Elucidation of the population structure and genetic diversity of Bipolaris oryzae associated with rice brown spot disease using SSR markers.

Brown spot disease, caused by Bipolaris oryzae, is one of the several disastrous diseases affecting rice. The brown spot fungus illustrates substantial pathogenic and genetic variability. To the best of our knowledge, extensive analysis utilizing specific SSR primers for B. oryzae genome is quite inadequate for the population structure and genetic diversity of Indian B. oryzae isolates. A total of 84 brown spot isolates were collected from rice-cultivating areas across southern and eastern Indian states, viz., Tamil Nadu, Andhra Pradesh, Odisha and Chhattisgarh. The pathogenicity and virulence characteristics of these isolates were assessed with the susceptible cultivar CR Dhan 201. Twelve genome-specific SSR markers of B. oryzae warranted the investigation of the population structure and genetic diversity among the isolates. These isolates were categorized based on their disease grade as highly virulent isolates (4 nos.), virulent isolates (8 nos.), moderately virulent isolates (47 nos.) and less virulent isolates (25 nos.). PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. The SSR markers produced a total of 35 alleles with 1 to 4 alleles per locus with a gene diversity ranging between 0.00 and 0.687 and a major allele frequency variation of 0.425-0.975. The PIC value ranged from 0.00 to 0.638 having a mean value of 0.34. Cluster analysis technique was applied to group the brown spot isolates into four distinct clusters. Principal coordinate and structure analysis identified two genetic clusters of B. oryzae isolates for individual states with some degree of distinctness complying with their virulence. Analysis of molecular variance revealed more genetic variation within populations and less among populations. The study outcome would expedite the comprehension of genetic diversity of B. oryzae across the southern and eastern states of India. Furthermore, we anticipate its guidance in the development of more effective disease management strategies as well as in the generation of novel resistant varieties through marker-assisted breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03347-4.

Expert Opinion on P2Y12 Inhibitors Use in Management of Acute Coronary Syndromes: Focus on Ticagrelor.

Ticagrelor is a potent, oral P2Y12 inhibitor used as a part of dual antiplatelet therapy (DAPT) in acute coronary syndromes (ACS). New evidence has emerged for its use in ACS, which may be crucial for the Indian context. This brought together nearly 150 experts in ACS management across the country who reviewed the current evidence and discussed the same through a series of 10 meetings on an online platform. With all experts' agreement, the key expert opinions for the P2Y12 inhibitors use in ACS management were finalized. These include the following. In ACS patients aged <75 years, with diabetes, a history of stroke/transient ischemic attack, and chronic kidney disease, ticagrelor may be preferred over other P2Y12 inhibitors. It may also be preferred in the elderly above 75 years with clopidogrel is a suitable alternative in patients at high-risk of bleeding. Rates of stent thrombosis are lower with ticagrelor than clopidogrel. In patients managed with fibrinolysis, use ticagrelor after 48 hours if streptokinase was the fibrinolytic agent or it can be used after 12 to 24 hours if fibrin-specific fibrinolytic was used. Rates of major bleeding in patients treated with fibrinolysis are similar to clopidogrel. Prehospital administration may be preferred over in-hospital administration with expected bleeding rates similar to clopidogrel. Switching among P2Y12 inhibitors should be done with due consideration of their pharmacodynamics. At present, DAPT should be continued for 12 months with discontinuation after three to six months in patients with high bleeding risk. The use of low dose ticagrelor may be considered in cases with high-bleeding risk. DAPT or ticagrelor continuation beyond one year should be individualized considering ischemic and bleeding risks. Dyspnea is a common, mild, and transient and does not necessitate ticagrelor discontinuation. Severe dyspnea should be investigated thoroughly. In conclusion, ticagrelor (180 mg, 90 mg, and 60 mg doses), a potent antiplatelet is expected to reshape the antiplatelet use in the management of ACS.

Role of climate change variables (standing water and rainfall) on dissipation of chlorantraniliprole from a simulated rice ecosystem.

Chlorantraniliprole (CAP) is extensively used for rice pest management. Lack of information on the role of standing water and amount and timing of rainfall on CAP dissipation in rice ecosystem could hamper its prospective use. Present study was performed to investigate the effects of different water regimes (saturated, 5 and 10 cm standing water) and simulated rainfall (40 and 100 mm occurred at 4, 8 and 24 h after CAP application) on leaching, surface runoff and dissipation of CAP into components of rice ecosystem. The results showed highest concentration of CAP residues in soil and plant under saturated condition followed by 5 and 10 cm standing water conditions. Whereas, the highest concentration of CAP in leachates was detected under 10 cm standing water (12.19 ng mL-1). The results revealed large amount of leaching (21.99 ng mL-1) and surface runoff (42.25 ng mL-1) losses of CAP when 100 mm rainfall occurred at 4 h after pesticide application. The total quantity of CAP residues in soil and plant was highest when rainfall occurred at 24 h after pesticide application under both the rainfall amounts. Water stagnation and high intensity rainfall occurred shortly after pesticide application will contribute to pesticide loss to non-target sites through surface run-off and leaching. There will be less pesticide available in soil for plant uptake which may not be sufficient to kill the target organisms.

Indigenous biobed to limit point source pollution of imidacloprid in tropical countries.

Point pollution of pesticides originating from the washing of spraying machines could be controlled by biobed system and it is in use in temperate countries. The biobed system is yet to be established in tropical countries. An indigenous biobed system was prepared using local resources like rice straw, farm yard manures (FYM) and paddy field soil to suit the tropical climate. Lowermost 3 cm layer of the biobed system was filled with rice husk biochar to prevent leaching of pesticides from the system. This model system was tested with high doses of imidacloprid (178 mg/column), a commonly used pesticide against number of insect-pests in different crops, for its degradation. The bio-mix trapped a major part of the imidacloprid on the top most layer of the biobed column and only a very small part of imidacloprid recovered from the leachate. The biobed system could degrade 70.13% of applied imidacloprid within 15 days of the experiment and only 5.27% of the total pesticide recovered 90 days after incubation. Addition of biochar layer adsorbed imidacloprid from the outgoing leachate from the biobed column. Biomixture boosted microbial activity more particularly fungal population, which might be responsible for imidacloprid degradation. Microbial biomass carbon, and soil enzymes indicated faster dissipation of imidacloprid from the top layer of the biobed. This simple but efficient biobed system using local resources can fulfill the need of the small and marginal farmers of Asian countries for pesticide decontamination.

Candidate screening of blast resistance donors for rice breeding.

Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21_79-3) corresponding to the blast resistance genes (Pi56(t) and pi21) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance. These associated genes could be introgressed through marker-assisted to develop durable blast resistant rice varieties. The selected resistant NRVs could be good donors for the blast resistance in rice crop improvement research.

Dissipation of chlorantraniliprole in contrasting soils and its effect on soil microbes and enzymes.

An experiment was set up to determine the rate of dissipation of chlorantraniliprole (CTP) from two soils with contrasting properties. The other objective of the study was to find out the effect of CTP on soil microorganisms (population, microbial biomass carbon and soil enzymes) under controlled environment. CTP residues when applied at recommended dose ((RD) (at 40 g a.i./ha)) could not be recovered either from alluvial soil or red soil at 60 days post application of CTP in a microcosm study. Higher clay content led to higher half-life in alluvial soil compared to red soil. CTP could not be recovered from RD treatment at 30 days after pesticide application under controlled environment. Faster dissipation of CTP was observed in rice rhizosphere soil with 23.89 and 34.65 days dissipation half-lives for RD and double the recommended dose (DRD) treatments, respectively. Different doses of chlorantraniliprole did not have considerable negative effect on actinomycetes, fungi, biological nitrogen fixers and phospahte solubilising bacteria except the bacteria population. Among the treatments, DRD recorded the lowest activity of dehyrodeganse, fluoresein diacetate hydrolase, acid and alkaline phosphatases followed by RD treatment. Microbial biomass carbon, ß -glycosidase and urease did not vary significantly among the different doses of CTP. In general, RD did not have negative effcts on soil microbes. Hence, CTP can be recommeded in rice pest managment maintaining existing soil microbes and soil enzymes activity.

Correction: Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers.

[This corrects the article DOI: 10.1371/journal.pone.0211061.].

Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers.

Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well-known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twenty-eight gene specific markers were investigated in landraces originated from nine diverse rice ecologies of India. Based on phenotypic evaluation, landraces were classified into three distinct groups: highly resistant (21), moderately resistant (70) and susceptible (70). The landraces harbour a range of five to nineteen genes representing blast resistance allele with the frequency varied from 4.96% to 100%. The cluster analysis grouped entire 161 landraces into two major groups. Population structure along with other parameters was also analyzed to understand the evolution of blast resistance gene in rice. The population structure analysis and principal coordinate analysis classified the landraces into two sub-populations. Analysis of molecular variance showed maximum (93%) diversity within the population and least (7%) between populations. Five markers viz; K3957, Pikh, Pi2-i, RM212and RM302 were strongly associated with blast disease with the phenotypic variance of 1.4% to 7.6%. These resistant landraces will serve as a valuable genetic resource for future genomic studies, host-pathogen interaction, identification of novel R genes and rice improvement strategies.

Effect of Abiotic Factors on Degradation of Imidacloprid.

The role of soil moisture, light and pH on imidacloprid dissipation was investigated. A high performance liquid chromatography (HPLC) based method was developed to quantify imidacloprid present in soil with a recovery of more than 82%. Rate of dissipation of imidacloprid from soil was faster in submerged condition compared to field capacity and air dried condition. Imidacloprid dissipated non-significantly between sterile and non-sterile soils, but at field capacity, the dissipation was faster in non-sterile soil compared to sterile soil after 60 days of incubation. Similarly, under submergence, the dissipation of imidacloprid was 66.2% and 79.8% of the initial in sterile and non-sterile soils, respectively. Imidacloprid was rather stable in acidic and neutral water but was prone to photo-degradation. Therefore, imidacloprid degradation will be faster under direct sunlight and at higher soil moisture.

A study on the impact of CYP2C19 genotype and platelet reactivity assay on patients undergoing PCI.

BACKGROUND: A thorough understanding of the patient's genotype and their functional response to a medication is necessary for improving event free survival. Several outcome studies support this view particularly if the patient is to be started on clopidogrel due to the prevalence of clopidogrel resistance. Such guided therapy has reduced the incidence of Major Adverse Cardiac Events (MACE) after stent implantation. METHODS: Between August 2013 and August 2014, 200 patients with coronary artery disease undergoing percutaneous coronary intervention (PCI) were prescribed any one of the anti-platelet medications such as clopidogrel, prasugrel or ticagrelor and offered testing to detect CYP2C19 gene mutations along with a platelet reactivity assay (PRA). Intended outcome was modification of anti-platelet therapy defined as either dose escalation of clopidogrel or replacement of clopidogrel with prasugrel or ticagrelor for the patients in clopidogrel arm, and replacement of ticagrelor or prasugrel with clopidogrel if those patients were non-carrier of mutant genes and also if they demonstrated bleeding tendencies in the ticagrelor and prasugrel arms. CONCLUSION: Clopidogrel resistance was observed to be 16.5% in our study population. PRA was useful in monitoring the efficacy of thienopyridines. By having this test, one can be safely maintained on clopidogrel in non-carriers, or with increased dose of clopidogrel in intermediate metabolizers or with newer drugs such as ticagrelor or prasugrel in poor metabolizers. Patients on ticagrelor and prasugrel identified as non-carriers of gene mutations for clopidogrel metabolism could be offered clopidogrel resulting in economic benefits to the patients. Patients at high risk of bleeding were also identified by the PRA.

Chimeric murine interferon regulatory factor-2 (IRF-2) binds to IRF-E (IRF binding element), VREß (virus response element) but not to VREα1.

Interferon regulatory factor-2 (IRF-2) is a multifunctional transcription factor having gene activation, repression and synergistic effect in conjunction with IRF-1. IRF-2 is also involved in type I IFN signalling by repressing INFß gene. So far, the molecular mechanism of its DNA binding activity remains elusive. We have carried out molecular sub-cloning, expression and electrophoretically mobility shift assay study of chimeric murine IRF-2. Here, we report expression of chimeric murine IRF-2 as GST-IRF-2 fusion protein in Escherichia coli/BL21 cells and demonstrated DNA binding activity by gel retardation technique using radio (32) P-labelled IRF-E motif (GAAAGT)4 , virus response element (VRE) of human INFß and IFNα1 gene. We observed five different masses DNA/GST-IRF-2 complexes (1-5) with IRF-E motif, three different masses DNA/GST-IRF-2 complexes (1-3) with VREß , but we could not observe any complex of DNA/GST-IRF-2 with VREα1 . The specific binding on IRF-E motif was confirmed by carrying out 100-X fold cold competition with (32) P-labelled IRF-E motif. In contrast to specific binding on VREß , we used negative control where we observed no binding complex, but we observed complexes with clones IPTG-induced extract. As far as binding on VREα1 is concerned, we could not observe any complex in negative control as well as in IPTG-inducible clones extract. Chimeric IRF-2 binds with IRF-E motif and VREß but not with VREα1. This study is first of its kind and paves the way to understand the differential DNA binding and molecular mechanism of DNA binding activity of the IRF-2 molecule, which is crucial for its function(s).

Microbial biomass and carbon mineralization in agricultural soils as affected by pesticide addition.

A laboratory study was conducted with four pesticides, viz. a fungicide (carbendazim), two insecticides (chlorpyrifos and cartap hydrochloride) and an herbicide (pretilachlor) applied to a sandy clay loam soil at a field rate to determine their effect on microbial biomass carbon (MBC) and carbon mineralization (C(min)). The MBC content of soil increased with time up to 30 days in cartap hydrochloride as well as chlorpyrifos treated soil. Thereafter, it decreased and reached close to the initial level by 90th day. However, in carbendazim treated soil, the MBC showed a decreasing trend up to 45 days and subsequently increased up to 90 days. In pretilachlor treated soil, MBC increased through the first 15 days, and thereafter decreased to the initial level. Application of carbendazim, chlorpyrifos and cartap hydrochloride decreased C(min) for the first 30 days and then increased afterwards, while pretilachlor treated soil showed an increasing trend.

Bilateral carotid angioplasty and stenting.

Bilateral carotid stenosis is generally treated by staged stenting procedure and rarely simultaneously due to concerns about hemodynamic impairment from stimulation of the carotid sinus baroreflex (severe bradycardia, hypotension) and the risk of cerebral hyperperfusion syndrome. Most of the accounts of bilateral carotid stenting are of small series. The aim of this study was to evaluate the feasibility and safety of simultaneous bilateral carotid angioplasty and stenting (CAS) in comparison with staged procedure. We retrospectively analyzed the procedural outcome and complications of bilateral CAS done between February 1995 and June 2004 in a consecutive series of 57 high-risk patients. Mean age was 64 +/- 9 years (male, 43; female 14). One hundred fifteen arteries were treated (one patient had bilateral internal carotid artery stenosis associated to an ostial common carotid artery stenosis). Thirty-nine patients were symptomatic (70%). Thirty-six patients had severe coronary artery disease. Seventeen patients underwent a simultaneous bilateral CAS (group 1), 40 in a staged manner (group 2). Among these 40 patients 10 were treated with a time interval of 24 hr, while the 30 other ones were treated with a time interval of 2 days to 2 months. A neuroprotection device was used in the last 42 patients. There was technical success in all patients and transient bradycardia and/or hypotension in 25 patients (44%). There was no prolonged bradycardia or hypotension. At 30 days, we observed in group 1 (simultaneous bilateral CAS) no transient ischemic attack (TIA), no minor stroke, one (5.8%) major stroke (hyperperfusion syndrome with brain hemorrhage leading to death in a patient under IIb/IIIa inhibitors), one myocardial infarction leading to death, and two (11.7%) death/stroke/myocardial infarction; in group 2 (staged procedure), two (5%) TIAs, no minor stroke, no major stroke, and one (2.5%) hyperperfusion syndrome with rapid recovery. Among the 10 patients treated with a time interval of 24 hr, we observed one TIA. Among carefully selected patients, bilateral CAS is feasible simultaneously or the day after, with a safety and complication rate comparable to that of large published series of CAS or endarterectomies in high-risk patients. Nevertheless, careful monitoring of the patient, blood pressure, and heart rate is mandatory to avoid complications related to hyperperfusion syndrome. Routine use of neuroprotection device and meticulous technique should improve the outcomes of bilateral CAS.

Percutaneous transluminal angioplasty using a cutting balloon for stenosis of the arch vessels in aortoarteritis.

Percutaneous transluminal angioplasty with or without stenting of steno-occlusions in the supra-aortic arch vessels in aortoarteritis is associated with suboptimal results and higher restenosis rates, particularly in those with diffuse disease. We report two cases of stand-alone cutting balloon angioplasty for patients who presented with critical stenosis of the common carotid artery, and occlusion of the subclavian artery, respectively.

Percutaneous transluminal angioplasty using a new peripheral cutting balloon for stenosis of arch vessels in aorto arteritis.

Percutaneous transluminal angioplasty (PTA) with or without stenting of steno-occlusions in the supra-aortic arch vessels in aortoarteritis is associated with higher residual stenosis and restenosis, particularly in those with diffuse disease. The use of the new peripheral cutting balloon (Boston Scientific Interventional Technologies, San Diego, CA, USA) in these lesions in aortoarteritis has not been described. We report here the first 2 cases of stand alone cutting angioplasty for 2 patients (3 arteries). One patient presented with a critical stenosis of the common carotid artery. We obtained a good immediate result but a restenosis appeared at 6 months, easily treated by a new angioplasty with cutting balloon and stent implantation. The second patient had an occlusion of the subclavian artery associated with a severe ostial vertebral artery stenosis. The immediate result was excellent and the 6-month clinical and angiographic control showed no restenosis.

Carotid artery stenting with filter protection.

BACKGROUND: Neurologic events associated with distal embolization of debris during percutaneous carotid artery stenting complicate the procedure. Filter devices for cerebral protection potentially reduce the risk of embolization and other neurologic events. We studied the feasibility, safety, and efficacy of carotid artery stenting with a filter device. METHODS AND RESULTS: Between January 2002 and January 2003, a total of 22 consecutive patients (30 lesions) who had >70% diameter stenosis of the internal carotid artery underwent carotid artery stenting with filter protection at our institute. The mean age of the patients was 64+/-9 years; 14 were men and 8 women, and 15 had neurologic symptoms. A stent was successfully implanted in 29 lesions. It was possible to position a filter device in all the 29 lesions. Neurologic complications during the procedure, in the hospital, and at 30-day clinical follow-up occurred in 2 patients. One patient suffered a minor stroke that resolved within 24 hours. None of the patients had a major embolic stroke. There was one death from intracerebral hemorrhage related to hyperperfusion and the use of a glycoprotein IIb/IIIa inhibitor. CONCLUSIONS: Filter protection during carotid artery stenting seems technically feasible, safe, and effective. In the present study, the incidence of embolic neurologic events was low.

Renal artery involvement in patients of coronary artery disease undergoing coronary angiography--a prospective study.

METHODS: We prospectively studied the angiographic incidence of renal artery stenosis in 1000 consecutive patients who underwent coronary angiography for clinically suspected coronary artery disease since December, 1998. Selective renal arteriography was performed in all the patients (mean age 57 years, 74.6% males) after coronary angiography. RESULTS: Systemic arterial hypertension was present in 52%, 29.1% were smokers, 21% had diabetes and 31.2% had hypercholesterolemia. Significant coronary artery diseases was found in 849 (84.9%) patients. Of the total patient cohort, 103 (10.3%) patients had renal artery disease; 78 (7.8%) had insignificant stenosis (> 50%) and significant renal artery stenosis (< 50%) was identified in 25 (2.5%) patients. Three had bilateral renal artery stenosis. Comparisons were made between renal artery stenosis and risk factor profile. There was no statistically significant association between renal artery stenosis and parameters like diabetes mellitus, hypertension, smoking, lipid levels and serum creatinine. CONCLUSION: In our study, the absolute number of cases with significant renal artery stenosis is small, so no statistical analysis could be performed to demonstrate the relationship of presence of renal artery stenosis with severity of CAD. However patients with severe coronary artery disease or having multiple risk factor showed a trend towards increased prevalence of renal artery stenosis, hence renal angiography should be done for this subset of patients.