Precision mapping and expression analysis of recessive bacterial blight resistance gene xa-45(t) from Oryza glaberrima.

BACKGROUND: Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice leading to huge yield losses in Southeast Asia. The recessive resistance gene xa-45(t) from Oryza glaberrima IRGC102600B, mapped on rice chromosome 8, spans 80 Kb with 9 candidate genes on Nipponbare reference genome IRGSP-1.0. The xa-45(t) gene provides durable resistance against all the ten Xanthomonas pathotypes of Northern India, thus aiding in the expansion of recessive bacterial blight resistance gene pool. Punjab Rice PR127, carrying xa-45(t), was released for wider use in breeding programs. This study aims to precisely locate the target gene among the 9 candidates conferring resistance to bacterial blight disease. METHODS AND RESULTS: Sanger sequencing of all nine candidate genes revealed seven SNPs and an Indel between the susceptible parent Pusa 44 and the resistant introgression line IL274. The genotyping with polymorphic markers identified three recombinant breakpoints for LOC_Os08g42370, and LOC_Os08g42400, 15 recombinants for LOC_Os08g423420 and 26 for LOC_Os08g42440 out of 190 individuals. Relative expression analysis across six time intervals (0, 8, 24, 48, 72, and 96 h) after bacterial blight infection showed over expression of LOC_Os08g42410-specific transcripts in IL274 compared to Pusa 44, with a significant 4.46-fold increase observed at 72 h post-inoculation. CONCLUSIONS: The Indel marker at the locus LOC_Os08g42410 was found co-segregating with the phenotype, suggesting its candidacy towards xa-45(t). The transcript abundance assay provides strong evidence for the involvement of LOC_Os08g42410 in the resistance conferred by the bacterial blight gene xa-45(t).

Viral Clearance with Neutrophil Recovery in a Patient with Active COVID-19 Infection and Refractory Acute Myeloid Leukemia Who Underwent Successful Reinduction with Cytarabine/Idarubicin.

Administering myelosuppressive chemotherapy to patients with aggressive malignant hematologic disorders typically poses serious infectious complications, which can be exacerbated by the presence of active COVID-19 infection. We report on a case of a successfully treated fit elderly woman with refractory acute myeloid leukemia (AML) who also had mild COVID-19 infection and detectable viral load at the time she was found to have recurrent disease. Prior to initiation of reinduction treatment with cytarabine/idarubicin, this 2-dose COVID-19-vaccinated patient received antiviral therapy with remdesivir with resolution of upper respiratory symptoms. This was followed by sotrovimab on the third day of chemotherapy. Throughout her hospital course, she remained hemodynamically stable with one episode of neutropenic fever without other identified infections. Symptomatic reactivation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 was not observed. After achieving biopsy-confirmed morphologic remission of AML and with neutrophil recovery, the patient gradually cleared the virus, eventually testing negative on polymerase chain reaction test of the nasopharynx. This case underlines the importance of considering initiation of timely chemotherapy, although myelosuppressive, in appropriate patients with aggressive hematologic malignancies and concomitant SARS-CoV-2. It demonstrates management of active COVID-19 infection in this group of patients and the dynamics of SARS-CoV-2 viral load during leukemia treatment.

Spectrum of Adrenal Lesions on Fine-Needle Aspiration Cytology: A Tertiary Care Centre Experience.

Introduction Fine-needle aspiration cytology (FNAC) is an easy, quick, and specialized technique to distinguish neoplastic from non-neoplastic adrenal lesions, yet limited to tertiary care centers. It helps in analyzing symptomatic, as well as incidental adrenal lesions with high sensitivity and specificity. Aim This study was conducted to determine the cytological spectrum of adrenal lesions in a tertiary care center. Material and Methods This was a retrospective study which included a total of 19 cases of adrenal FNAC received from June 2017 till June 2019 in a north Indian tertiary care university hospital. All the lesions were broadly classified into non-neoplastic and neoplastic categories. The non-neoplastic lesions were divided into infective causes and cystic lesions. Neoplastic lesions were further grouped into benign and malignant lesions. Immunohistochemical findings were retrieved from the hospital records wherever accessible. Results A total of 19 cases were aspirated, of which 16 cases (84.20%) yielded satisfactory material. Six cases (31.57%) showed non-neoplastic pathology of which one was a cystic lesion, three were infective (two histoplasmosis and one tuberculosis), and two showed only benign adrenal cortical cells in a setting of known extra-adrenal primary malignancy. The neoplastic group comprised of 10 cases (52.63%) of which 4 cases showed metastatic carcinomatous deposits from a known extra-adrenal primary malignancy and 6 cases showed primary adrenal neoplasm (one case of myelolipoma, one case of pheochromocytoma, and four cases of adrenal neoplasm) which were then subjected to biopsy and immunohistochemistry. A final diagnosis of pheochromocytoma was made in three cases, adrenocortical carcinoma in one case, and one case was inconclusive because of nonrepresentative biopsy. Conclusion Image-guided fine-needle aspiration cytology of adrenal lesions helps to determine the exact nature of the infection, avoids unnecessary surgery, and helps in targeted management. However, histopathological evaluation with immunohistochemistry remains the diagnostic modality of choice with regard to neoplastic lesions.

From Evolution to Revolution: Accelerating Crop Domestication through Genome Editing.

Crop domestication has a tremendous impact on socioeconomic conditions and human civilization. Modern cultivars were domesticated from their wild progenitors thousands of years ago by the selection of natural variation by humans. New cultivars are being developed by crossing two or more compatible individuals. But the limited genetic diversity in the cultivars severely affects the yield and renders the crop susceptible to many biotic and abiotic stresses. Crop wild relatives (CWRs) are the rich reservoir for many valuable agronomic traits. The incorporation of useful genes from CWR is one of the sustainable approaches for enriching the gene pool of cultivated crops. However, CWRs are not suited for urban and intensive cultivation because of several undesirable traits. Researchers have begun to study the domestication traits in the CWRs and modify them using genome-editing tools to make them suitable for extensive cultivation. Growing evidence has shown that modification in these genes is not sufficient to bring the desired change in the neodomesticated crop. However, the other dynamic genetic factors such as microRNAs (miRNAs), transposable elements, cis-regulatory elements and epigenetic changes have reshaped the domesticated crops. The creation of allelic series for many valuable domestication traits through genome editing holds great potential for the accelerated development of neodomesticated crops. The present review describes the current understanding of the genetics of domestication traits that are responsible for the agricultural revolution. The targeted mutagenesis in these domestication genes via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 could be used for the rapid domestication of CWRs.

Molecular mapping and transfer of a novel brown planthopper resistance gene bph42 from Oryza rufipogon (Griff.) To cultivated rice (Oryza sativa L.).

BACKGROUND: Brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests of rice accounting for 52% of annual yield loss. The breakdown of resistance against known BPH biotypes necessitates the identification and deployment of new genes from diverse sources. The current study aimed at mapping and transfer of a novel BPH resistance gene from the wild species of rice O. rufipogon accession CR100441 to the elite rice cultivar against BPH biotype 4. METHODS AND RESULTS: The phenotypic screening against BPH biotype 4 was conducted using the standard seedbox screening technique (SSST). Inheritance study using damage score caused by BPH infestation at the seedling stage indicated the presence of a single major recessive gene with the segregation ratio of susceptible to resistant plants in 3:1 (210:66, χ2c = 0.17 ≤ χ20.05,1 = 3.84). The genotyping of the mapping population was done using polymorphic microsatellite markers between PR122 and O.rufipogon acc.CR100441 spanning all the 12 chromosomes of rice. A total of 537 SSR markers were used to map a BPH resistance gene (designated as bph42) on the short arm of chromosome 4 between RM16282 and RM6659. QTL analysis identified a peak marker RM16335 contributing 29% of the phenotypic variance at 40.76 LOD. CONCLUSIONS: The identified marker co-segregates with the bph42 and hence could be efficiently used for marker-assisted selection (MAS) for the transfer of resistance into elite rice cultivars. The introgression lines with higher yield and BPH resistance were identified and are under advanced yield trails for further varietal release.

Pathogenic role of mitogen activated protein kinases in protozoan parasites.

Protozoan parasites with complex life cycles have high mortality rates affecting billions of human lives. Available anti-parasitic drugs are inadequate due to variable efficacy, toxicity, poor patient compliance and drug-resistance. Hence, there is an urgent need for the development of safer and better chemotherapeutics. Mitogen Activated Protein Kinases (MAPKs) have drawn much attention as potential drug targets. This review summarizes unique structural and functional features of MAP kinases and their possible role in pathogenesis of obligate intracellular protozoan parasites namely, Leishmania, Trypanosoma, Plasmodium and Toxoplasma. It also provides an overview of available knowledge concerning the target proteins of parasite MAPKs and the need to understand and unravel unknown interaction network(s) of MAPK(s).

High-resolution mapping of the quantitative trait locus (QTLs) conferring resistance to false smut disease in rice.

Rice false smut (RFS), an emerging major fungal disease worldwide caused by Ustilaginoidea virens, affects rice grain quality and yield. RFS cause 2.8-49% global yield loss depending upon disease severity and cultivars. In India, the yield loss due to RFS ranged from 2 to 75%. Identification of the genes or quantitative trait loci (QTLs) governing disease resistance would be of utmost importance towards mitigating the economic losses incurred due to RFS. Here, we report mapping of RFS resistance QTLs from a resistant breeding line RYT2668. The mapping population was evaluated for RFS resistance under the field condition in three cropping seasons 2013, 2015, and 2016. A positive correlation among infected panicle/plant, total smut ball/panicle, and disease score was observed in the years 2013, 2015, and the mean data. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 using 2326 single nucleotide polymorphism markers. Of these, two QTLs, qRFSr5.3 and qRFSr7.1a, were associated with the infected panicle per plant, one QTL qRFsr9.1 with total smut ball per panicle, and four QTLs qRFSr2.2, qRFSr4.3, qRFSr5.4, and qRFSr7.1b with disease score. Among them, a novel QTL qRFSr9.1 on chromosome 9 exhibits the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 revealed four nucleotide-binding sites-leucine-rich repeat (NBS-LRR) domain-containing disease resistance proteins. In summary, our findings mark the hotspot region of rice chromosomes carrying genes/QTLs for resistance to the RFS disease.

Comparative phosphoproteomic analysis unravels MAPK1 regulated phosphoproteins in Leishmania donovani.

Mitogen Activated Protein Kinase1 (MAPK1) of Leishmania donovani functions as key regulators of various cellular activities, which seem to be imperative for parasite survival, infectivity, drug resistance and post-translational modification of chaperones/co-chaperones. However, very less is known about LdMAPK1 target proteins. With recent advancements in proteomics, we aimed to identify phosphoproteins which were differentially expressed in LdMAPK1 overexpressing (Dd8++/++) and single replacement mutants (Dd8+/) as compared to wild type (Dd8+/+) parasites, utilizing LC-MS/MS approach. An in-depth label-free phospoproteomic analysis revealed that modulation of LdMAPK1 expression significantly modulates expression levels of miscellaneous phosphoproteins which may act as its targets/substrates. Out of 1974 quantified phosphoproteins in parasite, 140 were significantly differentially expressed in MAPK1 overexpressing and single replacement mutants. These differentially expressed phosphoproteins are majorly associated with metabolism, signal transduction, replication, transcription, translation, transporters and cytoskeleton/motor proteins, hence suggested that MAPK1 may act in concert to modulate global biological processes. The study further implicated possible role of LdMAPK1 in regulation and management of stress machinery in parasite through post translational modifications. Precisely, comparative phosphoproteomics study has elucidated significant role of LdMAPK1 in regulating various pathways contributing in parasite biology with relevance to future drug development. SIGNIFICANCE: MAPKinase1, the downstream kinase of MAPK signal transduction pathway, has drawn much attention as potential therapeutic drug target due to their indispensable role in survival and infectivity of Leishmania donovani. However, limited information is available about its downstream effector proteins/signaling networks. Utilizing label free LC-MS/MS analysis, phosphoproteome of LdMAPK1 over-expressing (Dd8++/++) and LdMAPK1 single replacement mutants (Dd8+/-) with wild type (Dd8+/+) parasites was compared and identified 140 LdMAPK1 modulated phosphoproteins, mainly involved in pathways like signal transduction, metabolism, transcriptional, translational, post-translational modification and regulation of heat shock proteins. Interestingly, LdMAPK1 interacts directly with only six phosphoproteins i.e. casein kinase, casein kinase II, HSP83/HSP90, LACK, protein kinase and serine/threonine protein kinase. Thus, the study elucidates significant role of LdMAPK1 in Leishmania biology which may drive drug-discovery efforts against visceral leishmaniasis.

Identification of potential anti-leishmanial agents using computational investigation and biological evaluation against trypanothione reductase.

Trypanothione reductase of Leishmania donovani is a flavin adenine dinucleotide containing homodimeric protein essential for parasite survival. The flavoenzyme utilizes nicotinamide adenine dinucleotide phosphate in the reaction to convert oxidized trypanothione to reduced trypanothione which is further used up by tryparedoxin/tryparedoxin peroxidase system to neutralize the reactive oxygen species generated by the macrophages. Some of the drugs previously reported against the disease include sodium stibogluconate, miltefosine and amphotericin B. However, due to the resistance and toxicity problem associated with these molecules, there is an urgent need to develop new drugs against L. donovani. Trypanothione reductase of L. donovani is one such essential target whose inhibition could lead to a decline in parasite growth. In this work, we have performed a computational studies using Maybridge library of chemical compounds to identify potential inhibitors of Trypanothione reductase of L. donovani. Structure-based virtual screening method in combination with molecular docking was employed to identify and prioritize 30 compounds which were further subjected to molecular dynamics simulation. Ten compounds which showed stable ligand root-mean-square deviation plot, c-alpha backbone and root-mean-square fluctuation were considered for trypanothione reductase inhibition assay and subsequent inhibition studies of parasite growth. Enzyme inhibition assay resulted in shortlisting of four compounds that were found to inhibit Trypanothione reductase of L. donovani. Subsequently, the anti-leishmanial screening highlighted one compound as the potential anti-leishmanial agent, with IC50 value of 15.2 µM, that can be further optimised with medicinal chemistry efforts to improve its activity. Communicated by Ramaswamy H. Sarma.

Metal- and Solvent-Free Multicomponent Decarboxylative A3-Coupling for the Synthesis of Propargylamines: Experimental, Computational, and Biological Investigations.

Decarboxylative A3-coupling of ortho-hydroxybenzaldehydes, secondary amines, and alkynoic acids is performed under catalyst and solvent-free conditions. The developed methodology provided a waste-free method for the synthesis of hydroxylated propargylamines which are versatile precursors for various bioactive heterocyclic scaffolds. The experimental and density functional theory studies revealed that the in situ-formed ortho-quinonoid intermediate (formed from ortho-hydroxybenzaldehyde and amine) undergoes a concerted Eschweiler-Clarke type decarboxylation with alkynoic acids. The synthesized compounds were evaluated for MAO-A, MAO-B, and AChE inhibitory activities as potential drug candidates for the treatment of various neurological disorders. Compound 4f was found to be the most potent and selective MAO-B (high selectivity over MAO-A) and AChE inhibitor in the series with IC50 values of 4.27 ± 0.07 and 0.79 ± 0.03 µM, respectively.

MAPK1 of Leishmania donovani interacts and phosphorylates HSP70 and HSP90 subunits of foldosome complex.

MAP kinases (MAPK) are the most downstream kinases in signal transduction cascades and regulate critical cellular activities such as cell proliferation, differentiation, mortality, stress response, and apoptosis. The Leishmania donovani MAPK1 (LdMAPK1) is involved in parasite viability and drug resistance, but its substrates have not been identified yet. Aiming to identify the possible targets(s) of LdMAPK1, we sought to isolate interacting partners by co-immunoprecipitation, gel electrophoresis and mass spectrometry. Out of fifteen analyzed protein bands, four were identified as subunits of the HSP90 foldosome complex, namely HSP 90, HSP70, STI and SGT. Western blot analysis not only confirmed that LdMAPK1 interacts with HSP70 and HSP90 but also demonstrated that MAPK1 abundance modulates their expression. The interaction is sensitive to treatment with AMTZD, a competitive ERK inhibitor. MAPK1 also displayed kinase activity with HSP90 or HSP70 as substrates. By phosphorylating HSPs in the foldosome complex, MAPK1 may regulate the stability and activity of the foldosome which in turn plays a pivotal role in the parasitic life cycle of L. donovani. Our study therefore implicates LdMAPK1 in the post-translational modification and possibly the regulation of heat shock proteins. Conversely, HSP90 and HSP70 are identified as the first substrates of LdMAPK1.

Pigmented Villonodular Synovitis of Thumb-A Cytological Diagnosis.

Pigmented Villonodular Synovitis (PVNS) is a unique benign proliferative process of unknown aetiology involving the synovial lined joints diffusely or focally. The entity remains a diagnostic challenge. This condition is attributed to an increased synovial proliferation causing villous or nodular changes of synovial lined joints leading to PVNS, Pigmented Villonodular Bursitis (PVNB) when arising from bursae or Pigmented Villonodular Tenosynovitis (PVNTS) originating from the tendon sheath. We present a case of a young female with nodular masses on right thumb with cytomorphological features on FNAC suggestive of PVNS which was finally confirmed by histopathology.

Parotid or carotid? Misled by site.

We present an interesting scenario where a 64 years old male presented with a long standing painless, infra-auricular swelling, which had progressively increased in size. Based on the site, the clinical impression was of a salivary gland lesion and FNAC was performed. The smears were unusually cellular and had necrotic background. The cytological diagnosis was a cystic neoplasm of salivary gland, possibly mucoepidermoid carcinoma. Warthin's tumor was also kept in differential. However, the radiological investigations, which were made available after the FNAC report were conflicting with cytological diagnosis of a malignancy and were characteristic of a carotid body tumor, generally a benign neoplasm. Surgical excision of the tumor with regional lymph node sampling was done and histopathological examination solved the puzzle by revealing metastasis of paraganglioma to right posterior triangle lymph nodes. This case is unique because of the unusual presentation of a malignant paraganglioma as an infra-auricular swelling, which was clinically considered as a parotid tumor. The clinician as well as the pathologist need to be aware of such diagnostic pitfall. Diagn. Cytopathol. 2017;45:569-573. © 2017 Wiley Periodicals, Inc.

Bilateral eosinophilic mastitis: an uncommon unheard entity.

We are reporting a case of bilateral eosinophilic mastitis which is rare and hardly heard. It is a mimicker of carcinoma breast both clinically & radiologically. A 30 years old non diabetic female presented with bilateral breast lumps with history of rhinitis off & on and peripheral eosinophilia. Mammography was suspicious while ultrasonography was diagnostic of bilateral mastitis. Aspiration cytology exhibited inflammatory lesion rich in eosinophils. Histopathology revealed the diagnosis of eosinophilic mastitis. Eosinophilic infiltration of the breast is a rare manifestation of tissue involvement in peripheral eosinophilia and bilateralism is even rarer.