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BACKGROUND: Aeromonas hydrophila is a widely recognized broad-spectrum pathogen that primarily targets the gastrointestinal tract. Type IV pili (T4P) are proteinaceous nano-machines located on the bacterial cell surface, playing a crucial role in host colonization and infection. Regrettably, the T4P systems of A. hydrophila remain largely underexplored. METHODS: A. hydrophila genomes with complete genome assembly and annotation reports up to 31 March 2023, were obtained from the NCBI Genome database or KEGG genome database, followed by a global search for T4P secretion system genes. Protein sequences of these manually curetted genes were used as secondary quarry for Synteny analysis. Protein-protein interaction analysis was performed by string analysis and in silico study of genomic islands. RESULTS: We identified 27 orthologs of type IV pili (T4P) nano-machine components in A. hydrophila. These orthologs are primarily distributed across three operons: pilABCD, pilMNOPQ, and pilVWXY. While the first two operons are commonly found in all experimental genomes, the presence of the pilVWXY operon, coding for 11 orthologs, is reported here for the first time in A. hydrophila. Notably, the complete pilVWXY operon is absent in nonvirulent strains. A genomic islands study between a nonvirulent and hypervirulent strain also confirms absence of most of the genes coded by pilVWXY in nonvirulent strain. Interestingly, among the 51 experimental genomes analyzed, the pilVWXY operon was completely absent in 10 strains, most of which are categorized as nonvirulent; Conclusions: The distribution of two major type IV pili (T4P) nano-machines, PilABCDMNOPQ and PilVWXY, is reported here for the first time in A. hydrophila. Additionally, this study suggests a potential role for the PilVWXY nano-machine in establishing human disease.

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Ralstonia solanacearum (Rs), the causative agent of devastating wilt disease in several major and minor economic crops, is considered one of the most destructive bacterial plant pathogens. However, the mechanism(s) by which Rs counteracts host-associated environmental stress is still not clearly elucidated. To investigate possible stress management mechanisms, orthologs of stress-responsive genes in the Rs genome were searched using a reference set of known genes. The genome BLAST approach was used to find the distributions of these orthologs within different Rs strains. BLAST results were first confirmed from the KEGG Genome database and then reconfirmed at the protein level from the UniProt database. The distribution pattern of these stress-responsive factors was explored through multivariate analysis and STRING analysis. STRING analysis of stress-responsive genes in connection with different secretion systems of Rs was also performed. Initially, a total of 28 stress-responsive genes of Rs were confirmed in this study. STRING analysis revealed an additional 7 stress-responsive factors of Rs, leading to the discovery of a total of 35 stress-responsive genes. The segregation pattern of these 35 genes across 110 Rs genomes was found to be almost homogeneous. Increasing interactions of Rs stress factors were observed in six distinct clusters, suggesting six different types of stress responses: membrane stress response (MSR), osmotic stress response (OSR), oxidative stress response (OxSR), nitrosative stress response (NxSR), and DNA damage stress response (DdSR). Moreover, a strong network of these stress responses was observed with type 3 secretion system (T3SS), general secretory proteins (GSPs), and different types of pili (T4P, Tad, and Tat). To the best of our knowledge, this is the first report on overall stress response management by Rs and the potential connection with secretion systems.

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Quantum cycles in established heat engines can be modeled with various quantum systems as working substances. For example, a heat engine can be modeled with an infinite potential well as the working substance to determine the efficiency and work done. However, in this method, the relationship between the quantum observables and the physically measurable parameters-i.e., the efficiency and work done-is not well understood from the quantum mechanics approach. A detailed analysis is needed to link the thermodynamic variables (on which the efficiency and work done depends) with the uncertainty principle for better understanding. Here, we present the connection of the sum uncertainty relation of position and momentum operators with thermodynamic variables in the quantum heat engine model. We are able to determine the upper and lower bounds on the efficiency of the heat engine through the uncertainty relation.

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Various techniques to tackle the black hole information paradox have been proposed. A new way out to tackle the paradox is via the use of a pseudo-density operator. This approach has successfully dealt with the problem with a two-qubit entangle system for a single black hole. In this paper, we present the interaction with a binary black hole system by using an arrangement of the three-qubit system of Greenberger-Horne-Zeilinger (GHZ) state. We show that our results are in excellent agreement with the theoretical value. We have also studied the interaction between the two black holes by considering the correlation between the qubits in the binary black hole system. The results depict a complete agreement with the proposed model. In addition to the verification, we also propose how modern detection of gravitational waves can be used on our optical setup as an input source, thus bridging the gap with the gravitational wave's observational resources in terms of studying black hole properties with respect to quantum information and entanglement.

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Established heat engines in quantum regime can be modeled with various quantum systems as working substances. For example, in the non-relativistic case, we can model the heat engine using infinite potential well as a working substance to evaluate the efficiency and work done of the engine. Here, we propose quantum heat engine with a relativistic particle confined in the one-dimensional potential well as working substance. The cycle comprises of two isothermal processes and two potential well processes of equal width, which forms the quantum counterpart of the known isochoric process in classical nature. For a concrete interpretation about the relation between the quantum observables with the physically measurable parameters (like the efficiency and work done), we develop a link between the thermodynamic variables and the uncertainty relation. We have used this model to explore the work extraction and the efficiency of the heat engine for a relativistic case from the standpoint of uncertainty relation, where the incompatible observables are the position and the momentum operators. We are able to determine the bounds (the upper and the lower bounds) of the efficiency of the heat engine through the thermal uncertainty relation.

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Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.

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BACKGROUND: Several strains of Klebsiella pneumoniae are responsible for causing pneumonia in lung and thereby causing death in immune-suppressed patients. In recent year, few investigations have reported the enhancement of K. pneumoniae population in patients using corticosteroid containing inhaler. OBJECTIVES: The biological mechanism(s) behind this increased incidence has not been elucidated. Therefore, the objective of this investigating was to explore the relation between Klebsiella pneumoniae and increment in carbapenamase producing Enterobacteriaceae score (ICS). METHODS: The available genomes of K. pneumoniae and the amino acid sequences of steroid catabolism pathway enzymes were taken from NCBI database and KEGG pathway tagged with UniPort database, respectively. We have used different BLAST algorithms (tBLASTn, BLASTp, psiBLAST, and delBLAST) to identify enzymes (by their amino acid sequence) involved in steroid catabolism. RESULTS: A total of 13 enzymes (taken from different bacterial candidates) responsible for corticosteroid degradation have been identified in the genome of K. pneumoniae. Finally, 8 enzymes (K. pneumoniae specific) were detected in four clinical strains of K. pneumoniae. This investigation intimates that this ability to catabolize corticosteroids could potentially be one mechanism behind the increased pneumonia incidence. CONCLUSION: The presence of corticosteroid catabolism enzymes in K. pneumoniae enhances the ability to utilize corticosteroid for their own nutrition source. This is the first report to demonstrate the corticosteroid degradation pathway in clinical strains of K. pneumoniae.

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The biotechnological production of fragrances is a recent trend that has expanded rapidly in the last two decades. Vanillin is the second most popular flavoring agent after saffron and is extensively used in various applications, e.g., as a food additive in food and beverages and as a masking agent in various pharmaceutical formulations. It is also considered a valuable product for other applications, such as metal plating and the production of other flavoring agents, herbicides, ripening agents, antifoaming agents, and personal and home-use products (such as in deodorants, air fresheners, and floor-polishing agents). In general, three types of vanillin, namely natural, biotechnological, and chemical/synthetic, are available on the market. However, only natural and nature-identical (biotechnologically produced from ferulic acid only) vanillins are considered as food-grade additives by most food-safety control authorities worldwide. In the present review, we summarize recent trends in fermentation technology for vanillin production and discuss the importance of the choice of raw materials for the economically viable production of vanillin. We also describe the key enzymes used in the biotechnological production of vanillin as well as their underlying genes. Research to advance our understanding of the molecular regulation of different pathways involved in vanillin production from ferulic acid is still ongoing. The enhanced knowledge is expected to offer new opportunities for the application of metabolic engineering to optimize the production of nature-identical vanillin. © 2018 Society of Chemical Industry.

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Bacillus thuringiensis (Bt) is a Gram-positive, spore-forming, soil bacterium, which is very popular bio-control agent in agricultural and forestry. In general, B. thuringiensis secretes an array of insecticidal proteins including toxins produced during vegetative growth phase (such as secreted insecticidal protein, Sip; vegetative insecticidal proteins, Vip), parasporal crystalline δ-endotoxins produced during vegetative stationary phase (such as cytolytic toxin, Cyt; and crystal toxin, Cry), and ß-exotoxins. Till date, a wide spectrum of Cry proteins has been reported and most of them belong to three-domain-Cry toxins, Bin-like toxin, and Etx_Mtx2-like toxins. To the best of our knowledge, neither Bt insecticidal toxins are exclusive to Bt nor all the strains of Bt are capable of producing insecticidal Bt toxins. The lacuna in their latest classification has also been discussed. In this review, the updated information regarding the insecticidal Bt toxins and their different mode of actions were summarized. Before applying the Bt toxins on agricultural field, the non-specific effects of toxins should be investigated. We also have summarized the problem of insect resistance and the strategies to combat with this problem. We strongly believe that this information will help a lot to the budding researchers in the field of modern pest control biotechnology.

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Disease in agricultural field is a big problem that causes a massive loss in production. In this present investigation, we have reported a soil-borne bacterium Bacillus cereus IB311 which is antagonistic to plant pathogens (Pseudomonas syringae and Agrobacterium tumefaciens), and could make a substantial contribution to the prevention of plant diseases. To prove the practical application, the strain was directly applied in agricultural field. The results demonstrated that B. cereus IB311 has increased the production (20% and 26% in term of average pod number per plant, average seed number per pod, and seed yield per experimental plot) in ground nut (Arachis hypogaea var. Koushal, G201) and sesame (Sesamum indicum var. Kanak), respectively. To reduce the production cost, the biomass production was optimized through response surface methodology (RSM). Interactions of three variables (glucose, beef extract and inoculum) were studied using Central Composite Design. According to our analysis, optimum production of Bacillus cereus IB311 (5.383 µg/ mL) may be obtained at glucose 1.985%, beef extract 1.615% and inoculums size 0.757%. Therefore, we strongly believe that the application of this strain in agricultural field as bio-controlling agent will definitely enhance the production yield and will reduce the disease risk.

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Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]. To solve this challenge, we have screened the four well-established candidate gene sequences (i.e., rbcL, matK, trnL-trnF IGS, and 18S-ITS1-5.8S-ITS2-28S nrDNA) of 65 Indian orchid species. We also have included 31 different species of Dendrobium to identify the suitable locus for resolving the phylogeny-related problem below the taxonomic rank of genus. The Consortium for the Barcode of Life has recommended the locus rbcL and matK for barcoding of all land plants, including orchids. However, in this study, matK and rbcL (species resolving capacity 52% and 48%, respectively) were found to work above the taxonomic limit of genus, and thus cannot be considered a suitable tool to resolve closely related species of Dendrobium, whereas, we found that the locus 18S-ITS1-5.8S-ITS2-28S nrDNA is the best choice with the highest species resolving ability (95.23%) and the highest mean Kimura 2-parameter distance (254 for intergeneric and 144 for intrageneric) for phylogeny construction, and thus have been taken as the most promising single-locus barcode for orchids.

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Food security and safety are the major concern in ever expanding human population on the planet earth. Each and every year insect pests cause a serious damage in agricultural field that cost billions of dollars annually to farmers. The loss in term of productivity and high cost of chemical pesticides enhance the production cost. Irrespective use of chemical pesticides (such as Benzene hexachloride, Endosulfan, Aldicarb, and Fenobucarb) in agricultural field raised several types of environmental issues. Furthermore, continuous use of chemical pesticides creates a selective pressure which helps in emerging of resistance pest. These excess chemical pesticide residues also contaminate the environment including the soil and water. Therefore, the biological control of insect pest in the agricultural field gains more importance due to food safety and environment friendly nature. In this regard, bacterial insecticides offer better alternative to chemical pesticides. It not only helps to establish food security through fighting against insect pests but also ensure the food safety. In this review, we have categorized insect pests and the corresponding bacterial insecticides, and critically analyzed the importance and mode of action of bacterial pesticides. We also have summarized the use of biopesticides in integrated pest management system. We have tried to focus the future research area in this field for the upcoming scientists.

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Biogas is a combination of methane, CO2, nitrogen, H2S and traces of few other gases. Almost any organic waste can be biologically transformed into biogas and other energy-rich organic compounds through the process of anaerobic digestion (AD) and thus helping in sustainable waste management. Although microbes are involved in each step of AD, knowledge about those microbial consortia is limited due to the lack of phylogenetic and metabolic data of predominantly unculturable microorganisms. However, culture-independent methods like PCR-based ribotyping has been successfully employed to get information about the microbial consortia involved in AD. Microbes identified have been found to belong mainly to the bacterial phyla of Proteobacteria, Chloroflexi, Firmicutes and Bacteroidetes. Among the archaeal population, the majority have been found to be methanogens (mainly unculturable), the remaining being thermophilic microbes. Thus, the AD process as a whole could be controlled by regulating the microbial consortia involved in it. Optimization in the feedstock, pH, temperature and other physical parameters would be beneficial for the microbial growth and viability and thus helpful for biogas production in AD. Besides, the biogas production is also dependent upon the activity of several key genes, ion-specific transporters and enzymes, like genes coding for methyl-CoM reductase, formylmethanofuran transferase, formate dehydrogenase present in the microbes. Fishing for these high-efficiency genes will ultimately increase the biogas production and sustain the production plant.

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Pathogenic Aeromonas hydrophila Strain AO1 bears a 21kb plasmid encoding several virulence determinants. Infection studies revealed that this isolate induced cytotoxicity in BALB/c mice splenic macrophages involving reactive oxygen species generation. DNA gel, Hoechst 33342, annexin-V and TUNEL assay documented macrophage death induced by 21kb plasmid bearing isolates to be apoptotic in nature. Apoptosis induced by the plasmid bearing isolates involved initiator caspase-8 and caspase-9 and executed by effector caspase-3. ELISA revealed the wild-type isolate as weak inducer of pro-inflammatory cytokine IL-1beta. Oral infection with wild-type isolates caused systemic infection in BALB/c mice. With plasmid curing the isolate looses several virulence attributes including cytotoxic potential. The cured isolate induced significant amounts of IL-1beta from infected macrophages, disseminated into Peyer's patches, spleen and liver but never attained the bacterial loads recorded with wild-type isolates and were rapidly cleared. Transformation of 21kb plasmid helped the cured bacteria regain wild-type virulence attributes, apoptotic potential and ability to cause systemic infection in mice. Thus the 21kb plasmid is a virulence factor in mice. It helps in suppressing the production of pro-inflammatory cytokine IL-1beta and induced apoptosis of host macrophages enabling A. hydrophila to evade host immune responses and establish systemic infection in mice.

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