Defining genomic landscape for identification of potential candidate resistance genes associated with major rice diseases through MetaQTL analysis.

Rice production is severely affected by various diseases such as bacterial leaf blight (BLB), brown spot (BS), false smut (FS), foot rot (FR), rice blast (RB), and sheath blight (SB). In recent years, several quantitative trait loci (QTLs) studies involving different populations have been carried out, resulting in the identification of hundreds of resistance QTLs for each disease. These QTLs can be integrated and analyzed using meta-QTL (MQTL) analysis for better understanding of the genetic architecture underlying multiple disease resistance (MDR). This study involved an MQTL analysis on 661 QTLs (378, 161, 21, 41, 44, and 16 QTLs for SB, RB, BLB, BS, FS, and FR, respectively) retrieved from 50 individual studies published from 1995 to 2021. Of these, 503 QTLs were projected finally onto the consensus map saturated with 6,275 markers, resulting in 73 MQTLs, including 27 MDR-MQTLs conferring resistance to three or more diseases. Forty-seven MQTLs were validated using marker-trait associations identified in published genome-wide association studies. A total of 3,310 genes, including both R and defense genes, were also identified within some selected high-confidence MQTL regions that were investigated further for the syntenic relationship with barley, wheat, and maize genomes. Thirty-nine high-confidence candidate genes were selected based on their expression patterns and recommended for future studies involving functional validation, genetic engineering, and gene editing. Nineteen MQTLs were co-localized with 39 known R genes for BLB and RB diseases. These results could pave the way to utilize candidate genes in a marker-assisted breeding program for MDR in rice.

Outcome of early detection approach in control of breast, cervical, and oral cancer: Experience from a rural cancer center in India.

In low- and middle-income countries most of the cancer patients attend the hospital at a late stage and treatment completion of these cases is challenging. The early detection program (EDP), in rural areas of Punjab state, India was initiated to identify breast, cervical, and oral cancer at an early stage by raising awareness and providing easy access to diagnosis and treatment. A total of 361 health education programs and 99 early detection clinics were organized. The symptomatic and self-interested (non-symptomatic individuals who opted for screening) cases visited the detection clinic. They were screened for breast, cervical, and/or oral cancer. Further diagnosis and treatment of screen-positive cases were carried out at Homi Bhabha Cancer Hospital (HBCH), Sangrur. Community leaders and healthcare workers were involved in all the activities. The EDP, Sangrur removed barriers between cancer diagnosis and treatment with the help of project staff. From 2019 to 2023, a total of 221,317 populations were covered. Symptomatic and self-interested individuals attended the breast (1627), cervical (1601), and oral (1111) examinations. 46 breast (in situ-4.3%; localized-52.2%), 9 cervical (localized-77.8%), and 12 oral (localized-66.7%) cancer cases were detected, and treatment completion was 82.6%, 77.8%, and 50.0%, respectively. We compared cancer staging and treatment completion of cases detected through EDP with the cases attended HBCH from Sangrur district in 2018; the difference between two groups is statistically significant. Due to the early detection approach, there is disease down-staging and improvement in treatment completion. This approach is feasible and can be implemented to control these cancers in low- and middle-income countries.

Exploring the unusual: a testosterone-secreting ovarian tumor.

Ovarian steroid cell tumors are rare, representing less than 0.1% of all ovarian neoplasms. Among the myriad causes of hirsutism, ovarian tumors account for 1% of the reported cases. We present the case of a 49-year-old parous postmenopausal woman who sought medical attention for hirsutism for 2 years. This case illustrates the unusual and interesting connection between rare ovarian pathology and the clinical manifestation of hirsutism in a postmenopausal patient. Her ultrasonography and MRI showed a right adnexal mass of solid-cystic consistency with thin septations. Her laboratory workup revealed high levels of total testosterone of 256 ng/ml (8.4-48.1ng/ml) and free testosterone of 7.36 pg/ml (0.2-4.1 pg/ml), while DHEAS - 234 µg/dl (35.4-256 µg/dl) and CA125 - 15.8U/L (0.0-35 U/L) were in the normal range. She underwent exploratory laparotomy with a total abdominal hysterectomy and oophorectomy. Histopathological examination and immunohistochemistry conclusively established the presence of a steroid cell tumor, specifically classified as "Not Otherwise Specified"(NOS), in the right ovary.

Exploring the unusual: a testosterone-secreting ovarian tumor

ABSTRACT Ovarian steroid cell tumors are rare, representing less than 0.1% of all ovarian neoplasms. Among the myriad causes of hirsutism, ovarian tumors account for 1% of the reported cases. We present the case of a 49-year-old parous postmenopausal woman who sought medical attention for hirsutism for 2 years. This case illustrates the unusual and interesting connection between rare ovarian pathology and the clinical manifestation of hirsutism in a postmenopausal patient. Her ultrasonography and MRI showed a right adnexal mass of solid-cystic consistency with thin septations. Her laboratory workup revealed high levels of total testosterone of 256 ng/ml (8.4-48.1ng/ml) and free testosterone of 7.36 pg/ml (0.2-4.1 pg/ml), while DHEAS - 234 µg/dl (35.4-256 µg/dl) and CA125 - 15.8U/L (0.0-35 U/L) were in the normal range. She underwent exploratory laparotomy with a total abdominal hysterectomy and oophorectomy. Histopathological examination and immunohistochemistry conclusively established the presence of a steroid cell tumor, specifically classified as "Not Otherwise Specified"(NOS), in the right ovary.

Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.

Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.

Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding.

Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima.

Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC1F1 population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.

Congenital Rubella Syndrome as a possible cause for persistent thrombocytopenia in early infancy: The Forgotten Culprit.

We present a case of a late preterm intrauterine growth-restricted neonate with isolated and persistent severe thrombocytopenia. At birth, the neonate did not have a complete clinical spectrum of congenital rubella syndrome (CRS) but later developed peculiar findings that helped clinch the diagnosis. The neonate also had interstitial pneumonia and died secondary to superimposed acute viral infection leading to acute respiratory distress syndrome. The serology was positive for IgM antibodies against the rubella virus. The constellation of clinical manifestations of congenital rubella in the presence of positive IgM antibody against rubella and consistent histopathology confirmed the diagnosis of CRS.

A Prospective Review on Selectable Marker-Free Genome Engineered Rice: Past, Present and Future Scientific Realm.

As a staple food crop, rice has gained mainstream attention in genome engineering for its genetic improvement. Genome engineering technologies such as transgenic and genome editing have enabled the significant improvement of target traits in relation to various biotic and abiotic aspects as well as nutrition, for which genetic diversity is lacking. In comparison to conventional breeding, genome engineering techniques are more precise and less time-consuming. However, one of the major issues with biotech rice commercialization is the utilization of selectable marker genes (SMGs) in the vector construct, which when incorporated into the genome are considered to pose risks to human health, the environment, and biodiversity, and thus become a matter of regulation. Various conventional strategies (co-transformation, transposon, recombinase systems, and MAT-vector) have been used in rice to avoid or remove the SMG from the developed events. However, the major limitations of these methods are; time-consuming, leftover cryptic sequences in the genome, and there is variable frequency. In contrast to these methods, CRISPR/Cas9-based marker excision, marker-free targeted gene insertion, programmed self-elimination, and RNP-based delivery enable us to generate marker-free engineered rice plants precisely and in less time. Although the CRISPR/Cas9-based SMG-free approaches are in their early stages, further research and their utilization in rice could help to break the regulatory barrier in its commercialization. In the current review, we have discussed the limitations of traditional methods followed by advanced techniques. We have also proposed a hypothesis, "DNA-free marker-less transformation" to overcome the regulatory barriers posed by SMGs.

Interaction of TiO2 nanoparticles with soil: Effect on microbiological and chemical traits.

Titanium dioxide (TiO2) nanoparticles (NPs) are the most widely used nanomaterials and their expanding use raises concerns about their impacts on soil ecosystems and functioning. The present study evaluates the potential impacts of TiO2 NPs applied at low doses (0, 1.0, 2.5, 5.0, 10.0 and 20.0 mg L-1) on soil chemical properties including the macro and micronutrient contents, microbial population and enzyme activities in rhizosphere soil of mung bean crop at different time intervals (7, 14, 28 and 56 days). A quantitative RT-PCR study was also performed to study the relative change in the gene expression of ammonia oxidizer and nitrogen fixers upon TiO2 NP supplementation. An increase in soil nutrient content viz., available N, P, Cu, Fe, Mn, nitrate-N and ammonical-N was observed with NP application except available K and Zn content. The TiO2 NPs stimulated the growth of soil microflora at low concentrations while an inhibitory effect was recorded at high concentrations. The soil fungi and actinobacteria emerged as the most sensitive groups of soil microbes towards TiO2 NP exposure exhibiting detrimental impacts on their growth at all concentrations. Similarly, the soil enzyme activities enhanced till TiO2 NPs (10.0 mg L-1) which was followed by decrease at higher concentrations. The qRT-PCR study showed that the ammonia oxidizers were more affected by TiO2 NPs application than nitrogen fixers. These findings suggest that TiO2 NPs can be used as stimulators of soil nutrients and soil microbial dynamics at low concentrations.

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.

Congenital Rubella Syndrome as a possible cause for persistent thrombocytopenia in early infancy: The Forgotten Culprit

Abstract We present a case of a late preterm intrauterine growth-restricted neonate with isolated and persistent severe thrombocytopenia. At birth, the neonate did not have a complete clinical spectrum of congenital rubella syndrome (CRS) but later developed peculiar findings that helped clinch the diagnosis. The neonate also had interstitial pneumonia and died secondary to superimposed acute viral infection leading to acute respiratory distress syndrome. The serology was positive for IgM antibodies against the rubella virus. The constellation of clinical manifestations of congenital rubella in the presence of positive IgM antibody against rubella and consistent histopathology confirmed the diagnosis of CRS.

Elucidating the morpho-physiological adaptations and molecular responses under long-term waterlogging stress in maize through gene expression analysis.

Waterlogging stress in maize is one of the emerging abiotic stresses in the current climate change scenario. To gain insights in transcriptional reprogramming during late hours of waterlogging stress under field conditions, we aimed to elucidate the transcriptional and anatomical changes in two contrasting maize inbreds viz. I110 (susceptible) and I172 (tolerant). Waterlogging stress reduced dry matter translocations from leaves and stems to ears, resulting in a lack of sink capacity and inadequate grain filling in I110, thus decreased the grain yield drastically. The development of aerenchyma cells within 48 h in I172 enabled hypoxia tolerance. The upregulation of alanine aminotransferase, ubiquitin activating enzyme E1, putative mitogen activated protein kinase and pyruvate kinase in I172 suggested that genes involved in protein degradation, signal transduction and carbon metabolism provided adaptive mechanisms during waterlogging. Overexpression of alcohol dehydrogenase, sucrose synthase, aspartate aminotransferase, NADP dependent malic enzyme and many miRNA targets in I110 indicated that more oxygen and energy consumption might have shortened plant survival during long-term waterlogging exposure. To the best of our knowledge, this is the first report of transcript profiling at late stage (24-96 h) of waterlogging stress under field conditions and provides new visions to understand the molecular basis of waterlogging tolerance in maize.

Cervico Medullary Junction "Intramedullary Schwannoma" Masquerading As Glioma: A Surprise During Surgery.

BACKGROUND: Intramedullary schwannomas (IS) at cervicomedullary junction (CMJ) are exceedingly uncommon. There is hardly any clinicoradiological marker for preoperative diagnosis and prognostication. CASE: We report a case of a 17-year-old boy with progressive spastic quadriparesis of six months duration. On radiology, there was a contrast-enhancing lesion expanding the cord extending from the medulla to C5 level. During surgery, the cord was expanded and the tumor was eccentric. Histopathology and immunohistochemistry were suggestive of schwannoma. In view of the ill-defined plane of separation from the normal neural tissue, only subtotal resection could be achieved. CONCLUSION: Schwannoma should be considered as a remote differential of intramedullary lesions. The extent of resection should be tailored according to the plane of dissection and intraoperative neuromonitoring guidance. Though a masquerader, schwannoma carries better prognosis than rest of the pathologies.

Computational identification of maize miRNA and their gene targets involved in biotic and abiotic stresses.

Plant interactions with biotic and abiotic stresses are complex and entail changes at the transcriptional, cellular and physiological level. MicroRNAs (miRNAs) are small (∼20-24 nt), non-coding RNAs that play a vital role in wide range of biological processes involved in regulation of gene expression through translation inhibition or degradation of their target mRNAs during stress conditions. Therefore, identification of miRNAs and their targets are of immense value in understanding the regulatory networks triggered during stress. Advancement in computational approaches has opened up ways for the prediction of miRNAs and their possible targets with functional pathways. Our objective was to identify miRNA and their potential targets involved in both biotic and abiotic stresses in maize. A total of 2,019,524 downloaded ESTs from dbEST were processed and trimmed by Seq Clean. The program trashed 264,000 and trimmed 284,979 sequences and the resulting 1,755,534 sequences were submitted for clustering and assembled to RepeatMasker and TGICL. A total of 30 miRNAs were found to hybridize with the potential targets of gene families such as CoA ligase, lipoxygenase 1, Terpenoideyclases, Zn finger, transducing, etc. Ten of the identified miRNAs targeted cytochrome c1 family. Zm_miR23 class targeted 11 different genes. The identified targets are involved in the plant growth and development during biotic and abiotic stresses in maize. These miRNAs may be further used for functional analysis. Furthermore, four and two of the miRNA targets were validated in response to waterlogging tolerance and southern leaf blight resistance, respectively, to understand the miRNA-assisted regulation of target miRNAs. The functional annotation of the predicted targets indicated that these stress-responsive miRNAs regulate cellular function; molecular function and biological process in maize at the post-transcriptional level. The present results have paved way towards better understanding the role of miRNAs in the mechanism of stress tolerance in maize.

An insight into the genome of extensively drug-resistant and uropathogenic Citrobacter werkmanii.

OBJECTIVE: Carbapenemase-producing bacteria pose a serious public-health threat. This study was performed to understand the emergence and genetic features of NDM-producers in hospital setting. METHODS: Samples were collected from a tertiary-care hospital. Isolate identification was performed by 16S rRNA sequencing. The genome of Citrobacter werkmanii (AK-8) was sequenced on an Illumina NextSeq 500 platform. Resistance determinants and pathogenicity islands were determined by ResFinder and PathogenFinder, respectively. MLST, two-component systems and transcription factors were identified by P2RP server, whilst variant calling and insertion sequence (IS) elements were determined by Galaxy and ISfinder, respectively. The genome of AK-8 was compared with uropathogenic Escherichia coli strain 536. RESULTS: This is the first report on whole-genome analysis of extensively drug-resistant NDM-6-producing uropathogenic C. werkmanii ST-104. Resistance genes for all antibiotics except colistin, fosfomycin, fusidic- acid, nitroimidazole, oxazolidinones, tetracycline and glycopeptides were detected in this strain. Genome analysis of AK-8 led to the identification of the BaeSR two-component system regulating production of multidrug efflux proteins. Virulence was regulated by CpxRA, ZraRS, RstAB, UhpAB, AcrAB, RcsBc and UvrY, whereas Bar-UvrY was found to control carbon metabolism, flagellum biosynthesis and biofilm formation. The AK-8 genome encodes 21 chemoreceptors involved in colonisation and pathogenesis. Fur family transcriptional regulator, cAMP receptor protein and RpoS were found to increase the virulence of AK-8. ntBLAST analysis showed 69.60% genetic identity with E. coli 536 as an adaptive feature for survival. CONCLUSION: The emergence of extensively drug-resistant pathogenic C. werkmanii is alarming and it should not be ignored as commensal.

Villous Morphology in Urinary Bladder Biopsy: An Approach to Diagnosis.

Villous morphology in urinary bladder biopsy is a relatively uncommon finding. Villi are slender, finger-like structures that are commonly seen in the small intestine or in neoplastic lesions of gastrointestinal lineage/differentiation. Importantly, placenta also exhibits villi that are morphologically and functionally different from the intestinal one. Majority of the neoplastic lesions of urinary bladder are urothelial in origin with a minor subset showing glandular differentiation. While the presence of benign villi in urinary bladder biopsy necessitates a search for an occult perforation, provided a sample mismatch is ruled out, cytoarchitecturally abnormal/dysplastic villi indicate a neoplastic lesion of the urinary bladder encompassing villous adenoma and adenocarcinoma and urothelial carcinoma with villoglandular differentiation. The dysplastic villi in urinary bladder also imply a lower gastrointestinal endoscopy to rule out a colorectal primary. The development of the villous lesions in the urinary bladder and the colorectum are embryologically related and pose a major diagnostic challenge to the clinicians and surgical pathologists due to identical histomorphology and immunohistochemistry. We tend to discuss the morphological differentials and diagnostic approach to the villous lesions in the urinary bladder biopsy.