Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses.

KEY MESSAGE: The differential compatibility responses of sugarcane to Colletotrichum falcatum pathotypes depend on the nature of both host primary defence signalling cascades and pathogen virulence. The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from ~ 54,699,263 raw reads, while 4022 contigs were assembled from ~ 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+, BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest clade to the perfect stage of C. falcatum (G. tucumanensis).

Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane.

Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03113-6.

Robustness of convolutional neural networks to physiological electrocardiogram noise.

The electrocardiogram (ECG) is a widespread diagnostic tool in healthcare and supports the diagnosis of cardiovascular disorders. Deep learning methods are a successful and popular technique to detect indications of disorders from an ECG signal. However, there are open questions around the robustness of these methods to various factors, including physiological ECG noise. In this study, we generate clean and noisy versions of an ECG dataset before applying symmetric projection attractor reconstruction (SPAR) and scalogram image transformations. A convolutional neural network is used to classify these image transforms. For the clean ECG dataset, F1 scores for SPAR attractor and scalogram transforms were 0.70 and 0.79, respectively. Scores decreased by less than 0.05 for the noisy ECG datasets. Notably, when the network trained on clean data was used to classify the noisy datasets, performance decreases of up to 0.18 in F1 scores were seen. However, when the network trained on the noisy data was used to classify the clean dataset, the decrease was less than 0.05. We conclude that physiological ECG noise impacts classification using deep learning methods and careful consideration should be given to the inclusion of noisy ECG signals in the training data when developing supervised networks for ECG classification. This article is part of the theme issue 'Advanced computation in cardiovascular physiology: new challenges and opportunities'.

Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen.

KEY MESSAGE: Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.

Knock-down of glucose transporter and sucrose non-fermenting gene in the hemibiotrophic fungus Colletotrichum falcatum causing sugarcane red rot.

Red rot caused by Colletotrichum falcatum, is one of the economically important disease of sugarcane and breeding for resistant varieties is considered to be the major solution to manage the disease. However, breakdown of red rot resistance become usual phenomenon due to development of newer races by culture adaptation on newly released varieties. Hence it is needed to characterize the genes responsible for pathogen virulence in order to take care of host resistance or to manage the disease by other methods. The transcript studies gave foundation to characterize the huge number of pathogenicity determinants and their role in pathogenesis. Here we studied role of two important genes viz., Glucose Transporter (GT) and Sucrose Non-Fermenting1 (SNF1) during pathogenesis of C. falcatum, which said to be involved in carbon source metabolism. Sugar metabolism has a vital role in disease progression of C. falcatum by regulating their cell growth, metabolism and development of the pathogen during various stages of infection. The present study was aimed to find out the role of GT and SNF1 genes in response to pathogenicity by RNA silencing (RNAi) approach. Knock-down of the target pathogenicity gene homologs in standard C. falcatum isolate Cf671 was carried out by amplifying sense and antisense fragments of targets individually using pSilent-1 vector. The expression cassette was cloned into the binary vector pCAMBIA1300 followed by fungal transformation through Agarobacterium mediated transformation. Resulted mutants of both the genes showed less virulence compared to wild type isolate. Simultaneously, both the mutants did not produce spores. Moreover, the molecular confirmation of the mutants displayed the expression of hygromycin gene with reduced expression of the target gene during host-pathogen interaction. Knockdown of the pathogenicity related genes (GT and SNF1) by RNAi approach corroborate the possible role of the genes in causing the disease.

Development and characterization of genomic SSR marker for virulent strain-specific Colletotrichum falcatum infecting sugarcane.

Colle totrichum falcatum, an intriguing pathogen causing red rot in sugarcane, exhibits enormous variation for pathogenicity under field conditions. A species-specific marker is very much needed to classify the virulence among the varying population and to identify the potential of a pathotype by mining the microsatellites, which are considered to be the largest genetic source to develop molecular markers for an organism. In this study, we have mined the C. falcatum genome using MISA database which yielded 12,121 SSRs from 48.1 Mb and 2745 SSRs containing sequences. The most frequent SSR types from the genome of C. falcatum was di-nucleotide which constitutes 50.89% followed by tri-nucleotide 39.60%, hepta-nucleotide 6.7%, hexa-nucleotide 1.38% and penta-nucleotide 1.3%. Over 90 SSR containing sequences from the genome were predicted using BlastX which are found to be non-homologs. Most of the annotated SSR containing sequences fell in CAZy superfamilies, proteases, peptidases, plant cell wall degrading enzymes (PCDWE) and membrane transporters which are considered to be pathogenicity gene clusters. Among them, glycosyl hydrolases (GH) were found to be abundant in SSR containing sequences which again proved our previous transcriptome results. Our in-silico results suggested that the mined microsatellites from C. falcatum genome show absence of homolog sequences which suggests that these markers could be used as an ideal species-specific molecular marker. Two virulence specific markers were characterized using conventional PCR assays from C. falcatum along with virulent species-specific (VSS) marker developed for C. gloeosporioides. The study lays the foundation for the development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence.

Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum.

The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.

Detection of the presence of Coxiella burnetii in a case of goat abortion: a first report from India.

Abortion is a major cause of economic loss to the goat industry. Coxiella burnetii the causative agent of Q fever is an important zoonotic agent known to be prevalent worldwide. In the present investigation, we detected the presence of Coxiella burnetii by the modified Ziehl Neelsen method of staining and its DNA by trans-PCR assay in the placenta obtained from the aborted goat. We also ruled out other common causes of abortion in this case. Based on a literature survey, this is the first report on the direct detection of Coxiella burnetii from an aborted goat to be reported from India.

Biomass Burning Smoke Climatology of the United States: Implications for Particulate Matter Air Quality.

We utilize the NOAA Hazard Mapping System smoke product for the period of 2005 to 2016 to develop climatology of smoke occurrence over the Continental United States (CONUS) region and to study the impact of wildland fires on particulate matter air quality at the surface. Our results indicate that smoke is most frequently found over the Great Plains and western states during the summer months. Other hotspots of smoke occurrence are found over state and national parks in the southeast during winter and spring, in the Gulf of Mexico southwards of the Texas and Louisiana coastline during spring season and along the Mississippi River Delta during the fall season. A substantial portion (20%) of the 24 h federal standard for particulate pollution exceedance events in the CONUS region occur when smoke is present. If the U.S. Environmental Protection Agency regulations continue to reduce anthropogenic emissions, wildland fire emissions will become the major contributor to particulate pollution and exceedance events. In this context, we show that HMS smoke product is a valuable tool for analysis of exceptional events caused by wildland fires and our results indicate that these tools can be valuable for policy and decision makers.

Comorbidity, age of onset and suicidality in obsessive-compulsive disorder (OCD): An international collaboration.

OBJECTIVES: To collate data from multiple obsessive-compulsive disorder (OCD) treatment centers across seven countries and five continents, and to report findings in relation to OCD comorbidity, age of onset of OCD and comorbid disorders, and suicidality, in a large clinical and ethnically diverse sample, with the aim of investigating cultural variation and the utility of the psychiatric diagnostic classification of obsessive-compulsive and related disorders. METHODS: Researchers in the field of OCD were invited to contribute summary statistics on current and lifetime psychiatric comorbidity, age of onset of OCD and comorbid disorders and suicidality in their patients with OCD. RESULTS: Data from 3711 adult patients with primary OCD came from Brazil (n=955), India (n=802), Italy (n=750), South Africa (n=565), Japan (n=322), Australia (n=219), and Spain (n=98). The most common current comorbid disorders were major depressive disorder (28.4%; n=1055), obsessive-compulsive personality disorder (24.5%, n=478), generalized anxiety disorder (19.3%, n=716), specific phobia (19.2%, n=714) and social phobia (18.5%, n=686). Major depression was also the most commonly co-occurring lifetime diagnosis, with a rate of 50.5% (n=1874). OCD generally had an age of onset in late adolescence (mean=17.9years, SD=1.9). Social phobia, specific phobia and body dysmorphic disorder also had an early age of onset. Co-occurring major depressive disorder, generalized anxiety disorder and psychotic disorders tended to have a later age of onset than OCD. Suicidal ideation within the last month was reported by 6.4% (n=200) of patients with OCD and 9.0% (n=314) reported a lifetime history of suicide attempt. CONCLUSIONS: In this large cross-continental study, comorbidity in OCD was common. The high rates of comorbid major depression and anxiety disorders emphasize the need for clinicians to assess and monitor for these disorders. Earlier ages of onset of OCD, specific phobia and social phobia may indicate some relatedness between these disorders, but this requires further study. Although there do not appear to be significant cultural variations in rates or patterns of comorbidity and suicidality, further research using similar recruitment strategies and controlling for demographic and clinical variables may help to determine whether any sociocultural factors protect against suicidal ideation or psychiatric comorbidity in patients with OCD.

Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum.

Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum.

Revisiting the susceptibility testing of Mycobacterium tuberculosis to ethionamide in solid culture medium.

BACKGROUND & OBJECTIVES: Increase in the isolation of drug resistant phenotypes of Mycobacterium tuberculosis necessitates accuracy in the testing methodology. Critical concentration defining resistance for ethionamide (ETO), needs re-evaluation in accordance with the current scenario. Thus, re-evaluation of conventional minimum inhibitory concentration (MIC) and proportion sensitivity testing (PST) methods for ETO was done to identify the ideal breakpoint concentration defining resistance. METHODS: Isolates of M. tuberculosis (n=235) from new and treated patients were subjected to conventional MIC and PST methods for ETO following standard operating procedures. RESULTS: With breakpoint concentration set at 114 and 156 µg/ml, an increase in specificity was observed whereas sensitivity was high with 80 µg/ml as breakpoint concentration. Errors due to false resistant and susceptible isolates were least at 80 µg/ml concentration. INTERPRETATION & CONCLUSIONS: Performance parameters at 80 µg/ml breakpoint concentration indicated significant association between PST and MIC methods.

Eating disorders in women.

Eating disorders, especially anorexia nervosa and bulimia nervosa have been classically described in young females in Western population. Recent research shows that they are also seen in developing countries including India. The classification of eating disorders has been expanded to include recently described conditions like binge eating disorder. Eating disorders have a multifactorial etiology. Genetic factor appear to play a major role. Recent advances in neurobiology have improved our understanding of these conditions and may possibly help us develop more effective treatments in future. Premorbid personality appears to play an important role, with differential predisposition for individual disorders. The role of cultural factors in the etiology of these conditions is debated. Culture may have a pathoplastic effect leading to non-conforming presentations like the non fat-phobic form of anorexia nervosa, which are commonly reported in developing countries. With rapid cultural transformation, the classical forms of these conditions are being described throughout the world. Diagnostic criteria have been modified to accommodate for these myriad presentations. Treatment of eating disorders can be quite challenging, given the dearth of established treatments and poor motivation/insight in these conditions. Nutritional rehabilitation and psychotherapy remains the mainstay of treatment, while pharmacotherapy may be helpful in specific situations.

Is late-onset OCD a distinct phenotype? Findings from a comparative analysis of "age at onset" groups.

OBJECTIVE: Significant differences in clinical profile and comorbidity patterns have been observed between "juvenile-onset" and "adult-onset" obsessive-compulsive disorder (OCD). There is little systematic research on onset of OCD after the fourth decade. The current study aims to compare the demographic, clinical, and comorbidity patterns of patients with "juvenile-onset" (<18 years), "adult-onset" (18-39 years), and "late-onset" (≥40 years) OCD. METHOD: Eight hundred two consecutive patients who consulted a specialty OCD clinic at a tertiary care hospital in India were evaluated with the Mini International Neuropsychiatric Interview, the Yale-Brown Obsessive-Compulsive Scale, and the Clinical Global Impression scale. RESULTS: 37.4%, 57.4%, and 5.2% of patients had juvenile-, adult-, and late-onset OCD, respectively. Late-onset OCD was associated with female gender (χ2=42, p<0.001); negative family history of OCD in first-degree relatives (χ2=20.4, p<0.001); and less aggressive obsessions (χ2=18.16, p<0.001), sexual obsessions (χ2=26.68, p<0.001), pathological doubts (χ2=19.41; p<0.001), and repeating rituals (χ2=44.28; p<0.001). On multinomial logistic regression, late-onset OCD was significantly associated with female gender, collecting compulsions, and less aggressive obsessions, in comparison with adult-onset OCD. In comparison with juvenile-onset, late-onset OCD was significantly associated with female gender, presence of precipitating factors, and less aggressive obsessions, sexual obsessions, and repeating compulsions. CONCLUSION: Late-onset OCD is characterized by female gender, lesser familial loading for OCD, and presence of precipitating factors, suggesting that it may have a distinct pathophysiology compared to juvenile- and adult-onset OCD. Systematic research is required to understand the family-genetic, neuropsychological, and neurobiological correlates of late-onset OCD.

Transformation of truncated gold octahedrons into triangular nanoprisms through the heterogeneous nucleation of silver.

Described is a straightforward procedure for forming organized substrate-immobilized nanoprisms which are single crystalline, surfactant-free and which form a heteroepitaxial relationship with the underlying substrate. The devised route utilizes truncated Au octahedrons formed through solid state dewetting techniques as high temperature heterogeneous nucleation sites for Ag adatoms which are arriving to the substrate surface in the vapour phase. Observed is a morphological and compositional transformation of the Au structures to triangular nanoprisms comprised of a homogeneous AuAg alloy. During this transformation, the localized surface plasmon resonance red-shifts, broadens and increases in strength. The shape transformation, which cannot be rationalized using thermodynamic arguments dependent on the surface energy minimization, is described in terms of a kinetically driven growth mode, previously predicted by molecular dynamic simulations. The so-formed structures, when coated with a thin layer of Pd, are demonstrated as plasmonic sensing elements for hydrogen detection.

N'-[(E)-3-Bromo-5-chloro-2-hy-droxy-benzyl-idene]furan-2-carbohydrazide.

In the title compound, C12H8BrClN2O3, the furan ring makes a dihedral angle of 17.2 (2)° with the six-membered ring. An intra-molecular O-H⋯N hydrogen bond stabilizes the mol-ecular conformation. In the crystal, N-H⋯O hydrogen bonds connect the mol-ecules into chains running along the c-axis direction. The crystal packing is additionally stabilized by C-H⋯O inter-actions into a three-dimensional supramolecular architecture.

Synthesis, characterization, structural analysis of metal(II) complexes of N'-[(E)-3-Bromo-5-Chloro-2-hydroxybenzidene]-4-hydroxybenzohydrazide-Multisubstituted Schiff base as a F(-) and Cu(2+) ions selective chemosensor.

New colorimetric chemosensor, N'-[(E)-3-Bromo-5-Chloro-2-hydroxybenzidene]-4-hydroxybenzohydrazide, containing OH and NH groups as binding sites have been synthesized and characterized by spectral UV, IR, NMR and ESR. The molecular structure of ligand is determined by X-ray crystallography and it has the monoclinic space group P21/c with cell parameters a=15.1058(6), b=14.3433(6), c=17.5800(8)Å and Z=8. The electronic spectral measurements show that Co(2+), Ni(2+) and Zn(2+) complexes have tetrahedral geometry, while Cu(2+) complex has square planar geometry. Magnetic measurements show that Cu(2+), Co(2+) and Ni(2+) complexes have paramagnetic behavior and Zn(2+) complex has diamagnetic behavior. Anion binding studies carried out using (1)H NMR and UV-visible spectrophotometric titrations revealed that these receptors exhibit selective recognition towards F(-) over other halide anions. The selectivity for F(-) among the halides is attributed mainly to the hydrogen-bond interaction of the receptor with F(-). Receptor (5 × 10(-5)M) shows color change from colorless to yellow in the presence of tetrabutylammonium fluoride (TBAF, 1.5 × 10(-3)M). Moreover, F(-)-induced color changes remain the same even in the presence of large excess of Cl(-), Br(-) and I(-). The binding constant is found to be higher towards F(-) ion and this may be due to presence of OH group, which offers extra binding site. Chromogenic receptor undergoes distinct color changes from colorless to green on gradual addition of Cu(2+) can be used as colorimetric probes for spectrophotometric and visual analysis of Cu(2+) in the presence of other transition metal ions such as Co(2+), Ni(2+) and Zn(2+).

Stratifying low level Isoniazid resistance using additional intermediate drug concentration.

Isoniazid (INH) susceptibility testing for 100 Mycobacterium tuberculosis performed by conventional minimum inhibitory concentration (MIC) method was stratified using additional drug concentrations. Introduction of additional drug concentrations did not greatly improve the discriminatory capacity, but can be used in specialized studies pertaining to cross resistance between structural analogues of INH.

Differential regulation of defense-related gene expression in response to red rot pathogen Colletotrichum falcatum infection in sugarcane.

Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum imposing a considerable economic loss annually in all sugarcane-producing countries. In this study, we analyzed the early resistance response of sugarcane to red rot fungus by comparing the differences between control and inoculated stalk tissues. Differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was employed to identify altered expression of genes in disease-resistant cv Co 93009, in response to pathogen infection. DD-RT-PCR identified 300 differentially expressed transcripts of which 112 were selected for further analysis. Cloning and sequence analysis of the isolated cDNA fragments resulted in functional categorization of these clones into five categories, of which the defense/stress/signaling group was the largest, with clones homologous to genes known to be actively involved in various pathogenesis-related functions in plant species. This group showed overexpression of several transcripts related to ethylene-mediated and jasmonic acid pathway of plant defense mechanisms. Of the 112 expressed sequence tags, validation of expression was carried out for five important genes whose role in plant defense mechanisms is well established. This is the first report of Colletotrichum-mediated gene regulation in sugarcane which has provided a set of candidate genes for detailed molecular dissection of signaling and defense responses in tropical sugarcane during the onset of red rot resistance.