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1.
Genome Res ; 31(4): 607-621, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33514624

RESUMEN

The establishment of centromeric chromatin and its propagation by the centromere-specific histone CENPA is mediated by epigenetic mechanisms in most eukaryotes. DNA replication origins, origin binding proteins, and replication timing of centromere DNA are important determinants of centromere function. The epigenetically regulated regional centromeres in the budding yeast Candida albicans have unique DNA sequences that replicate earliest in every chromosome and are clustered throughout the cell cycle. In this study, the genome-wide occupancy of the replication initiation protein Orc4 reveals its abundance at all centromeres in C. albicans Orc4 is associated with four different DNA sequence motifs, one of which coincides with tRNA genes (tDNA) that replicate early and cluster together in space. Hi-C combined with genome-wide replication timing analyses identify that early replicating Orc4-bound regions interact with themselves stronger than with late replicating Orc4-bound regions. We simulate a polymer model of chromosomes of C. albicans and propose that the early replicating and highly enriched Orc4-bound sites preferentially localize around the clustered kinetochores. We also observe that Orc4 is constitutively localized to centromeres, and both Orc4 and the helicase Mcm2 are essential for cell viability and CENPA stability in C. albicans Finally, we show that new molecules of CENPA are recruited to centromeres during late anaphase/telophase, which coincides with the stage at which the CENPA-specific chaperone Scm3 localizes to the kinetochore. We propose that the spatiotemporal localization of Orc4 within the nucleus, in collaboration with Mcm2 and Scm3, maintains centromeric chromatin stability and CENPA recruitment in C. albicans.


Asunto(s)
Candida albicans , Centrómero , Cromatina , Complejo de Reconocimiento del Origen/metabolismo , Candida albicans/genética , Centrómero/genética , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , Histonas/metabolismo , Cinetocoros , Origen de Réplica/genética
2.
Arch Microbiol ; 206(2): 81, 2024 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-38294553

RESUMEN

Enterobacter genus includes the bacteria occupying every aspect of environment, however, their adaptability at varying temperature is not clear. In the present study, we analyzed the transcriptome response of Enterobacter sp. S-33 and their functional genes under various temperatures (30-45 ℃) that were expressed and accumulated in cells under temperature-stress. During a temperature shift from 37 to 45 ℃, 165 genes showed differential expression including 112 up-regulated and 53 down-regulated. In particular, heat-shock genes such as CspA, 16 kDa heat shock protein A/B and transcriptional regulators such as LysR, TetR, and LuxR were differentially expressed, indicating the role of complex molecular mechanism of Enterobacter adapting to temperature stress. Similarly, genes associated to signal transduction, ABC transporters, iron homeostasis, and quorum sensing were also induced. The Gene ontology enrichment analysis of differentially expressed genes (DEGs) were categorized into "transmembrane transport", "tRNA binding", "hydrogen sulfide biosynthetic process" and "sulfate assimilation" terms. In addition, Kyoto Encyclopedia of Genes and Genomes pathways showed that ABC transporter as well as quorum sensing pathways were significantly enriched. Overall, current study has contributed to explore the adaptive molecular mechanisms of Enterobacter spp. upon temperature change, which further opens new avenues for future in-depth functional studies.


Asunto(s)
Enterobacter , Transcriptoma , Enterobacter/genética , Temperatura , Transporte Biológico , Ontología de Genes
3.
Mol Cell Biochem ; 2024 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-38413478

RESUMEN

Cancer remains a major global health concern with high mortality rates mainly due to late diagnosis and poor prognosis. Long non-coding RNAs (lncRNAs) are emerging as key regulators of gene expression in human cancer, functioning through various mechanisms including as competing endogenous RNAs (ceRNAs) and indirectly regulating miRNA expression. LncRNAs have been found to have both oncogenic and tumor-suppressive roles in cancer, with the former promoting cancer cell proliferation, migration, invasion, and poor prognosis. Recent research has shown that lncRNAs are expressed in various immune cells and are involved in cancer cell immune escape and the modulation of the tumor microenvironment, thus highlighting their potential as targets for cancer immunotherapy. Targeting lncRNAs in cancer or immune cells could enhance the anti-tumor immune response and improve cancer immunotherapy outcomes. However, further research is required to fully understand the functional roles of lncRNAs in cancer and the immune system and their potential as targets for cancer immunotherapy. This review offers a comprehensive examination of the multifaceted roles of lncRNAs in human cancers, with a focus on their potential as targets for cancer immunotherapy. By exploring the intricate mechanisms underlying lncRNA-mediated regulation of cancer cell proliferation, invasion, and immune evasion, we provide insights into the diverse therapeutic applications of these molecules.

4.
Funct Integr Genomics ; 23(3): 245, 2023 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-37460717

RESUMEN

Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.


Asunto(s)
Enterobacter , Genoma Bacteriano , Humanos , Enterobacter/genética , ARN Ribosómico 16S , Genómica , Carbohidratos , Filogenia
5.
BMC Microbiol ; 23(1): 192, 2023 07 18.
Artículo en Inglés | MEDLINE | ID: mdl-37464310

RESUMEN

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.


Asunto(s)
Paenibacillus , Rauwolfia , Rauwolfia/genética , Paenibacillus/genética , Composición de Base , Filogenia , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , Análisis de Secuencia de ADN , Ácidos Grasos , Microbiología del Suelo
6.
Int Microbiol ; 2023 Dec 04.
Artículo en Inglés | MEDLINE | ID: mdl-38044418

RESUMEN

Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.

7.
Curr Microbiol ; 80(3): 88, 2023 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-36719538

RESUMEN

Members of the Enterobacter genus include many pathogenic microbes of humans and plants, secrete proteins that contribute to the interactions of bacteria and their environment. Therefore, understanding of secreted proteins is vital to understand bacterial physiology and behavior. Here, we explored the secretome of an environmental isolate Enterobacter sp. S-16 by nanoLC-MS/MS and identified 572 proteins in the culture supernatant. Gene ontology (GO) analysis indicated that proteins were related to biological processes, molecular as well as cellular functions. The majority of the identified proteins are involved in microbial metabolism, chemotaxis & motility, flagellar hook-associated proteins, biosynthesis of antibiotics, and molecular chaperones to assist the protein folding. Bioinformatics analysis of the secretome revealed the presence of type I and type VI secretion system proteins. Presence of these diverse secretion system proteins in Enterobacter sp. S-16 are likely to be involved in the transport of various proteins including nutrient acquisition, adhesion, colonization, and homeostasis maintenance. Among the secreted bacterial proteins with industrial importance, lignocellulolytic enzymes play a major role, therefore, we analyzed our secretome results for any presence of glycoside hydrolases (GHs) and other hydrolytic enzymes (CAZymes). Overall, the secreted proteins may be considered an attractive reservoir of potential antigens for drug development, diagnostic markers, and other biomedical applications.


Asunto(s)
Espectrometría de Masas en Tándem , Factores de Virulencia , Humanos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Glicósido Hidrolasas , Factores de Virulencia/genética , Enterobacter/aislamiento & purificación
8.
Curr Microbiol ; 80(6): 202, 2023 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-37145205

RESUMEN

Acinetobacter species is currently ranked as high-priority pathogen for their extraordinary ability to become resistant to almost all existing antibiotics. The diverse range of effectors secreted by Acinetobacter spp. constitutes a significant proportion of the virulence arsenal. Therefore, our study aims to characterize the secretome of Acinetobacter pittii S-30. Analysis of extracellular secreted proteins of A. pittii S-30 revealed the presence of transporter proteins, outer membrane proteins, molecular chaperones, porins, and several proteins of unknown function. Additionally, proteins related to metabolism, as well as those involved in gene expression and protein translation, type VI secretion system (T6SS) proteins, and stress response-related proteins were also identified in the secretome. The comprehensive analysis of secretome revealed putative protein antigens which could elicit substantial immune response. The limited availability of effective antibiotics and the worldwide growth of secretome data make this approach appealing in the development of effective vaccines against Acinetobacter and other bacterial pathogens.


Asunto(s)
Infecciones por Acinetobacter , Acinetobacter , Humanos , Infecciones por Acinetobacter/microbiología , Secretoma , Acinetobacter/genética , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo
9.
Biotechnol Lett ; 45(3): 309-331, 2023 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-36683130

RESUMEN

Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.


Asunto(s)
Sistemas de Secreción Tipo VI , Sistemas de Secreción Tipo VI/química , Sistemas de Secreción Tipo VI/metabolismo , Proteínas Bacterianas/metabolismo , Bacterias/metabolismo , Sistemas de Secreción Bacterianos , Factores de Virulencia/metabolismo
10.
Biophys J ; 121(14): 2794-2812, 2022 07 19.
Artículo en Inglés | MEDLINE | ID: mdl-35672951

RESUMEN

Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation, and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction-strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its three-dimensional organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid- and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops.


Asunto(s)
Cromatina , Polímeros , Cromosomas , Entropía , Epigenómica , Humanos
11.
Arch Microbiol ; 204(11): 662, 2022 Oct 05.
Artículo en Inglés | MEDLINE | ID: mdl-36198868

RESUMEN

Enterobacter species are responsible for causing infections of the lower respiratory tract, urinary tract, meninges, etc. Proteins secreted by these species may act as determinants of host-pathogen interaction and play a role in virulence. Among the secreted proteins, the Type VI secretion system (T6SS) acts as a molecular nanomachine to deliver many effector proteins directly into prey cells in a contact-dependent manner. The secreted proteins may provide an idea for the interaction of bacteria to their environment and an understanding of the role of these proteins for their role in bacterial physiology and behaviour. Therefore, aim of this study was to characterize the secreted proteins in the culture supernatant by a T6SS bacterium Enterobacter sp. S-33 using nano-LC-MS/MS tool. Using a combined mass spectrometry and bioinformatics approach, we identified a total of 736 proteins in the secretome. Bioinformatics analysis predicting subcellular localization identified 110 of the secreted proteins possessed signal sequences. By gene ontology analysis, more than 80 proteins of the secretome were classified into biological or molecular functions. More than 20 percent of secretome proteins were virulence proteins including T6SS proteins, proteins involved in adherence and fimbriae formation, molecular chaperones, outer membrane proteins, serine proteases, antimicrobial, biofilm, exotoxins, etc. In summary, the results of the present study of the S-33 secretome provide a basis for understanding the possible pathogenic mechanisms and future investigation by detailed experimental approach will provide a confirmation of secreted virulence proteins in the exact role of virulence using the in vivo model.


Asunto(s)
Sistemas de Secreción Tipo VI , Proteínas Bacterianas/metabolismo , Enterobacter/genética , Enterobacter/metabolismo , Exotoxinas/metabolismo , Proteínas de la Membrana/metabolismo , Señales de Clasificación de Proteína , Secretoma , Serina Proteasas/metabolismo , Espectrometría de Masas en Tándem , Sistemas de Secreción Tipo VI/genética , Sistemas de Secreción Tipo VI/metabolismo , Virulencia
12.
Biophys J ; 118(9): 2193-2208, 2020 05 05.
Artículo en Inglés | MEDLINE | ID: mdl-32389215

RESUMEN

The three-dimensional (3D) organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state-accessibility and amount of gene expression-of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs, but not on the interaction strength that leads to these contact counts. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In this work, a novel inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the α-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. The results presented for multiple normalization methods suggest that all measurable quantities may crucially depend on the nature of normalization. We argue that by experimentally measuring predicted quantities, one may infer the appropriate form of normalization.


Asunto(s)
Cromatina , Cromosomas , Conformación Molecular , Probabilidad
13.
Soft Matter ; 15(39): 7876-7887, 2019 Oct 09.
Artículo en Inglés | MEDLINE | ID: mdl-31531489

RESUMEN

The universality of the swelling of the radius of gyration of a homopolymer relative to its value in the θ state, independent of polymer-solvent chemistry, in the crossover regime between θ and athermal solvent conditions, is well known. Here we study, by Brownian dynamics, a polymer model where a subset of monomers is labelled as "stickers". The mutual interaction of the stickers is more attractive than those of the other ("backbone") monomers, and has an additional important characteristic of "functionality" φ, i.e., the maximum number of stickers that can locally bind to a given sticker. A saturated bond formed in this manner remains bound until it breaks due to thermal fluctuations, a requirement which can be viewed as an additional Boolean degree of freedom that describes the bonding. This, in turn, makes the question of the order of the collapse transition a non-trivial one. Nevertheless, for the parameters that we have studied (in particular, φ = 1), we find a standard second-order θ collapse, using a renormalised solvent quality parameter that takes into account the increased average attraction due to the presence of stickers. We examine the swelling of the radius of gyration of such a sticky polymer relative to its value in the altered θ state, using a novel potential to model the various excluded volume interactions that occur between the monomers on the chain. We find that the swelling of such sticky polymers is identical to the universal swelling of homopolymers in the thermal crossover regime. Additionally, for our model, the Kuhn segment length under θ conditions is found to be the same for chains with and without stickers.

14.
J Org Chem ; 83(15): 8225-8232, 2018 08 03.
Artículo en Inglés | MEDLINE | ID: mdl-29847121

RESUMEN

A urea tag was incorporated at the C-4 position of proline, cis to its COOH group, in order to explore the prospect of a synergistic effect between the two functional groups in the transition state of the enamine route to the asymmetric aldol reaction. The catalyst proved to be an excellent performer, delivering aldols in high yields and with excellent enantio- and diastereoselectivities using just 2 mol % loading in the presence of water; it also exhibited good levels of recyclability under aqueous conditions. The favorable results reveal the interesting possibility of an intramolecular host-guest interaction between the urea and the amino acid moieties, exerting a beneficial effect on catalysis. The concept could certainly offer a new direction toward more efficient catalyst design.

15.
Indian J Ophthalmol ; 72(1): 51-55, 2024 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-38131569

RESUMEN

PURPOSE: The efficacy of posterior optic capture (POC) in reducing posterior capsule opacification (PCO) in pediatric cataract is well recognized. The purpose of this paper was to identify the surgical challenges when attempting this technique and highlight the etiquettes to follow when performing this maneuver. METHODS: Prospective observational noncomparative case series. Children diagnosed with congenital or developmental cataracts undergoing cataract surgery and primary IOL implantation with posterior optic capture (and no anterior vitrectomy) from June 2017 to April 2022 at a tertiary care referral institute were included. Records of all intraoperative findings and postoperative complications until the last follow-up were noted. RESULTS: Posterior optic capture was attempted in 53 eyes of 49 children aged 2.4 ± 1.98 years. The mean follow-up of the patients was 16.5 ± 14.2 months (range 6 months-5 years). Successful POC could be performed in 46 eyes (86.8%). Two eyes developed posterior capsular opacification at the last follow-up. In eyes where POC could not be performed, five of these (83%) were children below 12 months of age with half of them having a preexisting posterior capsular defect. CONCLUSION: Posterior optic capture is technically challenging with a steep learning curve that can be mastered over time. Adequate relative sizing of the anterior and posterior capsulorhexis is important. Caution is advised when using this technique in infants and in cases with posterior capsular defects.


Asunto(s)
Extracción de Catarata , Catarata , Cápsula del Cristalino , Lentes Intraoculares , Humanos , Lactante , Capsulorrexis/métodos , Catarata/etiología , Extracción de Catarata/efectos adversos , Cápsula del Cristalino/cirugía , Implantación de Lentes Intraoculares/métodos , Lentes Intraoculares/efectos adversos , Complicaciones Posoperatorias/cirugía , Vitrectomía/métodos , Preescolar
16.
Front Microbiol ; 15: 1351161, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38741743

RESUMEN

A newly isolated bacterium Acinetobacter pittii 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 A. pittii genomes. The isolate showed metal-resistant behavior and was able to survive up to 5 mM of ZnSO4. 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 A. pittii 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 A. pittii 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 A. pittii strains was performed to understand the population expansion hypothesis of A. pittii strains. To our knowledge, this is the first report demonstrating the detailed genomic characterization of a heavy metal-resistant bacterium belonging to A. pittii. Therefore, the A. pittii S-30 could be a good candidate for the promotion of plant growth and other biotechnological applications.

17.
Genes Genomics ; 46(6): 671-687, 2024 06.
Artículo en Inglés | MEDLINE | ID: mdl-38687436

RESUMEN

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.


Asunto(s)
Enterobacter , Regulación Bacteriana de la Expresión Génica , Estrés Fisiológico , Transcriptoma , Enterobacter/genética , Enterobacter/metabolismo , Concentración de Iones de Hidrógeno , Estrés Fisiológico/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo
18.
Indian J Ophthalmol ; 72(7): 1017-1020, 2024 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-38454863

RESUMEN

PURPOSE: To study the pupil dynamics with premixed intracameral anesthetic mydriatic combination of phenylephrine (0.31%), tropicamide (0.02%), and lidocaine (1%) in pediatric cataract surgery. METHODS: Consecutive children aged ≤12 years planned for cataract surgery were recruited. A commercially available premixed combination of phenylephrine (0.31%), tropicamide (0.02%), and lidocaine (1%) was injected at the beginning of surgery without any topical/infusion drugs for mydriasis. Pupil sizes at various points of surgery were studied. RESULTS: We recruited 75 patients with a mean age of 24.3 ± 33.4 months (range: 1 month-11 years). Adequate mydriasis with a single injection was achieved in 93.5% (n = 73 eyes of 70 patients) without additional pharmacotherapy or intervention. The mean pupillary diameter increased from 1.8 ± 0.79 to 6.1 ± 1.4 mm after injection (mean change of 4.2 ± 1.25 mm from baseline). The mean variability in pupillary diameter was 0.73 ± 1.3 mm. In five eyes, good dilatation was not possible even after repeat injection. CONCLUSION: Fixed-dose premixed intracameral injection is effective in pupil dilatation. It alleviates the need for any topical dilators or additional intraoperative supplementation for pediatric cataract surgery.


Asunto(s)
Extracción de Catarata , Midriáticos , Fenilefrina , Pupila , Tropicamida , Humanos , Midriáticos/administración & dosificación , Preescolar , Masculino , Lactante , Femenino , Extracción de Catarata/métodos , Pupila/efectos de los fármacos , Niño , Tropicamida/administración & dosificación , Fenilefrina/administración & dosificación , Lidocaína/administración & dosificación , Cámara Anterior/efectos de los fármacos , Catarata , Estudios Prospectivos , Estudios de Seguimiento , Soluciones Oftálmicas/administración & dosificación , Relación Dosis-Respuesta a Droga
19.
Artículo en Inglés | MEDLINE | ID: mdl-38457114

RESUMEN

The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.

20.
Cureus ; 16(1): e52266, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38352100

RESUMEN

BACKGROUND: Orthodontists, like any other medical professional, are susceptible to cumulative stressors and their undesirable consequences. The study aims to assess the self-perceived occupational stress levels and the psychological link between predictors and stress among orthodontic practitioners in India. MATERIALS AND METHODS: The participants in this cross-sectional study are active members of the Indian Orthodontic Society (IOS). The data for the survey were collected by a previously validated closed-ended occupational stress assessment (OSA) questionnaire and a job satisfaction questionnaire, which were sent through the registered e-mails. A five-point Likert scale was used to assess the severity of individual stressors, and an overall severity score was obtained by summing up the individual scores. The predictors of stress based on socio-demographic parameters were assessed using a binomial multiple logistic equation. Statistical significance was set at a p-value of <0.05. RESULTS: A total of 311 responses were received. Male orthodontists, unmarried, in the age group of 30-40 years, working in urban areas without any academic attachment were more stressed compared to the other groups in the respective categories. Tiredness/headache (39%) was reported as the most common consequence of occupational stress. The most concerning stressor was patients not wearing retainers. Orthodontists showed overall job satisfaction that is negatively correlated to overall stress (p <0.0001)(r = -0.260). CONCLUSION: A profound variation in stress levels was found among the orthodontists with their socio-demographic and professional characteristics. Despite the stress, orthodontists were highly satisfied with their careers.

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