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Marine Environmental Research Jun 2024We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3...
We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.
PubMed: 38941665
DOI: 10.1016/j.marenvres.2024.106615 -
PloS One 2024Prenatal alcohol exposure (PAE) causes cognitive impairment and a distinctive craniofacial dysmorphology, due in part to apoptotic losses of the pluripotent cranial...
Prenatal alcohol exposure (PAE) causes cognitive impairment and a distinctive craniofacial dysmorphology, due in part to apoptotic losses of the pluripotent cranial neural crest cells (CNCs) that form facial bones and cartilage. We previously reported that PAE rapidly represses expression of >70 ribosomal proteins (padj = 10-E47). Ribosome dysbiogenesis causes nucleolar stress and activates p53-MDM2-mediated apoptosis. Using primary avian CNCs and the murine CNC line O9-1, we tested whether nucleolar stress and p53-MDM2 signaling mediates this apoptosis. We further tested whether haploinsufficiency in genes that govern ribosome biogenesis, using a blocking morpholino approach, synergizes with alcohol to worsen craniofacial outcomes in a zebrafish model. In both avian and murine CNCs, pharmacologically relevant alcohol exposure (20mM, 2hr) causes the dissolution of nucleolar structures and the loss of rRNA synthesis; this nucleolar stress persisted for 18-24hr. This was followed by reduced proliferation, stabilization of nuclear p53, and apoptosis that was prevented by overexpression of MDM2 or dominant-negative p53. In zebrafish embryos, low-dose alcohol or morpholinos directed against ribosomal proteins Rpl5a, Rpl11, and Rps3a, the Tcof homolog Nolc1, or mdm2 separately caused modest craniofacial malformations, whereas these blocking morpholinos synergized with low-dose alcohol to reduce and even eliminate facial elements. Similar results were obtained using a small molecule inhibitor of RNA Polymerase 1, CX5461, whereas p53-blocking morpholinos normalized craniofacial outcomes under high-dose alcohol. Transcriptome analysis affirmed that alcohol suppressed the expression of >150 genes essential for ribosome biogenesis. We conclude that alcohol causes the apoptosis of CNCs, at least in part, by suppressing ribosome biogenesis and invoking a nucleolar stress that initiates their p53-MDM2 mediated apoptosis. We further note that the facial deficits that typify PAE and some ribosomopathies share features including reduced philtrum, upper lip, and epicanthal distance, suggesting the facial deficits of PAE represent, in part, a ribosomopathy.
Topics: Animals; Neural Crest; Zebrafish; Ribosomes; Ethanol; Tumor Suppressor Protein p53; Apoptosis; Mice; Proto-Oncogene Proteins c-mdm2; Cell Nucleolus; Ribosomal Proteins; Skull; Zebrafish Proteins
PubMed: 38941348
DOI: 10.1371/journal.pone.0304557 -
Current Microbiology Jun 2024Three novel bacterial strains, FE4, FE10, and LA51, which are phylogenetically affiliated to the genera Pseudoalteromonas, Vibrio, or Marinobacter, respectively,...
The Description of Pseudoalteromonas apostichopi sp. nov., Vibrio apostichopi sp. nov., and Marinobacter apostichopi sp. nov. from the Fertilized Eggs and Larvae of Apostichopus japonicus.
Three novel bacterial strains, FE4, FE10, and LA51, which are phylogenetically affiliated to the genera Pseudoalteromonas, Vibrio, or Marinobacter, respectively, isolated from fertilized eggs and juveniles of sea cucumber Apostichopus japonicus were characterized by a genome-based taxonomical approach including multilocus sequence analysis (MLSA) combined with classical phenotypic and chemotaxonomic characterizations. A molecular network reconstructed on the basis of nucleotide sequences of four phylogenetic maker protein genes revealed that the strains FE4, FE10, and LA51 were closely related to Pseudoalteromonas shioyasakiensis, Vibrio lentus, and Marinobacter similis, respectively. Average nucleotide identity (ANI) comparisons against phylogenetically related species to FE4, FE10, and LA51 demonstrated that each newly described strain could not be identified as any previously described species within each genus showing < 95% ANI: 91.3% of FE4 against P. shioyasakiensis JCM 18891, 92.6% of FE10 against "V. bathopelagicus" Sal10, and 92.6% of LA51 against M. similis A3d10, in maximum, respectively. Here, we show molecular phylogenetic, genomic, phenotypic, and chemotaxonomic features of the newly described species FE4, FE10, and LA51. We also propose Pseudoalteromonas apostichopi sp. nov. with FE4 (JCM 36173 = LMG 33143) as the type strain, Vibrio apostichopi sp. nov. with FE10 (JCM 36174 = LMG 33144) as the type strain, and Marinobacter apostichopi sp. nov. with LA51 (JCM 36175 = LMG 33145) as the type strain.
Topics: Pseudoalteromonas; Animals; Phylogeny; Vibrio; Stichopus; Marinobacter; Larva; Multilocus Sequence Typing; DNA, Bacterial; Bacterial Typing Techniques; RNA, Ribosomal, 16S; Zygote; Genome, Bacterial; Fatty Acids
PubMed: 38940874
DOI: 10.1007/s00284-024-03751-4 -
International Journal of Systematic and... Jun 2024A Gram-negative, strictly aerobic bacterial strain was isolated from asymptomatic leaf tissue of a wild yam plant. Optimal growth was observed at 28 °C and pH 7, and...
A Gram-negative, strictly aerobic bacterial strain was isolated from asymptomatic leaf tissue of a wild yam plant. Optimal growth was observed at 28 °C and pH 7, and catalase and oxidase activities were detected. Polyphasic taxonomic and comparative genomics revealed that strain LMG 33091 represents a novel species of . The nearest phylogenetic neighbours of strain LMG 33091 were NBRC 14164 (with 99.79 % 16S rRNA sequence identity), KL28 (99.28 %) and (99.07 %) ATCC 23835. MALDI-TOF MS analysis yielded distinct profiles for strain LMG 33091 and the nearest phylogenetic neighbours. Average nucleotide identity analyses between the whole genome sequence of strain LMG 33091 and of the type strains of its nearest-neighbour taxa yielded values below the species delineation threshold and thus confirmed that the strain represented a novel species, for which we propose the name sp. nov., with strain LMG 33091 (=GMI12077= CFBP 9143) as the type strain.
Topics: Pseudomonas; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Plant Leaves; Sequence Analysis, DNA; Bacterial Typing Techniques; Dioscorea; Whole Genome Sequencing; Base Composition; Fatty Acids; Genome, Bacterial
PubMed: 38940814
DOI: 10.1099/ijsem.0.006395 -
Journal of Virology Jun 2024Viruses have evolved a range of strategies to utilize or manipulate the host's cellular translational machinery for efficient infection, although the mechanisms by which...
UNLABELLED
Viruses have evolved a range of strategies to utilize or manipulate the host's cellular translational machinery for efficient infection, although the mechanisms by which infectious bronchitis virus (IBV) manipulates the host translation machinery remain unclear. In this study, we firstly demonstrate that IBV infection causes host shutoff, although viral protein synthesis is not affected. We then screened 23 viral proteins, and identified that more than one viral protein is responsible for IBV-induced host shutoff, the inhibitory effects of proteins Nsp15 were particularly pronounced. Ribosome profiling was used to draw the landscape of viral mRNA and cellular genes expression model, and the results showed that IBV mRNAs gradually dominated the cellular mRNA pool, the translation efficiency of the viral mRNAs was lower than the median efficiency (about 1) of cellular mRNAs. In the analysis of viral transcription and translation, higher densities of RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) reads were observed for structural proteins and 5' untranslated regions, which conformed to the typical transcriptional characteristics of nested viruses. Translational halt events and the number of host genes increased significantly after viral infection. The translationally paused genes were enriched in translation, unfolded-protein-related response, and activation of immune response pathways. Immune- and inflammation-related mRNAs were inefficiently translated in infected cells, and IBV infection delayed the production of IFN-β and IFN-λ. Our results describe the translational landscape of IBV-infected cells and demonstrate new strategies by which IBV induces host gene shutoff to promote its replication.
IMPORTANCE
Infectious bronchitis virus (IBV) is a γ-coronavirus that causes huge economic losses to the poultry industry. Understanding how the virus manipulates cellular biological processes to facilitate its replication is critical for controlling viral infections. Here, we used Ribo-seq to determine how IBV infection remodels the host's biological processes and identified multiple viral proteins involved in host gene shutoff. Immune- and inflammation-related mRNAs were inefficiently translated, the translation halt of unfolded proteins and immune activation-related genes increased significantly, benefitting IBV replication. These data provide new insights into how IBV modulates its host's antiviral responses.
PubMed: 38940559
DOI: 10.1128/jvi.00830-24 -
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