Comparative Genomic and Functional Analyses for Insights into Pantoea agglomerans Strains Adaptability in Diverse Ecological Niches.

Pantoea agglomerans inhabit diverse ecological niches, ranging from epiphytes and endophytes in plants, body of animals, and occasionally in the human system. This multifaceted bacterium contributes substantially to plant growth promotion, stress resilience, and biocontrol but can also act as a pathogen to its host. The genetic determinants underlying these diverse functions remain largely unfathomed and to uncover this phenomenon, nineteen strains of Pantoea agglomerans were selected and analyzed. Genome-to-Genome Distance Calculator (GGDC) which uses the Genome Blast Distance Phylogeny (GBDP) technique to calculate digital DDH values. Phylogenetic analysis via Genome-to-Genome distance, Average Nucleotide Identity, and Amino Acid Identity calculation revealed that all strains belonged to the genus Pantoea. However, strain 33.1 had a lower value than the threshold for the same species delineation. Bacterial Pan Genome Analysis (BPGA) Pipeline and MinPath analysis revealed genetic traits associated with environmental resilience, such as oxidative stress, UV radiation, temperature extremes, and metabolism of distinct host-specific carbohydrates. Protein-protein interactome analysis illustrated osmotic stress proteins closely linked with core proteins, while heavy metal tolerance, nitrogen metabolism, and Type III and VI secretion systems proteins generally associated with pathogenicity formed a separate network, indicating strain-specific characteristics. These findings shed new light on the intricate genetic architecture of Pantoea agglomerans, revealing its adaptability to inhabit diverse niches and thrive in varied environments.

Draft genome sequence of halotolerant plant growth-promoting Bacillus paralicheniformis MHN12.

Bacillus paralicheniformis MHN12 possesses a 4,245,453-base pair genome with 45.9% G + C content, including 1 CRISPR, 80 tRNA, 8 rRNA genes, and 4,418 predicted coding sequences . MHN12 exhibits high salinity tolerance and plant growth-promoting abilities, making it a promising bioinoculant for enhancing plant growth in saline soils.

The PPE2 protein of Mycobacterium tuberculosis is secreted during infection and facilitates mycobacterial survival inside the host.

Mycobacterium tuberculosis secrets various effector proteins to evade host immune responses for facilitating its intracellular survival. The bacterial genome encodes several unique PE/PPE family proteins, which have been implicated to play important role in mycobacterial pathogenesis. A member of this family, PPE2 have been shown to contain a monopartite nuclear localization signal (NLS) and a DNA binding domain. In this study, we demonstrate that PPE2 protein is present in the sera of mice infected with either M. smegmatis expressing PPE2 or a clinical strain of M. tuberculosis (CDC1551). It was found that exogenously added PPE2 can permeate through the macrophage cell membrane and eventually translocate into the nucleus which requires the presence of NLS which showed considerable homology to HIV-tat like cell permeable peptides. Exogenously added PPE2 could inhibit NO production and decreased mycobacterial survival in macrophages. PPE2-null mutant of M. tuberculosis failed to inhibit NO production and had poor survival in macrophages which could be rescued by complementation with full-length PPE2. PPE2-null mutants also had poor survival in the lungs of infected mice indicating that PPE2 even when present in the bloodstream can confer a survival advantage to mycobacteria.

The cause-effect relation of tuberculosis on incidence of diabetes mellitus.

Tuberculosis (TB) is one of the oldest human diseases and is one of the major causes of mortality and morbidity across the Globe. Mycobacterium tuberculosis (Mtb), the causal agent of TB is one of the most successful pathogens known to mankind. Malnutrition, smoking, co-infection with other pathogens like human immunodeficiency virus (HIV), or conditions like diabetes further aggravate the tuberculosis pathogenesis. The association between type 2 diabetes mellitus (DM) and tuberculosis is well known and the immune-metabolic changes during diabetes are known to cause increased susceptibility to tuberculosis. Many epidemiological studies suggest the occurrence of hyperglycemia during active TB leading to impaired glucose tolerance and insulin resistance. However, the mechanisms underlying these effects is not well understood. In this review, we have described possible causal factors like inflammation, host metabolic changes triggered by tuberculosis that could contribute to the development of insulin resistance and type 2 diabetes. We have also discussed therapeutic management of type 2 diabetes during TB, which may help in designing future strategies to cope with TB-DM cases.

Mild-to-moderate severity of psoriasis may be assessed remotely based on photographs and self-reported extent of skin involvement.

Background: Remote monitoring was used to assess and manage skin diseases. Objective: To investigate to what extent smartphone photographs along with a self-reported body region (BR) score can be used to evaluate psoriasis severity. Methods: Psoriasis severity was assessed in the clinic using the psoriasis area and severity index and the physician's global assessment. On the same day, the patients took a photograph of a representative lesion from 4 BR (head/neck, upper limbs, trunk, and lower limbs) and completed a questionnaire about BR score. The photographs were rated by 5 dermatologists. Intraclass correlation coefficients with 95% CIs were calculated. Results: Overall, 32 were included, of which 6% had almost clear, 69% had mild, and 25% had moderate psoriasis. Perfect agreement between the self-reported and the doctors' BR score was observed for 59%, and near-perfect agreement (deviation of maximum 1 score) was 92%. The intraclass correlation coefficient between clinical and photographic psoriasis area and severity index was 0.78 (95% CI, 0.55-0.90), and for physician's global assessment, perfect agreement was 53%. Conclusions: The agreement between psoriasis severity assessed clinically and by photographs was good in a study setting. This gives the opportunity to remotely assess psoriasis severity by combining photographs with self-reported BR scores.

Assessing anatomical distribution of atopic dermatitis identifies a cluster of patients with late onset and low risk of asthma and allergy: An observational study.

Background and Aims: A better understanding of distinct subgroups in atopic dermatitis (AD) is warranted. The aim was to identify and determine characteristics of clusters based on anatomical location of AD. Methods: In this 8-week, observational, decentralized study, patients with AD completed a baseline questionnaire about anatomical location and severity of AD, and a principal component analysis (PCA) was applied to identify clusters. The Patient-Oriented Eczema Measure (POEM) was completed weekly and photographs of affected body areas were captured by the participants' own smartphones. From the weekly photographs, the AD severity was evaluated using the intensity part of the SCORing Atopic Dermatitis. Results: Fifty-five participants were recruited, of which 53 completed the baseline questionnaire with a mean POEM of 14.5 (SD: 5.6). The PCA analysis revealed three clusters, with AD predominantly on the shins, knees, and genitals (Cluster 1), with involvement of the upper body (Cluster 2), and with AD on the hands and feet (Cluster 3). Cluster 1 had a lower mean POEM score (11.12, SD: 5.3) compared with Clusters 2 (12.64, SD: 4.5) and 3 (15.98, SD: 4.7), respectively (p = 0.007). Further, Cluster 1 had the highest age of AD onset (mean 9.5 vs. 2.5 and 4.7 years, p = 0.02) and the lowest proportion of asthma/allergy (47% vs. 82% and 90%, p = 0.01). Conclusion: Three clusters of patients with AD based on affected body areas were identified. The cluster with involvement of legs and genitals was characterized by the oldest age of AD onset and the lowest prevalence of asthma/allergy.

Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte.

Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.

Biogenic Synthesis of Zinc Nanoparticles, Their Applications, and Toxicity Prospects.

Nanofertilizers effectively deliver the micronutrients besides reducing the phytotoxicity and environmental damage associated with chemical fertilizers. Zinc, an essential micronutrient, is significant for chloroplast development, activation of certain enzymes, and primary metabolism. Nano zinc oxide (ZnO) is the most widely used zinc nanoparticle. Concerns regarding the toxicity of conventional physical and chemical methods of synthesizing the nanoparticles have generated the need for a green approach. It involves the biogenic synthesis of metallic nanoparticles using plants and microorganisms. Microbe-mediated biogenic synthesis of metallic nanoparticles is a bottom-up approach in which the functional biomolecules of microbial supernatant reduce the metal ions into its nanoparticles. This review discusses the biological synthesis of nano-ZnO from microorganisms and related aspects such as the mechanism of synthesis, factors affecting the same, methods of application, along with their role in conferring drought stress tolerance to the plants and challenges involved in their large-scale synthesis and applications.

Endophytism: A Multidimensional Approach to Plant-Prokaryotic Microbe Interaction.

Plant growth and development are positively regulated by the endophytic microbiome via both direct and indirect perspectives. Endophytes use phytohormone production to promote plant health along with other added benefits such as nutrient acquisition, nitrogen fixation, and survival under abiotic and biotic stress conditions. The ability of endophytes to penetrate the plant tissues, reside and interact with the host in multiple ways makes them unique. The common assumption that these endophytes interact with plants in a similar manner as the rhizospheric bacteria is a deterring factor to go deeper into their study, and more focus was on symbiotic associations and plant-pathogen reactions. The current focus has shifted on the complexity of relationships between host plants and their endophytic counterparts. It would be gripping to inspect how endophytes influence host gene expression and can be utilized to climb the ladder of "Sustainable agriculture." Advancements in various molecular techniques have provided an impetus to elucidate the complexity of endophytic microbiome. The present review is focused on canvassing different aspects concerned with the multidimensional interaction of endophytes with plants along with their application.

Modified Artificial Bee Colony Algorithm-Based Strategy for Brain Tumor Segmentation.

Medical image segmentation is a technique for detecting boundaries in a 2D or 3D image automatically or semiautomatically. The enormous range of the medical image is a considerable challenge for image segmentation. Magnetic resonance imaging (MRI) scans to aid in the detection and existence of brain tumors. This approach, however, requires exact delineation of the tumor location inside the brain scan. To solve this, an optimization algorithm will be one of the most successful techniques for distinguishing pixels of interest from the background, but its performance is reliant on the starting values of the centroids. The primary goal of this work is to segment tumor areas within brain MRI images. After converting the gray MRI image to a color image, a multiobjective modified ABC algorithm is utilized to separate the tumor from the brain. The intensity determines the RGB color generated in the image. The simulation results are assessed in terms of performance metrics such as accuracy, precision, specificity, recall, F-measure, and the time in seconds required by the system to segment the tumor from the brain. The performance of the proposed algorithm is computed with other algorithms like the single-objective ABC algorithm and multiobjective ABC algorithm. The results prove that the proposed multiobjective modified ABC algorithm is efficient in analyzing and segmenting the tumor from brain images.

Mild to moderate atopic dermatitis severity can be reliably assessed using smartphone-photographs taken by the patient at home: A validation study.

BACKGROUND: The use of photographs to diagnose and monitor skin diseases is gaining ground. OBJECTIVES: To investigate the validity and reliability of photographic assessments of atopic dermatitis (AD) severity. METHODS: AD severity was evaluated in the clinic by two assessors using the Eczema Area and Severity Index (EASI), SCOring Atopic Dermatitis (SCORAD), and Investigator's Global Assessment (IGA). Participants photographed the lesions with their own smartphone and completed a questionnaire about the extent of eczema the same day from home. The photographs were assessed twice with an 8 weeks interval by five dermatologists experienced in photographic evaluations. Intraclass correlation coefficients (ICC) with 95% confidence interval (CI) were applied. RESULTS: Seventy-nine participants were enrolled. The ICC between clinical EASI and photographic EASI was 0.88 (95% CI 0.81-0.93), and 0.86 (0.70-0.93) between clinical SCORAD and photographic SCORAD. Perfect agreement between clinical IGA and photograph IGA was observed for 62%, with the difference between the two never deviating with more than 1 score. The inter-rater ICC for photographic EASI and photographic SCORAD, respectively, was 0.90 (0.85-0.94), and 0.96 (0.91-0.98). The intra-rater agreements between the first and second assessments varied from 0.95 to 0.98 for photographic EASI, and from 0.86 to 0.94 for photographic SCORAD. CONCLUSION: There was high agreement between mild to moderate AD severity assessed clinically and based on smartphone photographs. Further, the photographic assessments can be reproduced with high reliability.

Aeromonas hydrophila inhibits autophagy triggering cytosolic translocation of mtDNA which activates the pro-apoptotic caspase-1/IL-1ß-nitric oxide axis in headkidney macrophages.

The molecular mechanisms underlying Aeromonas hydrophila-pathogenesis are not well understood. Using head kidney macrophages (HKM) of Clarias gariepinus, we previously reported the role of ER-stress in A. hydrophila-induced pathogenesis. Here, we report that PI3K/PLC-induced cytosolic-Ca2+ imbalance induces the expression of pro-apoptotic ER-stress marker, CHOP in A. hydrophila-infected HKM. CHOP promotes HKM apoptosis by inhibiting AKT activation and enhancing JNK signaling. Elevated mitochondrial ROS (mtROS) was recorded which declined significantly by ameliorating ER-stress and in the presence of ER-Ca2+ release modulators (2-APB and dantrolene) and mitochondrial-Ca2+ uptake inhibitor, Ru360, together suggesting the role of ER-mitochondrial Ca2+ dynamics in mtROS generation. Inhibiting mtROS production reduced HKM death implicating the pro-apoptotic role of mtROS in A. hydrophila-pathogenesis. The expression of autophagic proteins (LC3B, beclin-1, and atg 5) was suppressed in the infected HKM. Our results with autophagy-inducer rapamycin demonstrated that impaired autophagy favored the cytosolic accumulation of mitochondrial DNA (mtDNA) and the process depended on mtROS levels. Enhanced caspase-1 activity and IL-1ß production was detected and transfection studies coupled with pharmacological inhibitors implicated mtROS/mtDNA axis to be crucial for activating the caspase-1/IL-1ß cascade in infected HKM. RNAi studies further suggested the involvement of IL-1ß in generating pro-apoptotic NO in A. hydrophila-infected HKM. Our study suggests a novel role of ER-mitochondria cross-talk in regulating A. hydrophila pathogenesis. Based on our observations, we conclude that A. hydrophila induces ER-stress and inhibits mitophagy resulting in mitochondrial dysfunction which leads to mtROS production and translocation of mtDNA into cytosol triggering the activation of caspase-1/IL-1ß-mediated NO production, culminating in HKM apoptosis.

Remote Rating of Atopic Dermatitis Severity Using Photo-Based Assessments: Proof-of-Concept and Reliability Evaluation.

BACKGROUND: Digital imaging of dermatological patients is a novel approach to remote assessment and has recently become more relevant since telehealth and remote decentralized clinical trials are gaining ground. OBJECTIVE: We aimed to investigate whether photographs taken by a smartphone are of adequate quality to allow severity assessments to be made and to explore the usefulness of an established atopic dermatitis severity assessment instrument on photograph evaluation. METHODS: During scheduled visits in a previously published study, the investigating doctor evaluated the severity of atopic dermatitis using the Scoring AD (SCORAD) index and took photographs of the most representative lesions (target lesions) with both a smartphone and a digital single-lens reflex camera (DSLR). The photographs were then assessed by 5 dermatologists using the intensity items of the SCORAD (iSCORAD), which consists of erythema, oedema/papulation, excoriations, lichenification, oozing/crusts, and dryness (scale 0-3, maximum score 18). The mean iSCORAD of the photographs was calculated and compared with in-person assessments using Pearson correlation and Bland-Altman plots. Intraclass correlation coefficients were used for interrater reliability. RESULTS: A total of 942 photographs from 95 patients were assessed. The iSCORAD based on smartphone photographs correlated strongly with the evaluations performed in person (iSCORAD: r=0.78, P<.001; objective SCORAD: r=0.81, P<.001; and total SCORAD: r=0.78, P<.001). For iSCORAD specifically, a Bland-Altman plot showed a difference in mean score of 1.31 for in-person and remote iSCORAD. In addition, the interrater agreement between the 5 rating dermatologists was 0.93 (95% CI 0.911-0.939). A total of 170 lesions were photographed, and the difference in mean scores was 1.32, 1.13, and 1.43 between in-person and remote evaluations based on photographs taken by a DSLR camera, a smartphone without flash, and a smartphone with flash, respectively. CONCLUSIONS: In terms of quality, remote atopic dermatitis severity assessments based on photographs are comparable to in-person assessments, and smartphone photos can be used to assess atopic dermatitis severity to a similar degree as photographs from a DSLR camera. Further, the variation in how the dermatologists in this study rated the iSCORAD based on the photographs was very low.

mtROS Induced via TLR-2-SOCE Signaling Plays Proapoptotic and Bactericidal Role in Mycobacterium fortuitum-Infected Head Kidney Macrophages of Clarias gariepinus.

The mechanisms underlying Mycobacterium fortuitum-induced mycobacteriosis remain unexplored. Using head kidney macrophages (HKM) from catfish (Clarias gariepinus), we report that Ca2+ surge across mitochondrial-Ca2+ uniporter (MICU), and consequent mitochondrial ROS (mtROS) production, is imperative for mycobactericidal activity. Inhibition of mtROS alleviated HKM apoptosis and enhanced bacterial survival. Based on RNA interference (RNAi) and inhibitor studies, we demonstrate that the Toll-like receptor (TLR)-2-endoplasmic reticulum (ER) stress-store-operated calcium entry (SOCE) axis is instrumental for activating the mt-Ca2+/mtROS cascade in M. fortuitum-infected HKM. Additionally, pharmacological inhibition of mtROS attenuated the expression of CHOP, STIM1, and Orai1, which suggests a positive feedback loop between ER-stress-induced SOCE and mtROS production. Elevated tumor necrosis factor alpha (TNF-α) levels and caspase-8 activity were observed in HKM consequent to M. fortuitum infection, and our results implicate that mtROS is crucial in activating the TNF-mediated caspase-8 activation. Our results for the first time demonstrate mitochondria as an innate immune signaling center regulating mycobacteriosis in fish. We conclude that M. fortuitum-induced persistent SOCE signaling leads to mtROS production, which in turn activates the TNF-α/caspase-8 axis culminating in HKM apoptosis and bacterial clearance.

The coordinated outcome of STIM1-Orai1 and superoxide signalling is crucial for headkidney macrophage apoptosis and clearance of Mycobacterium fortuitum.

The mechanisms underlying M. fortuitum-induced pathogenesis remains elusive. Using headkidney macrophages (HKM) from Clarias gariepinus, we report that TLR-2-mediated internalization of M. fortuitum is imperative to the induction of pathogenic effects. Inhibiting TLR-2 signalling alleviated HKM apoptosis, thereby favouring bacterial survival. Additionally, TLR-2-mediated cytosolic calcium (Ca2+)c elevation was instrumental for eliciting ER-stress in infected HKM. ER-stress triggered the activation of membrane-proximal calcium entry channels comprising stromal interaction molecule 1 (STIM1) and calcium-release activated calcium channel 1 (Orai1). RNAi studies suggested STIM1-Orai1 signalling initiate calpain-mediated cleavage of nitric oxide synthase interacting protein, prompting the release of pro-apoptotic nitric oxide. Inhibiting STIM1-Orai1 signalling attenuated superoxide production (O2•-) and vice versa. We conclude, TLR-2-induced ER-stress triggers STIM1/Orai1 expression and that the reciprocal association between STIM1-Orai1 signalling and oxidative stress is critical for sustaining (Ca2+)c level, thereby prolonging ER-stress and maintenance of pro-oxidant rich environment to induce HKM apoptosis and bacterial clearance.