Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase.

The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.

Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis.

Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of high-priority transcription factors (TFs), dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We identified distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficient nodes. Dynamic transcriptional regulatory modeling of integrated TF targets and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs, as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that could potentially be used in future genetic crop engineering programs.

Comparative study of the efficacy of Ionic Silver Solution and Super Oxidized Solution in the management of chronic wounds.

Background: Chronic wounds are of many etiologies and difficult to treat. Many commercial products to manage such wounds are available, which claim to have good outcomes. Aim of this study was to compare the efficacy of Ionic Silver Solution and Super Oxidized Solution in the management of chronic wounds. Methods: Patients with chronic wounds were randomly placed in two groups-Group A (Ionic Silver Solution) and Group B (Super Oxidized Solution) with 30 patients each. The dressings were continued until the wound healed completely or the wound was ready for a definitive procedure. Wound parameters were recorded as per Bates Jensen Wound Assessment Tool (BJWAT) Score. Results: FIfty patients completed the study. The scores were compared at the initiation and endpoint of treatment. The pretreatment total for BJWAT was 916 and 924 in group A and group B respectively, which was not statistically significant. Post-treatment improvement was noticed in both the groups and the score decreased to 510 and 675 in group A and group B respectively (p = 0.001). Ionic Silver Solution and Super Oxidized Solution both were found to be effective in improving the overall wound condition. However, Ionic Silver Solution was found to be more effective than Super Oxidized Solution in the healing of chronic wounds. Complete healing was noticed in a small number (6%) of patients. These agents can therefore best prepare the wounds for early surgical intervention. Conclusion: Both the agents were found to be safe and useful in the management of chronic wounds. However, Ionic Silver Solution was found to be more effective than the super oxidized solution in this study.

Salvage of Infected Cardiac Implantable Electrical Devices with Subpectoral Plane Pocket Revision.

Introduction Infection of cardiac implantable electrical devices (CIEDs) may lead to serious complications. Complete CIED explantation is expensive, requires expertise, not free from complications, and may not be an option in patients with device dependence. Aim To highlight that carefully selected infected CIEDs can be salvaged by placing the device in a subpectoral pocket below the pectoralis major muscle. We conducted a retrospective descriptive observational study. Material and Methods Twelve patients (10 male and two female) with erosion, exposure or infection of infraclavicular, subcutaneously placed CIED were treated over a 30-month period between July 2018 and December 2020. The technique involved debridement and excision of a peridevice capsule, creating a subpectoral pocket beneath the pectoralis major muscle, and placing the CIED in a new pocket with total muscle coverage and closure of skin without tension. Results Twelve patients ( m = 10; f = 2) with a mean age of 65 years (range, 46-82 years) presented with infection of CIED within 9 months of implantation. None had sepsis or endocarditis. In nine patients, CIEDs were successfully salvaged with relocation to subpectoral pocket. Mean follow-up was 20 months (range, 8-30 months). Three out of 12 developed reinfection that ultimately required CIED explantation. There was no mortality. Conclusion In the absence of sepsis or endocarditis, infected CIEDs may be attempted at salvage by subpectoral pocket placement. This obviates the need for potentially risky explantation or replacement of expensive CIEDs.

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum).

Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD-associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD-infested Mac7 and validated RNA-Seq data with qPCR on 24 independent genes. We performed co-expression network and pathway analysis for regulation of geminivirus/betasatellite-interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co-expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite-interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus-induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub-genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.

Systems Biology and Machine Learning in Plant-Pathogen Interactions.

Systems biology is an inclusive approach to study the static and dynamic emergent properties on a global scale by integrating multiomics datasets to establish qualitative and quantitative associations among multiple biological components. With an abundance of improved high throughput -omics datasets, network-based analyses and machine learning technologies are playing a pivotal role in comprehensive understanding of biological systems. Network topological features reveal most important nodes within a network as well as prioritize significant molecular components for diverse biological networks, including coexpression, protein-protein interaction, and gene regulatory networks. Machine learning techniques provide enormous predictive power through specific feature extraction from biological data. Deep learning, a subtype of machine learning, has plausible future applications because a domain expert for feature extraction is not needed in this algorithm. Inspired by diverse domains of biology, we here review classic systems biology techniques applied in plant immunity thus far. We also discuss additional advanced approaches in both graph theory and machine learning, which may provide new insights for understanding plant-microbe interactions. Finally, we propose a hybrid approach in plant immune systems that harnesses the power of both network biology and machine learning, with a potential to be applicable to both model systems and agronomically important crop plants.

Methanol leaves extract Hibiscus micranthus Linn exhibited antibacterial and wound healing activities.

BACKGROUND: Infectious diseases are the most common causes of morbidity and mortality in developing countries. Wound and wound infections are also major health problem. Nowadays, medicinal plants play a major role in treatment of infectious diseases and wound healing and they are easily available and more affordable as compared to synthetic compounds. The aim of this study is therefore, to investigate the antibacterial and wound healing activities of 80% methanol extract of Hibiscus micranthus leaves using disc diffusion methods and rat excision model respectively. METHODS: In vitro antibacterial screening was carried out against S. aureus, S.pneumoniae, S. pyogenes, E. coli, P. aeruginosa, K. pneumoniae and P. mirabilis bacterial strains using disc-well diffusion assay. Would healing activity was done in rats divided into four groups each consisting of six animals. Group I was served as a negative control (ointment base), Group II served as a positive control Nitrofurazone (NFZ 0.2% ointment), Groups III and IV was treated 5 and 10% extracts respectively. The acute oral toxicity test and skin sensitivity test were also performed before conducting the actual study. The extract was analyzed for secondary metabolites using standard methods. RESULTS: Preliminary phytochemical screening have revealed the presence of alkaloids, flavonoids, saponins, tannins, steroids, phenols, diterpines, anthraquinones and the absence of glycosides, terpinoides and triterpines. Based on acute oral toxicity test the extract was found to be safe up to a dose of 2 g/kg. In addition, acute dermal toxicity test indicated no sign of skin irritation. The leaves extract exhibited varying degrees of sensitivity with zones of inhibition ranging from 14.00 ± 0.333 (S.pyogenes) to 22.67 ± 1.202 mm (S.aureus). It was found that S. aureus and S. pneumonia (p < 0.05) were the most sensitive to the extracts of the leaves at concentrations of 800 µg/ml and 400 µg/ml respectively followed by P. aeuruginosa [(18.33 ± .333 mm) (p < 0.05)] at a concentration of 400 µg/ml. However, E. coli and P. mirabilis were found to be resistant to the extract at any of the applied doses. In the wound healing study, the 5 and 10% w/w extract exhibited significant wound contraction rate of 99.30% and 99.13% as compared to NFZ ointment and simple ointment base treated groups from 6th to 16th day, respectively (p < 0.05). CONCLUSION: The present study suggests that the methanol extract of the leaves exhibited a potential antibacterial activity against the tested microorganisms and wound healing activity.

Harvesting split thickness costal cartilage graft.

AIM: There are few complications associated with harvesting of full thickness coastal cartilage grafts i.e., pneumothorax (0.9%), contour deformities and prolonged post-operative pain. To address these issues, authors devised special scalpel to harvest split-thickness costal cartilage grafts. MATERIALS AND METHODS: Standard inframammary incision was used for harvesting rib. Incision was made directly over the desired rib. Specially designed scalpel was used to cut through the rib cartilage to the half of the thickness. The study was conducted in two parts - cadaveric and clinical. RESULTS: There was significantly less pain and no pneumothorax in the patients in whom the split thickness graft was harvested. Wounds healed without any complication. DISCUSSION: Thus, newly devised angulated scalpel used in the current study, showed the potential to supply the reconstructive surgeon with split thickness rib graft without risk of complications such as pneumothorax or warping contour deformities and post-operative pain.

PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill).

BACKGROUND: Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. RESULTS: A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. CONCLUSIONS: PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

A Descriptive Study on Imperiled Cochlear Implant Salvage Using Double Flap Cover-What We Learned in 6 Years.

Cochlear implant surgery is the standard of care for severe sensorineural hearing loss. Infection followed by implant extrusion is an infrequent complication of this surgery. The ideal treatment is explantation of the implant. However, implant removal and reimplantation is a challenging surgery and may have poor speech reception outcomes. The cost of a new implant especially in developing countries is also a deterrent. Our study dwells on the feasibility of salvaging exposed cochlear implants by a combination of pericranial flaps followed by a scalp flap cover. The study was done in a tertiary care hospital over a period of six years. Out of 303 cochlear implant surgeries, 12 patients had implant exposure and extrusion. Patients having meningitis and sepsis were excluded from the study. All patients underwent debridement and cover with double flap (Pericranial flaps and scalp rotation flap). The average operating time was 2.17 h. The surgery is technically simple with a short learning curve. It brings in rich blood supply and there is fair amount of tissue mobility. In 11 patients we were able to salvage the implant. Patients were followed for a period of 01 year post operatively. Our study suggests that salvage of infected implant should be attempted as it is feasible, durable and effective in appropriate patients.

SGLT2 inhibition: a novel prospective strategy in treatment of diabetes mellitus.

The role of the kidney in glucose homeostasis and the potential of the kidney as a therapeutic target in type 2 diabetes is little appreciated. Hyperglycemia is an important pathogenic component in the development of microvascular and macrovascular complications in type 2 diabetes mellitus. Inhibition of renal tubular glucose re-absorption that leads to glycosuria has been proposed as a new mechanism to attain normoglycemia and thus prevent and diminish these complications, thus representing an innovative therapeutic strategy for the treatment of hyperglycemia and/or obesity in patients with type 1 or type 2 diabetes by enhancing glucose and energy loss through the urine. Sodium glucose co-transporter 2 (SGLT2) has a key role in re-absorption of glucose in kidney. Competitive inhibitors of SGLT2 have been discovered and a few of them have also been advanced in clinical trials for the treatment of diabetes.

Integrative systems biology framework discovers common gene regulatory signatures in multiple mechanistically distinct inflammatory skin diseases.

More than 20% of the population across the world is affected by non-communicable inflammatory skin diseases including psoriasis, atopic dermatitis, hidradenitis suppurativa, rosacea, etc. Many of these chronic diseases are painful and debilitating with limited effective therapeutic interventions. However, recent advances in psoriasis treatment have improved the effectiveness and provide better management of the disease. This study aims to identify common regulatory pathways and master regulators that regulate molecular pathogenesis. We designed an integrative systems biology framework to identify the significant regulators across several inflammatory skin diseases. With conventional transcriptome analysis, we identified 55 shared genes, which are enriched in several immune-associated pathways in eight inflammatory skin diseases. Next, we exploited the gene co-expression-, and protein-protein interaction-based networks to identify shared genes and protein components in different diseases with relevant functional implications. Additionally, the network analytics unravels 55 high-value proteins as significant regulators in molecular pathogenesis. We believe that these significant regulators should be explored with critical experimental approaches to identify the putative drug targets for more effective treatments. As an example, we identified IKZF1 as a shared significant master regulator in three inflammatory skin diseases, which can serve as a putative drug target with known disease-derived molecules for developing efficacious combinatorial treatments for hidradenitis suppurativa, atopic dermatitis, and rosacea. The proposed framework is very modular, which can indicate a significant path of molecular mechanism-based drug development from complex transcriptomics data and other multi-omics data.

NK and NKT cells in the pathogenesis of Hidradenitis suppurativa: Novel therapeutic strategy through targeting of CD2.

Hidradenitis suppurativa (HS) is a chronic debilitating inflammatory skin disease with poorly understood pathogenesis. Single-cell RNAseq analysis of HS lesional and healthy individual skins revealed that NKT and NK cell populations were greatly expanded in HS, and they expressed elevated CD2, an activation receptor. Immunohistochemistry analyses confirmed significantly expanded numbers of CD2+ cells distributed throughout HS lesional tissue, and many co-expressed the NK marker, CD56. While CD4+ T cells were expanded in HS, CD8 T cells were rare. CD20+ B cells in HS were localized within tertiary follicle like structures. Immunofluorescence microscopy showed that NK cells (CD2 + CD56 dim ) expressing perforin, granzymes A and B were enriched within the hyperplastic follicular epidermis and tunnels of HS and juxtaposed with apoptotic cells. In contrast, NKT cells (CD2 + CD3 + CD56 bright ) primarily expressed granzyme A and were associated with α-SMA expressing fibroblasts within the fibrotic regions of the hypodermis. Keratinocytes and fibroblasts expressed high levels of CD58 (CD2 ligand) and they interacted with CD2 expressing NKT and NK cells. The NKT/NK maturation and activating cytokines, IL-12, IL-15 and IL-18, were significantly elevated in HS. Inhibition of cognate CD2-CD58 interaction with blocking anti-CD2 mAb in HS skin organotypic cultures resulted in a profound reduction of the inflammatory gene signature and secretion of inflammatory cytokines and chemokines in the culture supernate. In summary, we show that a cellular network of heterogenous NKT and NK cell populations drives inflammation, tunnel formation and fibrosis in the pathogenesis of HS. Furthermore, CD2 blockade is a viable immunotherapeutic approach for the management of HS.

Investigating the effect of CoCl2 administration on diabetic nephropathy and associated aortic dysfunction.

AIM: Endothelial dysfunction appears to be a consistent finding in diabetic nephropathy. The study aimed to investigate the effect of cobalt chloride in the amelioration of endothelial dysfunction in uninephrectomized diabetic rats. METHODS: We examined the effect of CoCl(2) (10 mg/kg, i.p., OD = once a day) treatment on contractile responses to angiotensin II (10(-10) to 10(-6)M) in an aortic preparation of control rats and uninephrectomized diabetic control rats. Blood glucose, plasma urea, creatinine, uric acid, aortic endothelial nitric oxide synthase (eNOS), nitrate/nitrite (NOx), superoxide dismutase, catalase and reduced glutathione levels were checked in the different groups. RESULTS: A significant attenuation of the augmented responses to angiotensin II was observed in CoCl(2)-treated animals along with a fall in plasma urea, creatinine and uric acid levels. A significant reduction in blood glucose and an increase in aortic eNOS and NOx levels along with antioxidants levels were observed. CONCLUSION: Chronic hypoxia augments angiotensin II responses in the thoracic aorta of uninephrectomized diabetic control rats. CoCl(2) attenuates these enhanced vascular responses with a significant decrease in blood glucose signifying stabilization of the hypoxia-inducible factor in the alleviation of endothelial dysfunction in diabetic nephropathy.

A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets.

Network science identifies key players in diverse biological systems including host-pathogen interactions. We demonstrated a scale-free network property for a comprehensive rice protein-protein interactome (RicePPInets) that exhibits nodes with increased centrality indices. While weighted k-shell decomposition was shown efficacious to predict pathogen effector targets in Arabidopsis, we improved its computational code for a broader implementation on large-scale networks including RicePPInets. We determined that nodes residing within the internal layers of RicePPInets are poised to be the most influential, central, and effective information spreaders. To identify central players and modules through network topology analyses, we integrated RicePPInets and co-expression networks representing susceptible and resistant responses to strains of the bacterial pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola (Xoc) and generated a RIce-Xanthomonas INteractome (RIXIN). This revealed that previously identified candidate targets of pathogen transcription activator-like (TAL) effectors are enriched in nodes with enhanced connectivity, bottlenecks, and information spreaders that are located in the inner layers of the network, and these nodes are involved in several important biological processes. Overall, our integrative multi-omics network-based platform provides a potentially useful approach to prioritizing candidate pathogen effector targets for functional validation, suggesting that this computational framework can be broadly translatable to other complex pathosystems.

Protective effect of Celastrus paniculatus on cognitive function in glutamate-induced brain-injured mice by reducing the intracellular influx of Ca.

Present investigation evaluates the protective effect of Celastrus paniculatus (CP) on the cognitive function in neuronal injured mice. Neuronal injury was induced by oral administration of monosodium glutamate (MSG) at a dose of 1.66 g/kg/day for 30 days. Mice in the CP-treated group receives CP 30 mg/kg ip and CP + GGA-treated group received CP 30 mg/kg ip and glutamic acid (GGA, 1.5 mg/kg, ip) 30 min prior to the administration of MSG for 30 days. Assessment of cognitive function was done using Morris water maze. Level of inflammatory cytokines and production of reactive oxygen species (ROS) was estimated in the brain tissue of brain-injured mice. Moreover, intracellular concentration of Ca+ ion was estimated in the brain tissue and expression of Bcl-2, Bax, and caspase-3 protein was estimated in the brain tissue by western blot assay. Cognitive function was attenuated in CP-treated glutamate-injured mice. Data of the study suggest that treatment with CP reduces the level of inflammatory cytokines and production of ROS in the brain tissue compared to negative control group. There was reduction in the concentration of Ca+ ion in the neuronal cells in CP-treated group than negative control group of mice. Treatment with CP ameliorates the expression of Bax, Bcl-2, and caspase-3 in the brain tissue of glutamate-induced brain-injured mice. In conclusion, data of the study suggest that treatment with CP attenuates the cognitive function and neuronal apoptosis in glutamate-induced neuronal injury by reducing the concentration of intracellular Ca+ ion.

A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions.

Investigating the complexity of host-pathogen interactions is challenging. Here, we outline a pipeline to identify important proteins and signaling molecules in human-viral interactomes. Firstly, we curate a comprehensive human interactome. Subsequently, we infer viral targets and transcriptome-specific human interactomes (VTTSHI) for papillomavirus and herpes viruses by integrating viral targets and transcriptome data. Finally, we reveal the common and shared nodes and pathways in viral pathogenesis following network topology and pathway enrichment analyses. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2020).

Sparking a sulfur war between plants and pathogens.

The biochemical versatility of sulfur (S) lends itself to myriad roles in plant-pathogen interactions. This review evaluates the current understanding of mechanisms by which pathogens acquire S from their plant hosts and highlights new evidence that plants can limit S availability during the immune responses. We discuss the discovery of host disease-susceptibility genes related to S that can be genetically manipulated to create new crop resistance. Finally, we summarize future research challenges and propose a research agenda that leverages systems biology approaches for a holistic understanding of this important element's diverse roles in plant disease resistance and susceptibility.

Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC.

With the advent of recent next-generation sequencing (NGS) technologies in genomics, transcriptomics, and epigenomics, profiling single-cell sequencing became possible. The single-cell RNA sequencing (scRNA-seq) is widely used to characterize diverse cell populations and ascertain cell type-specific regulatory mechanisms. The gene regulatory network (GRN) mainly consists of genes and their regulators-transcription factors (TF). Here, we describe the lightning-fast Python implementation of the SCENIC (Single-Cell reEgulatory Network Inference and Clustering) pipeline called pySCENIC. Using single-cell RNA-seq data, it maps TFs onto gene regulatory networks and integrates various cell types to infer cell-specific GRNs. There are two fast and efficient GRN inference algorithms, GRNBoost2 and GENIE3, optionally available with pySCENIC. The pipeline has three steps: (1) identification of potential TF targets based on co-expression; (2) TF-motif enrichment analysis to identify the direct targets (regulons); and (3) scoring the activity of regulons (or other gene sets) on single cell types.