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).

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.

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.

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.

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.

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.

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.

Modification of proportion sensitivity testing method for ethionamide.

Standardized methodology for drug susceptibility testing of second line drugs is vital for treatment of multi/extensively drug resistant tuberculosis. Discrepancy between laboratory methods and clinical interpretation is well established for bacteriostatic drugs such as ethionamide. Optimization of the standard proportion sensitivity testing (PST) method for ethionamide was under taken in 235 Mycobacterium tuberculosis isolates from new and previously treated pulmonary tuberculosis patients. An additional higher concentration of 57 µg/ml was evaluated against at the standard 40 µg/ml concentration in PST method. Performance parameters and agreement between the two drug concentrations was higher indicating the efficiency of PST method at its present format at 40 µg/ml and additional higher concentration of 57 µg/ml as an alternative when required.

Altering the dewetting characteristics of ultrathin gold and silver films using a sacrificial antimony layer.

Solid state dewetting of ultrathin films is the most straightforward means of fabricating substrate-supported noble metal nanostructures. This assembly process is, however, quite inflexible, yielding either densely packed smaller structures or widely spaced larger structures. Here, we demonstrate the utility of introducing a sacrificial antimony layer between the substrate and noble metal overlayer. We observe an agglomeration process which is radically altered by the concurrent sublimation of antimony. In stark contrast with conventional dewetting, where the thickness of the deposited metal film determines the characteristic length scales of the assembly process, it is the thickness of the sacrificial antimony layer which dictates both the nanoparticle size and interparticle spacing. The result is a far more flexible self-assembly process where the nanoparticle size and areal density can be varied widely. Demonstrations show nanoparticle areal densities which are varied over four orders of magnitude assembled from the identical gold layer thickness, where the accompanying changes to nanostructure size see a systematic shift in the wavelength of the localized surface plasmon resonance. As a pliable self-assembly process, it offers the opportunity to tailor the properties of an ensemble of nanostructures to meet the needs of specific applications.

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.

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.

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.

Satellite remote sensing of particulate matter air quality: the cloud-cover problem.

Satellite assessments of particulate matter (PM) air quality that use solar reflectance methods are dependent on availability of clear sky; in other words, mass concentrations of PM less than 2.5 microm in aerodynamic diameter (PM2.5) cannot be estimated from satellite observations under cloudy conditions or bright surfaces such as snow/ice. Whereas most ground monitors measure PM2.5 concentrations on an hourly basis regardless of cloud conditions, space-borne sensors can only estimate daytime PM2.5 in cloud-free conditions, therefore introducing a bias. In this study, an estimate of this clear-sky bias is provided from monthly to yearly time scales over the continental United States. One year of the Moderate Resolution Imaging Spectroradiometer (MODIS) 550-nm aerosol optical depth (AOD) retrievals from Terra and Aqua satellites, collocated with 371 U.S. Environmental Protection Agency (EPA) ground monitors, have been analyzed. The results indicate that the mean differences between PM2.5 reported by ground monitors and PM2.5 calculated from ground monitors during the satellite overpass times during cloud-free conditions are less than +/- 2.5 microg m(-3), although this value varies by season and location. The mean differences are not significant as calculated by t tests (alpha = 0.05). On the basis of this analysis, it is concluded that for the continental United States, cloud cover is not a major problem for inferring monthly to yearly PM2.5 from space-borne sensors.

2-{[4-(Diethyl-amino)-phen-yl]imino-methyl}-4,6-diiodo-phenol.

In the title compound, C(17)H(18)I(2)N(2)O, the dihedral angle between the aromatic rings is 5.4 (1)°. An intra-molecular O-H⋯N hydrogen bond generates an S(6) ring motif. The crystal packing is stabilized by C-H⋯π and π-π inter-actions [centroid-centroid distance = 3.697 (1) Å].

Remote sensing of particulate pollution from space: have we reached the promised land?

The recent literature on satellite remote sensing of air quality is reviewed. 2009 is the 50th anniversary of the first satellite atmospheric observations. For the first 40 of those years, atmospheric composition measurements, meteorology, and atmospheric structure and dynamics dominated the missions launched. Since 1995, 42 instruments relevant to air quality measurements have been put into orbit. Trace gases such as ozone, nitric oxide, nitrogen dioxide, water, oxygen/tetraoxygen, bromine oxide, sulfur dioxide, formaldehyde, glyoxal, chlorine dioxide, chlorine monoxide, and nitrate radical have been measured in the stratosphere and troposphere in column measurements. Aerosol optical depth (AOD) is a focus of this review and a significant body of literature exists that shows that ground-level fine particulate matter (PM2.5) can be estimated from columnar AOD. Precision of the measurement of AOD is +/-20% and the prediction of PM2.5 from AOD is order +/-30% in the most careful studies. The air quality needs that can use such predictions are examined. Satellite measurements are important to event detection, transport and model prediction, and emission estimation. It is suggested that ground-based measurements, models, and satellite measurements should be viewed as a system, each component of which is necessary to better understand air quality.

Fatal cerebral abscess caused by Cladophialophora bantiana.

Primary cerebral phaeohyphomycosis is caused by pigmented fungi that exhibit distinct neurotropism often in immunocompetent individuals. A 20-yr-old male presented with multiple brain abscess which was subsequently proven microbiologically to be due to Cladophialophora Bantiana. In spite of near total excision and appropriate antifungal agents succumbed to his illness. We report this case to highlight its rarity and high mortality in an immunocompetent host. There is no initial clinical or laboratory feature that makes a preoperative diagnosis possible and relies on microbiological confirmation.