Molecular and functional characterization of chemosensory genes from the root-knot nematode Meloidogyne graminicola.

BACKGROUND: Root-knot nematode Meloidogyne graminicola has emerged as a major threat in rice agroecosystems owing to climate change-induced changes in cultivation practices. Synthetic nematicides are continually being withdrawn from the nematode management toolbox because of their ill effects on the environment. A sustainable strategy would be to develop novel nematicides or resistant plants that would target nematode sensory perception, which is a key step in the host finding biology of plant-parasitic nematodes (PPNs). However, compared to the extensive literature on the free-living nematode Caenorhabditis elegans, negligible research has been performed on PPN chemosensory biology. RESULTS: The present study characterizes the five chemosensory genes (Mg-odr-7, Mg-tax-4, Mg-tax-4.1, Mg-osm-9, and Mg-ocr-2) from M. graminicola that are putatively associated with nematode host-finding biology. All the genes were highly transcribed in the early life stages, and RNA interference (RNAi)-induced downregulation of each candidate gene perturbed the normal behavioural phenotypes of M. graminicola, as determined by examining the tracking pattern of juveniles on Pluronic gel medium, attraction to and penetration in rice root tip, and developmental progression in rice root. In addition, a detrimental effect on nematode chemotaxis towards different volatile and nonvolatile organic compounds and host root exudates was documented. CONCLUSION: Our findings enrich the existing literature on PPN chemosensory biology and can supplement future research aimed at identifying a comprehensive chemosensory signal transduction pathway in PPNs.

A rice root-knot nematode Meloidogyne graminicola-resistant mutant rice line shows early expression of plant-defence genes.

MAIN CONCLUSION: Resistance to rice root-knot nematode Meloidogyne graminicola in a mutant rice line is suggested to be conferred by higher expression of several genes putatively involved in damage-associated molecular pattern recognition, secondary metabolite biosynthesis including phytoalexins, and defence-related genes. Meloidogyne graminicola has emerged as the most destructive plant-parasitic nematode disease of rice (Oryza sativa L.). Genetic resistance to M. graminicola is one of the most effective methods for its management. A M. graminicola-resistant O. sativa ssp. indica mutant line-9 was previously identified through a forward genetic screen (Hatzade et al. Biologia 74:1197-1217, 2019). In the present study, we used RNA-Sequencing to investigate the molecular mechanisms conferring nematode resistance to the mutant line-9 compared to the susceptible parent JBT 36/14 at 24 h post-infection. A total of 674 transcripts were differentially expressed in line-9. Early regulation of genes putatively related to nematode damage-associated molecular pattern recognition (e.g., wall-associated receptor kinases), signalling [Nucleotide-binding, Leucine-Rich Repeat (NLRs)], pathogenesis-related (PR) genes (PR1, PR10a), defence-related genes (NB-ARC domain-containing genes), as well as a large number of genes involved in secondary metabolites including diterpenoid biosynthesis (CPS2, OsKSL4, OsKSL10, Oscyp71Z2, oryzalexin synthase, and momilactone A synthase) was observed in M. graminicola-resistant mutant line-9. It may be suggested that after the nematode juveniles penetrate the roots of line-9, early recognition of invading nematodes triggers plant immune responses mediated by phytoalexins, and other defence proteins such as PR proteins inhibit nematode growth and reproduction. Our study provides the first transcriptomic comparison of nematode-resistant and susceptible rice plants in the same genetic background and adds to the understanding of mechanisms underlying plant-nematode resistance in rice.

RNAi-mediated disruption of neuropeptide genes, nlp-3 and nlp-12, cause multiple behavioral defects in Meloidogyne incognita.

Owing to the current deficiencies in chemical control options and unavailability of novel management strategies, root-knot nematode (M. incognita) infections remain widespread with significant socio-economic impacts. Helminth nervous systems are peptide-rich and appear to be putative drug targets that could be exploited by antihelmintic chemotherapy. Herein, to characterize the novel peptidergic neurotransmitters, in silico mining of M. incognita genomic and transciptomic datasets revealed the presence of 16 neuropeptide-like protein (nlp) genes with structural hallmarks of neuropeptide preproproteins; among which 13 nlps were PCR-amplified and sequenced. Two key nlp genes (Mi-nlp-3 and Mi-nlp-12) were localized to the basal bulb and tail region of nematode body via in situ hybridization assay. Mi-nlp-3 and Mi-nlp-12 were greatly expressed (in qRT-PCR assay) in the pre-parasitic juveniles and adult females, suggesting the association of these genes in host recognition, development and reproduction of M. incognita. In vitro knockdown of Mi-nlp-3 and Mi-nlp-12 via RNAi demonstrated the significant reduction in attraction and penetration of M. incognita in tomato root in Pluronic gel medium. A pronounced perturbation in development and reproduction of NLP-silenced worms was also documented in adzuki beans in CYG growth pouches. The deleterious phenotypes obtained due to NLP knockdown suggests that transgenic plants engineered to express RNA constructs targeting nlp genes may emerge as an environmentally viable option to manage nematode problems in crop plants.

Assessment of Pulmonary Functions in Parkinson's Disease and Unveiling the Role of Levodopa Therapy: A Cross-Sectional Study.

INTRODUCTION: This investigation aimed to thoroughly characterize the range of pulmonary function abnormalities present in individuals with Parkinson's disease (PD) and to evaluate the effects of levodopa therapy on these respiratory dysfunctions. METHODS:  Ninety-five PD patients diagnosed via the UK Parkinson's Disease Society Brain Bank Diagnostic Criteria were recruited, excluding those with a smoking history or unable to perform pulmonary function tests (PFTs). Severity was assessed using the Hoehn and Yahr Scale. Spirometry-measured PFT parameters (forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), and peak expiratory flow rate (PEFR)) were compared against matched predicted values. The changes in PFT parameters post-levodopa challenge were assessed. RESULTS: Most of the PD patients were aged between 51-60 years, with a mean age of 55.89 ± 8.37 years. Of these, 65.3% were male. A significant proportion of the cohort exhibited restrictive pulmonary patterns (73.7%), while a smaller fraction displayed obstructive (7.4%) or normal (18.9%) pulmonary function patterns. Notably, levodopa treatment correlated with marked improvements in all measured PFT parameters, especially evident in the enhancements from the "off" medication stage to the "on" stage for FVC and FEV1 (P=0.0001). A weak positive correlation between the severity of respiratory restriction and the duration of PD (r = 0.139, P = 0.021) was found, suggesting that PD's progression exerts an increasingly adverse effect on respiratory function over time. CONCLUSION:  The findings of this study illustrate that restrictive pulmonary abnormalities are more prevalent than obstructive patterns in PD patients and that these patients respond favorably to levodopa therapy.

Induced knockdown of Mg-odr-1 and Mg-odr-3 perturbed the host seeking behavior of Meloidogyne graminicola in rice.

Root-knot nematode Meloidogyne graminicola is one of the most destructive plant parasites in upland as well as direct seeded rice. As an integral part of nematode biology, host finding behavior involves perceiving and responding to different chemical cues originating from the rhizosphere. A sustainable management tactic may include retardation of nematode chemoreception that would impair them to detect and discriminate the host stimuli. Deciphering the molecular basis of nematode chemoreception is vital to identify chokepoints for chemical or genetic interventions. However, compared to the well-characterized chemoreception mechanism in model nematode Caenorhabditis elegans, plant nematode chemoreception is yet underexplored. Herein, the full-length cDNA sequences of two chemotaxis-related genes (Mg-odr-1 and Mg-odr-3) were cloned from M. graminicola. Both the genes were markedly upregulated in the early developmental stages of M. graminicola suggesting their involvement in host finding processes. RNAi-induced independent knockdown of Mg-odr-1 and Mg-odr-3 caused behavioral aberration in second-stage juveniles of M. graminicola which in turn perturbed the nematodes' host finding ability and parasitic success inside rice roots. Additionally, nematodes' chemotactic response to different host root exudates, volatile and nonvolatile compounds was affected. Our results demonstrating the role of specific chemosensory genes in modulating M. graminicola host seeking behavior can enrich the existing knowledge of plant nematode chemoreception mechanism, and these genes can be targeted for novel nematicide development or in planta RNAi screens.

Socioepidemiological status and clinical outcome of MDR TB patients in a tertiary medical college in Southern Odisha.

Introduction: India accounts for one-fourth of the global TB burden. The load of drug-resistant TB is of foremost attention and concern at international, regional, and national levels. As per estimates of TB burden in India in 2018, the MDR/RR-TB incidence was 1.30 lakhs. Objectives: Socioepidemiological status and clinical outcome of MDR TB patients in a teaching hospital in tribal area of southern Odisha from 2012-2020. Material and Methods: This is a retrospective observational study accepted by the Institutional Ethics Committee of this tertiary medical college & hospital to which the DRTB centre is attached with the agreement of the program administrators. Inclusion Criteria: Patients with >15 years of age, those patients with pulmonary and extrapulmonary tuberculosis with normal liver enzymes. Exclusion Criteria: Patients having abnormal liver enzymes before treatment, pregnant ladies and children <15 years of age. Results: A total of 40 MDR TB patients were included. The patients' mean age was 36.65 ± 11.75 years. 65% of the patients had BMI below 18.5 kg/m2. 17.5% of patients had comorbidities. Approximately 45% had successful treatment outcomes. Poor treatment outcome includes loss to follow-up in 22.5% and mortality in 12.5%. We did not find any treatment failure. Conclusion: Treatment success outcomes occurred in less than half of the cases. The main predictors of mortality among MDR-TB patients were the presence of comorbidities like anaemia, baseline leucocytosis or lymphopenia, hypoproteinaemia, HIV sero-positivity and smaller baseline BMI.

Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines.

Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238-553,648 unique SNPs and 32,395-65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.

Psoriasis Lesion Detection Using Hybrid Seeker Optimization-based Image Clustering.

BACKGROUND: In recent years, there has been a massive increase in the number of people suffering from psoriasis. For proper psoriasis diagnosis, psoriasis lesion segmentation is a prerequisite for quantifying the severity of this disease. However, segmentation of psoriatic lesions cannot be evaluated just by visual inspection as they exhibit inter and intra variability among the severity classes. Most of the approaches currently pursued by dermatologists are subjective in nature. The existing conventional clustering algorithm for objective segmentation of psoriasis lesion suffers from limitations of premature local convergence. OBJECTIVE: An alternative method for psoriatic lesion segmentation with objective analysis is sought in the present work. The present work aims at obtaining optimal lesion segmentation by adopting an evolutionary optimization technique that possesses a higher probability of global convergence for psoriasis lesion segmentation. METHODS: A hybrid evolutionary optimization technique based on the combination of two swarm intelligence algorithms, namely Artificial Bee Colony and Seeker Optimization algorithm, has been proposed. The initial population for the hybrid technique is obtained from the two conventional local- based approaches, i.e., Fuzzy C-means and K-means clustering algorithms. RESULTS: The initial population selection from the convergence of classical techniques reduces the effect of population dynamics on the final solution and hence yields precise lesion segmentation with a Jaccard Index of 0.91 from 720 psoriasis images. CONCLUSION: The performance comparison reflects the superior performance of the proposed algorithm over other swarm intelligence and conventional clustering algorithms.

An improved draft genome assembly of Meloidogyne graminicola IARI strain using long-read sequencing.

The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.

Swarm intelligence based clustering technique for automated lesion detection and diagnosis of psoriasis.

BACKGROUND: In psoriasis skin disease, psoriatic cells develop rapidly than the normal healthy cells. This speedy growth causes accumulation of dead skin cells on the skin's surface, resulting in thick patches of red, dry, and itchy skin. This patches or psoriatic skin legions may exhibit similar characteristics as healthy skin, which makes lesion detection more challenging. However, for accurate disease diagnosis and severity detection, lesion segmentation has prime importance. In that context, our group had previously performed psoriasis lesion segmentation using the conventional clustering algorithm. However, it suffers from the constraint of falling into the local sub-optimal centroids of the clusters. OBJECTIVE: The main objective of this paper is to implement an optimal lesion segmentation technique with aims at global convergence by reducing the probability of trapping into the local optima. This has been achieved by integrating swarm intelligence based algorithms with conventional K-means and Fuzzy C-means (FCMs) clustering algorithms. METHODOLOGY: There are a total of eight different suitable combinations of conventional clustering (i.e., K-means and Fuzzy C-means (FCMs)) and four swarm intelligence (SI) techniques (i.e., seeker optimization (SO), artificial bee colony (ABC), ant colony optimization (ACO) and particle swarm optimization (PSO)) have been implemented in this study. The experiments are performed on the dataset of 780 psoriasis images from 74 patients collected at Psoriasis Clinic and Research Centre, Psoriatreat, Pune, Maharashtra, India. In this study, we are employing swarm intelligence optimization techniques in combination with the conventional clustering algorithms to increase the probability of convergence to the optimal global solution and hence improved clustering and detection. RESULTS: The performance has been quantified in terms of four indices, namely accuracy (A), sensitivity (SN), specificity (SP), and Jaccard index (JI). Among the eight different combinations of clustering and optimization techniques considered in this study, FCM + SO outperformed with mean JI = 0.83, mean A = 90.89, mean SN = 92.84, and mean SP = 88.27. FCM + SO found statistical significant than other approaches with 96.67 % of the reliability index. CONCLUSION: The results obtained reflect the superiority of the proposed techniques over conventional clustering techniques. Hence our research development will lead to an objective analysis for automatic, accurate, and quick diagnosis of psoriasis.

Wrapper-filter feature selection algorithm using a memetic framework.

This correspondence presents a novel hybrid wrapper and filter feature selection algorithm for a classification problem using a memetic framework. It incorporates a filter ranking method in the traditional genetic algorithm to improve classification performance and accelerate the search in identifying the core feature subsets. Particularly, the method adds or deletes a feature from a candidate feature subset based on the univariate feature ranking information. This empirical study on commonly used data sets from the University of California, Irvine repository and microarray data sets shows that the proposed method outperforms existing methods in terms of classification accuracy, number of selected features, and computational efficiency. Furthermore, we investigate several major issues of memetic algorithm (MA) to identify a good balance between local search and genetic search so as to maximize search quality and efficiency in the hybrid filter and wrapper MA.

An unusual case of spontaneous esophagopleural fistula.

Esophago-pleural fistula (EPF) is an uncommon condition, despite of an anatomical proximity of these structures. Causes of EPF include pneumonectomy for suppurative or tubercular disease of lung and carcinoma lung, malignancy of esophagus. Benign EPF is rare and may be due to trauma or infection. The most common infectious cause is tuberculosis. Spontaneous development of fistula between esophagus and pleura is rarely described in literature. We, hereby present a spontaneous case of such a rare entity in a middle-aged male.