High light intensity plays a major role in emergence of population level variation in Arabidopsis thaliana along an altitudinal gradient

Environmental conditions play an important role in the emergence of genetic variations in natural populations. We identified genome-wide patterns of nucleotide variations in the coding regions of natural Arabidopsis thaliana populations. These populations originated from 700 m to 3400 m a.m.s.l. in the Western Himalaya. Using a pooled RNA-Seq approach, we identified the local and global level population-specific SNPs. The biological functions of the SNP-containing genes were primarily related to the high light intensity prevalent at high-altitude regions. The novel SNPs identified in these genes might have arisen de novo in these populations. In another approach, the F_STs of SNP-containing genes were correlated with the corresponding climatic factors. ‘Radiation in the growing season’ was the only environmental factor found to be strongly correlated with the gene-level F_STs. In both the approaches, the high light intensity was identified as the primary abiotic stress associated with the variations in these populations. The differential gene expression analysis between field and controlled condition grown plants also showed high light intensity as the primary abiotic stress, particularly for the high altitude populations. Our results provide a genome-wide perspective of nucleotide variations in populations along altitudinal gradient and their putative role in emergence of these variations.

Urinary osteoprotegerin: a potential biomarker of lupus nephritis disease activity

OBJECTIVES

Urinary biomarkers may help in identification, treatment and assessment of response in patients with lupus nephritis (LN). Osteoprotegerin (OPG) is produced by the kidneys and lymphoid cells and may reflect renal disease activity better. The data on its utility are sparse.

METHODS

Fifty-eight patients with active LN (AN), 24 with active non-renal disease (ANR) and 39 with inactive disease (ID) were included. Median disease duration was 32 (1-204) months and median age was 27 (12-50) years. AN patients were followed up every three months for one year. Urine and serum samples were collected for OPG measurement by ELISA (pg/ml) and urinary values were normalised for creatinine excretion (pg/mg). Urine samples from 24 healthy individuals (HCs) and 20 patients each of rheumatoid arthritis (RA) and diabetic nephropathy (DM) served as controls. Variables were expressed as median (range).

RESULTS

At baseline, normalised urinary OPG (uOPG) was significantly higher (p < 0.001) in AN (1229 (0-8577)) than ANR (236 (0-14713)), ID (463 (7-4253)), HCs (366 (120-2849)) and DM (350 (127-1577)) but it was not different from RA (1511 (122-8849)). uOPG correlated modestly with rSLEDAI (r = 0.4, p < 0.001) and SLEDAI (r = 0.31, p < 0.001) but not with serum OPG (sOPG). uOPG but not sOPG could differentiate between AN and ANR groups. In the longitudinal study, uOPG and sOPG decreased significantly with treatment at all follow-up visits but the trend of fall in sOPG was erratic. uOPG values at baseline, 3, 6, 9 and 12 months were 1229 (0-8577), 466 (3-4874), 104 (0-1598), 325 (0-4025) and 555 (6-6771) pg/mg, respectively. uOPG but not sOPG rose before conventional markers in three patients who had a relapse of LN. In two patients who developed chronic kidney disease, uOPG remained persistently high. For differentiating AN from ANR patients, uOPG performed the best on receiver operator characteristics analysis (AUC = 0.72) when compared with anti-dsDNA antibodies, C3, C4 and sOPG.

CONCLUSION

uOPG is derived from kidneys and helps differentiate active SLE patients with and without LN. It shows modest correlation with disease activity and has a potential to predict poor response to therapy and relapse of LN.

Overview of ion source characterization diagnostics in INTF

INdian Test Facility (INTF) is envisaged to characterize ITER diagnostic neutral beam system and to establish the functionality of its eight inductively coupled RF plasma driver based negative hydrogen ion source and its beamline components. The beam quality mainly depends on the ion source performance and therefore, its diagnostics plays an important role for its safe and optimized operation. A number of diagnostics are planned in INTF to characterize the ion source performance. Negative ions and its cesium contents in the source will be monitored by optical emission spectroscopy (OES) and cavity ring down spectroscopy. Plasma near the extraction region will be studied using standard electrostatic probes. The beam divergence and negative ion stripping losses are planned to be measured using Doppler shift spectroscopy. During initial phase of ion beam characterization, carbon fiber composite based infrared imaging diagnostics will be used. Safe operation of the beam will be ensured by using standard thermocouples and electrical voltage-current measurement sensors. A novel concept, based on plasma density dependent plasma impedance measurement using RF electrical impedance matching parameters to characterize the RF driver plasma, will be tested in INTF and will be validated with OES data. The paper will discuss about the overview of the complete INTF diagnostics including its present status of procurement, experimentation, interface with mechanical systems in INTF, and integration with INTF data acquisition and control systems.

Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing

miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna.

Soil quality index for evaluation of reclaimed coal mine spoil

Success in the remediation of mine spoil depends largely on the selection of appropriate tree species. The impacts of remediation on mine soil quality cannot be sufficiently assessed by individual soil properties. However, combination of soil properties into an integrated soil quality index provides a more holistic status of reclamation potentials of tree species. Remediation potentials of four tree species (Acacia auriculiformis, Cassia siamea, Dalbergia sissoo, and Leucaena leucocephala) were studied on reclaimed coal mine overburden dumps of Jharia coalfield, Dhanbad, India. Soil samples were collected under the canopies of the tree species. Comparative studies on the properties of soils in the reclaimed and the reference sites showed improvements in soil quality parameters of the reclaimed site: coarse fraction (-20.4%), bulk density (-12.8%), water holding capacity (+0.92%), pH (+25.4%), EC (+2.9%), cation exchange capacity (+46.6%), organic carbon (+91.5%), N (+60.6%), P (+113%), K (+19.9%), Ca (+49.6%), Mg (+12.2%), Na (+19.6%), S (+46.7%), total polycyclic aromatic hydrocarbons (-71.4%), dehydrogenase activity (+197%), and microbial biomass carbon (+115%). Principal component analysis (PCA) was used to identify key mine soil quality indicators to develop a soil quality index (SQI). Selected indicators include: coarse fraction, pH, EC, soil organic carbon, P, Ca, S, and dehydrogenase activity. The indicator values were converted into a unitless score (0-1.00) and integrated into SQI. The calculated SQI was significantly (P<0.001) correlated with tree biomass and canopy cover. Reclaimed site has 52-93% higher SQI compared to the reference site. Higher SQI values were obtained for sites reclaimed with D.sissoo (+93.1%) and C.siamea (+86.4%).

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.

Purification and characterization of laccase secreted by Phellinus linteus MTCC-1175 and its role in the selective oxidation of aromatic methyl group

A laccase from the culture filtrate of Phellinus linteus MTCC-1175 has been purified to homogeneity. The method involved concentration of the culture filtrate by ammonium sulphate precipitation and an anion exchange chro- matography on DEAE-cellulose. The SDS-PAGE and native-PAGE gave single protein band indicating that the enzyme preparation was pure. The molecular mass of the enzyme determined from SDS-PAGE analysis was 70 kDa. Using 2,6-dimethoxyphenol, 2,2'[azino-bis-(3-ethylbonzthiazoline-6-sulphonic acid) diammonium salt] (ABTS) and 4-hydroxy-3,5-dimethoxybenzaldehyde azine as the substrates, the Kin, kcat and kt/Km values of the laccase were found to be 160 microM, 6.85 s(-1), 4.28 x 10(4) M(-1) s(-1), 42 microM, 6.85 s(-1), 16.3 x 10(4) M(-1) s(-1) and 92 microM, 6.85 s(-1), 7.44 x 10(4) M(-1) s(-1), respectively. The pH and the temperature optima of the P. linteus MTCC-1175 laccase were 5.0 and 45 degrees C, respectively. The activation energy for thermal denaturation of the enzyme was 38.20 kJ/mole/K. The enzyme was the most stable at pH 5.0 after 1 h reaction. In the presence ofABTS as the mediator, the enzyme transformed toluene, 3-nitrotoluene and 4-chlorotoluene to benzaldehyde, 3-nitroben-zaldehyde and 4-chlorobenzaldehyde, respectively.

Acaricidal activity of ethanolic extract of Artemisia absinthium against Hyalomma anatolicum ticks

The aim of the study was to evaluate the in vitro efficacy of different concentrations of ethanolic extract obtained from the aerial parts of Artemisia absinthium in comparison to amitraz on adults, eggs and larvae of Hyalomma anatolicum using the adult immersion test (AIT), egg hatchability test and larval packet test (LPT), respectively. Four concentrations of the extract (2.5, 5, 10 and 20%) with three replications for each concentration were used in all the bioassays. In AIT, the mortality rates at 2.5, 5 and 10% were significantly different (p < 0.05) in comparison to the control group; however, at 20%, it was similar to the positive control group. Maximum mortality of 86.7% was recorded at 20%. The LC50 and LC95 values were calculated as 6.51 and 55.43%, respectively. The oviposition was reduced significantly by 36.8 and 59.1% at concentrations of 10 and 20%, respectively. Egg hatchability was reduced significantly at all concentrations (2.5-20%) in comparison to the control. In LPT, the extract caused 100% mortality of larvae at all the concentrations after 24 h. The results show that ethanolic extract obtained from the aerial parts of A. absinthium has acaricidal properties and could be useful in controlling H. anatolicum.

Urinary sCD25 as a biomarker of lupus nephritis disease activity

OBJECTIVES

T cells play an important role in the pathogenesis of lupus nephritis (LN). We studied the role of urinary soluble CD25 (sCD25) as a biomarker of LN disease activity in a cross-sectional and longitudinal study.

METHODS

Patients with systemic lupus erythematosus were classified as active LN (AN), inactive disease (ID) and active non-renal (ANR) based on disease activity and renal involvement at the time of enrolment. Urine and serum samples were collected at baseline from all patients and at 3-monthly follow-up from patients with AN. SLE disease activity index (SLEDAI) was used for disease activity assessment at all visits. sCD25 was measured by ELISA and normalized to urinary creatinine excretion and is expressed as pg/mg. Urine samples from 10 healthy individuals (HC) served as controls.

RESULTS

There were 119 patients (111 females, median age 27 years, 57 AN, 43 ID, 19 ANR). Median SLEDAI was 18, 2 and 8 in AN, ID and ANR groups, respectively. Median renal SLEDAI in AN was 8. Mean (±SD) urinary sCD25 in the AN, ID, ANR and HC groups at baseline was 741.1 (±794.9), 407.8 (±511.1), 735.4 (±667.7) and 250.9 (±122.2) pg/mg respectively (p = 0.019). Mean (±SD) serum sCD25 in AN, ID and ANR was 8285.25 (±5922.2), 6044 (±3501.92) and 6568.72 (±4333.62) pg/ml, respectively. Urinary sCD25 correlated with SLEDAI (r = 0.22; p = 0.015) but did not correlate with serum sCD25 or proteinuria. Urinary sCD25 compares well with traditional markers of disease activity in differentiating active from inactive renal disease. On follow-up mean urinary sCD25 decreased to 470.0 (±449.6; p < 0.05) at 3 months, 496.7 (±465.8; p = 0.006) at 6 months, 471.9 (±303.2; p = 0.041) at 9 months and 358.6 (±496.9; p = 0.007) at 12 months from baseline value of 741.1 (±794.9). In four patients who either had relapse, persistent disease activity or developed chronic kidney disease, urinary sCD25 showed rise preceding traditional abnormalities on urine examination.

CONCLUSIONS

Urinary sCD25 is a good biomarker for follow-up of LN. It may also have the potential to predict poor response and relapse.

Measurement of the cosmic microwave background polarization lensing power spectrum with the POLARBEAR experiment

Gravitational lensing due to the large-scale distribution of matter in the cosmos distorts the primordial cosmic microwave background (CMB) and thereby induces new, small-scale B-mode polarization. This signal carries detailed information about the distribution of all the gravitating matter between the observer and CMB last scattering surface. We report the first direct evidence for polarization lensing based on purely CMB information, from using the four-point correlations of even- and odd-parity E- and B-mode polarization mapped over ∼30 square degrees of the sky measured by the POLARBEAR experiment. These data were analyzed using a blind analysis framework and checked for spurious systematic contamination using null tests and simulations. Evidence for the signal of polarization lensing and lensing B modes is found at 4.2σ (stat+sys) significance. The amplitude of matter fluctuations is measured with a precision of 27%, and is found to be consistent with the Lambda cold dark matter cosmological model. This measurement demonstrates a new technique, capable of mapping all gravitating matter in the Universe, sensitive to the sum of neutrino masses, and essential for cleaning the lensing B-mode signal in searches for primordial gravitational waves.

First Report of a New Subgroup 16Sr II-M 'Candidatus Phytoplasma aurantifolia' Associated with Witches'-Broom Disease of Tephrosia purpurea in India

Wild indigo (Tephrosia purpurea (L.) Pers.) grows as a common weed throughout the Indian subcontinent. The plant has pinnate leaves, white or purplish flowers, and flat hairy pods, and is cultivated as a green manure crop. The plant extracts contain compounds such as tephrosin, an aromatic ester, prenylated flavonoid, and sesquiterpene (2) that have medicinal properties. The newly recognized disease, Tephrosia purpurea witches' broom (TPWB), was characterized by chlorosis, stunting, and proliferative branching, which were suggestive of phytoplasma infection during a field survey conducted in November 2013. To determine the presence of phytoplasma, 2 g of compound leaves from three symptomatic and asymptomatic plants were used for total DNA extraction using the CTAB method. The phytoplasma 16S rRNA gene was detected in all three symptomatic plants using nested PCR with universal phytoplasma primer pairs, P1/P7 followed by R16F2n/R16R2 (4). No amplification was observed in DNA isolated from asymptomatic plants. PCR fragments (1,246 bp in length) generated from symptomatic T. purpurea plants were sequenced directly using five different primers viz. 343R, 536F, 704F, 907R, and 1103F. TPWB phytoplasma 16S rRNA gene sequence (GenBank Accession No. HG792252) showed 99.12% homology with a 'Candidatus Phytoplasma aurantifolia' strain WBDL (U15442) when compared using the EzTaxon 16S rRNA database (3). Virtual restriction fragment length polymorphism (RFLP) analysis was carried out on the obtained sequence using iPhyClassifier (5). The virtual RFLP pattern derived from the HG792252 sequence was different to the reference patterns of previously established 16Sr groups and subgroups. The reference pattern of the 16Sr group II, subgroup C (AJ293216) was most similar with a similarity coefficient of 0.92, which placed it in a new subgroup, 16Sr II-M (1). Furthermore, virtual RFLP results were confirmed by digesting R16F2n/R16R2 amplicon with BstUI, DraI, HinfI, HpaI, and MseI restriction enzymes according to manufacturer's instructions. To our knowledge, this is the first report of a 'Ca. P. aurantifolia'-related strain associated with witches'-broom disease of T. purpurea in India. References: (1) H. Cai et al. Int. J. Syst. Evol. Microbiol. 58:1448, 2008. (2) A. K. Khalafalah et al. Pharmacognosy Res. 2:72, 2010. (3) O.-S. Kim et al. Int. J. Syst. Evol. Microbiol. 62:716, 2012. (4) C. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996. (5) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

Evidence for gravitational lensing of the cosmic microwave background polarization from cross-correlation with the cosmic infrared background

We reconstruct the gravitational lensing convergence signal from cosmic microwave background (CMB) polarization data taken by the Polarbear experiment and cross-correlate it with cosmic infrared background maps from the Herschel satellite. From the cross spectra, we obtain evidence for gravitational lensing of the CMB polarization at a statistical significance of 4.0σ and indication of the presence of a lensing B-mode signal at a significance of 2.3σ. We demonstrate that our results are not biased by instrumental and astrophysical systematic errors by performing null tests, checks with simulated and real data, and analytical calculations. This measurement of polarization lensing, made via the robust cross-correlation channel, not only reinforces POLARBEAR auto-correlation measurements, but also represents one of the early steps towards establishing CMB polarization lensing as a powerful new probe of cosmology and astrophysics.