First Report of 'Candidatus Phytoplasma citri' related strain (16SrII-C subgroup) associated with phyllody disease of cumin in India.

Cumin (Cuminum cyminum L.), is an important export-oriented seed spice crop for India. Cumin is popularly used for flavouring food, including soups, pickles and vegetables, and for herbal medicine. India is the largest producer, consumer and exporter of cumin seed with an annual production of 0.795 million tones over an area of 1.09 million hectares. During 2020-21, India exported about 0.299 million tons of cumin worth of Rs 33280 million (Anonymous, 2021). Recently, phytoplasma suspected symptoms were observed in cumin at Agricultural Research Station, Mandor, Jodhpur, Rajasthan, India from 2019. The symptoms related to phytoplasma infection were first recorded after 70-75 days of sowing in the month of January of the years 2019 to 2022. The major symptoms recorded were yellowing, phyllody, witches-broom, yellowing and deformed elongated seeds. Disease incidence was recorded as 0.25-1.0%, 0.5-1.5%, 0.5-2.5 % and 0.5-10.6% during the years 2019, 2020, 2021 and 2022, respectively using quadrate method. In 2022, among different genotypes assessed GC 4, MCU 73, MCU 105, and MCU 32 exhibited lower disease incidences ranging from 0.5% to 1.5%, while MCU 78 recorded the highest disease incidence at 10.6%. To detect the association of phytoplasma with symptomatic cumin samples, genomic DNA was extracted from four representative cumin genotypes (CuPP-MND-01 to CuPP-MND-04) and one asymptomatic cumin plant using the Qiagen DNeasy plant mini kit (Germany). The extracted DNA was amplified using nested PCR assays with universal phytoplasma detection primers for 16S rRNA gene (P1/P7 and R16F2n/R16R2) (Schneider et al., 1995; Gundersen and Lee, 1996) and secA gene specific primers (SecAfor1/SecArev3 followed by nested PCR primers SecAfor5/ SecArev2) (Hodgetts et al. 2008; Bekele et al. 2011). The amplicons of ∼1.25 kb with 16S rRNA gene and ∼600 bp with secA gene specific primers were amplified in all symptomatic cumin plant samples and positive control of brinjal little leaf. PCR amplified products from the four selected positive samples (CuPP-MND-01 to CuPP-MND-04) of 16S rRNA gene and secA gene, were sequenced from both ends. The 1,245 bp sequences were deposited in GenBank (OQ299007-10), which showed 100% sequence identity with each other and 99.4% identity with 'Candidatus Phytoplasma citri' reference strain (GenBank accession: U15442) (Rodrigues Jardim et al. 2023). The phylogenetic analysis and virtual RFLP analysis using 17 restriction enzymes of 16S rRNA gene sequences through iPhyclassifier allowed affiliating the cumin phytoplasma strains with 16SrII-C subgroup strain with a similarity coefficient of 1 to the reference pattern of 16Sr group II, subgroup C (GenBank accession: AJ293216) (Zhao et al. 2009). In addition, the phylogenetic analysis of the secA gene-based sequences (OQ305073-76) further confirmed the close association of 16SrII-C group phytoplasmas with phyllody and witches' broom disease of cumin. Earlier 16SrII-C subgroup phytoplasma has been reported from various crops and weeds in India (Rao et al. 2021). However, no phytoplasma association has been reported earlier with cumin in India and abroad. To the best of our knowledge, this is the first report on the association of 16SrII-C group phytoplasma causing phyllody, witches' broom in cumin genotypes. This report has economic and epidemiological implications and needs immediate attention to reduce export losses due to phytoplasma disease in cumin and to prevent the potential spread to other crops.

The Interplay Between Cholesterol and Amyloid-ß on HT22 Cell Viability, Morphology, and Receptor Tyrosine Kinase Signaling.

BACKGROUND: There is a lack of understanding in the molecular and cellular mechanisms of Alzheimer's disease that has hindered progress on therapeutic development. The focus has been on targeting toxic amyloid-ß (Aß) pathology, but these therapeutics have generally failed in clinical trials. Aß is an aggregation-prone protein that has been shown to disrupt cell membrane structure in molecular biophysics studies and interfere with membrane receptor signaling in cell and animal studies. Whether the lipid membrane or specific receptors are the primary target of attack has not been determined. OBJECTIVE: This work elucidates some of the interplay between membrane cholesterol and Aß42 on HT22 neuronal cell viability, morphology, and platelet-derived growth factor (PDGF) signaling pathways. METHODS: The effects of cholesterol depletion by methyl-ß-cyclodextrin followed by treatment with Aß and/or PDGF-AA were assessed by MTT cell viability assays, western blot, optical and AFM microscopy. RESULTS: Cell viability studies show that cholesterol depletion was mildly protective against Aß toxicity. Together cholesterol reduction and Aß42 treatment compounded the disruption of the PDGFα receptor activation. Phase contrast optical microscopy and live cell atomic force microscopy imaging revealed that cytotoxic levels of Aß42 caused morphological changes including cell membrane damage, cytoskeletal disruption, and impaired cell adhesion; cell damage was ameliorated by cellular cholesterol depletion. CONCLUSIONS: Cholesterol depletion impacted the effects of Aß42 on HT22 cell viability, morphology, and receptor tyrosine kinase signaling.

First Report of Candidatus Phytoplasma asteris (16SrI-B Subgroup) associated with phyllody disease of moth bean in world.

Moth bean (Vigna aconitifolia), a drought and heat-resistant legume from the Fabaceae family, is commonly cultivated in arid and semi-arid regions of the Indian subcontinent In September 2022, phyllody symptoms (Figure 1) were observed on 50-days-old moth bean plants at the ICAR-NBPGR research farm in Jodhpur, Rajasthan, India. The disease incidence ranged from 10 to 25%. To investigate the cause, ten symptomatic VacoJod (1-10) and ten asymptomatic VacoJod (11-20) Vigna aconitifolia plants were collected. Insect populations were also collected from the vicinity using the sweep-net method to examine the role of insect vectors. The leafhopper was identified based on morphological characterization as Empoasca sp. at the Division of Entomology, ICAR-IARI, New Delhi. DNA was extracted from midribs of all collected plants and the Empoasca sp., using Qiagen DNeasy Plant Mini Kit and Blood and Tissue kit, respectively. Nested polymerase chain reaction (Nested-PCR) with universal primers P1/P7 and R16F2n/R16R2 (Deng and Hiruki, 1991; Gundersen and Lee, 1996), and secA gene primers (secAfor1/secArev3 and secAfor2/secArev3) (Hodgetts et al., 2008) were employed to determine phytoplasma species association. Out of the 10 symptomatic plants and 10 leafhopper samples, 6 leafhopper samples and all symptomatic plants produced expected band sizes for the 16S rRNA (approximately 1.25 kb) and secA gene (480 bp). The PCR products were cloned, sequenced, and sequences (two each from moth bean and leafhopper) were submitted to NCBI GenBank with accession numbers OP941130, OP941132, OP941133 and OP941134 for 16S rRNA and OP958868, OP958869, OP958870, and OP958871 for secA gene sequences. Nucleotide BLAST analysis of 16S rRNA sequences revealed a minimum of 99.92% similarity with 'Primula acaulis' yellows phytoplasma (KJ494340) from Czech Republic. All 100% hits corresponded to 16SrI-B group phytoplasmas, for example rapeseed phyllody phytoplasma (CP055264) from Taiwan. Similarly, nucleotide BLAST analysis of secA sequences revealed a minimum of 99.15% sequence similarity with Paulownia witches'-broom phytoplasma (secA) (OP124308) from China. All 100% hits were of 16SrI-B group phytoplasmas, for example Ageratum conyzoides yellowing phytoplasma (MW401697, secA) from India. Phylogenetic analysis using MEGA11 (Tamura et al., 2021) clustered the moth bean and Empoasca sp. phytoplasma strains with 16SrI-B phytoplasma reference strains. iPhyClassifier tool classified the 16S rRNA gene sequences into 16Sr group I, subgroup B, with a similarity coefficient of 1.0 (Figure 2a, 2b). This marks the first report of the association of 'Ca. P. asteris' 16SrI-B related phytoplasma strain with moth bean plants globally. The 16SrI-B phytoplasma strain is prevalent in various crops in India (Singh et al., 2023). This report emphasizes the epidemiological studies and highlights the need for further research and preventive measures to manage the spread of this phytoplasma strain, which could impact crop production and food security in hot and dry regions.

Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection.

Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E1, E2, E3, E4, E5, E5, E6, and E7). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.

First Report of Candidatus Phytoplasma asteris (16SrI-B subgroup) associated with phyllody disease of fenugreek in the world.

Fenugreek (Trigonella foenum-graecum) is a leafy vegetable and spice crop, native to Indian subcontinent and Eastern Mediterranean region. Phytoplasma infection symptoms were observed in fenugreek at ICAR-National Bureau of Plant Genetic Resources Regional Station, Jodhpur and Agricultural Research Station Mandore Jodhpur, Rajasthan, India. The first appearance of phytoplasma suspected symptoms of little leaf was recorded after 50 days of sowing in the months of January 2022. The major symptoms recorded were virescence, phyllody, shoot proliferation, witches-broom, little leaf, yellowing and overall stunted growth in 146 germplasm accessions at NBPGR research farm, Jodhpur and one major commercially cultivated variety RMT 305 at Mandore Jodhpur. Ten samples from symptomatic and five samples from asymptomatic fenugreek plants were collected and processed for total DNA extraction using the Qiagen DNeasy plant mini kit (Germany). The extracted DNA was amplified using nested PCR assays with universal phytoplasma detection primers for 16S rRNA gene (P1/P7 and R16F2n/R16R2) and secA gene specific primers (SecAfor1/SecArev3 and SecAfor2/SecArev3) (Schneider et al. 1995; Gundersen and Lee 1996; Hodgetts et al. 2008). The amplicons of ∼1.25 kb with 16S rRNA and ∼480 bp with secA gene specific primers were amplified in all symptomatic fenugreek samples. In negative control (asymptomatic plants) no amplification was observed with either of gene specific primers in gel electrophoresis. PCR amplified products from the six selected positive samples (FPP-NBPGR-J-01 to FPP-NBPGR-J-04 and FPP-MND-01 to FPP-MND-02) of 16S rRNA and secA gene, were sequenced from both ends. Sequences were deposited in the NCBI GenBank with accession numbers ON756108-ON756113 for 16S rRNA gene sequences and ON745809 to ON745814 for secA gene sequences. BLAST analysis of 16S rRNA and secA sequences revealed 100% sequence identity among themselves and 99.95 to 100% sequence identity with the earlier reported phytoplasma strains of aster yellows group related phytoplasma strains (GenBank Acc. No. MN239504, MN080270) belonging to Ca. P. asteris (16SrI group). Further analyses of the 16S rRNA and secA gene-based phylogenetic tree and the iPhyClassifier-based virtual RFLP analysis of 16S rRNA gene study demonstrated that the phytoplasma associated with fenugreek phyllody belonged to 16Sr group I ('Ca. P. asteris') and subgroup B (GenBank accession AP006628), with similarity coefficient of 1.0. Earlier association of 16Sr-II-D subgroup (Ca. P. australasiae) with fenugreek as host was reported from Pakistan (Malik et al., 2020). To the best of our knowledge, this is the first report of a 'Ca. P. asteris', 16SrI-B subgroup related phytoplasma strain associated with fenugreek phyllody in the world. The 16SrI-B phytoplasma strain is a widely distributed strain associated with several agricultural and horticultural crops of India (Rao 2021). This is not only the first instance of fenugreek phyllody disease found in India, but also the first instance of fenugreek phyllody caused by 16SrI-B subgroup phytoplasma worldwide. This report has epidemiological significance and needs immediate attention, as fenugreek is one of the most common seed spice crop being grown all over India.

First report of 'Candidatus phytoplasma asteris' (16SrI) from Cassia fistula showing symptoms of flat stem and witches'-broom in India.

Cassia fistula commonly known as 'golden shower tree' is a deciduous tree with a greenish-gray bark and complex leaves with lovely clusters of yellow blossoms that is also utilized for several purposes in traditional medicine offer therapeutic characteristics (Pawar et al., 2017). Random spotting of flat stem symptoms along with unopened flower beds was observed in C. fistula plant during March 2022 in IISER (Indian Institute of Science Education and Research), Thiruvananthapuram, Kerala, India and during May 2022 in SKUAST (Sher-e-Kashmir University of Agricultural Sciences and Technology), Jammu, which were suggestive of phytoplasma infection (Fig. 1 a-e). Surge of leaf hoppers was also observed in and around the tree. The leaf samples were collected from 3 individual C. fistula trees showing suspected symptoms of phytoplasma and one sample from asymptomatic plant of both the states. Leafhopper (LH) species were collected using sweep net method from both the locations. DNA was extracted using CTAB (Cetyl trimethyl ammonium bromide) method and nested universal PCR primers P1/P7 and R16F2n/R16R2 for the 16S rRNA gene (Deng and Hiruki 1991; Gundersen and Lee 1996) and secAfor1/secArev3 and SecAfor2/ SecArev3 for SecA gene (Hodgetts et al. 2008) were employed for the analysis of the phytoplasma strain association. The symptomatic plants and leaf hopper species showed positive bands of 1.2kb and 480bp for 16S rRNA and SecA gene respectively along with. Purified PCR products of both the genes (16Sr RNA and sec A) were ligated into pGEM ®T vector and cloned in Escherichia coli (DH5-α) were sequenced at Agri Genome labs, Kerala, India. The comparative sequence analysis using the BLASTn tool results showed 16S rRNA sequences acquired from plant samples (GenBank Acc. No. OP950857, OP950858) and the leafhoppers Hishimonus phycitis (OP538583) and Orosius albicinctus (OP538584) of Kerala had the minimum of 99.84% of similarity with Bitter gourd little leaf phytoplasma from Myanmar and maximum sequence identity (100%) with the Rapeseed phyllody phytoplasma strain from Taiwan. The sequences of phytoplasma strains from Jammu trees (Genbank Acc. No. OP801671 & OP801672) and H. phycitis (OP801673) shared 100% similarity with each other as well as with North American grapevine yellows and a minimum of 97.65% with Beta vulgaris phytoplasma from Poland. The pairwise comparison results were completely supported by the corresponding phylogenetic sequence analysis of 16S rRNA and SecA gene sequences of all the isolates in the study which clustered with 16SrI-B subgroup related strains. Virtual RFLP analysis through iPhyClassifer results that were derived from in silico digestions of R16F2n/R2 region of 16S rRNA gene using 17 restriction endonucleases enzymes indicated that all the samples produced similar virtual RFLP profiles identical to the reference strain of 16SrI-B phytoplasma subgroup (aster yellows: Acc. No. M30790) with a similarity coefficient value of 1.0. To the best of our knowledge, this is the first report of the phytoplasma association of 'Ca. P. asteris' (16SrI-B) subgroup with Cassia fistula in the world.

Leuconostoc, a masquerading pathogen in oral cancer patient: A rare case report.

Osteoradionecrosis is the most common cause of mandibular osteomyelitis. Here we are reporting a case of osteomyelitis of the mandible caused by Leuconostoc mesenteroides spp cremoris. The frequency of Leuconostoc infections are under reported mainly due to its difficult identification. Non pathogenic organism like leuconostoc can cause infection in the immunocompromised and should warrant proper microbial identification and adequate targeted treatment to manage the patients.

Non-alcoholic fatty liver disease in polycystic ovarian syndrome in Indian women.

Non-alcoholic fatty liver disease (NAFLD) is a frequent occurrence in polycystic ovarian syndrome (PCOS). We studied the frequencies and characteristics of NAFLD in PCOS women. We compared various methods of detection of advanced fibrosis/cirrhosis. One hundred and forty women with PCOS and seventy controls, matched for age, were evaluated for the presence of NAFLD. Anthropometric variables, serum levels of aminotransferases, glucose, lipids and transient elastography were done. Thirty-six percent of the NAFLD patients had abnormal aminotransferases. In women presenting to an infertility clinic, NAFLD was higher in both obese and non-obese PCOS women, being present in 117 (83.6%) of PCOS cases and 32 (45.7%) of non-PCOS controls (p< .001). Fibroscan is helpful in evaluating for liver fibrosis in patients with NAFLD.Impact StatementWhat is already known on this subject? Polycystic ovarian syndrome (PCOS) has been associated with many long-term health complications including endometrial cancer, diabetes, hypertension and metabolic syndrome. The association of PCOS with NAFLD has been suggested. NAFLD is recognised as a leading cause of liver dysfunction which can progress to long-term sequel of cirrhosis.What do the results of this study add? In this study, asymptomatic women seeking treatment of infertility were screened for presence of NAFLD. The study shows a high prevalence of NAFLD in young Indian women. The prevalence was significantly higher in women with PCOS than non-PCOS women.What are the implications of these findings for clinical practice and/or further research? The findings of the study suggest that all infertile women, especially those with PCOS, should be screened for NAFLD. This will help in early identification and management of this condition and to avoid long-term consequences of liver dysfunction and cirrhosis. PCOS is an independent risk factor for the development of NAFLD in obese women. Liver ultrasound, serum levels of transaminases clinch the diagnosis. Short of liver biopsy, non-invasive tests like Fibroscan and NAFLD fibrosis score are useful to assess the stage of fibrosis.

Transcriptome profiling and differential gene expression analysis provides insights into Lr24-based resistance in wheat against Puccinia triticina.

Leaf rust caused by Puccinia triticina is an important disease of wheat and Lr24 gene confers resistance to all known pathotypes of P. triticina in India. Transcripts associated with the Lr24 mediated resistance were identified through transcriptome sequencing and further expression analysis of differentially regulated genes was performed using qPCR technique. De novo transcriptome assembly showed 66,415 and 68,688 transcripts in resistant and susceptible genotypes, respectively. The study revealed that 5873 genes unique to resistant; 6782 genes unique to susceptible, while 10,841 genes were common to both. Gene Ontology distribution statistics showed 1030 and 1068 CDS in biological processes; 1234 and 1326 CDS in cellular processes; 1321 and 1352 CDS in molecular functions, respectively. A total of 659 genes were found to be differentially expressed, of which 349 were upregulated and 310 were downregulated in resistant genotype. Pathway analysis of transcripts appeared in resistant genotype revealed that 279 transcripts had homology with genes involved in signal transduction, 18 transcripts in membrane transport, one transcript in signaling molecules. Real-time PCR study showed that most of the up-regulated defense related genes expressed in early hours indicating that a cascade of defense starts early in Lr24 mediated resistance, which successfully inhibited pathogen establishment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02972-9.

Gastric secretion in patients with caustic ingestion: A prospective study.

BACKGROUND: Caustic ingestion can lead to structural changes in the upper gastrointestinal tract. However, there are limited data on the effect of caustic ingestion on gastric secretion. This study was planned to determine the changes in gastric acid output in patients with caustic ingestion. METHODS: It was a prospective study done at a tertiary care center in northern India. Twenty consecutive patients in chronic phase of caustic ingestion were evaluated for the study. The gastric secretory function was estimated in the basal state and following pentagastrin stimulation. These results were compared with normal values for our laboratory. RESULTS: The mean age of the included patients (n = 20) was 27.35 ± 2.96 years and 14 patients were male. Sixteen (80%) patients had a history of acid ingestion. Patients with caustic ingestion had significantly lower mean gastric acid secretion (0.8 ± 0.4 mEq/h vs. 4 ± 0.4 mEq/h; p < 0.001) compared to controls. After pentagastrin stimulation, the mean gastric juice volume (31.8 ± 6 mL/h vs. 62.3 ± 11.7 mL/h; p < 0.01) and acidity (15.3 ± 5.1 mEq/L vs. 39.6 ± 9.3 mEq/L; p < 0.001) increased in patients with caustic ingestion, but were lower than those in control subjects. Patients with a lower esophageal stricture (n = 6) had decreased maximum acid output (0.62 ± 0.32 mEq/h vs. 6.05 ± 0.55 mEq/h; p < 0.05) compared to patients with stricture in the upper or middle esophagus. CONCLUSION: Caustic ingestion is associated with reduced gastric juice volume and acid output. Patients with stricture in the lower one third of the esophagus are at a higher risk of hypochlorhydria compared to patients with stricture in either the upper or middle esophagus.

Utility of narrow band imaging in predicting histology in celiac disease.

BACKGROUND: Narrow band imaging (NBI) with magnification better visualizes the duodenal microsurface and mucosal vascularity. NBI delineates villous atrophy better than conventional white light endoscopy. AIMS: This study was conducted to evaluate the diagnostic accuracy of narrow band imaging with magnification (NBI-ME) in celiac disease (CD). METHODS: In this prospective study, consecutive patients of suspected CD and controls were subjected to tissue transglutaminase antibody test and endoscopic evaluation initially with white light followed by NBI-ME, and biopsies were taken from duodenum. Duodenal villous patterns on NBI were interpreted as normal, blunted distorted, and absent. Severity of villous atrophy was reported according to the modified Marsh criteria. RESULTS: One hundred and twenty-two patients (mean age of 27.53 ± 13.37 years and a male to female ratio of 1:1.26) and 40 controls were studied. The sensitivity and specificity of NBI-ME in predicting villous atrophy were found to be 95.54% and 90%, respectively. The specificity and negative predictive value of NBI-ME in predicting villous atrophy amongst controls was 100% and 97.5%, respectively. Abnormal findings (blunted and absent villous patterns) combined with elevated transglutaminase antibody (> 5-fold) were found to have high accuracy in predicting villous atrophy. CONCLUSION: NBI with magnification has high sensitivity and specificity in predicting villous atrophy in patients with celiac disease.

First Draft Genome Sequence of Wheat Spot Blotch Pathogen Bipolaris sorokiniana BS_112 from India, Obtained Using Hybrid Assembly.

Bipolaris sorokiniana is a devastating fungal pathogen causing spot blotch of wheat. We report here the first draft genome of Bipolaris sorokiniana strain BS_112 from India using sequence reads from the Ion Torrent, Illumina HiSeq, and Nanopore platforms. The genome size was estimated at 35.64 Mb with an average G+C content of 50.20%.

Patterns of alcohol consumption and nutrition intake in patients with alcoholic liver disease and alcoholic pancreatitis in North Indian men.

BACKGROUND AND AIM: Chronic alcoholism and nutrition play an important role in liver and pancreatic diseases. To compare drinking habits and nutritional data in patients with alcoholic liver disease (ALD) and alcoholic pancreatitis (ALP). METHODS: Clinical, anthropometric, dietary intake, laboratory, and imaging data were recorded in consecutive patients of ALD and ALP. RESULTS: In 150 patients of ALP (n = 76) and ALD (n = 74), the age of starting alcohol consumption (19.03 ± 3.78 vs 18.0 ± 2.59 years) and the mean amount of alcohol consumed per day (165.63 ± 87.99 vs 185.50 ± 113.54 g; P = 0.230) were similar. Patients with ALD consumed alcohol on a daily basis more frequently (90.5 vs 72.3%; P = 0.003) and had a longer duration of alcohol intake (21.6 + 0.2 vs 14.5 + 6.9 years; P < 0.0001) than patients in the ALP group. Binge drinking was more common in patients with ALP compared to patients with ALD (60.5 vs 20.3%); P < 0.0001). Patients with ALP had a lower body mass index (19.9 ± 3.49 vs 22.64 ± 4.88 kg/m2; P = 0.001) and more frequent decrease in mid arm circumference (57.9 vs 44.6%; P = 0.042) and triceps skin fold thickness (67.1 vs 52.7%; P = 0.072) compared to patients with ALD. CONCLUSION: There was no difference in the age of starting alcohol consumption and mean amount of alcohol consumption per day between the groups. Patients with ALD were more likely to be daily drinkers with a longer duration of alcohol intake. However, binge drinking and malnourishment was more common in the ALP group.

Vitamin D deficiency in adult patients with ulcerative colitis: Prevalence and relationship with disease severity, extent, and duration.

BACKGROUND: Vitamin D plays a key role in gut immunity and maintenance of the mucosal barrier. Vitamin D deficiency (VDD) worsens ulcerative colitis (UC) and its supplementation ameliorates the disease in mouse models. The prevalence and predictors of VDD in UC are not known. METHODS: Consecutive patients with UC (n = 80) underwent clinical, endoscopic, and histological evaluation to assess the extent, severity using UC disease activity index (UCDAI) score, and duration of illness. An equal number of age and gender-matched healthy adults without any features of inflammatory bowel disease (IBD) living in the same latitude were identified as controls. The serum 25-hydroxy vitamin D3 level was estimated. The subjects were classified as deficient (< 20 ng/mL), insufficient (20-32 ng/mL), sufficient (32-80 ng/mL), and optimal (> 80 ng/mL) based on vitamin D levels. Chi-square test and Mann-Whitney U test were done to identify factors associated with vitamin D deficiency. RESULTS: The patients and controls were similar in age and gender (40 ± 11.4 years, 51% male vs. 40 ± 12 years, 51% male; p = 1.000). Median vitamin D levels among patients were lower than the controls (18.1 ng/mL [IQR 14] vs. 32.5 ng/mL [IQR 36]; p < 0.001). Patients were more often VDD (56% vs. 40%) or insufficient (34% vs. 9%) and less often sufficient (9% vs. 40%) or optimal (1% vs. 11%), in contrast to controls (p < 0.001). Median vitamin D levels were lower in those with UCDAI > 6 (15 vs. 21 ng/mL; p = 0.01), having pancolitis (13 vs. 21 ng/mL, p = 0.01), and longer duration of illness > 2 years (13.8 vs. 20.8; p = 0.025). Vitamin D levels showed a negative correlation with frequency of stools (rho = - 0.244, p = 0.05), disease duration (rho = - 0.244, p = 0.007) and UCDAI score (r = - 0.348, p = 0.002). CONCLUSION: VDD is highly prevalent among patients with UC. Patients with longer disease duration, more severe symptoms, and pancolitis are likely to have lower vitamin D levels.

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification.

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 µM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease.

Hypotension in the first week of acute pancreatitis and APACHE II score predict development of infected pancreatic necrosis.

BACKGROUND: Hypotension and intestinal mucosal ischemia lead to bacterial translocation from the gut lumen into systemic circulation. AIM: The purpose of this study was to determine the strength of association between different types of organ failure (OF): hypotension (cardiovascular system failure), renal failure, respiratory failure, CNS failure and coagulopathy in the first week of acute pancreatitis (AP) and the subsequent development of infected pancreatic necrosis (IN). METHODS: Consecutive patients with AP were evaluated for OF and its severity in the first week of hospital admission. Modified multiple organ failure score (MOFS) was used to identify and grade severity of OF. MOFS of ≥2, lasting for more than 48 h was defined as OF. Occurrence of IN (isolation of bacteria in necrosectomy specimen or image guided fine needle aspiration of pancreatic necrosis) was compared between groups with and without OF. RESULTS: Of the 81 patients, mean age was 40.1 ± 14.4 years and 55 were males; 60 (74 %) patients had OF and 13 (16 %) patients had IN. Occurrence of IN was not significantly different between patients with OF (18.3 %) and without OF (14.3 %), p = 0.48. However IN occurred in 10 % of patients without and 33.7 % patients with hypotension, p = 0.01. The rest of the organ systems analyzed did not show any significant difference in occurrence of infected necrosis. On multivariate analysis independent predictors of occurrence of IN were hypotension (odds ratio, OR 2.5, p < 0.001) and APACHE II score at 24 h of hospital admission (OR 4.77, p < 0.001). CONCLUSION: Hypotension in the first week of AP and APACHE II score predict development of IN.

Clinical, endoscopic and endoscopic ultrasound features of duodenal varices: A report of 10 cases.

BACKGROUND: Duodenal varices (DV) although an uncommon cause, are an important cause due to the severe nature of the bleed and associated adverse outcome. MATERIALS AND METHODS: We retrospectively evaluated patients with DV seen at our institution over past 4 years. RESULTS: A total of 10 patients (nine males; mean age was 35.8 ± 7.68 years) with DV were studied. Five patients had underlying cirrhosis and five had DV because of non-cirrhotic portal hypertension (four patients had extra-hepatic portal venous obstruction and one patient had non-cirrhotic portal fibrosis). Five patients presented with upper gastrointestinal (GI) bleed, whereas in the remaining five patients DV were detected on endoscopy performed for evaluation of portal hypertension. Endoscopy revealed submucosal lesion in nine patients, whereas in one patient an initial endoscopic diagnosis of Dieulafoy's lesion was made. However endoscopic ultrasound (EUS) could clearly identify DV in all patients. Of five patients presenting with upper GI bleed, three had the esophageal varices eradicated and two presented 1(st) time with bleed form DV and did not have esophagogastric varices. All patients with acute upper GI bleed were initially treated with intravenous terlipressin followed by glue (n-butyl cyanoacrylate) injection in 4/5 patients with one patient refusing further endoscopic therapy. The variceal obliteration was documented by EUS in all these four patients and there has been no recurrence of bleed in these four patients over a follow-up period of 4-46 months. The five non-bleeding DV were already on beta- blockers and the same were continued. Two of these five patients succumbed to progressive liver failure with none of these five patients having GI bleed on follow-up. CONCLUSION: EUS is a useful investigational modality for evaluating patients with DV and endoscopic injection of glue is an effective therapy for controlling and preventing recurrence of bleed from DV.

Implementation of the Asia-Pacific guidelines of obesity classification on the APACHE-O scoring system and its role in the prediction of outcomes of acute pancreatitis: a study from India.

AIMS: We studied the role of obesity and the Acute Physiology and Chronic Health Evaluation (APACHE) O score in predicting the outcome in patients with acute pancreatitis (AP) using the Asia-Pacific obesity classification. METHODS: Two hundred eighty AP patients were classified into three different groups, normal weight [body mass index (BMI) = 18.5-22.9 kg/m(2)], overweight (BMI = 23-24.9 kg/m(2)) and obese (BMI > 25 kg/m(2)), according to the Asia-Pacific obesity classification. For all patients APACHE II scores and modified APACHE O (i.e., APACHE Oap) scores that included a factor for obesity were calculated. The patients were managed using a standard protocol, and the outcome measures were compared for different obesity groups. RESULTS: Of the 280 patients (mean age 40.7 years), 46.8% were normal weight, 29.6% overweight and 23.6% obese. Forty-six (16.4%) patients underwent surgery, and 61 (21.8%) patients died. Patients with higher BMI had worse radiological indices of severity, more infected necrosis (p < 0.001), more persistent organ failure (p < 0.001) and higher requirement for percutaneous drain insertion (p = 0.04), surgery (p = 0.008) and mortality (p < 0.001). The area under the curve for predicting mortality was 0.879 for APACHE II and 0.886 for APACHE Oap; at a cutoff of 8.5, the APACHE II score had a sensitivity of 88.2% and specificity of 68.7%, and APACHE Oap 90.2 and 64.0%, respectively. CONCLUSIONS: BMI ≥ 23 kg/m(2) was an important predictor of a severe disease course and fatal outcome in patients with AP. However, the predictive accuracy of APACHE Oap for mortality was similar to APACHE II.

Dynamic nature of organ failure in severe acute pancreatitis: the impact of persistent and deteriorating organ failure.

BACKGROUND AND AIMS: In acute pancreatitis (AP), patients with persistent organ failure [POF, duration of organ failure (OF) ≥48 h] and transient organ failure (TOF, duration of OF <48 h) have different outcomes. We have compared the clinical course and outcome of patients with severe AP (SAP) with TOF and POF in the first week of hospitalization as well as the impact of change in the OF score in the first week on patient outcome. METHODS: Consecutive patients with SAP were evaluated for OF and its dynamics during the first week of hospitalization. The modified multiple organ failure score (MOFS) was used to identify OF, grade its severity and monitor its progression. The clinical course and outcome of patients were studied. RESULTS: Of 114 patients, mean age 39.2 ± 13.7 years, 37 (32.5%) patients had no OF, 34 (29.8%) had TOF and 43(37.7%) had POF. Patients with POF had the higher infected necrosis, increased requirement for percutaneous drain placement, surgery and higher mortality as compared with those with TOF. The odds ratio for mortality with persistent and deteriorating OF was 26.2 [confidence interval (CI) 5.1-134.9] compared with only persistent OF. CONCLUSION: The dynamics of OF in the first week of SAP predicts the clinical course and outcome. Persistent and deteriorating OF indicates a poor outcome.

Non-surgical management of pancreatic pseudocysts associated with arterial pseudoaneurysm.

BACKGROUND: Pseudoaneurysms associated with pancreatic pseudocysts are different from simple, isolated pancreatic pseudoaneurysms and there is paucity of published data on their non surgical treatment. AIM: To retrospectively analyze results of combination of angioembolisation or thrombin injection followed by endoscopic transpapillary drainage for management of pseudoaneurysms associated with pancreatic pseudocysts. METHODS: Eight patients (all males; mean age ± SD: 31.2 ± 6.1 years; age range: 21-38 years) underwent radiological management of the pseudoaneurysm followed by endoscopic drainage of the pseudocysts. RESULTS: All patients had pseudocysts (median size 4 cm) with underlying chronic pancreatitis. All patients had abdominal pain on presentation and 7/8 (87.5%) patients had presented with overt gastrointestinal bleeding. The size of the pseudoaneurysms varied from 1 to 4 cm. Two patients were treated with percutaneous thrombin injection whereas six patients underwent digital subtraction angiography and angioembolisation. All patients underwent successful endoscopic transpapillary drainage through the major (5) or minor papilla (3) and resolution of pseudocysts was noted within 6 weeks (median 4 weeks). No significant complication of the procedure was noted in any of the patients. CONCLUSIONS: Pseudoaneurysms associated with pancreatic pseudocysts can be successfully and safely treated with a combination of radiological obliteration of the pseudoaneurysm followed by endoscopic transpapillary drainage.