A prophage tail-like protein facilitates the endophytic growth of Burkholderia gladioli and mounting immunity in tomato.

A prophage tail-like protein (Bg_9562) of Burkholderia gladioli strain NGJ1 possesses broad-spectrum antifungal activity, and it is required for the bacterial ability to forage over fungi. Here, we analyzed whether heterologous overexpression of Bg_9562 or exogenous treatment with purified protein can impart disease tolerance in tomato. The physiological relevance of Bg_9562 during endophytic growth of NGJ1 was also investigated. Bg_9562 overexpressing lines demonstrate fungal and bacterial disease tolerance. They exhibit enhanced expression of defense genes and activation of mitogen-activated protein kinases. Treatment with Bg_9562 protein induces defense responses and imparts immunity in wild-type tomato. The defense-inducing ability lies within 18-51 aa region of Bg_9562 and is due to sequence homology with the bacterial flagellin epitope. Interaction studies suggest that Bg_9562 is perceived by FLAGELLIN-SENSING 2 homologs in tomato. The silencing of SlSERK3s (BAK1 homologs) prevents Bg_9562-triggered immunity. Moreover, type III secretion system-dependent translocation of Bg_9562 into host apoplast is important for elicitation of immune responses during colonization of NGJ1. Our study emphasizes that Bg_9562 is important for the endophytic growth of B. gladioli, while the plant perceives it as an indirect indicator of the presence of bacteria to mount immune responses. The findings have practical implications for controlling plant diseases.

Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors.

Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor non-canonical helix-turn-helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin-antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.

The alternative sigma factors, rpoN1 and rpoN2 are required for mycophagous activity of Burkholderia gladioli strain NGJ1.

Bacteria utilize RpoN, an alternative sigma factor (σ54) to grow in diverse habitats, including nitrogen-limiting conditions. Here, we report that a rice-associated mycophagous bacterium Burkholderia gladioli strain NGJ1 encodes two paralogues of rpoN viz. rpoN1 and rpoN2. Both of them are upregulated during 24 h of mycophagous interaction with Rhizoctonia solani, a polyphagous fungal pathogen. Disruption of either one of rpoNs renders the mutant NGJ1 bacterium defective in mycophagy, whereas ectopic expression of respective rpoN genes restores mycophagy in the complementing strains. NGJ1 requires rpoN1 and rpoN2 for efficient biocontrol to prevent R. solani to establish disease in rice and tomato. Further, we have identified 17 genes having RpoN regulatory motif in NGJ1, majority of them encode potential type III secretion system (T3SS) effectors, nitrogen assimilation, and cellular transport-related functions. Several of these RpoN regulated genes as well as certain previously reported T3SS apparatus (hrcC and hrcN) and effector (Bg_9562 and endo-ß-1,3-glucanase) encoding genes are upregulated in NGJ1 but not in ΔrpoN1 or ΔrpoN2 mutant bacterium, during mycophagous interaction with R. solani. This highlights that RpoN1 and RpoN2 modulate T3SS, nitrogen assimilation as well as cellular transport systems in NGJ1 and thereby promote bacterial mycophagy.

Calcium regulates the mycophagous ability of Burkholderia gladioli strain NGJ1 in a type III secretion system-dependent manner.

BACKGROUND: A rice associated bacterium Burkholderia gladioli strain NGJ1 demonstrates mycophagy, a phenomenon wherein bacteria feed on fungi. Previously, we have reported that NGJ1 utilizes type III secretion system (T3SS) to deliver a prophage tail-like protein (Bg_9562) into fungal cells to establish mycophagy. RESULTS: In this study, we report that calcium ion concentration influences the mycophagous ability of NGJ1 on Rhizoctonia solani, an important fungal pathogen. The calcium limiting condition promotes mycophagy while high calcium environment prevents it. The expression of various T3SS apparatus encoding genes of NGJ1 was induced and secretion of several potential T3SS effector proteins (including Bg_9562) into extracellular milieu was triggered under calcium limiting condition. Using LC-MS/MS proteome analysis, we identified several calcium regulated T3SS effector proteins of NGJ1. The expression of genes encoding some of these effector proteins was upregulated during mycophagous interaction of NGJ1 with R. solani. Further, mutation of one of these genes (endo-ß-1, 3- glucanase) rendered the mutant NGJ1 bacterium defective in mycophagy while complementation with full length copy of the gene restored its mycophagous activity. CONCLUSION: Our study provides evidence that low calcium environment triggers secretion of various T3SS effectors proteins into the extracellular milieu and suggests the importance of cocktail of these proteins in promoting mycophagy.

Benefits of an Android Based Tablet Application in Primary Screening for Eye Diseases in a Rural Population, India.

To investigate the effectiveness, efficiency and cost gains in collecting patient eye health information from remote rural villages of India by trained field investigators through an Android Based Tablet Application namely 'Sankara Electronic Remote Vision Information System (SERVIS)". During January and March 2016, a population based cross-sectional study was conducted in three Indian states employing SERVIS and manual method. The SERVIS application has a 48-items survey instrument programed into the application. Data on 281 individuals were collected for each of these methods as part of screening. The demographic details of individuals between both screening methods were comparable (P>0.05). The mean time (in minutes) to screen an individual by SERVIS was significantly less when compared to manual method (6.57±1.46 versus 11.93±1.53) (P<0.0001). The efficiency of SERVIS in screening was significantly evident as 26% (n = 73) of the patients screened have been referred to campsite and 69.8% (n = 51) of those referred were visited the campsite for a detailed eye examination by an ophthalmologist. The cost of screening through SERVIS is significantly less when compared to manual method; INR 7,633 (USD 113.9) Versus INR 24,780 (USD 370). SERVIS is an effective and efficient tool in terms of patients' referral conversion to the camp site leading to timely detection of potential blinding eye conditions and their appropriate treatment. This ensures timely prevention of avoidable blindness and visual impairment. In addition, the storage and access of eye health epidemiological quality data is helpful to plan appropriate blindness prevention initiatives in rural India.

Acute Kidney Injury among Neonates with Perinatal Asphyxia in a Tertiary Care Centre.

Introduction: Perinatal asphyxia is a very common cause of morbidity and mortality in both term and preterm neonates and ranks the second most important cause of neonatal death. The incidence and importance of acute kidney injury in the neonatal period are becoming increasingly apparent. Early diagnosis and timely management of acute kidney injury is very important in these newborns to avoid other long-term adverse events. This study aimed to find out the prevalence of acute kidney injury among neonates with perinatal asphyxia in a tertiary care centre. Methods: A descriptive cross-sectional study was conducted at the neonatal intensive care unit and nursery in a tertiary care hospital of Eastern Nepal from 1 November 2021 to 31 October 2022 after obtaining ethical approval from the Institutional Review Committee. A convenience sampling method was used. The point estimate was calculated at a 95% Confidence Interval. Results: Among 97 neonates, the prevalence of acute kidney injury was seen among 60 (61.86%) (50.25-69.75, 95% Confidence Interval) neonates. Out of which 42 (70%) were males and 18 (30%) were female. Conclusions: The prevalence of acute kidney injury among neonates with perinatal asphyxia was found to be higher than other studies done in a similar setting. Keywords: acute kidney injury; neonates; prevalence.

Carbon quantum dot-nanocomposite hydrogel as Denovo Nexus in rapid chondrogenesis.

The incapability of cartilage to naturally regenerate and repair chronic muscular injuries urges the development of competent bionic rostrums. There is a need to explore faster strategies for chondrogenic engineering using mesenchymal stem cells (MSCs). Along these lines, rapid chondrocyte differentiation would benefit the transplantation demand affecting osteoarthritis (OA) and rheumatoid arthritis (RA) patients. In this report, a de novo nanocomposite was constructed by integrating biogenic carbon quantum dot (CQD) filler into synthetic hydrogel prepared from dimethylaminoethyl methacrylate (DMAEMA) and acrylic acid (AAc). The dominant structural integrity of synthetic hydrogel along with the chondrogenic differentiation potential of garlic peel derived CQDs led to faster chondrogenesis within 14 days. By means of extensive chemical and morphological characterization techniques, we illustrate that the hydrogel nanocomposite possesses lucrative features to influence rapid chondrogenesis. These results were further corroborated by bright field imaging, Alcian blue staining and Masson trichome staining. Thus, this stratagem of chondrogenic engineering conceptualizes to be a paragon in clinical wound care for the rapid manufacturing of chondrocytes.

Nicotinic Acid Catabolism Modulates Bacterial Mycophagy in Burkholderia gladioli Strain NGJ1.

Burkholderia gladioli strain NGJ1 exhibits mycophagous activity on a broad range of fungi, including Rhizoctonia solani, a devastating plant pathogen. Here, we demonstrate that the nicotinic acid (NA) catabolic pathway in NGJ1 is required for mycophagy. NGJ1 is auxotrophic to NA and it potentially senses R. solani as a NA source. Mutation in the nicC and nicX genes involved in NA catabolism renders defects in mycophagy and the mutant bacteria are unable to utilize R. solani extract as the sole nutrient source. As supplementation of NA, but not FA (fumaric acid, the end product of NA catabolism) restores the mycophagous ability of ΔnicC/ΔnicX mutants, we anticipate that NA is not required as a carbon source for the bacterium during mycophagy. Notably, nicR, a MarR-type of transcriptional regulator that functions as a negative regulator of the NA catabolic pathway is upregulated in ΔnicC/ΔnicX mutant and upon NA supplementation the nicR expression is reduced to the basal level in both the mutants. The ΔnicR mutant produces excessive biofilm and is completely defective in swimming motility. On the other hand, ΔnicC/ΔnicX mutants are compromised in swimming motility as well as biofilm formation, potentially due to the upregulation of nicR. Our data suggest that a defect in NA catabolism alters the NA pool in the bacterium and upregulates nicR which in turn suppresses bacterial motility as well as biofilm formation, leading to mycophagy defects. IMPORTANCE Mycophagy is an important trait through which certain bacteria forage over fungal mycelia and utilize fungal biomass as a nutrient source to thrive in hostile environments. The present study emphasizes that nicotinic acid (NA) is important for bacterial motility and biofilm formation during mycophagy by Burkholderia gladioli strain NGJ1. Defects in NA catabolism potentially alter the cellular NA pool, upregulate the expression of nicR, a negative regulator of biofilm, and therefore suppress bacterial motility as well as biofilm formation, leading to mycophagy defects.

Orthopedic Scaffolds: Evaluation of Structural Strength and Permeability of Fluid Flow via an Open Cell Neovius Structure for Bone Tissue Engineering.

The ability of bone to regenerate itself through mechanobiological responses is its dynamic property. Mechanical cues from a neighboring environment produce the structural strain to promote blood flow and bone marrow mobility that in turn aids the bone regeneration process. Occurrences of these phenomena are crucial for the success of metallic scaffolds implanted in the host bone tissue. Thus, permeability and fluid flow-induced wall shear stress (WSS) are two parameters that directly influence cell bioactivities inside a scaffold and are crucial for effective bone tissue regeneration. Given that the scaffolds shall be implanted in the body, permeability assessment was carried out using non-Newtonian fluid. In this work, the triply periodic minimal surface scaffolds with Neovius architectures were fabricated by using selective laser melting technology. The estimation of fluid flow was carried out using computational fluid dynamics (CFD) analysis with a non-Newtonian blood fluid model. Further, the structural strength of various open cell Neovius lattices was evaluated using a static compression test, and in vitro cell culture using Alamar blue assay was evaluated. Results revealed that the values of intrinsic blood flow permeability of the three-dimensional (3D)-printed open cell porous scaffold with Neovius architecture were of the same order of magnitude as those of human bone, ranging from 0.0025 × 10-9 to 0.0152 × 10-9 m2. The structural elastic modulus and compressive strength of NOCL40, NOCL50, and NOCL60 lattices range from 3.27 to 3.71 GPa and 194 to 205 MPa, respectively. All of the values are comparable to the human bone, thus making these lattices a suitable alternative for orthopedic applications.

N-Terminus Plays a Critical Role for Stabilizing the Filamentous Assembly and the Antifungal Activity of Bg_9562.

Bg_9562, a prophage tail-like protein was earlier shown to be required for bacterial mycophagy by Burkholderia gladioli strain NGJ1. The purified protein exhibited broad-spectrum antifungal activity; however, the structural and mechanistic details vis-à-vis its activity remained elusive. In this study, we have structurally characterized the protein Bg_9562 using negatively stained transmission electron microscopy, molecular modeling and mutagenesis. We find that Bg_9562 shows structural similarity to Gp13, a tail assembly chaperone. The transmission electron microscopy revealed that, Bg_9562 forms long flexible tubular structures. Molecular modeling of the filament like structure divulges that the inter subunit contacts are meditated largely through hydrophobic interactions. Using mutagenesis, we demonstrate that the N-terminal residues of the protein when deleted results in reduced activity and destabilization of filament formation. Overall, structure-function analysis opens up avenues for further utilization of the protein as a potent antifungal molecule. IMPORTANCE Burkholderia gladioli strain NGJ1, isolated from healthy rice seedling, was earlier demonstrated to have mycophagous properties on a broad range of fungi, including Rhizoctonia solani, a causal agent of deadly sheath blight disease of rice. The purified Bg_9562 protein exerts broad-spectrum antifungal activity. The protein also inhibits the growth of laboratory strain of Candida, an opportunistic human pathogen. In this study, we structurally characterize Bg_9562 using a combination of negative staining transmission electron microscopy, molecular modeling, mutagenesis, and functional antifungal assay. We show that the protein assembles into long filament like structures stabilized by N-terminus residues and this region is important for its activity. Our study has implications in utilizing Bg_9562 or its derivatives as antifungal molecule(s) which will provide environmentally friendly control of fungal diseases of plants and animals.

Intraretinal Layer Segmentation Using Cascaded Compressed U-Nets.

Reliable biomarkers quantifying neurodegeneration and neuroinflammation in central nervous system disorders such as Multiple Sclerosis, Alzheimer's dementia or Parkinson's disease are an unmet clinical need. Intraretinal layer thicknesses on macular optical coherence tomography (OCT) images are promising noninvasive biomarkers querying neuroretinal structures with near cellular resolution. However, changes are typically subtle, while tissue gradients can be weak, making intraretinal segmentation a challenging task. A robust and efficient method that requires no or minimal manual correction is an unmet need to foster reliable and reproducible research as well as clinical application. Here, we propose and validate a cascaded two-stage network for intraretinal layer segmentation, with both networks being compressed versions of U-Net (CCU-INSEG). The first network is responsible for retinal tissue segmentation from OCT B-scans. The second network segments eight intraretinal layers with high fidelity. At the post-processing stage, we introduce Laplacian-based outlier detection with layer surface hole filling by adaptive non-linear interpolation. Additionally, we propose a weighted version of focal loss to minimize the foreground-background pixel imbalance in the training data. We train our method using 17,458 B-scans from patients with autoimmune optic neuropathies, i.e., multiple sclerosis, and healthy controls. Voxel-wise comparison against manual segmentation produces a mean absolute error of 2.3 µm, outperforming current state-of-the-art methods on the same data set. Voxel-wise comparison against external glaucoma data leads to a mean absolute error of 2.6 µm when using the same gold standard segmentation approach, and 3.7 µm mean absolute error in an externally segmented data set. In scans from patients with severe optic atrophy, 3.5% of B-scan segmentation results were rejected by an experienced grader, whereas this was the case in 41.4% of B-scans segmented with a graph-based reference method. The validation results suggest that the proposed method can robustly segment macular scans from eyes with even severe neuroretinal changes.

Prior optic neuritis detection on peripapillary ring scans using deep learning.

BACKGROUND: The diagnosis of multiple sclerosis (MS) requires demyelinating events that are disseminated in time and space. Peripapillary retinal nerve fiber layer (pRNFL) thickness as measured by optical coherence tomography (OCT) distinguishes eyes with a prior history of acute optic neuritis (ON) and may provide evidence to support a demyelinating attack. OBJECTIVE: To investigate whether a deep learning (DL)-based network can distinguish between eyes with prior ON and healthy control (HC) eyes using peripapillary ring scans. METHODS: We included 1033 OCT scans from 415 healthy eyes (213 HC subjects) and 510 peripapillary ring scans from 164 eyes with prior acute ON (140 patients with MS). Data were split into 70% training, 15% validation, and 15% test data. We included 102 OCT scans from 80 healthy eyes (40 HC) and 61 scans from 40 ON eyes (31 MS patients) from an independent second center. Receiver operating characteristic curve analyses with area under the curve (AUC) were used to investigate performance. RESULTS: We used a dilated residual convolutional neural network for the classification. The final network had an accuracy of 0.85 and an AUC of 0.86, whereas pRNFL only had an AUC of 0.77 in recognizing ON eyes. Using data from a second center, the network achieved an accuracy of 0.77 and an AUC of 0.90 compared to pRNFL, which had an AUC of 0.84. INTERPRETATION: DL-based disease classification of prior ON is feasible and has the potential to outperform thickness-based classification of eyes with and without history of prior ON.

Serum glial fibrillary acidic protein correlates with retinal structural damage in aquaporin-4 antibody positive neuromyelitis optica spectrum disorder.

BACKGROUND: Aquaporin-4 immunoglobulin-G positive (AQP4-IgG+) neuromyelitis optica spectrum disorder (NMOSD) is an autoimmune astrocytopathy associated with optic neuritis (ON). Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is an oligodendrocytopathy with a similar phenotype. Serum glial fibrillary acidic protein (sGFAP), an astrocyte-derived protein, is associated with disease severity in AQP4-IgG+ NMOSD. Serum neurofilament light (sNfL) indicates neuroaxonal damage. The objective was to investigate the association of sGFAP and sNfL with subclinical afferent visual system damage in clinically stable AQP4-IgG+ NMOSD and MOGAD patients. METHODS: In this cross-sectional study, clinically stable patients with AQP4-IgG+ NMOSD (N = 33) and MOGAD (N = 16), as diseased controls, underwent sGFAP and sNfL measurements by single molecule array, retinal optical coherence tomography and visually evoked potentials. RESULTS: Higher sGFAP concentrations were associated with thinner ganglion cell-inner plexiform layer (ß (95% confidence interval (CI)) = -0.75 (-1.23 to -0.27), p = 0.007) and shallower fovea (average pit depth: ß (95%CI) = -0.59 (-0.63 to -0.55), p = 0.020) in NMOSD non-ON eyes. Participants with pathological P100 latency had higher sGFAP (median [interquartile range]: 131.32 [81.10-179.34] vs. 89.50 [53.46-121.91] pg/ml, p = 0.024). In MOGAD, sGFAP was not associated with retinal structural or visual functional measures. CONCLUSIONS: The association of sGFAP with structural and functional markers of afferent visual system damage in absence of ON suggests that sGFAP may be a sensitive biomarker for chronic disease severity in clinically stable AQP4-IgG+ NMOSD.

Enzymatic and non-enzymatic functional attributes of plant microbiome.

Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.

COVID-19 in Iran: Forecasting Pandemic Using Deep Learning.

COVID-19 has led to a pandemic, affecting almost all countries in a few months. In this work, we applied selected deep learning models including multilayer perceptron, random forest, and different versions of long short-term memory (LSTM), using three data sources to train the models, including COVID-19 occurrences, basic information like coded country names, and detailed information like population, and area of different countries. The main goal is to forecast the outbreak in nine countries (Iran, Germany, Italy, Japan, Korea, Switzerland, Spain, China, and the USA). The performances of the models are measured using four metrics, including mean average percentage error (MAPE), root mean square error (RMSE), normalized RMSE (NRMSE), and R 2. The best performance was found for a modified version of LSTM, called M-LSTM (winner model), to forecast the future trajectory of the pandemic in the mentioned countries. For this purpose, we collected the data from January 22 till July 30, 2020, for training, and from 1 August 2020 to 31 August 2020, for the testing phase. Through experimental results, the winner model achieved reasonably accurate predictions (MAPE, RMSE, NRMSE, and R 2 are 0.509, 458.12, 0.001624, and 0.99997, respectively). Furthermore, we stopped the training of the model on some dates related to main country actions to investigate the effect of country actions on predictions by the model.

Robust and High Fidelity Mesh Denoising.

This paper presents a simple and effective two-stage mesh denoising algorithm, where in the first stage, face normal filtering is done by using bilateral normal filtering in a robust statistics framework. Tukey's bi-weight function is used as similarity function in the bilateral weighting, which is a robust estimator and stops the diffusion at sharp edges to retain features and removes noise from flat regions effectively. In the second stage, an edge-weighted Laplace operator is introduced to compute a differential coordinate. This differential coordinate helps the algorithm to produce a high-quality mesh without any face normal flips and makes the method robust against high-intensity noise.

Mesh Denoising Based on Normal Voting Tensor and Binary Optimization.

This paper presents a two-stage mesh denoising algorithm. Unlike other traditional averaging approaches, our approach uses an element-based normal voting tensor to compute smooth surfaces. By introducing a binary optimization on the proposed tensor together with a local binary neighborhood concept, our algorithm better retains sharp features and produces smoother umbilical regions than previous approaches. On top of that, we provide a stochastic analysis on the different kinds of noise based on the average edge length. The quantitative results demonstrate that the performance of our method is better compared to state-of-the-art smoothing approaches.

Fluctuating nonlinear hydrodynamics of flocking.

Starting from a microscopic model, the continuum field theoretic description of the dynamics of a system of active ingredients or "particles" is presented. The equations of motion for the respective collective densities of mass and momentum follow exactly from that of a single element in the flock. The single-particle dynamics has noise and anomalous momentum dependence in its frictional terms. The equations for the collective densities are averaged over a local equilibrium distribution to obtain the corresponding coarse grained equations of fluctuating nonlinear hydrodynamics (FNH). The latter are the equations used frequently for describing active systems on the basis of intuitive arguments. The transport coefficients which appear in the macroscopic FNH equations are determined in terms of the parameters of the microscopic dynamics.

Optic nerve head three-dimensional shape analysis.

We present a method for optic nerve head (ONH) 3-D shape analysis from retinal optical coherence tomography (OCT). The possibility to noninvasively acquire in vivo high-resolution 3-D volumes of the ONH using spectral domain OCT drives the need to develop tools that quantify the shape of this structure and extract information for clinical applications. The presented method automatically generates a 3-D ONH model and then allows the computation of several 3-D parameters describing the ONH. The method starts with a high-resolution OCT volume scan as input. From this scan, the model-defining inner limiting membrane (ILM) as inner surface and the retinal pigment epithelium as outer surface are segmented, and the Bruch's membrane opening (BMO) as the model origin is detected. Based on the generated ONH model by triangulated 3-D surface reconstruction, different parameters (areas, volumes, annular surface ring, minimum distances) of different ONH regions can then be computed. Additionally, the bending energy (roughness) in the BMO region on the ILM surface and 3-D BMO-MRW surface area are computed. We show that our method is reliable and robust across a large variety of ONH topologies (specific to this structure) and present a first clinical application.