Urinary extracellular vesicles (uEVs) are rich in valuable biomolecule information which are increasingly recognized as potential biomarkers for various diseases. uEV...
Urinary extracellular vesicles (uEVs) are rich in valuable biomolecule information which are increasingly recognized as potential biomarkers for various diseases. uEV long RNAs are among the critical cargos capable of providing unique transcriptome information of the source cells. However, consensus regarding ideal reference genes for relative long RNAs quantification in uEVs is not available as of date. Here we explored stable reference genes through profiling the long RNA expression by RNA-seq following unsupervised analysis and validation studies. Candidate reference genes were identified using four algorithms: NormFinder, GeNorm, BestKeeper and the Delta Ct method, followed by validation. RNA profile showed uEVs contained abundant long RNAs information and the core transcriptome was related to cellular structures, especially ribosome which functions mainly as translation, protein and RNA binding molecules. Analysis of RNA-seq data identified RPL18A, RPL11, RPL27, RACK1, RPSA, RPL41, H1-2, RPL4, GAPDH, RPS27A as candidate reference genes. RT-qPCR validation revealed that RPL41, RPSA and RPL18A were reliable reference genes for long RNA quantification in uEVs from patients with diabetes mellitus (DM), diabetic nephropathy (DN), IgA nephropathy (IgAN) and prostate cancer (PCA). Interestingly, RPL41 also outperformed traditional reference genes in renal tissues of DN and IgAN, as well as in plasma EVs of several types of cancers. The stable reference genes identified in this study may facilitate development of uEVs as novel biomarkers and increase the accuracy and comparability of biomarker studies.
PubMed: 38938675
DOI: 10.1002/jex2.136 -
Journal of Extracellular Biology Sep 2023Extracellular vesicles (EVs) recently emerged as important players in the pathophysiology of parasitic infections. While the protist parasite can produce EVs, their...
Extracellular vesicles (EVs) recently emerged as important players in the pathophysiology of parasitic infections. While the protist parasite can produce EVs, their role in giardiasis remains obscure. can disrupt gut microbiota biofilms and transform commensal bacteria into invasive pathobionts at sites devoid of colonizing trophozoites via unknown mechanisms. We hypothesized that EVs could modify gut bacterial behaviour via a novel mode of trans-kingdom communication. Our findings indicate that EVs exert bacteriostatic effects on HB101 and TW1, increasing their swimming motility. EVs also decreased the biofilm-forming ability of HB101 but not by TW1, supporting the hypothesis that these effects are, at least in part, bacteria-selective. HB101 and TW1 exhibited increased adhesion/invasion onto small intestine epithelial cells when exposed to EVs. EVs labelled with PKH67 revealed colocalization with HB101 and TW1 bacterial cells. Small RNA sequencing revealed a high abundance of ribosomal RNA (rRNA)- and transfer RNA (tRNA)-derived small RNAs, short-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) within EVs. Proteomic analysis of EVs uncovered the presence of RNA chaperones and heat shock proteins that can facilitate the thermal stability of EVs and its sRNA cargo, as well as protein-modifying enzymes. In vitro, RNase heat-treatment assays showed that total RNAs in EVs, but not proteins, are responsible for modulating bacterial swimming motility and biofilm formation. small RNAs of EVs, but not proteins, were responsible for the increased bacterial adhesion to intestinal epithelial cells induced upon exposure to EVs. Together, the findings indicate that EVs contain a heat-stable, RNase-sensitive cargo that can trigger the development of pathobiont characteristics in Enterobacteria, depicting a novel trans-kingdom cross-talk in the gut.
PubMed: 38938375
DOI: 10.1002/jex2.109 -
Animal Bioscience Jun 2024This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus).
OBJECTIVE
This study aimed to identify, discover and explore the characteristics of the mtDNA genomes of Cemani chicken (Gallus gallus).
METHODS
This study used gDNA of Cemani chicken isolated from liver tissue. mtDNA sequencing was performed using WGS mtDNA analysis with nanopore technology by Oxford Nanopore Technologies GridION. Bioinformatics and data analysis were then performed.
RESULTS
This study showed that the length of the mtDNA genome is 16,789 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), and a noncoding control region (Dloop). Furthermore, analysis showed there were polymorphic sites and amino acid alterations when mtDNA Cemani chicken was aligned with references from GenBank.
CONCLUSION
Site (988T>*) in Dloop genes and (328A>G) in ND3 genes which alter glycine to stop codon, were specific markers found only in Cemani chicken.
PubMed: 38938041
DOI: 10.5713/ab.23.0513 -
Journal of Microbiology and... Jun 2024The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in...
The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as , , , , and dominated the intestine, while , , and prevailed in the stomach and hepatopancreas. It is particularly notable that , which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.
Topics: Animals; Penaeidae; Hepatopancreas; RNA, Ribosomal, 16S; Bacteria; Gastrointestinal Microbiome; Republic of Korea; Intestines; Phylogeny; Stomach; Biodiversity; Aquaculture; DNA, Bacterial
PubMed: 38938005
DOI: 10.4014/jmb.2403.03039