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Seed health testing, using the blotter method, revealed some fungal growth on the seed surface of one accession of Indian trumpet flower/Broken bones tree (Oroxylum indicum (L.) Kurz) collected from Kokrajhar, Assam, India. The fungus was identified as Diaporthe phaseolorum (Cooke & Ellis) Sacc. based on morphological characters. Later, the identity was re-confirmed by DNA sequencing using ITS gene sequencing (NCBI Sequence Id: MT154253.1) and a large subunit of rRNA (NCBI Sequence Id: OL798081.1). Literature reveals that D. phaseolorum is a destructive pathogen causing severe yield losses in various host crops. However, detection of D. phaseolorum in Indian trumpet flower seed followed by pathogenicity on its seedlings confirms that O. indicum is a new host record. Being a destructive pathogen of several other crops, such as seed decay and stem canker in soybean, it may pose a serious threat to future cultivation of this herbal plant.

The present study was entitled “Study of genetic variability and character association in elite lines of finger millet [Eleusine coracana (L.)] Suitable for the eastern plain zone of Uttar Pradesh” was carried out to estimate the genetic variability, genetic advance, correlation, between yield and yield contributing traits and direct and indirect effect of yield component on yield through path analysis (18). The present investigation concluded genotype acquiring the less for grain yield per plant were IC NO 0474166 (FIN NO 5126) (0.41 t/ha). The genotype IC NO 0473932 (FIN NO 4980) (2.22 t/ha) was high ear head length. This genotype was the highest grain yield per plant than CHECK GPU 67 (0.55 t/ha). The genotype IC NO 0473932 (FIN NO 4980) (2.22 t/ha) was 1.67 t/ha higher yield than CHECK GPU 67 (0.55 t/ha). The highest genotypic variance observed were finger length, harvest index, grain yield per plant. The highest phenotypic coefficient of variance observed were test weight, finger length, harvest index, grain yield per plant. The highest heritability were recorded in harvest index, grain yield per plant, flag leaf width, plant height, Number of days to 50% flowering, Days to Maturity, finger width, finger length. The traits Number of days to 50% flowering, biological yield per plant, plant height, days to Maturity exhibited moderate genetic advance. The traits were biological yield per plant, test weight, finger width, harvest index, finger length, grain yield per plant recorded high genetic advance as percentage of mean. Genotypic correlation coefficient reveals that single plant yield significantly positive correlation with number of finger fingers per, harvest index, biological yield per plant, finger length, ear head length, finger width, no. of tillers per plant, flag leaf length. For phenotypic correlation traits were harvest index, test weight, biological yield per plant, number of finger per ear, ear head length, flag leaf length, number of tillers per plant, flag leaf width showed significantly positive correlation with grain yield per plant. The traits harvest index, flag leaf length, flag leaf width, number of finger per ear showed higher positive direct effect on grain yield per plant at genotypic level. The traits harvest index, biological yield, plant height showed higher positive direct effect on grain yield per plant at phenotypic level (6).

Wheat is the most important cereal crop in the world that ranks first position in terms of production and trade. In Nepal this is the third most cultivated crop after rice and maize. Various environmental constraints including heat stress have been determined to be a great factor to limit world wheat production. High temperature leaves a devastating impact in wheat production by affecting different stages including germination, plant growth, anthesis and grain filling etc. heat stress also affects photosynthesis process and responsible for the lower biomass yield. Various studies have shown that the reproductive stages of wheat plant are more susceptible to heat stress than vegetative stages. Heat stress hinders germination, reduce plant growth, decrease number of plant population per unit area and causes leaf senescence. Water relation disturbance and oxidative damage to plants are other harmful effects of heat stress in wheat plants. Plant also has tolerance mechanism against such heat induced stresses. Such mechanisms include avoidance against heat stress, production of heat shock protein and antioxidant mechanisms.

Background: Morphological characters are stable across environments owing to oligogeneic nature. Hence, they serve as morphological markers which can be used in varietal or genotypic identification, varietal purification and even in seed production. Genetic diversity analysis is being used to identify the divergent genotypes and to utilize these genotypes to exploit heterosis and also help to select desirable segregants. Methods: A total of 266 pigeonpea germplasm lines along with three checks were evaluated in augmented block design (ABD) at ZARS, Kalaburagi, during kharif, 2020. Observations are recorded on nine quantitative and fourteen morphological triats. Result: Grouping of 266 germplasm lines into twelve clusters indicated a wider genetic diversity for the traits studied, in which cluster I and cluster II are the largest comprising 105 genotypes each, while clusters V, VI, VIII, IX, X, XI, XII were solitary with one entry each. Germplasm lines IC339062, IC343954, IC339074, IC418976, IC343931, IC437078, IC355599 and IC384490 fall into solitary cluster and are more often likely to have some unique characters which make them divergent. The genotypes IC 355599 and IC 343931 are trait specific for both seed weight and pods per plant.

9 páginas, 4 figuras, 1 tabla., Background: Molecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: A candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: 15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: This first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes. Funding: UNITAID, Wellcome, MRC, BMGF., Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

Oxidative reactive species play an important role in pathological conditions such as aging, fatty liver and cancers. Secondary metabolites enriched fraction derived from medicinal plants showed the inhibition of free radical generation by playing an important role in precluding various diseases. The aim of present study was to evaluate the antioxidant activity of different extracts by using the DPPH method. We assayed the free radicals scavenging activity of extracts at 50, 100, 200, 400 and 500 µg/ml concentration and phytochemical study of Petroleum ether, Chloroform, Methanol and Aqueous whole plant extracts of Catharanthus roseus. Amid the five absorption concentrations tested, it was observed that dose of 500 µg/ml showed the higher antioxidant activity for each extract. All samples displayed an increasing antioxidant effect with increase in concentration i.e. concentration dependant. The IC50 value of Petroleum ether, Chloroform, Methanol and Aqueous extract was found as 330.73 µg/ml, 596.13 µg/ml, 801.92 µg/ml and 504.12 µg/ml respectively. The petroleum ether extract at the concentration of 500 µg/ml showed the highest % inhibition of 67.441% compare to other extracts. DPPH method provides an easy and fast way to analyze potential antioxidants. The C. roseus extracts can be considered a rich natural source of antioxidants and can be used to develop pharmaceutical products for therapeutic treatment of various disorders caused by free radicals in human body.

Studies on infection indexing and distribution profiling of seed-borne fungi of sorghum germplasm in india for safe and healthy

Background Molecular mechanisms determining the transmission and prevalence of drug resistant tuberculosis (DR-TB) in Papua New Guinea (PNG) are poorly understood. We used genomic and drug susceptibility data to explore the evolutionary history, temporal acquisition of resistance and transmission dynamics of DR-TB across PNG. Methods We performed whole genome sequencing on isolates from Central Public Health Laboratory, PNG, collected 2017–2019. Data analysis was done on a composite dataset that also included 100 genomes previously sequenced from Daru, PNG (2012–2015). Results Sampled isolates represented 14 of the 22 PNG provinces, the majority (66/94; 70%) came from the National Capital District (NCD). In the composite dataset, 91% of strains were Beijing 2.2.1.1, identified in 13 provinces. Phylogenetic tree of Beijing strains revealed two clades, Daru dominant clade (A) and NCD dominant clade (B). Multi-drug resistance (MDR) was repeatedly and independently acquired, with the first MDR cases in both clades noted to have emerged in the early 1990s, while fluoroquinolone resistance emerged in 2009 (95% highest posterior density 2000–2016). We identified the presence of a frameshift mutation within Rv0678 (p.Asp47fs) which has been suggested to confer resistance to bedaquiline, despite no known exposure to the drug. Overall genomic clustering was significantly associated with rpoC compensatory and inhA promoter mutations (p Conclusions The acquisition and evolution of drug resistance among the major clades of Beijing strain threaten the success of DR-TB treatment in PNG. With continued transmission of this strain in PNG, genotypic drug resistance surveillance using whole genome sequencing is essential for improved public health response to outbreaks. With occurrence of resistance to newer drugs such as bedaquiline, knowledge of full drug resistance profiles will be important for optimal treatment selection.

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively. Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation. Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC. Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing. Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples. Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.

Background Studies to date show contrasting conclusions when comparing intracorporeal and extracorporeal anastomoses for minimally invasive right colectomy. Large multi-center prospective studies comparing perioperative outcomes between these two techniques are needed. The purpose of this study was to compare intracorporeal and extracorporeal anastomoses outcomes for robotic assisted and laparoscopic right colectomy. Methods Multi-center, prospective, observational study of patients with malignant or benign disease scheduled for laparoscopic or robotic-assisted right colectomy. Outcomes included conversion rate, gastrointestinal recovery, and complication rates. Results There were 280 patients: 156 in the robotic assisted and laparoscopic intracorporeal anastomosis (IA) group and 124 in the robotic assisted and laparoscopic extracorporeal anastomosis (EA) group. The EA group was older (mean age 67 vs. 65 years, p = 0.05) and had fewer white (81% vs. 90%, p = 0.05) and Hispanic (2% vs. 12%, p = 0.003) patients. The EA group had more patients with comorbidities (82% vs. 72%, p = 0.04) while there was no significant difference in individual comorbidities between groups. IA was associated with fewer conversions to open and hand-assisted laparoscopic approaches (p = 0.007), shorter extraction site incision length (4.9 vs. 6.2 cm; p ≤ 0.0001), and longer operative time (156.9 vs. 118.2 min). Postoperatively, patients with IA had shorter time to first flatus, (1.5 vs. 1.8 days; p ≤ 0.0001), time to first bowel movement (1.6 vs. 2.0 days; p = 0.0005), time to resume soft/regular diet (29.0 vs. 37.5 h; p = 0.0014), and shorter length of hospital stay (median, 3 vs. 4 days; p ≤ 0.0001). Postoperative complication rates were comparable between groups. Conclusion In this prospective, multi-center study of minimally invasive right colectomy across 20 institutions, IA was associated with significant improvements in conversion rates, return of bowel function, and shorter hospital stay, as well as significantly longer operative times compared to EA. These data validate current efforts to increase training and adoption of the IA technique for minimally invasive right colectomy.

In a manufacturer-independent laboratory validation study, the Xpert MTB/XDR® assay demonstrated equivalent limit of detection to Xpert MTB/RIF®, detected 100% of tested resistance mutations and showed some utility for resistance detection in strain mixtures. The Xpert MTB/XDR assay is a reliable, sensitive assay for tuberculosis and expanded resistance detection.

Background: Chickpea is the largest produced food legume in South Asia. It is mainly grown in dry or rainfed area, where patchy plant stand often results due to delayed and non-uniform emergence. Moreover, genotypes vary for seed germination and seedling vigour. Therefore, the study was undertaken to find most appropriate seed treatment for enhancement of planting value of desi and kabuli type chickpeas. Methods: Study was conducted at ICAR-IARI, New Delhi with fresh, 2 and 4 years stored seed lots of desi (Pusa 2028) and kabuli (Pusa 1108) varieties. The lots were compared with untreated (control) for quality and vigour parameters after giving seed enhancement treatments (SET); osmopriming, halopriming, solid matrix priming (SMP), thiram and neem khali. Result: Investigations revealed that SMP and thiram seed treatments significantly enhanced germination and field performance of fresh as well as aged seeds in these varieties. Effectiveness of treatments was found more pronounced in kabuli than desi type and thus confirmed the usefulness of SETs for poor vigour seeds. Results also showed that seed quality and vigour of both the types were significantly affected with time in storage. However, desi variety maintained satisfactory germination and field performance up to 2 years under ambient conditions of storage.

Sorghum genetic resource conservations involve multiple strategies and collaboration to ensure the continued safeguarding of this valuable genetic resource. Curations of such worldwide collections require commitments to the acquisition, maintenance, distribution, evaluation, and utilization of such collections. In sorghum, a major challenge to its curation has been the standardization of protocols and techniques that each country deploys in evaluating their own collections. Information and documentation of these various collections has been a challenge; however, the two largest collections from the USA and ICRISAT have attempted to update their databases to reflect the rich sources of information available on their collections. In 2007, a panel of sorghum experts met to develop a “Strategy for the Global Ex Situ Conservation of Sorghum Genetic Diversity” and from this a review of the various collections is presented within this chapter. This review looked at various collections and evaluated the collections based on passport and characterization data. Collections reflected sorghum accessions from many different parts of the world and highlight some of the genetic stocks and phenotypic information available for utilization. As world populations increase and climate change challenges our ability to feed our population, the safety and curation of these types of collection allow us to respond to both biotic and abiotic stresses that will put pressure on the world’s population to feed itself. These irreplaceable collections are in greater need of curation than ever before, but in order to understand the needs, one must first understand what is already present in these collections.

Morpho-physiological and biochemical analyses were carried out in eight diverse indigenous muskmelon (Cucumis melo L.) genotypes exposed to different degrees of water deficit (WD). The ability of genotypes MM-7, and especially MM-6, to counteract better the negative effect of WD was associated with maintaining higher relative water content (RWC), photosynthetic rate, efficiency of PSII, and photosynthetic pigments compare to other genotypes. Furthermore, MM-6 showed a better ability to maintain cellular homeostasis than the others. It was indicated by a stimulated antioxidative defense system, i.e., higher activities of antioxidant enzymes, accumulation of nonenzymatic antioxidants together with lower concentration of reactive oxygen species and malondialdehyde. However, the genotypes MM-2 and MM-5 suffered greatly due to WD and showed reduced RWC, photosynthetic rates, pigment content, and exhibited higher oxidative stress observed as lower antioxidant enzyme activities.

The aim of this study was to assess the performance of the GeneXpert MTB/RIF assay on extrapulmonary (EP) and respiratory (non-sputum) clinical samples of patients suspected of having tuberculosis (TB) from Queensland, Australia. A total of 269 EP and respiratory (non-sputum) clinical samples collected from Qld patients who were suspected of having TB were subjected to the GeneXpert MTB/RIF analysis, Ziehl-Neelsen (ZN) staining, Mycobacterium tuberculosis (MTB) culture and drug susceptibility testing. Phenotypic and genotypic data were compared. The overall performance analysis of the GeneXpert MTB/RIF assay for detection of MTB complex demonstrated sensitivity of 89%, specificity of 95%, PPV of 89% and NPV of 95% using culture as a reference standard. The GeneXpert MTB/RIF analysis of acid-fast bacilli (AFB) smear positive samples and AFB smear negative samples showed sensitivities of 100% and 77%, respectively. Looking at individual EP and respiratory (non-sputum) sample types, the sensitivity ranged from 60% to 100% although the specificity ranged from 33% to 100% with the specificity of lymph node tissue biopsy being the lowest. The GeneXpert MTB/RIF assay detected 11% more TB cases than culture and 27% more cases than ZN microscopy. Due to insufficient numbers of presenting rifampicin resistance cases, performance analysis of the GeneXpert MTB/RIF assay on rifampicin resistance could not be carried out. The GeneXpert MTB/RIF assay is potentially valuable for TB diagnosis in the majority of the EP and respiratory (other than sputum) samples in our setting. Although the GeneXpert MTB/RIF assay provides rapid diagnostic results, the overall sensitivity to rule out the disease is suboptimal for some specimen types. Performance varied according to specimen type and AFB smear status. The sensitivity and specificity of lymph node tissue was 63% and 33%. Care must be taken when using the GeneXpert MTB/RIF assay for detection of MTB in lymph node tissue samples. All samples should be cultured regardless of the GeneXpert MTB/RIF assay result.

Objectives Mycobacterium triplex is a slow-growing nontuberculous mycobacteria (NTM) and is a rare cause of human disease. The pathogenicity, natural history and spectrum of disease is unknown. The aim of this study was to review the clinical features, outcomes and drug susceptibility testing (DST) of all M. triplex isolates in Queensland, Australia to guide management of this rare NTM infection in the future. Methods This retrospective study included all patients who isolated M. triplex in Queensland, Australia from the 1st January 2000 to 31st December 2016. Clinical information was obtained from medical records to determine the clinical significance of isolates, natural history of disease and treatment outcomes. DST was performed on 15 isolates. Results Forty-three patients (21 male) had positive cultures for M. triplex. Thirty-nine patients had isolates from pulmonary specimens and 17 (43.6%) met the American Thoracic Society criteria for NTM lung disease. Six patients with pulmonary infection received antimicrobial therapy with 5 patients demonstrating treatment success. Four patients had localised extrapulmonary disease and were cured with surgical management ± antimicrobial therapy. DST suggests 93% of isolates are susceptible to macrolides. Conclusion This is the largest case series of M. triplex isolates and confirms it is a rare human pathogen. Extrapulmonary disease responded well to surgical management. Treatment of M. triplex pulmonary disease is challenging, and the optimal antimicrobial regimen is unknown. However, the DST data suggests macrolide resistance is rare and macrolides should be included in treatment regimens.

BACKGROUND Nano-size and wide-range solubility of amphiphilic polymers (having both hydrophilic and hydrophobic blocks) can improve uniformity in seed coatings. An investigation was carried out to assess the positive effect of amphiphilic polymers over hydrophilic or hydrophobic polymers as seed coating agents and pesticide carriers. RESULTS Amphiphilic polymers with 127.5-354 nm micelle size were synthesized in the laboratory using polyethylene glycols and aliphatic di-acids. After 6 months of storage, germination of uncoated soybean seeds decreased drastically from 97.80 to 81.55%, while polymer-coated seeds showed 89.44-95.92% germination. Similarly, vigour index-1 was reduced from 3841.10 to 2813.06 for control seeds but ranged from 3375.59 to 3844.60 for polymer-coated seeds after 6 months. The developed imidacloprid formulations retained more pesticide on soybean seed coatings than did a commercial formulation (Gaucho(®) 600 FS). The time taken for 50% release of imidacloprid from seed coatings in water was 7.12-9.11 h for the developed formulations and 0.41 h for the commercial formulation. CONCLUSION Nano-range amphiphilic polymers can be used to protect soybean seeds from ageing. Formulations as seed treatments may produce improved and sustained efficacy with minimum environmental contamination. © 2016 Society of Chemical Industry.

Global spread of aggressive mycobacteria Many mycobacteria, in addition to those causing leprosy and tuberculosis, are capable of infecting humans. Some can be particularly dangerous in patients suffering from immunosuppression or chronic disease, such as cystic fibrosis (CF). Bryant et al. observed clusters of near-identical isolates of drug-resistant Mycobacterium abscessus in patients reporting to CF clinics. The similarity of the isolates suggests transmission between patients, rather than environmental acquisition. Although this bacterium is renowned for its environmental resilience, the mechanism for its long-distance transmission among the global CF patient community remains a puzzle. Science , this issue p. 751

Chickpea (Cicer arietinum L.) is the second largest pulse crop grown worldwide and ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. is the most devastating disease of the crop in all chickpea growing areas across the continents. The pathogen A. rabiei is highly variable. The resistant sources available are not sufficient and new sources needs to be identified from time to time as resistance breakdown in existing chickpea varieties is very frequent due to fast evolution of new pathotypes of the pathogen. Therefore, this work was undertaken to evaluate the existing chickpea germplasm diversity conserved in Indian National Genebank against the disease under artificial epiphytotic conditions. An artificial standard inoculation procedure was followed for uniform spread of the pathogen. During the last five winter seasons from 2014-15 to 2018-19, a total of 1,970 accessions have been screened against the disease and promising accessions were identified and validated. Screening has resulted in identification of some promising chickpea accessions such as IC275447, IC117744, EC267301, IC248147 and EC220109 which have shown the disease resistance (disease severity score ≤3) in multiple seasons and locations. Promising accessions can serve as the potential donors in chickpea improvement programs. The frequency of resistant and moderately resistant type accessions was comparatively higher in accessions originated from Southwest Asian countries particularly Iran and Syria than the accessions originated from Indian sub-continent. Further large scale screening of chickpea germplasm originated from Southwest Asia may result in identifying new resistant sources for the disease.

A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99.92 % assembly accuracy. Incorporation of complementary short read sequences (Illumina) as part of consensus error correction resulted in a 4 404 064 bp genome with 99.98 % assembly accuracy. This assembly had an average nucleotide identity of 99.7 % relative to the reference genome, H37Rv. We assembled nearly all GC-rich repetitive PE/PPE family genes (166/168) and identified variants within these genes. With an estimated genotypic error rate of 5.3 % from MinION data, we demonstrated identification of variants to include the conventional drug resistance mutations, and those that contribute to the resistance phenotype (efflux pumps/transporter) and virulence. Reference-based alignment of the assembly allowed detection of deletions and insertions. MinION sequencing provided a fully annotated assembly of a transmissible XDR strain from an endemic setting and showed its utility to provide further understanding of genomic processes within Mycobacterium tuberculosis.

Introduction. We describe the first detailed case report of human infection with Mycobacterium stomatepiae. Infection with non-tuberculous mycobacteria (NTM) related to M. stomatepiae is well described, despite the lack of previous confirmed reports of M. stomatepiae-related human disease. Localised cervical lymphadenitis is the most common NTM disease in children, with species closely related to M. stomatepiae, such as Mycobacterium triplex and Mycobacterium florentinum, having been shown to be rare causative agents. Case presentation. A 19-month-old girl presented with persistent unilateral neck lumps which developed following a facial laceration. Both lumps were fluctuant with overlying erythema and no fistulae present. Incision and drainage with curettage was performed. The operative sample of purulent fluid revealed pleomorphic bacilli on Ziehl–Neelsen staining. The isolate cultured was referred for further genotypic identification via 16S rRNA gene sequencing, identifying the organism as M. stomatepiae. Conclusion. We describe the first detailed case report of human infection with M. stomatepiae. This organism can now be added to the growing list of NTM that are opportunistic human pathogens, though it is likely to remain a very rare causative agent of this clinical syndrome. Early diagnosis relies on clinical suspicion by the treating doctor, flagging potential cases to the microbiology laboratory and hence allowing correct specimen set-up. Laboratory diagnosis requires incubation of cultures at lower temperatures, and definitive identification is best performed by sequencing methods, including 16S rRNA gene sequencing. The description of novel species of NTM causing human disease is likely to increase with further advancements in diagnostic methods.

Objective: To determine the proportion of non-tuberculous mycobacteria (NTM) in samples of pulmonary tuberculosis (TB) cases from Papua New Guinea who were diagnosed using acid-fast microscopy. Methods: As part of a case detection study for TB, conducted in three provincial hospitals in Papua New Guinea, sputum samples of suspected tuberculous cases aged 15 years or older were collected from November 2010 to July 2012. Mycobacterial species isolated from sputum and grown in culture were examined to distinguish between NTM and the Mycobacterium tuberculosis complex (MTBC). Results: NTM were detected in 4% (9/225) of sputum samples grown in culture. Five (2.2%) of them were identified as NTM only and four (1.8%) were identified as mixed cultures containing both MTBC and NTM. Four different NTM species were identified; M. fortuitum, M. intracellulare, M. terrae and M. avium. Discussion: This is the first report from Papua New Guinea identifying NTM in three different locations. As NTM cannot be distinguished from M. tuberculosis through smear microscopy, the presence of NTM can lead to a false-positive diagnosis of tuberculosis. The prevalence of NTM should be determined and a diagnostic algorithm developed to confirm acid-fast bacilli in a smear as M. tuberculosis.

Seed storage is being affected by factors viz. seed moisture content, temperature and relative humidity. The effects of four drying methods using silica gel, saturated salt solution of lithium chloride, concentrated sulphuric acid and dryer drying on different physiological and biochemical characteristics of genotypes CSH 16 and CSV 18 of sorghum (Sorghum bicolor (L.) Moench) were investigated. Faster drying rate was observed in acid and silica gel while dryer and saturated salt solution of lithium chloride exhibited slow drying rate. Acid drying was efficient in drying, but detrimental to the seed quality. Results obtained by silica gel and lithium chloride salt solution drying were comparable with those obtained by seed dryer. Among the various parameters investigated, germination, vigour, total protein content, dehydrogenase, amylase, superoxide dismutase (SOD) and peroxidase activity were found to show a decreasing trend, whereas electrical conductivity (EC) increased during storage irrespective of drying methods. Seed quality was preserved in conventional drying method (drying chamber at 15°C and 15% RH), which was comparable to the quality of seeds dried using lithium chloride; though drying rate was slow. Silica gel resulted in faster rate of drying to maintain moisture content and seed quality. Key words: Sorghum, silica gel, acid, dryer, lithium chloride, drying methods, seed quality.

One thousand sorghum germplasm accessions were evaluated and characterized at SDAU Deesa (Gujarat) under Consortium Research Platform on Agro-biodiversity and majority of accession showed good early vigour, dark green leaves, non-tan type, drooping leaf orientation, white mid rib color, non-senescence, awn less, semi compact ear head, oblong ear head shape, half glum covered, bold and white seeded. The quantitative characters also showed wide variation and the potential germplasm may be utilized for further breeding program.

A study was conducted on the spatial dimension of crop diversity in Jutpani Village Development Committee (VDC) in central Nepal. Many crop diversity studies focus only on home gardens, but this study aimed to investigate the crop diversity among different production systems, and the factors affecting variations in the crop diversity on a household level. A survey of inter-household variation in cultivated crop diversity in different land-use types among 134 households indicates that 96 different types of annual crops, perennial crops and fruit trees are cultivated. Individual farms cultivated an average of 26 different crops, with this number ranging from 11 to 45. Crops were used as food by the households and, based on their adaptive characters, they were grown either in home gardens or in upland, Tandikhet and lowland. Research showed that home gardens have the highest crop diversity (a total of 78 different crops grown) compared to upland, Tandikhet and lowland. Statistical analysis to understand the factors affecting the variation in crop diversity in the household level showed that the total number of crops grown (crop diversity) on a farm is significantly higher (PIndo-Aryan ethnic group compared to the Tibeto-Burman group. Farmers with three different production domains maintained higher (PP

The shift from double-season rice (DSR) to single-season rice (SSR) in the Yangtze River Valley in China has led to a decrease in the area of rice sown since the early 1980s and a decline in output since 1997. In this paper, changes in rice cropping patterns are described and a neoclassical household model is used to analyse differences in rice cropping patterns. The authors use the Probit model to analyse the impact on rice cropping patterns in the physical characteristics of plots, household economic characteristics and regional factors. They find that, in addition to the physical characteristics of plots, non-farm wage rates, land/labour ratios and ownership of labour-saving machinery all have significant impacts on rice cropping. Higher non-farm wages and higher land/labour ratios are associated with SSR; conversely, ownership of labour-saving machinery is associated with DSR. The policy implications are discussed.

Rice (Oryza sativa) is the main crop of Nepal. Farmers in Nepal mostly use seed from their stock in the form of informal seed systems which is around 92.3% of total seed requirements. In Nepal, formal seed of rice is distributed mostly by public institutions and very nominal amount by private seed dealers. Unavailability of quality seed of preferred variety is the key issue for rice seed systems. This study tries to attempt to address existing rice seed supply systems in Nepal thereby understanding its opportunities and constraints. The study was undertaken by collecting information from various documented sources and primary data from the household survey done at Chitwan and some seed related institutions during 2010/11. Formal and the informal are the two dimensions of the seed system for rice. Farm saved seed and farmers- to- farmers exchange of seed are informal seed system whereas private seed dealers and public institutions’ involvement in the seed sector are formal seed systems. Due to dominant of informal seed systems, there is the low seed replacement rate of 8.7% for rice. Nevertheless, breeder seed is solely produced by different Research Centers of Nepal Agriculture Research Council (NARC), whereas foundation seed is produced by NARC Research Centers and other institutes as well. This amount of source seed does not seem enough to cover rice areas of the country. To tackle problem of seed insufficiency, quality of source seed should be maintained by public institutions aside from creating awareness to farmers by service providers about the importance of producing certified seed by using foundation seed in farmers’ field. DOI: http://dx.doi.org/10.3126/ajn.v2i0.7531 Agronomy Journal of Nepal (Agron JN) Vol. 2: 2011 pp.157-167

Kodo millet (Paspalum scrobiculatum L.) is known for its high nutritive value, dietary fiber, antioxidant activity, as well as for drought tolerance. It is primarily grown as a grain in India and in Africa it is either cultivated or harvested in wild. Neutral—ISSR (inter simple sequence repeat) as well as functional—SCoT (start codon targeted) and SRAP (sequence-related amplified polymorphism) markers were employed for genetic diversity studies in 96 accessions of kodo millet collected from diverse regions of India. The genetic diversity parameters like average bands per primer, Polymorphic information content, Nei’s gene diversity and Shannon’s information index of 11.22, 9.69; 0.12, 0.11; 0.15 ± 0.14, 0.13 ± 0.13 and 0.26 ± 0.21, 0.22 ± 0.19 was observed with neutral and functional markers respectively. Neutral markers were showing higher values as compared to functional markers for the genetic diversity parameters as discussed. Structure based analysis placed all the accessions into four sub-groups not strictly according to their geographical locations. The accessions from Bihar followed by Karnataka were showing high diversity based on both the marker systems useful for designing exploration, conservation and germplasm enrichment strategies. Further, the set of diverse accessions selected based on these markers would serve as potential sources of unique alleles and may be exploited in future for enhancement and utilization of kodo millet germplasm. Usage of African gene pool and wild species for broadening the genetic base of Indian kodo millet was also suggested based on the present studies.

This study aimed to investigate the changes in rice-growing area over a decade (2000–2009) using remote-sensing techniques in combination with socioeconomic information and national statistics. Temporal rice area and land-use changes in Nepal were mapped using MODIS (MOD09A1) 500 m time-series data and spectral matching techniques (SMTs). This analysis presents mapped agricultural cropland change detected over a large area, where fuzzy classification accuracies range between 67% and 91% for various rice classes, with an accuracy of 82% for field-plot data. The MODIS-derived rice areas for the districts were highly correlated with national statistical data with R 2 values of 0.9918. We observed a significant decline (13%) in rice cultivated area in 2006 compared with the average over the remaining years. The higher reduction in rice area was mainly restricted to the rainfed districts of the eastern, central, and midwestern regions due to severe drought incidence, particularly in 2006. The area under the rainfed rice ecosystem continues to predominate, recording the largest share among rice classes across all the years from 2000 to 2009. The use of remote-sensing techniques is a rapid, cost-effective, and reliable measure to monitor changes in rice cultivated area over long periods of time and estimate the reduction in area cultivated due to climatic stress such as drought. Reinforced with methods and information in socioeconomics, these techniques could be used for mapping agricultural land-use changes, production planning, and targeting. Agricultural research and development institutions in Nepal can use these techniques for better planning, regular monitoring of land-use changes, and technology transfer.

An analysis of the patterns of technology adoption by upland rice farmers in southern Yunnan and of the impact of technologies was conducted using farm–household data collected during 2005. The technologies considered were improved upland rice varieties and terraces. The results indicate that these technologies are now spreading in upland areas. Farmers who have adopted both technology components have been able to increase the upland rice yield substantially. Income from rice production was similarly found to be higher for adopters than for nonadopters. In addition, there was evidence that increased rice yield helped reduce the pressure from intensifying food production in these fragile uplands because farmers were able to meet their food needs from smaller areas. Implications of these findings for sustainable development of uplands in Yunnan and in countries in the region are drawn.

The present paper assesses the impact of improved upland rice technology on farmers’ well-being. The study uses propensity-score matching to address the problem of ‘self-selection,’ because technology adoption is not randomly assigned. It applies this procedure to household survey data collected in Yunnan, China in 2000, 2002 and 2004. The findings indicate that improved upland rice technology has a robust and positive effect on farmers’ well-being, as measured by income levels and the incidence of poverty. The effect of technology on well-being shows a diminishing impact on producers’ incomes. This implies that newer innovations are continuously needed to replace older technologies that have reached their saturation points. asej_2033 141..159

Drought is a major constraint affecting rice production, especially in rainfed areas of Asia. Despite its importance in rice-growing areas, the magnitude of economic losses arising from drought, its impact on farm households, and farmers' drought coping mechanisms are poorly understood. This article provides insights into these aspects of drought based on a cross-country comparative analysis of rainfed rice-growing areas in southern China, eastern India, and northeast Thailand. The economic cost of drought is found to be substantially higher in eastern India than in the other two countries. Higher probability and greater spatial covariance of drought and less diversified farming systems with rice accounting for a larger share of household income are the main reasons for this higher cost of drought in eastern India. Farmers deploy various coping mechanisms but such mechanisms are largely unable to prevent a reduction in income and consumption, especially in eastern India. As a result, welfare consequences on poor farmers are substantial with a large number of people falling back into poverty during drought years. The overall implications for technology design and for policy improvements for drought mitigation and drought relief are discussed in the light of the empirical findings of the study.

Allocation of research resources between favorable and unfavorable rice-growing environments is analyzed in this paper using the case of India. The resource allocation in rice research for all ecosystems of India is approximated by the full-time equivalent (FTE) of scientist time spent in research. This was estimated through a survey of all major public research organizations involved in rice research. The FTEs were adjusted for any cost differences per scientist time across the rice growing environments. Unadjusted FTEs indicated a high congruence in resource allocation while adjusted FTEs showed slight under investment in rainfed environment. The use of equity weights amplified the extent of under investment in rainfed environments. It is concluded that, in the case of rice research, rainfed environments in India remain under-invested moderately. Options for addressing this imbalance and the overall implications for resource allocation are discussed.

Rice, the staple crop in northern Laos, has traditionally been grown in shifting cultivation systems (upland rice). Government policies and increasing population pressure have resulted in declining productivity of this system. Farmers need alternative and sustainable rice production systems to meet their rice needs. One alternative is the production of rice in flooded, terraced fields (montane paddy). This option is not new; however, farmers are developing these montane paddy fields much more now than in the past. The objectives of the study were to understand why farmers have begun developing montane paddy, the effect of paddy rice production on farmer livelihood activities, and the economics and costs associated with developing paddy land. The survey focused on 9 highland villages in northern Laos. In all villages, farmers reported declining upland rice yields. Between 1998 and 2002, the paddy area in these villages increased by over 240%. The main reasons cited for developing new paddy area we...

The value of rainfall forecasts for rainfed rice production in the Philippines is estimated under the assumption that farmers adjust the quantities of fertilizer and labor if rainfall forecasts are available. Using a panel of 46 rice farmers in Tarlac, Philippines, a heteroskedastic production function with growing season rainfall (July to October) as one of the independent variables is estimated. The expected value of rainfall forecasts under the assumption of simultaneous adjustments in both fertilizer and labor was estimated to be slightly more than 1% of the net return from rice production. Taking the rainfed rice area in the Philippines of 1.2 million ha and a net return of $446/ha, the total value of the forecast was estimated to be $6.6 million per year. The expected value was also estimated under the assumption that, instead of forecasts of rainfall amounts for each year, forecasts made are for rainfall “above average”, “average”, or “below average”. The value of rainfall forecasts was found to be highest and ranged between 1.4%-4.5% of the net return when the forecast is ‘above average’. The Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA) could help farmers by investing more of its resource for the accurate prediction of ‘above average’ rainfall events.