Diverse begomovirus-betasatellite complexes cause tomato leaf curl disease in the western India.

In the Indian sub-continent, tomato leaf curl disease (ToLCD) of tomato caused by begomoviruses has emerged as a major limiting factor for tomato cultivation. Despite the spread of this disease in the western India, a systematic study on the characterization of virus complexes with ToLCD is lacking. Here, we report the identification of a complex of begomoviruses including 19 DNA-A and 4 DNA-B as well as 15 betasatellites with ToLCD in the western part of the country. Additionally, a novel betasatellite and an alphasatellite were also identified. The recombination breakpoints were detected in the cloned begomoviruses and betasatellites. The cloned infectious DNA constructs cause disease on the tomato (a moderately virus-resistant cultivar) plants, thus fulfilling Koch's postulates for these virus complexes. Further, the role of non-cognate DNA B/betasatellite with ToLCD-associated begomoviruses on disease development was demonstrated. It also emphasizes the evolutionary potential of these virus complexes in breaking disease resistance and plausible expansion of its host range. This necessitates to investigate the mechanism of the interaction between resistance breaking virus complexes and the infected host.

Improving the assessment of polluted sites using an integrated bio-physico-chemical monitoring framework.

Soil - water pollution resulting from anthropogenic activities is a growing concern internationally. Effective monitoring techniques play a crucial role in the detection, prevention, and remediation of polluted sites. Current pollution monitoring practices in many geographical locations are primarily based on physico-chemical assessments which do not always reflect the potential toxicity of contaminant 'cocktails' and harmful chemicals not screened for routinely. Biomonitoring provides a range of sensitive techniques to characterise the eco-toxicological effects of chemical contamination. The bioavailability of contaminants, in addition to their effects on organisms at the molecular, cellular, individual, and community level allows the characterisation of the overall health status of polluted sites and ecosystems. Quantifying bioaccumulation, changes to community structure, faunal morphology, behavioural, and biochemical responses are standard procedures employed in biomonitoring studies in many High-Income Countries (HICs). This review highlights the need to integrate biomonitoring tools alongside physico-chemical monitoring techniques by using 'effect-based' tools to provide more holistic information on the ecological impairment of soil-water systems. This paper considers the wider implementation of biomonitoring methods in Low to Middle Income Countries (LMICs) and their significance in pollution investigations and proposes an integrated monitoring framework that can identify toxicity drivers by utilising 'effect-based' and 'risk-based' monitoring approaches.

Floodplains landforms, clay deposition and irrigation return flow govern arsenic occurrence, prevalence and mobilization: A geochemical and isotopic study of the mid-Gangetic floodplains.

This article attempts to understand the evolution of groundwater chemistry in the mid Gangetic floodplain through the identification of hydrogeochemical processes including the impact of surface recharge and geological features. Isotopic investigations identified that irrigation return flow is partly responsible for arsenic (As) enrichment through preferential vertical recharge. Further, the floodplain geomorphological attributes and associated As hydrogeochemical behaviour traced through isotopes tracers highlighted that meandering and ox-bow like geomorphological features owing to clay deposition leads to the anoxic condition induced reductive microbial dissolution of As-bearing minerals causing the arsenic contamination in the investigated aquifer of the mid-Gangetic plain (MGP). To achieve the objectives, 146 water samples for water chemistry and 62 samples for the isotopic study were collected from Bhojpur district, Bihar (district bounded by the river Ganges in the north and Son in the east) located in MGP during the pre-monsoon season of 2018. The chemical results revealed high arsenic concentration (BDL to 206 µg.L-1, 32% samples are exceeding the 10 µg.L-1 limit) in the Holocene recent alluviums which are characterized by various geomorphological features such as meander scars and oxbow lake (northern part of the district). Arsenic is more concentrated in the depth range of 15-40 m below ground surface. All other trace metals viz. Ni, Pb, Zn, Cd and Al were found in low concentration except Fe and Mn. The geochemical analyses suggest that rock-water interaction is controlling the hydro-geochemistry while the chemical constituent of the groundwater is mainly controlled by carbonate weathering with limited contribution from silicate weathering. The isotopic signatures revealed that the Son river is recharging groundwater while the groundwater is contributing to the Ganges river. A clear pattern of fast vertical recharge in the arsenic contaminated area is observed in the proximity to the river Ganges with an elevated nitrate concentration resulted from the reduced As dissolution. The origin of groundwater is local precipitation with low to high evaporation enrichment effect which is further indicating the vertical mixing of groundwater from the irrigation return flow and/or recharge from domestic discharge causing enhanced As mobilization through microbial assisted reductive dissolution of As-bearing minerals.

Bhendi Yellow Vein Mosaic Virus and Bhendi Yellow Vein Mosaic Betasatellite Cause Enation Leaf Curl Disease and Alter Host Phytochemical Contents in Okra.

Whitefly (Bemisia tabaci)-transmitted begomoviruses cause severe diseases in numerous economically important dicotyledonous plants. Okra enation leaf curl disease (OELCuD) has emerged as a serious threat to okra (Abelmoschus esculentus L. Moench) cultivation in the Indian subcontinent. This study reports the association of a monopartite begomovirus (bhendi yellow vein mosaic virus; BYVMV) and betasatellite (bhendi yellow vein mosaic betasatellite; BYVB) with OELCuD in the Mau region of Uttar Pradesh, India. The BYVMV alone inoculated Nicotiana benthamiana and A. esculentus cv. Pusa Sawani plants developed mild symptoms. Co-inoculation of BYVMV and BYVB resulted in a reduced incubation period, an increased symptom severity, and an enhanced BYVMV accumulation by Southern hybridization and quantitative real-time PCR. This is the first study that satisfies Koch's postulates for OELCuD in its natural host. Activities of various antioxidative enzymes were significantly increased in the virus-inoculated okra plants. Differential responses in various biochemical components (such as photosynthetic pigments, phenol, proline, and sugar) in diseased okra plants were observed. This change in phytochemical responses is significant in understanding its impact on virus pathogenesis and disease development.

Two distinct monopartite begomovirus-betasatellite complexes in western India cause tomato leaf curl disease.

In India, begomovirus infection causing tomato leaf curl disease (ToLCD) is a major constraint for tomato productivity. Here, we have identified two distinct monopartite begomovirus and betasatellite complexes causing ToLCD in the western part of India. A new monopartite begomovirus (Tomato leaf curl Mumbai virus, ToLCMumV) and betasatellite (Tomato leaf curl Mumbai betasatellite, ToLCMumB) were isolated from the Mumbai sample. A distinct Tomato leaf curl Gandhinagar virus (ToLCGanV) and Tomato leaf curl Gandhinagar betasatellite (ToLCGanB) were identified from the Gandhinagar sample. Both of the cloned begomoviruses were recombinants. The demonstration of systemic infection caused by begomovirus (ToLCGanV or ToLCMumV) alone in N. benthamiana and tomato (a virus resistant variety) emphasizes that they were monopartite begomoviruses. Co-inoculation of cognate begomovirus and betasatellite reduces the incubation period and increases symptom severity. Thus, Koch's postulates were satisfied for these virus complexes. Further, an enhanced accumulation of ToLCGanV was detected in the presence of cognate ToLCGanB, however ToLCMumB did not influence the level of ToLCMumV in the agro-inoculated tomato plants. Our results indicate that the cloned viruses form potential virus resistance breaking disease complexes in India. This necessitates to investigate the spread of these disease complexes to major tomato growing regions in the country.

A novel monopartite begomovirus and satellites associated with yellow mosaic disease of Sida spp. in India.

Begomoviruses (family Geminiviridae) cause severe diseases in many economically important crops and non-cultivated plants in the warmer regions of the world. Non-cultivated weeds have been reported to act as natural virus reservoirs. In January 2016, Sida plants with yellow mosaic symptoms were found at the edge of an agricultural field in Gujarat, India. Sequence analysis of the viral genomic components cloned from a diseased Sida plant indicated the presence of a distinct monopartite begomovirus (proposed as sida yellow mosaic Gujarat virus) along with a betasatellite (ludwigia leaf distortion betasatellite) and an alphasatellite (malvastrum yellow mosaic alphasatellite). Our results emphasize that this weed may harbor a begomovirus-alphasatellite-betasatellite complex. This host serves as a potential source of virus inoculum, which can be transmitted by whiteflies to other cultivated crops.

STrategically Acquired Gradient Echo (STAGE) imaging, part III: Technical advances and clinical applications of a rapid multi-contrast multi-parametric brain imaging method.

One major thrust in radiology today is image standardization with a focus on rapidly acquired quantitative multi-contrast information. This is critical for multi-center trials, for the collection of big data and for the use of artificial intelligence in evaluating the data. Strategically acquired gradient echo (STAGE) imaging is one such method that can provide 8 qualitative and 7 quantitative pieces of information in 5 min or less at 3 T. STAGE provides qualitative images in the form of proton density weighted images, T1 weighted images, T2* weighted images and simulated double inversion recovery (DIR) images. STAGE also provides quantitative data in the form of proton spin density, T1, T2* and susceptibility maps as well as segmentation of white matter, gray matter and cerebrospinal fluid. STAGE uses vendors' product gradient echo sequences. It can be applied from 0.35 T to 7 T across all manufacturers producing similar results in contrast and quantification of the data. In this paper, we discuss the strengths and weaknesses of STAGE, demonstrate its contrast-to-noise (CNR) behavior relative to a large clinical data set and introduce a few new image contrasts derived from STAGE, including DIR images and a new concept referred to as true susceptibility weighted imaging (tSWI) linked to fluid attenuated inversion recovery (FLAIR) or tSWI-FLAIR for the evaluation of multiple sclerosis lesions. The robustness of STAGE T1 mapping was tested using the NIST/NIH phantom, while the reproducibility was tested by scanning a given individual ten times in one session and the same subject scanned once a week over a 12-week period. Assessment of the CNR for the enhanced T1W image (T1WE) showed a significantly better contrast between gray matter and white matter than conventional T1W images in both patients with Parkinson's disease and healthy controls. We also present some clinical cases using STAGE imaging in patients with stroke, metastasis, multiple sclerosis and a fetus with ventriculomegaly. Overall, STAGE is a comprehensive protocol that provides the clinician with numerous qualitative and quantitative images.

Quantitative Flow Imaging in Human Umbilical Vessels In Utero Using Nongated 2D Phase Contrast MRI.

BACKGROUND: Volumetric assessment of afferent blood flow rate provides a measure of global organ perfusion. Phase-contrast magnetic resonance imaging (PCMRI) is a reliable tool for volumetric flow quantification, but given the challenges with motion and lack of physiologic gating signal, such studies, in vivo on the human placenta, are scant. PURPOSE: To evaluate and apply a nongated (ng) PCMRI technique for quantifying blood flow rates in utero in umbilical vessels. STUDY TYPE: Prospective study design. STUDY POPULATION: Twenty-four pregnant women with median gestational age (GA) 30 4/7 weeks and interquartile range (IQR) 8 1/7 weeks. FIELD STRENGTH/SEQUENCE: All scans were performed on a 3.0T Siemens Verio system using the ng-PCMRI technique. ASSESSMENT: The GA-dependent increase in umbilical vein (UV) and arterial (UA) flow was compared to previously published values. Systematic error to be expected from ng-PCMRI, in the context of pulsatile UA flow and partial voluming, was studied through Monte-Carlo simulations, as a function of resolution and number of averages. STATISTICAL TESTS: Correlation between the UA and UV was evaluated using a generalized linear model. RESULTS: Simulations showed that ng-PCMRI measurement variance reduced by increasing the number of averages. For vessels on the order of 2 voxels in radius, partial voluming led to 10% underestimation in the flow. In fetuses, the average flow rates in UAs and UV were measured to be 203 ± 80 ml/min and 232 ± 92 ml/min and the normalized average flow rates were 140 ± 59 ml/min/kg and 155 ± 57 ml/min/kg, respectively. Excellent correlation was found between the total arterial flow vs. corresponding venous flow, with a slope of 1.08 (P = 0.036). DATA CONCLUSION: Ng-PCMRI can provide accurate volumetric flow measurements in utero in the human umbilical vessels. Care needs to be taken to ensure sufficiently high-resolution data are acquired to minimize partial voluming-related errors. LEVEL OF EVIDENCE: 2 Technical Efficacy Stage 1 J. Magn. Reson. Imaging 2017.

Magnetic resonance angiography of fetal vasculature at 3.0 T.

Magnetic resonance angiography has not been used much previously for visualizing fetal vessels in utero for reasons that include a contraindication for the use of exogenous contrast agents, maternal respiratory motion and fetal motion. In this work, we report the feasibility of using an appropriately modified clinical time-of-flight magnetic resonance imaging sequence for non-contrast angiography of human fetal and placental vessels at 3.0 T. Using this 2D angiography technique, it is possible to visualize fetal vascular networks in late pregnancy. KEY POINTS: • 3D-visualization of fetal vasculature is feasible using non-contrast MRA at 3.0 T. • Visualization of placental vasculature is also possible with this method. • Fetal MRA can serve as a vascular localizer for quantitative MRI studies. • This method can be extended to 1.5 T.

Evidence for presence of mismatch repair gene expression positive Lynch syndrome cases in India.

Lynch syndrome (LS), the most common form of familial CRC predisposition that causes tumor onset at a young age, is characterized by the presence of microsatellite instability (MSI) in tumors due to germline inactivation of mismatch repair (MMR) system. Two MMR genes namely MLH1 and MSH2 account for majority of LS cases while MSH6 and PMS2 may account for a minor proportion. In order to identify MMR genes causing LS in India, we analyzed MSI and determined expression status of the four MMR genes in forty eight suspected LS patient colorectal tumor samples. Though a majority exhibited MSI, only 58% exhibited loss of MMR expression, a significantly low proportion compared to reports from other populations. PCR-DNA sequencing and MLPA-based mutation and exonic deletion/duplication screening respectively, revealed genetic lesions in samples with and without MMR gene expression. Interestingly, tumor samples with and without MMR expression exhibited significant differences with respect to histological (mucin content) and molecular (instability exhibited by mononucleotide microsatellites) features. The study has revealed for the first time a significant proportion of LS tumors not exhibiting loss of MMR expression.

Biodegradation of Toluene Under Seasonal and Diurnal Fluctuations of Soil-Water Temperature.

An increasing interest in bioremediation of hydrocarbon polluted sites raises the question of the influence of seasonal and diurnal changes on soil-water temperature on biodegradation of BTEX, a widespread group of (sub)-surface contaminants. Therefore, we investigated the impact of a wide range of varying soil-water temperature on biodegradation of toluene under aerobic conditions. To see the seasonal impact of temperature, three sets of batch experiments were conducted at three different constant temperatures: 10°C, 21°C, and 30°C. These conditions were considered to represent (1) winter, (2) spring and/or autumn, and (3) summer seasons, respectively, at many polluted sites. Three additional sets of batch experiments were performed under fluctuating soil-water temperature cases (21<>10°C, 30<>21°C, and 10<>30°C) to mimic the day-night temperature patterns expected during the year. The batches were put at two different temperatures alternatively to represent the day (high-temperature) and night (low-temperature) times. The results of constant- and fluctuating-temperature experiments show that toluene degradation is strongly dependent on soil-water temperature level. An almost two-fold increase in toluene degradation time was observed for every 10°C decrease in temperature for constant-temperature cases. Under fluctuating-temperature conditions, toluene degraders were able to overcome the temperature stress and continued thriving during all considered weather scenarios. However, a slightly longer time was taken compared to the corresponding time at daily mean temperature conditions. The findings of this study are directly useful for bioremediation of hydrocarbon-polluted sites having significant diurnal and seasonal variations of soil-water temperature.