Inhibition of endoribonuclease/kinase Ire1 has shown beneficial effects in many proteotoxicity‐induced pathology models. The mechanism by which this occurs has not been elucidated completely. Using a ...proteotoxic yeast model of Huntington's disease, we show that the deletion of Ire1 led to lower protein aggregation at longer time points. The rate of protein degradation was higher in ΔIre1 cells. We monitored the two major protein degradation mechanisms in the cell. The increase in expression of Rpn4, coding for the transcription factor controlling proteasome biogenesis, was higher in ΔIre1 cells. The chymotrypsin‐like proteasomal activity was also significantly enhanced in these cells at later time points of aggregation. The gene and protein expression levels of the autophagy gene Atg8 were higher in ΔIre1 than in wild‐type cells. Significant increase in autophagy flux was also seen in ΔIre1 cells at later time points of aggregation. The results suggest that the deletion of Ire1 activates UPR‐independent arms of the proteostasis network, especially under conditions of aggravated stress. Thus, the inhibition of Ire1 may regulate UPR‐independent cellular stress‐response pathways under prolonged stress.
The role of endoribonuclease/kinase Ire1 in cellular proteostasis has been investigated. Deletion of Ire1 led to lower protein aggregation at longer time points in a yeast model of Huntington's disease. Activation of unfolded protein response (UPR)‐independent arms of the proteostasis network was observed under conditions of aggravated stress. Proteasomal activity and autophagy were enhanced. Thus, the inhibition of Ire1 may regulate UPR‐independent cellular stress‐response pathways under prolonged stress.
This paper aims to investigate and map the spatial distribution of urban green spaces (UGSs) in Bathinda City, India. Since urban green spaces affect the quality of life and provide various ...ecological, socio-cultural and economic benefits to a city, the spatial distribution of UGSs and per capita availability deserve greater consideration in urban planning and research. The UGSs are extracted from freely available Sentinel 2 image with spatial resolutions of 10 m (blue, green, red, and near infrared bands). The result indicates that the planned urban setups have higher area under UGSs as compared to the rest of the city. Analysis and intra-city comparison (ward wise) of distribution of green spaces and per capita availability indicate that there is an inequitable distribution of UGSs in Bathinda City. The study also attempts to accentuate the scope of green initiatives in the various wards of the city to ensure the well-being of people.
Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we ...characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes.
Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability.
The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.
Bio-inspired quantum dots have received widespread attention in recent years due to their great potential for biological applications. Herein, we report a one pot hydrothermal synthesis of ...nitrogen-phosphorus-sulphur (NPS)-codoped carbon quantum dots from endophytic bacteria without using any additional doping precursor. The synthesized CQDs were thoroughly characterized and interestingly found to have a graphene like structure. The synthesized CQDs were then utilized in bactericidal activities against Gram-negative bacteria like
Salmonella typhi
,
Pseudomonas aeruginosa
and Gram-positive bacteria like the
Bacillus subtilis
strain. The strains were treated with different concentrations ranging from 5-100 µg ml
−1
. The 5 µg ml
−1
concentration appeared to be the MIC (minimum inhibitory concentration) and 100 µg ml
−1
is the MBC (minimum bactericidal concentration) maintaining a short incubation period of one hour. A simple, cost-effective and eco-friendly approach to synthesize multi-elemental doped CQDs would certainly cause the method to be used in future for diverse biological applications. As compared to the broadly used antibiotics, the developed CQDs have some added advantages including lower cytotoxicity, excellent photo-stability and high selectivity.
A bio-inspired route has been described to synthesize NPS-codoped CQDs having enhanced antibacterial and antioxidant activities.
This study examines the Sundarijal Water Supply System in Nepal, which involves over a century of experience on a multipurpose water supply project. Research findings suggest that the liberal idea of ...justice as fairness in the distribution of risks and benefits fails to appreciate the political nature of state interventions to transfer rural water for urban municipal use. The research rejects the neoliberal idea of procedural justice as creating non-argumentative spaces for decision-making common in collaborative governance in favour of the political ecological approach to developing argumentative spaces to facilitate contested co-production of legitimacy.
A newly isolated bacterium
S-30 was recovered from waste-contaminated soil in Ranchi, India. The isolated bacterium belongs to the ESKAPE organisms which represent the major nosocomial pathogens that ...exhibit high antibiotic resistance. Furthermore, average nucleotide identity (ANI) analysis also showed its closest match (>95%) to other
genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO
. Whole genome sequencing and annotations revealed the occurrence of various genes involved in stress protection, motility, and metabolism of aromatic compounds. Moreover, genome annotation identified the gene clusters involved in secondary metabolite production (biosynthetic gene clusters) such as arylpolyene, acinetobactin like NRP-metallophore, betalactone, and hserlactone-NRPS cluster. The metabolic potential of
S-30 based on cluster of orthologous, and Kyoto Encyclopedia of Genes and Genomes indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux systems etc., which is relatively rare in
strains. Additionally, the presence of various carbohydrate-active enzymes such as glycoside hydrolases (GHs), glycosyltransferases (GTs), and other genes associated with lignocellulose breakdown suggests that strain S-30 has strong biomass degradation potential. Furthermore, an analysis of genetic diversity and recombination in
strains was performed to understand the population expansion hypothesis of
strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to
Therefore, the
S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead ...dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
Background
Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the ...establishment of efficient microbial populations in their natural niches. The survival of
Enterobacter
species under acidic stress remains poorly understood.
Objective
This study aimed to investigate the survival of an environmental isolate
Enterobacter
sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes.
Methods
We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions.
Results
A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that
Enterobacter
reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress.
Conclusions
The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of
Enterobacter
bacterium.
