De novo Assembly and Characterization of Cajanus scarabaeoides (L.) Thouars Transcriptome by Paired-End Sequencing

Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR) in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop. Bud and leaf tissue of Cajanus scarabaeoides, a wild relative of pigeon pea were used for transcriptome profiling. Approximately 30 million clean reads filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (3.02 gigabase pairs) were generated by Illumina paired-end RNA-seq technology. All of these clean reads were pooled and assembled de novo into 1,17,007 transcripts using the Trinity. Finally, a total of 98,664 unigenes were derived with mean length of 396 bp and N50 values of 1393. The assembly produced significant mapping results (73.68%) in BLASTN searches of the Glycine max CDS sequence database (Ensembl). Further, uniprot database of Viridiplantae was used for unigene annotation; 81,799 of 98,664 (82.90%) unigenes were finally annotated with gene descriptions or conserved protein domains. Further, a total of 23,475 SSRs were identified in 27,321 unigenes. This data will provide useful information for mining of functionally important genes and SSR markers for pigeonpea improvement.

Molecular prevalence of Babesia bigemina in Rhipicephalus microplus ticks infesting cross-bred cattle of Punjab, India

Babesiosis is an economically important tick-borne apicomplexan protozoan disease of cattle in tropical and subtropical regions. In the present study, Rhipicephalus microplus engorged female ticks were collected from 135 apparently healthy cattle from different agro-climatic zones of Punjab, India, to investigate the carrier status of Babesia bigemina infection in vector tick by using microscopy and PCR based assays. PCR when applied on DNA extracted from the egg masses harvested from ticks showed 1.48% (2/135) samples as positive, whereas 4.44% (6/135) samples were positive when product of primary PCR was used as template in nPCR. Further, among the DNA samples isolated from the unfed larval stages that emerged from egg masses laid by ticks, only 1.48% (2/135) samples were detected as positive for B. bigemina in PCR, while 7.41% (10/135) samples were detected positive in nPCR assay. Statistically, non-significant (p > 0.05) difference in prevalence rates was observed across different agro-climatic zones and between different age groups of cattle from which engorged ticks were collected. It can, thus, be concluded that prevalence of B. bigemina in the vector tick, R. microplus in Punjab state of India indicates an endemic status of the organism and a further study is needed for the management and control of the bovine babesiosis.

A Young Boy with L-asparaginase-Induced Seizure

L-Asparaginase is a critical component in the treatment of acute lymphoblastic leukemia in children. It is known to cause coagulation abnormalities, thrombosis and hemorrhage in the central nervous system in addition to vasculitis and hypersensitivity reactions. This syndrome generally occurs after a few weeks of therapy and may occur after L-asparaginase therapy is completed. Seizures are uncommon symptoms. We report a case of seizure associated with L-asparaginase therapy but no evidence of hemorrhagic or thrombotic cerebrovascular events, completed in the department of Hematology of Bangabandhu Sheikh Mujib Medical University during March & April 2016.

Sparse feature selection for classification and prediction of metastasis in endometrial cancer

Background

Metastasis via pelvic and/or para-aortic lymph nodes is a major risk factor for endometrial cancer. Lymph-node resection ameliorates risk but is associated with significant co-morbidities. Incidence in patients with stage I disease is 4–22% but no mechanism exists to accurately predict it. Therefore, national guidelines for primary staging surgery include pelvic and para-aortic lymph node dissection for all patients whose tumor exceeds 2cm in diameter. We sought to identify a robust molecular signature that can accurately classify risk of lymph node metastasis in endometrial cancer patients. 86 tumors matched for age and race, and evenly distributed between lymph node-positive and lymph node-negative cases, were selected as a training cohort. Genomic micro-RNA expression was profiled for each sample to serve as the predictive feature matrix. An independent set of 28 tumor samples was collected and similarly characterized to serve as a test cohort.

Results

A feature selection algorithm was designed for applications where the number of samples is far smaller than the number of measured features per sample. A predictive miRNA expression signature was developed using this algorithm, which was then used to predict the metastatic status of the independent test cohort. A weighted classifier, using 18 micro-RNAs, achieved 100% accuracy on the training cohort. When applied to the testing cohort, the classifier correctly predicted 90% of node-positive cases, and 80% of node-negative cases (FDR = 6.25%).

Conclusion

Results indicate that the evaluation of the quantitative sparse-feature classifier proposed here in clinical trials may lead to significant improvement in the prediction of lymphatic metastases in endometrial cancer patients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3604-y) contains supplementary material, which is available to authorized users.

Detection of amitraz and malathion resistance in field populations of Rhipicephalus (Boophilus) microplus (Acari: Ixodidae) in Jammu region of India

Detection of resistance levels against amitraz and malathion in Rhipicephalus (Boophilus) microplus collected from four districts of Jammu region (India) was carried out using the adult immersion test. The regression graphs of probit mortality of ticks plotted against log values of concentration of drugs were utilised for the determination of slope of mortality, lethal concentration for 50% (LC₅₀), 95% (LC₉₅) and resistance factor (RF). On the basis of the data generated on variables (mortality, egg mass weight, reproductive index and percentage inhibition of oviposition) the resistance level was categorised as I, II, III and IV. Out of these four districts, resistance to amitraz was detected at level I in Udhampur (RF = 2.81), Jammu (RF = 2.53) and Samba isolates (RF = 2.24) whereas Rajouri isolate was found susceptible (RF = 1.0). Resistance to malathion was detected at level I in Udhampur (RF = 4.01) and Jammu isolates (RF = 1.76) whereas Rajouri (RF = 0.472) and Samba (RF = 0.199) isolates were found susceptible. The data generated on amitraz and malathion resistance status will help in formulating a tick control strategy in the region.

Augmentation of arsenic enhances lipid yield and defense responses in alga Nannochloropsis sp

The present study was conducted with microalga Nannochloropsis sp. to evaluate its tolerance responses and biofuel perspectives under different arsenic regime (0-1000μM As(III)). Results showed that optimal biomass (61.00±3.72mg/L/d) and lipid productivity (20.27mg/L/d) were obtained in culture treated with 100μM As(III) in comparison to other treatments. In addition, fatty acid profile of alga was in accordance with European biodiesel standards (EN 14214), which reflects good oxidative stability of oil. High antioxidants viz., ascorbic acid, GSH and cysteine tolerance responses as well as lipid yield at 100μM As(III), opens a new insight in the field of algal biology. Thus, microalgae Nannochloropsis sp. may be employ in remediation as well as biodiesel production.

Synthesis of Enantiopure Alicyclic Ethers and Their Activity on the Chemosensory Organ of the Ectoparasite of Honey Bees, Varroa destructor

The preparation of enantiopure conformationally restricted alicyclic ethers and their inhibitory activities on the chemosensory organ of the Varroa destructor, a parasite of honey bees, are reported in this article. We tested the effect of enantiopure ethers of cis-5-(2'-hydroxyethyl)cyclopent-2-en-1-ol on the Varroa chemosensory organ by electrophysiology, for their ability to inhibit the responses to two honey bee-produced odors that are important for the mite to locate its host: nurse bee head space odor and (E)-β-ocimene, a honey bee brood pheromone. Previous work with the racemic compounds showed that they suppress the mite's olfactory response to its bee host, which led to incorrect host choice. Based on a structure-activity relationship, we predicted that the two most active compounds-cis-1-butoxy-5-(2'-methoxyethyl)cyclopent-2-ene, cy{4,1}, and (cis-1-ethoxy-5-(2'ethoxyethyl)cyclopent-2-ene, cy{2,2}-could have opposite active enantiomers. Here we studied the enantiomers of both ethers, whose preparation involved enzymatic resolution of racemic diol cis-5-(2'-hydroxyethyl)cyclopent-2-en-1-ol using Lipase AK with vinyl acetate. The racemic diol was prepared from commercially available 2,5-norbornadiene. We observed that the responses of the chemosensory organ to honey bee head space volatiles were significantly decreased by both enantiomers of cy{4,1} and cy{2,2}, but that responses to (E)-β-ocimene were decreased significantly only by (+)-cy{4,1} (1R,5S) and (-)-cy{2,2} (1S,5R) and not by their respective enantiomers. The importance of this result is that the racemates could be used to inhibit olfactory detection of bee odors by mites, without a loss in activity relative to the more expensive enantiopure compounds.

Hemin, a heme oxygenase-1 inducer, restores the attenuated cardioprotective effect of ischemic preconditioning in isolated diabetic rat heart

BACKGROUND

Attenuated cardioprotective effect of ischemic preconditioning (IPC) by reduced nitric oxide (NO) is a hallmark during diabetes mellitus (DM). Recently, we reported that the formation of caveolin-endothelial nitric oxide synthase (eNOS) complex decreases the release of NO, which is responsible for attenuation of IPC-induced cardioprotection in DM rat heart. Heme oxygenase-1 (HO-1) facilitates release of NO by disrupting caveolin-eNOS complex. The activity of HO-1 is decreased during DM. This study was designed to investigate the role of hemin (HO-1 inducer) in attenuated cardioprotective effect of IPC in isolated diabetic rat heart.

METHODS

DM was induced in male Wistar rat by single dose of streptozotocin. Cardioprotective effect was assessed in terms of myocardial infarct size and release of lactate dehydrogenase and creatine kinase in coronary effluent. The release of NO was estimated indirectly by measuring the release of nitrite in coronary effluent. Perfusion of sodium nitrite, a precursor of NO, was used as a positive control.

RESULT

IPC-induced cardioprotection and increased release of nitrite were significantly attenuated in a diabetic rat as compared to a normal rat. Pretreatment with hemin and daidzein, a caveolin inhibitor, alone or in combination significantly restored the attenuated cardioprotection and increased the release of nitrite in diabetic rat heart. Zinc protoporphyrin, a HO-1 inhibitor, significantly abolished the observed cardioprotection and decreased the release of nitrite in hemin pretreated DM rat heart.

CONCLUSION

Thus, it is suggested that hemin restores the attenuated cardioprotective effect in diabetic rat heart by increasing the activity of HO-1 and subsequently release of NO.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

Background

The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940–2013), conserved in the National Gene Bank of India using SSR markers.

Result

A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend.

Conclusion

Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0437-7) contains supplementary material, which is available to authorized users.

Arsenic and other heavy metal accumulation in plants and algae growing naturally in contaminated area of West Bengal, India

The present study was conducted to quantify the arsenic (As) and other heavy metal concentrations in the plants and algae growing naturally in As contaminated blocks of North-24-Pargana and Nandia district, West Bengal, India to assess their bioaccumulation potential. The plant species included five macrophytes and five algae were collected from the nine selected sites for estimation of As and other heavy metals accumulated therein by using Inductively Coupled Plasma Mass Spectrophotometer (ICP-MS). Results revealed that maximum As concentration (117mgkg(-1)) was recorded in the agricultural soil at the Barasat followed by Beliaghat (111mgkg(-1)) sites of North-24-Pargana. Similarly, concentration of selenium (Si, 249mgkg(-1)), lead (Pb, 79.4mgkg(-1)), chromium (Cr, 138mgkg(-1)) was also found maximum in the soil at Barasat and cadmium (Cd, 163mgkg(-1)) nickel (Ni, 36.5mgkg(-1)) at Vijaynagar site. Among the macrophytes, Eichhornia crassipes found more dominating species in As contaminated area and accumulate As (597mgkg(-1)) in the shoot at kanchrapara site. The Lemna minor found to accumulate maximum As (735mgkg(-1)) in the leaves at Sonadanga and Pistia stratiotes accumulated minimum As (24.5mgkg(-1)) in the fronds from Ranaghat site. In case of diatoms, maximum As (760mgkg(-1)) was accumulated at Kanchrapara site followed by Hydrodictiyon reticulatum (403mgkg(-1)) at the Ranaghat site. High concentration of As and other heavy metal in soil indicates long term effects of irrigation with contaminated ground water, however, high concentration of heavy metals in naturally growing plants and algae revealed their mobilization through leaching and possible food chain contamination. Therefore, efficient heavy metal accumulator macrophytes Eichhornia crassipes, Lemna minor, Spirodela polyrhiza may be exploited in removing metals from contaminated water by developing a plant based treatment system. However, As accumulator algal species may be used as a bioresource for understanding algae mediated As detoxification and bioindication studies.

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka

Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.

Hydro-Climatological Influences on Long-Term Dissolved Organic Carbon in a Mountain Stream of the Southeastern United States

In the past decade, significant increases in surface water dissolved organic carbon (DOC) have been reported for large aquatic ecosystems of the Northern Hemisphere and have been attributed variously to global warming, altered hydrologic conditions, and atmospheric deposition, among other factors. We analyzed a 25-yr DOC record (1988-2012) available for a forested headwater stream in the United States and documented two distinct regimes of stream DOC trends. From 1988 to 2001, annual mean volume-weighted DOC concentration (DOC, mg L) and annual DOC flux (kg ha yr) declined by 34 and 56%, respectively. During 1997 to 2012, the decline in DOC and DOC flux increased by 141 and 165%, respectively. Declining DOC from 1988 to 2001 corresponded to a decline in growing season runoff, which has the potential to influence mobilization of DOC from uplands to streams. Increasing DOC from 1997 to 2012 corresponded to increased precipitation early in the growing season and to an increase in the number and intensity of short-duration fall storms capable of mobilizing long-accrued DOC from forest litter and soils. In contrast, total annual runoff declined throughout the period. Rising air temperature, atmospheric acid deposition, and nitrogen depositions did not offer any plausible explanation for the observed bidirectional annual trends of stream DOC. Our study highlights the critical role of long-term datasets and analyses for understanding the impacts of climate change on carbon and water cycles and associated functions of aquatic and terrestrial ecosystems.

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins

Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.

Identification and gene-silencing of a putative odorant receptor transcription factor in Varroa destructor: possible role in olfaction

The ectoparasitic mite Varroa destructor is one of the major threats to apiculture. Using a behavioural choice bioassay, we determined that phoretic mites were more successful in reaching a bee than reproductive mites, suggesting an energy trade-off between reproduction and host selection. We used both chemo-ecological and molecular strategies to identify the regulation of the olfactory machinery of Varroa and its association with reproduction. We focused on transcription regulation. Using primers designed to the conserved DNA binding region of transcription factors, we identified a gene transcript in V. destructor homologous to the pheromone receptor transcription factor (PRTF) gene of Pediculus humanus corporis. Quantitative PCR (qPCR) revealed that this PRTF-like gene transcript is expressed in the forelegs at higher levels than in the body devoid of forelegs. Subsequent comparative qPCR analysis showed that transcript expression was significantly higher in the phoretic as compared to the reproductive stage. Electrophysiological and behavioural studies revealed a reduction in the sensitivity of PRTF RNA interference-silenced mites to bee headspace, consistent with a reduction in the mites' ability to reach a host. In addition, vitellogenin expression was stimulated in PRTF-silenced mites to similar levels as found in reproductive mites. These data shed light upon the regulatory mechanism of host chemosensing in V. destructor.

Amelioration of arsenic toxicity in rice: Comparative effect of inoculation of Chlorella vulgaris and Nannochloropsis sp. on growth, biochemical changes and arsenic uptake

The present study was conducted to assess the responses of rice (Oryza sativa L. var. Triguna) by inoculating alga; Chlorella vulgaris and Nannochlropsis sp. supplemented with As(III) (50µM) under hydroponics condition. Results showed that reduced growth variables and protein content in rice plant caused by As toxicity were restored in the algae inoculated plants after 7d of treatment. The rice plant inoculated with Nannochloropsis sp. exhibited a better response in terms of increased root, shoot length and biomass than C. vulgaris under As(III) treatment. A significant reduction in cellular toxicity (thiobarbituric acid reactive substances) and antioxidant enzyme (SOD, APX and GR) activities were observed in algae inoculated rice plant under As(III) treatment in comparison to uninoculated rice. In addition, rice treated with As(III), accumulated 35.05mgkg(-1)dw arsenic in the root and 29.96mgkg(-1)dw in the shoot. However, lower accumulation was observed in As(III) treated rice inoculated with C. vulgaris (24.09mg kg(-1)dw) and Nannochloropsis sp. (20.66mgkg(-1)dw) in the roots, while in shoot, it was 20.10mgkg(-1)dw and 11.67mgkg(-1)dw, respectively. Results demonstrated that application of these algal inoculum ameliorates toxicity and improved tolerance in rice through reduced As uptake and modulating antioxidant enzymes. Thus, application of algae could provide a low-cost and eco-friendly mitigation approach to reduce accumulation of arsenic in edible part of rice as well as higher yield in the As contaminated agricultural field.

Performance of fenugreek bioinoculated with Rhizobium meliloti strains under semi-arid condition

Rhizobium meliloti strains were isolated from the fields of S.D. Agricultural University (Gujarat, India) and were maintained in the Congo Red Yeast Extract Mannitol Agar medium. These strains were tested for their effectiveness for fenugreek crop grown under semi-arid condition. Among the six Rhizobium strains, FRS-7 strain showed best plant growth parameters like shoot length, shoot dry weight, shoot total nitrogen, root length, root dry weight, root total nitrogen, seed yield, 1000 grain weight, number of root nodules, and nodules fresh and dry weight. The performance of this strain was better as compared to 20 kgN ha(-1) treatment through urea and was even far better over control plot. Seed yields obtained with FRS-7 during two years were 10.14 and 9.66 q ha(-1); which was about 36.8% and 45.9% high over control. This strain resulted in saving of about 20 kgN ha(-1) accompanied with better crop yield and soil health. Results of the present experiments can be utilized in integrated nutrient management for cultivation of fenugreek in semi-arid areas to provide sustainability to agricultural productivity in such regions.

From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network

Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.

Molecular detection of Babesia bigemina infection in apparently healthy cattle of central plain zone of Punjab

Bovine babesiosis is an important tick-borne disease caused by the parasites belonging to the genus Babesia, distributed worldwide and infecting a wide range of domesticated and wild cattle, occasionally man. The present study was conducted to determine the prevalence of B. bigemina infection in apparently healthy cattle from central plain zone of Punjab, India. Examination of Giemsa-stained peripheral thin blood smears revealed 2.45 % (5/204) animals to be positive for piroplasms of B. bigemina. However, genomic DNA isolated from these blood samples when subjected to primary PCR revealed a positivity of 7.35 % (15/204) as detected by the amplification of a 278-bp product in the agarose gel. PCR products obtained from the primary PCR of B. bigemina, when employed as template in nested PCR produced the amplicons of desired size (170 bp) was detected in 30.39 % (62/204) of the samples. It can thus be concluded that B. bigemina infection is prevalent in apparently healthy cattle population of this region and PCR assays can serve as a valuable tool for epidemiological studies in endemic areas.

Syndrome of remitting seronegative symmetrical synovitis with pitting edema: a case series

Remitting Seronegative Symmetrical Synovitis with Pitting Edema (RS3PE) is a rare clinical entity that is easily missed due to lack of knowledge. It was formerly considered as a subset of rheumatoid arthritis (RA), but is now regarded as a distinct disease/syndrome. The diagnosis of RS3PE is not easy, as it is always hindered by the lack of definite diagnostic criteria and presence of other much common rheumatological disorders that mimic it. We report a series of seven cases that attended our clinic in the last year, which highlight the salient features of the disease. The disease was found to have a heterogeneous presentation. Immunogenetic, clinical, laboratory, radiological, and possible etiological factors and associations with the neoplasm are described, as also other peculiar presentations. Finally, a comparison with other common rheumatological disorders is made to alert the clinician about this rare, but easily treatable disease.

Deltamethrin resistance in field populations of Rhipicephalus (Boophilus) microplus (Acari: Ixodidae) in Jammu and Kashmir, India

Detection of resistance levels against deltamethrin in Rhipicephalus (Boophilus) microplus collected from six districts of Jammu and Kashmir (India) was carried out using the adult immersion test. The regression graphs of probit mortality of ticks plotted against log values of concentration of drug were utilised for the determination of slope of mortality, lethal concentration for 50% (LC50), 95% (LC95) and resistance factor (RF). On the basis of the data generated on mortality, egg mass weight, reproductive index and percentage inhibition of oviposition, the resistance level was categorised as I, II, III and IV. Out of these six districts, resistance to deltamethrin at level I was detected in one district (RF = 1.9), at level II in two districts (RF = 7.08-10.07) and at level IV in three districts (RF = 96.08-288.72). The data generated on deltamethrin resistance status will help in formulating tick control strategy in the region.

In vitro acaricidal activity of ethanolic and aqueous floral extracts of Calendula officinalis against synthetic pyrethroid resistant Rhipicephalus (Boophilus) microplus

Detection of resistance levels against deltamethrin and cypermethrin in Rhipicephalus (Boophilus) microplus collected from Jammu (India) was carried out using larval packet test (LPT). The results showed the presence of resistance level II and I against deltamethrin and cypermethrin, respectively. Adult immersion test (AIT) and LPT were used to evaluate the in vitro efficacy of ethanolic and aqueous floral extracts of Calendula officinalis against synthetic pyrethroid resistant adults and larvae of R. (B.) microplus. Four concentrations (1.25, 2.5, 5 and 10 %) of each extract with four replications for each concentration were used in both the bioassays. A concentration dependent mortality was observed and it was more marked with ethanolic extract. In AIT, the LC50 values for ethanolic and aqueous extracts were calculated as 9.9 and 12.9 %, respectively. The egg weight of the live ticks treated with different concentrations of the ethanolic and aqueous extracts was significantly lower than that of control ticks; consequently, the reproductive index and the percent inhibition of oviposition values of the treated ticks were reduced. The complete inhibition of hatching was recorded at 10 % of ethanolic extract. The 10 % extracts caused 100 % mortality of larvae after 24 h. In LPT, the LC50 values for ethanolic and aqueous extracts were determined to be 2.6 and 3.2 %, respectively. It can be concluded that the ethanolic extract of C. officinalis had better acaricidal properties against adults and larvae of R. (B.) microplus than the aqueous extract.