Neuronal Population Encoding of Identity in Primate Prefrontal Cortex

The ventrolateral prefrontal cortex (VLPFC) shows robust activation during the perception of faces and voices. However, little is known about what categorical features of social stimuli drive neural activity in this region. Since perception of identity and expression are critical social functions, we examined whether neural responses to naturalistic stimuli were driven by these two categorical features in the prefrontal cortex. We recorded single neurons in the VLPFC, while two male rhesus macaques (Macaca mulatta) viewed short audiovisual videos of unfamiliar conspecifics making expressions of aggressive, affiliative, and neutral valence. Of the 285 neurons responsive to the audiovisual stimuli, 111 neurons had a main effect (two-way ANOVA) of identity, expression, or their interaction in their stimulus-related firing rates; however, decoding of expression and identity using single-unit firing rates rendered poor accuracy. Interestingly, when decoding from pseudo-populations of recorded neurons, the accuracy for both expression and identity increased with population size, suggesting that the population transmitted information relevant to both variables. Principal components analysis of mean population activity across time revealed that population responses to the same identity followed similar trajectories in the response space, facilitating segregation from other identities. Our results suggest that identity is a critical feature of social stimuli that dictates the structure of population activity in the VLPFC, during the perception of vocalizations and their corresponding facial expressions. These findings enhance our understanding of the role of the VLPFC in social behavior.

Multiplexed Host-Induced Gene Silencing of Aspergillus flavus Genes Confers Aflatoxin Resistance in Groundnut

Aflatoxins are immunosuppressive and carcinogenic secondary metabolites, produced by the filamentous ascomycete Aspergillus flavus, that are hazardous to animal and human health. In this study, we show that multiplexed host-induced gene silencing (HIGS) of Aspergillus flavus genes essential for fungal sporulation and aflatoxin production (nsdC, veA, aflR, and aflM) confers enhanced resistance to Aspergillus infection and aflatoxin contamination in groundnut (<20 ppb). Comparative proteomic analysis of contrasting groundnut genotypes (WT and near-isogenic HIGS lines) supported a better understanding of the molecular processes underlying the induced resistance and identified several groundnut metabolites that might play a significant role in resistance to Aspergillus infection and aflatoxin contamination. Fungal differentiation and pathogenicity proteins, including calmodulin, transcriptional activator-HacA, kynurenine 3-monooxygenase 2, VeA, VelC, and several aflatoxin pathway biosynthetic enzymes, were downregulated in Aspergillus infecting the HIGS lines. Additionally, in the resistant HIGS lines, a number of host resistance proteins associated with fatty acid metabolism were strongly induced, including phosphatidylinositol phosphate kinase, lysophosphatidic acyltransferase-5, palmitoyl-monogalactosyldiacylglycerol Δ-7 desaturase, ceramide kinase-related protein, sphingolipid Δ-8 desaturase, and phospholipase-D. Combined, this knowledge can be used for groundnut pre-breeding and breeding programs to provide a safe and secure food supply.

CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects

Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.

Loss-of-function of triacylglycerol lipases are associated with low flour rancidity in pearl millet [Pennisetum glaucum (L.) R. Br.]

Pearl millet is an important cereal crop of semi-arid regions since it is highly nutritious and climate resilient. However, pearl millet is underutilized commercially due to the rapid onset of hydrolytic rancidity of seed lipids post-milling. We investigated the underlying biochemical and molecular mechanisms of rancidity development in the flour from contrasting inbred lines under accelerated aging conditions. The breakdown of storage lipids (triacylglycerols; TAG) was accompanied by free fatty acid accumulation over the time course for all lines. The high rancidity lines had the highest amount of FFA by day 21, suggesting that TAG lipases may be the cause of rancidity. Additionally, the high rancidity lines manifested substantial amounts of volatile aldehyde compounds, which are characteristic products of lipid oxidation. Lipases with expression in seed post-milling were sequenced from low and high rancidity lines. Polymorphisms were identified in two TAG lipase genes (PgTAGLip1 and PgTAGLip2) from the low rancidity line. Expression in a yeast model system confirmed these mutants were non-functional. We provide a direct mechanism to alleviate rancidity in pearl millet flour by identifying mutations in key TAG lipase genes that are associated with low rancidity. These genetic variations can be exploited through molecular breeding or precision genome technologies to develop elite pearl millet cultivars with improved flour shelf life.

Graph deep network for optic disc and optic cup segmentation for glaucoma disease using retinal imaging

The fundus imaging method of eye screening detects eye diseases by segmenting the optic disc (OD) and optic cup (OC). OD and OC are still challenging to segment accurately. This work proposes three-layer graph-based deep architecture with an enhanced fusion method for OD and OC segmentation. CNN encoder-decoder architecture, extended graph network, and approximation via fusion-based rule are explored for connecting local and global information. A graph-based model is developed for combining local and overall knowledge. By extending feature masking, regularization of repetitive features with fusion for combining channels has been done. The performance of the proposed network is evaluated through the analysis of different metric parameters such as dice similarity coefficient (DSC), intersection of union (IOU), accuracy, specificity, sensitivity. Experimental verification of this methodology has been done using the four benchmarks publicly available datasets DRISHTI-GS, RIM-ONE for OD, and OC segmentation. In addition, DRIONS-DB and HRF fundus imaging datasets were analyzed for optimizing the model's performance based on OD segmentation. DSC metric of methodology achieved 0.97 and 0.96 for DRISHTI-GS and RIM-ONE, respectively. Similarly, IOU measures for DRISHTI-GS and RIM-ONE datasets were 0.96 and 0.93, respectively, for OD measurement. For OC segmentation, DSC and IOU were measured as 0.93 and 0.90 respectively for DRISHTI-GS and 0.83 and 0.82 for RIM-ONE data. The proposed technique improved value of metrics with most of the existing methods in terms of DSC and IOU of the results metric of the experiments for OD and OC segmentation.

Pearl Millet Aquaporin Gene PgPIP2;6 Improves Abiotic Stress Tolerance in Transgenic Tobacco

Pearl millet [Pennisetum glaucum (L) R. Br.] is an important cereal crop of the semiarid tropics, which can withstand prolonged drought and heat stress. Considering an active involvement of the aquaporin (AQP) genes in water transport and desiccation tolerance besides several basic functions, their potential role in abiotic stress tolerance was systematically characterized and functionally validated. A total of 34 AQP genes from P. glaucum were identified and categorized into four subfamilies, viz., plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin-26-like intrinsic proteins (NIPs), and small basic intrinsic proteins (SIPs). Sequence analysis revealed that PgAQPs have conserved characters of AQP genes with a closer relationship to sorghum. The PgAQPs were expressed differentially under high vapor pressure deficit (VPD) and progressive drought stresses where the PgPIP2;6 gene showed significant expression under high VPD and drought stress. Transgenic tobacco plants were developed by heterologous expression of the PgPIP2;6 gene and functionally characterized under different abiotic stresses to further unravel their role. Transgenic tobacco plants in the T2 generations displayed restricted transpiration and low root exudation rates in low- and high-VPD conditions. Under progressive drought stress, wild-type (WT) plants showed a quick or faster decline of soil moisture than transgenics. While under heat stress, PgPIP2;6 transgenics showed better adaptation to heat (40°C) with high canopy temperature depression (CTD) and low transpiration; under low-temperature stress, they displayed lower transpiration than their non-transgenic counterparts. Cumulatively, lower transpiration rate (Tr), low root exudation rate, declined transpiration, elevated CTD, and lower transpiration indicate that PgPIP2;6 plays a role under abiotic stress tolerance. Since the PgPIP2;6 transgenic plants exhibited better adaptation against major abiotic stresses such as drought, high VPD, heat, and cold stresses by virtue of enhanced transpiration efficiency, it has the potential to engineer abiotic stress tolerance for sustained growth and productivity of crops.

Optical coherence tomography versus angiography to guide percutaneous intervention: a real-world single center propensity-matched analysis

Funding Acknowledgements

Type of funding sources: None.

Background

Optical coherence tomography (OCT) with its superior resolution has several benefits over coronary angiography (CA) to guide percutaneous coronary intervention (PCI).  Despite the benefits of OCT in comparison with angiography, it is not widely used in developing countries like India data is limited in India specifically in all comer population to meet unmet need.

Objective

Here we aim to determine the clinical efficacy and safety outcomes of OCT versus CA alone in guiding PCI in all-comer patients.

Methods

This was a retrospective study which included 434 all comer patients which were propensity matched. These patients underwent PCI at our center between December 2018 and June 2020.  The primary endpoint was MACE, a composite of cardiovascular death, repeat revascularization, stent thrombosis, recurrent ischemia and target vessel myocardial infarction (TV-MI) at 6 months. Secondary endpoint was target lesion failure (TLF), composite of stent thrombosis and in-stent restenosis. Safety endpoints were post-PCI s. creatinine and hospital stay and other outcome includes post PCI rise in CK-MB.

Results

A total of 217 patients were included in each group: the OCT group and conventional angiography guided PCI (angio group) after propensity matching. Compared to angio group, patients presenting with unstable angina, NSTEMI were significantly higher in the OCT group (55.7% vs 43.3%, p = 0.0095; 17.5% vs 10%, p = 0.02, respectively) while patients with STEMI were significantly low in the OCT (23.5% vs 41.5%, p = 0.00005). Number of balloons, maximum balloon size and left main interventions and contrast volume were more in OCT group than angio group (4.21 ± 1.67 vs 3.86 ± 1.76, P= 0.0034; 3.77 ± 0.63 mm vs 3.51 ± 0.52 mm,P &lt; 0.0001; 24.52% vs 13.36 %,P = 0.003 and 202.53 ± 73.15 ml vs 161.91 ± 69.23 ml, P&lt; 0.0001 respectively). The incidence of MACE at 6 months was numerically lower in the OCT group vs angio group but the difference was not statistically significant (15 [6.9%] vs 21 [9.7%]; p = 0.2964). No cases of TV-MI, TLF (stent thrombosis or in-stent restenosis) is observed in both the groups. Post procedure rise in CKMB was more in Angio group in comparison to OCT group (6.16 ± 31.28 ng/ml vs 39.5 ± 108.71 ng/ml, p &lt; 0.001). Optimal stent expansion (&gt;80%) was seen in 71.5% patients in post OCT-guided PCI. In OCT guided PCI group, OCT identified stent underexpansion in 28.5%, stent malapposition in 3.7%, stent edge dissection in 4.1%, and tissue prolapse in 10% of the patients.

Conclusion

In this large retrospective study, OCT guided PCI is feasible and OCT-guided PCI has tendency to improve clinical outcomes at six months follow up compared to conventional angiography guided PCI in all comer patients. Abstract Figure. central illustration  Abstract Figure. Identification of PCI complications

Functional characterization of late embryogenesis abundant genes and promoters in pearl millet (Pennisetum glaucum L.) for abiotic stress tolerance

Late embryogenesis abundant (LEA) genes display distinct functions in response to abiotic stresses in plants. In pearl millet (Pennisetum glaucum L.), a total of 21 PgLEA genes were identified and classified into six groups including LEA1, LEA2, LEA3, LEA5, LEA7, and dehydrins (DHN). Open reading frames (ORFs) of PgLEAs range from 291 bp (PgLEA1-1) to 945 bp (PgLEA2-11) and distributed randomly among the seven chromosomes. Phylogenetic analysis revealed that all PgLEA proteins are closely related to sorghum LEA proteins. The PgLEAs were found to be expressed differentially under high progressive vapor pressure deficit (VPD), PgLEA7 was significantly expressed under high VPD and was selected for functional validation. In silico analysis of the PgLEA promoter regions revealed abiotic stress-specific cis-acting elements such as ABRE, CCAAT, MYBS, and LTRE. Based on the type of motifs, PgLEAPC promoter (758 bp), its deletion 1 (PgLpd1, 349 bp) and deletion 2 (PgLpd2, 125 bp) were cloned into the plant expression vector pMDC164 having the promoter-less uidA gene. All the three plant expression vectors were introduced into tobacco through Agrobacterium tumefaciens-mediated transformation to obtain T₁ and T₂ generations of transgenic plants. Based on expression of the uidA gene, tissue-specific expression was observed in mature stems, roots and seedlings of PgLEAPC and PgLpd1 carrying transgenics only. While the transgenic PgLEAPC plants displayed significantly higher uidA expression in the stem and root tissues under salt, drought, heat, and cold stresses, very low or no expression was observed in PgLpd1 and PgLpd2 transgenics under the tested stress conditions. The results of this study indicate that the complete promoter of PgLEAPC plays a role in developing abiotic stress tolerance in plants.

Precision Postbiotics and Mental Health: the Management of Post-COVID-19 Complications

The health catastrophe originated by COVID-19 pandemic construed profound impact on a global scale. However, a plethora of research studies corroborated convincing evidence conferring severity of infection of SARS-CoV-2 with the aberrant gut microbiome that strongly speculated its importance for development of novel therapeutic modalities. The intense exploration of probiotics has been envisaged to promote the healthy growth of the host, and restore intestinal microecological balance through various metabolic and physiological processes. The demystifying effect of probiotics cannot be defied, but there exists a strong skepticism related to their safety and efficacy. Therefore, molecular signature of probiotics termed as "postbiotics" are of paramount importance and there is continuous surge of utilizing postbiotics for enhancing health benefits, but little is explicit about their antiviral effects. Therefore, it is worth considering their prospective role in post-COVID regime that pave the way for exploring the pastoral vistas of postbiotics. Based on previous research investigations, the present article advocates prospective role of postbiotics in alleviating the health burden of viral infections, especially SARS-CoV-2. The article also posits current challenges and proposes a futuristic model describing the concept of "precision postbiotics" for effective therapeutic and preventive interventions that can be used for management of this deadly disease.

Bio-mimetic synthesis of catalytically active nano-silver using Bos taurus (A-2) urine

Herein we have synthesized silver nanoparticles (Ag NPs) using liquid metabolic waste of Bos taurus (A-2 type) urine. Various bio-molecules present in cow urine, are effectively used to reduce silver (Ag) ions into silver nanoparticles in one step. This is bio-inspired electron transfer to Ag ion for the formation of base Ag metal and is fairly prompt and facile. These nanoparticles act as a positive catalyst for various organic transformation reactions. The structural, morphological, and optical properties of the as-synthesized Ag NPs are widely characterized by X-ray diffraction spectroscopy, ultraviolet–visible spectroscopy, scanning electron microscope, Fourier transmission infra-red spectroscopy, and atomic force microscopy. The as-synthesized bio-mimetic Ag NPs show potential activity for several reduction reactions of nitro groups. The Ag NPs were also used for degradation of hazardous dyes such as Methylene blue and Crystal violet with good degradation rate constant.

Translating Fear Circuitry: Amygdala Projections to Subgenual and Perigenual Anterior Cingulate in the Macaque

Rodent fear-learning models posit that amygdala–infralimbic connections facilitate extinction while amygdala–prelimbic prefrontal connections mediate fear expression. Analogous amygdala–prefrontal circuitry between rodents and primates is not established. Using paired small volumes of neural tracers injected into the perigenual anterior cingulate cortex (pgACC; areas 24b and 32; a potential homologue to rodent prelimbic cortex) and subgenual anterior cingulate cortex (sgACC, areas 25 and 14c; a potential homologue to rodent infralimbic cortex) in a single hemisphere, we mapped amygdala projections to the pgACC and sgACC within single subjects. All injections resulted in dense retrograde labeling specifically within the intermediate division of the basal nucleus (Bi) and the magnocellular division of the accessory basal nucleus (ABmc). Areal analysis revealed a bias for connectivity with the sgACC, with the ABmc showing a greater bias than the Bi. Double fluorescence analysis revealed that sgACC and pgACC projections were intermingled within the Bi and ABmc, where a proportion were double labeled. We conclude that amygdala inputs to the ACC largely originate from the Bi and ABmc, preferentially connect to the sgACC, and that a subset collaterally project to both sgACC and pgACC. These findings advance our understanding of fear extinction and fear expression circuitry across species.

Natural antioxidants for neuroinflammatory disorders and possible involvement of Nrf2 pathway: A review

The transcription factor Nrf2 (nuclear factor-erythroid 2 p45-related factor 2) play a crucial role in cellular redox and metabolic system. Activation of Nrf2 may be an effective therapeutic approach for neuroinflammatory disorders, through activation of antioxidant defences system, lower the inflammation, line up the mitochondrial function, and balancing of protein homeostasis. Various recent studies revealed that many of active substance obtained from plants have been found to activate the Nrf2 and to exert neuroprotective effects in various experimental models, raising the possibility that activation of Nrf2 may be an effective therapeutic approaches for neuroinflammatory disorders. The objective of this review was to evaluate the neuroprotective property of natural substance against neuroinflammatory disorders by reviewing the studies done till today. The outcomes of various in vitro and in vivo examinations have shown that natural compounds producing neuroprotective effects in neuronal system via activation of Nrf2. Herein, we also reviewed the studies to understand the role of Nrf2 for curing CNS disorders. Here we can conclude, herbal/natural moieties having potency to fight and prevent from neuroinflammatory disorders due to their abilities to activate Nrf2 pathway.

Functional characterization of the promoter of pearl millet heat shock protein 10 (PgHsp10) in response to abiotic stresses in transgenic tobacco plants

In the present study, the promoter region of the pearl millet heat shock protein 10 (PgHsp10) gene was cloned and characterized. The PgHsp10 promoter (PgHsp10pro) sequence region has all the cis-motifs required for tissue and abiotic stress inducibility. The complete PgHsp10pro (PgHsp10PC) region and a series of 5' truncations of PgHsp10 (PgHsp10D1 and PgHsp10D2) and an antisense form of PgHsp10pro (PgHsp10AS) were cloned into a plant expression vector (pMDC164) through gateway cloning. All four constructs were separately transformed into tobacco through Agrobacterium-mediated genetic transformation, and PCR-confirmed transgenic plants progressed to T1 and T2 generations. The T2 transgenic tobacco plants comprising all PgHsp10pro fragments were used for GUS histochemical and qRT-PCR assays in different tissues under control and abiotic stresses. The PgHsp10PC pro expression was specific to stem and seedlings under control conditions. Under different abiotic stresses, particularly heat stress, PgHsp10PCpro had relatively higher activity than PgHsp10D1pro, PgHsp10D2pro and PgHsp10ASpro. PgHsp10pro from a stress resilient crop like pearl millet responds positively to a range of abiotic stresses, in particular heat, when expressed in heterologous plant systems such as tobacco. Hence, PgHsp10pro appears to be a potential promoter candidate for developing heat and drought stress-tolerant crop plants.

Gut-organ axis: a microbial outreach and networking

Human gut microbiota (GM) includes a complex and dynamic population of microorganisms that are crucial for well-being and survival of the organism. It has been reported as diverse and relatively stable with shared core microbiota, including Bacteroidetes and Firmicutes as the major dominants. They are the key regulators of body homeostasis, involving both intestinal and extra-intestinal effects by influencing many physiological functions such as metabolism, maintenance of barrier homeostasis, inflammation and hematopoiesis. Any alteration in GM community structures not only trigger gut disorders but also influence other organs and cause associated diseases. In recent past, the GM has been defined as a 'vital organ' with its involvement with other organs; thus, establishing a link or a bi- or multidirectional communication axis between the organs via neural, endocrine, immune, humoral and metabolic pathways. Alterations in GM have been linked to several diseases known to humans; although the exact interaction mechanism between the gut and the organs is yet to be defined. In this review, the bidirectional relationship between the gut and the vital human organs was envisaged and discussed under several headings. Furthermore, several disease symptoms were also revisited to redefine the communication network between the gut microbes and the associated organs.

Sleep apnea detection from ECG using variational mode decomposition

Sleep apnea is a pervasive breathing problem during night sleep, and its repetitive occurrence causes various health problems. Polysomnography is commonly used for apnea screening which is an expensive, time-consuming, and complex process. In this paper, a simple but efficient technique based on the variational mode decomposition (VMD) for automated detection of sleep apnea from single-lead ECG is proposed. The heart rate variability and ECG-derived respiration signals obtained from ECG are decomposed into different modes using the VMD, and these modes are used for extracting different features including spectral entropies, interquartile range, and energy. The principal component analysis is employed to reduce the dimension of the feature vector. The experiments are conducted using the Apnea-ECG dataset, and the classification performance of various classifiers is investigated. In per-segment classification, an accuracy of about 87.5% (Sens: 84.9%, Spec: 88.2%) is achieved using the K-nearest neighbor classifier. In per-recording classification, the proposed technique using the linear discriminant analysis model outperformed the existing apnea detection approaches by achieving the accuracy of 100%. The algorithm also provided the best agreement between the estimated and reference apnea-hypopnea index (AHI) values. These results show that the algorithm has the potential to be used for home-based apnea screening systems.

An update and perspectives on the use of promoters in plant genetic engineering

Genetically engineered plants have varied applications in agriculture for enhancing the values of food and feed. Genetic engineering aims to introduce selected genetic regions with desirable traits into target plants for both spatial and temporal expressions. Promoters are the key elements responsible for regulating gene expressions by modulating the transcription factors (TFs) through recognition of RNA polymerases. Based on their recognition and expression, RNA polymerases were categorized into RNA pol II and pol III promoters. Promoter activity and specificity are the two prime parameters in regulating the transgene expression. Since the use of constitutive promoters like Cauliflower mosaic virus (CaMV) 35S may lead to adverse effects on nontarget organisms or ecosystem, inducible/tissue specific promoters and/or the RNA pol III promoters provide myriad opportunities for gene expressions with controlled regulation and with minimum adverse effects. Besides their role in transgene expression, their influence in synthetic biology and genome editing are also discussed. This review provides an update on the importance, current prospects, and insight into the advantages and disadvantages of promoters reported thus far would help to utilize them in the endeavour to develop nutritionally and agronomically improved transgenic crops for commercialization.

Isolation and functional characterization of three abiotic stress-inducible (Apx, Dhn and Hsc70) promoters from pearl millet (Pennisetum glaucum L.)

Pearl millet is a C4 cereal crop that grows in arid and semi-arid climatic conditions with the remarkable abiotic stress tolerance. It contributed to the understanding of stress tolerance not only at the physiological level but also at the genetic level. In the present study, we functionally cloned and characterized three abiotic stress-inducible promoters namely cytoplasmic Apx1 (Ascorbate peroxidase), Dhn (Dehydrin), and Hsc70 (Heat shock cognate) from pearl millet. Sequence analysis revealed that all three promoters have several cis-acting elements specific for temporal and spatial expression. PgApx pro, PgDhn pro and PgHsc70 pro were fused with uidA gene in Gateway-based plant transformation pMDC164 vector and transferred into tobacco through leaf-disc method. While PgApx pro and PgDhn pro were active in seedling stages, PgHsc70 pro was active in stem and root tissues of the T2 transgenic tobacco plants under control conditions. Higher activity was observed under high temperature and drought, and less in salt and cold stress conditions. Further, all three promoters displayed higher GUS gene expression in the stem, moderate expression in roots, and less expression in leaves under similar conditions. While RT-qPCR data showed that PgApx pro and PgDhn pro were expressed highly in high temperature, salt and drought, PgHsc70 pro was fairly expressed during high temperature stress only. Histochemical and RT-qPCR assays showed that all three promoters are inducible under abiotic stress conditions. Thus, these promoters appear to be immediate candidates for developing abiotic stress tolerant crops as these promoter-driven transgenics confer high degree of tolerance in comparison with the wild-type (WT) plants.

Clinical Profile, Risk Factors and Outcomes in Patients with Cerebral Venous Sinus Thrombosis: A Study from Western India

AIM

Study of cause and clinical profile of venous sinus thrombosis in Western India.

SETTINGS AND DESIGN

A retrospective study was conducted to ascertain the clinical profile, etiology, and follow up of patients with venous sinus thrombosis.

METHODS AND MATERIAL

Hospital database of patients suffering from venous sinus thrombosis from two tertiary care hospitals in West India were studied. A telephonic follow up was taken for assessment of outcome. Inclusion criteria were a) Age more than 15 years of age b) clinically symptomatic patients c) Diagnosis confirmed by Magnetic resonance Venography (MRV) or CT Venography (CT Venography) Exclusion criteria: Patients with infarct in arterial territory, hypertensive hemorrhage, metabolic encephalopathy and eclampsia were excluded from the study.

STATISTICAL ANALYSIS USED

Descriptive statistic was performed as frequency, mean and standard deviation or percentages. Difference in continuous variables was evaluated by using independent t-test while chi-square test was performed in categorical variables. Statistical P<0.05 was considered statistically significant.

RESULTS

We conducted a retrospective study of patients with venous sinus thrombosis in Rajasthan in western India. Out of 71 patients in our study group the mean age of presentation was 36.64 years. 42 patients were male (59.2%) and 29 were female (40.8%). Only 9 patients (12.6%) had pregnancy or puerperium related venous sinus thrombosis. The most common presenting feature was headache 47/71(66.2), followed by seizures 33 (46.5%), paresis 20/71 (28.16%) and coma 15/71(21.1%). MRI Brain recorded infarcts in 32/71 patients and predominant hemorrhage was recorded in 34/71. 4 cases were associated with malignancy (one CNS, one outside CNS and 2 hematological). Raised homocysteine level was found in 26/35 (74.3%) patients in whom they were measured. 9 patients had moderately elevated homocysteine levels (15-30), another 9 had intermediate values (31-64) and 5 patients had elevated homocysteine level >65. Hyperhomocysteinemia was the commonest causative factor and was far more common in men (21/25) than in women (5/10). (p value 0.019). 24 out of 71 patients were found to be anemic (33.8%). Anemia was far more common in women than in men. (p value .002). Protein C level was found abnormal in 5/27 patients, Protein S in 6/27 patients and Anti thrombin III in 1/23 patient studied respectively. History of oral contraceptive intake was recorded in only a minority of women with venous sinus thrombosis 7(24.1%) compared to the western data where most of the venous sinus thrombosis are related to the contraceptive pills.

CONCLUSION

The clinical presentation of venous sinus thrombosis in tertiary care centers is changing outside the traditional peurperium / pregnancy related venous sinus thrombosis. Common risk factors include hyperhomocysteinemia, anemia, coagulopathy, pregnancy related, vasculitis, malignancy and oral contraceptive usage. Male involvement was far more common than females and was usually associated with a higher level of homocysteine.

Comprehensive evaluation of candidate reference genes for real-time quantitative PCR (RT-qPCR) data normalization in nutri-cereal finger millet [Eleusine Coracana (L.)]

Finger millet (Eleusine coracana L.) is an annual herbaceous self-pollinating C4 cereal crop of the arid and semi-arid regions of the world. Finger millet is a food security crop proven to have resilience to changing climate and scores very high in nutrition. In the current study, we have assessed sixteen candidate reference genes for their appropriateness for the normalization studies in finger millet subjected to experimental regimes and treatments. Ten candidate reference genes (GAPDH, β-TUB, CYP, EIF4α, TIP41, UBC, G6PD, S24, MACP and MDH) were cloned and six (ACT, ELF1α, PP2A, PT, S21 and TFIID) were mined from the NCBI database as well as from the literature. Expression stability ranking of the finger millet reference genes was validated using four different statistical tools i.e., geNorm, NormFinder, BestKeeper, ΔCt and RefFinder. From the study, we endorse MACP, CYP, EIF4α to be most stable candidate reference genes in all 'tissues', whereas PT, TFIID, MACP ranked high across genotypes, β-TUB, CYP, ELF1α were found to be best under abiotic stresses and 'all samples set'. The study recommends using minimum of two reference genes for RT-qPCR data normalizations in finger millet. All in all, CYP, β-TUB, and EF1α, in combination were found to be best for robust normalizations under most experimental conditions. The best and the least stable genes were validated for confirmation by assessing their appropriateness for normalization studies using EcNAC1 gene. The report provides the first comprehensive list of suitable stable candidate reference genes for nutritional rich cereal finger millet that will be advantageous to gene expression studies in this crop.

Detection of Wolbachia Phage (WO) in Indian Lac Insect [Kerria lacca (Kerr.)] and Its Implications

Wolbachia, a maternally inherited bacterium induces reproductive alterations in its hosts such as feminization of males, male killing and parthenogenesis. It is the most diverse endosymbiont infecting more than 70% of the insects ranging from pests to pollinators. Kerria lacca-a hemipteran is a sedentary, oriental insect known to produce lac-the only resin of animal origin. The present study was conducted to screen the presence of Wolbachia and its associated phages in the two infrasubspecific forms (four insect lines) of K. lacca viz. kusmi and rengeeni differing from each other on the basis of host preference. Wolbachia and its associated phage were found to be prevalent in all the insect lines analyzed. We, hereby, report the presence of WO-phage (Wolbachia phage) for the first time in K. lacca. Further, phylogenetic data differentiated the kusmi and rengeeni infrasubspecific forms into two different groups on the basis of WO-phage sequences.

A novel mitochondrial orf147 causes cytoplasmic male sterility in pigeonpea by modulating aberrant anther dehiscence

KEY MESSAGE

A novel open reading frame (ORF) identified and cloned from the A4 cytoplasm of Cajanus cajanifolius induced partial to complete male sterility when introduced into Arabidopsis and tobacco. Pigeonpea (Cajanus cajan L. Millsp.) is the only legume known to have commercial hybrid seed technology based on cytoplasmic male sterility (CMS). We identified a novel ORF (orf147) from the A4 cytoplasm of C. cajanifolius that was created via rearrangements in the CMS line and co-transcribes with the known and unknown sequences. The bi/poly-cistronic transcripts cause gain-of-function variants in the mitochondrial genome of CMS pigeonpea lines having distinct processing mechanisms and transcription start sites. In presence of orf147, significant repression of Escherichia coli growth indicated its toxicity to the host cells and induced partial to complete male sterility in transgenic progenies of Arabidopsis thaliana and Nicotiana tabacum where phenotype co-segregated with the transgene. The male sterile plants showed aberrant floral development and reduced lignin content in the anthers. Gene expression studies in male sterile pigeonpea, Arabidopsis and tobacco plants confirmed down-regulation of several anther biogenesis genes and key genes involved in monolignol biosynthesis, indicative of regulation of retrograde signaling. Besides providing evidence for the involvement of orf147 in pigeonpea CMS, this study provides valuable insights into its function. Cytotoxicity and aberrant programmed cell death induced by orf147 could be important for mechanism underlying male sterility that offers opportunities for possible translation for these findings for exploiting hybrid vigor in other recalcitrant crops as well.

Peanuts that keep aflatoxin at bay: a threshold that matters

Aflatoxin contamination in peanuts poses major challenges for vulnerable populations of sub-Saharan Africa and South Asia. Developing peanut varieties to combat preharvest Aspergillus flavus infection and resulting aflatoxin contamination has thus far remained a major challenge, confounded by highly complex peanut-Aspergilli pathosystem. Our study reports achieving a high level of resistance in peanut by overexpressing (OE) antifungal plant defensins MsDef1 and MtDef4.2, and through host-induced gene silencing (HIGS) of aflM and aflP genes from the aflatoxin biosynthetic pathway. While the former improves genetic resistance to A. flavus infection, the latter inhibits aflatoxin production in the event of infection providing durable resistance against different Aspergillus flavus morphotypes and negligible aflatoxin content in several peanut events/lines well. A strong positive correlation was observed between aflatoxin accumulation and decline in transcription of the aflatoxin biosynthetic pathway genes in both OE-Def and HIGS lines. Transcriptomic signatures in the resistant lines revealed key mechanisms such as regulation of aflatoxin synthesis, its packaging and export control, besides the role of reactive oxygen species-scavenging enzymes that render enhanced protection in the OE and HIGS lines. This is the first study to demonstrate highly effective biotechnological strategies for successfully generating peanuts that are near-immune to aflatoxin contamination, offering a panacea for serious food safety, health and trade issues in the semi-arid regions.

ECG-derived respiration based on iterated Hilbert transform and Hilbert vibration decomposition

Monitoring of the respiration using the electrocardiogram (ECG) is desirable for the simultaneous study of cardiac activities and the respiration in the aspects of comfort, mobility, and cost of the healthcare system. This paper proposes a new approach for deriving the respiration from single-lead ECG based on the iterated Hilbert transform (IHT) and the Hilbert vibration decomposition (HVD). The ECG signal is first decomposed into the multicomponent sinusoidal signals using the IHT technique. Afterward, the lower order amplitude components obtained from the IHT are filtered using the HVD to extract the respiration information. Experiments are performed on the Fantasia and Apnea-ECG datasets. The performance of the proposed ECG-derived respiration (EDR) approach is compared with the existing techniques including the principal component analysis (PCA), R-peak amplitudes (RPA), respiratory sinus arrhythmia (RSA), slopes of the QRS complex, and R-wave angle. The proposed technique showed the higher median values of correlation (first and third quartile) for both the Fantasia and Apnea-ECG datasets as 0.699 (0.55, 0.82) and 0.57 (0.40, 0.73), respectively. Also, the proposed algorithm provided the lowest values of the mean absolute error and the average percentage error computed from the EDR and reference (recorded) respiration signals for both the Fantasia and Apnea-ECG datasets as 1.27 and 9.3%, and 1.35 and 10.2%, respectively. In the experiments performed over different age group subjects of the Fantasia dataset, the proposed algorithm provided effective results in the younger population but outperformed the existing techniques in the case of elderly subjects. The proposed EDR technique has the advantages over existing techniques in terms of the better agreement in the respiratory rates and specifically, it reduces the need for an extra step required for the detection of fiducial points in the ECG for the estimation of respiration which makes the process effective and less-complex. The above performance results obtained from two different datasets validate that the proposed approach can be used for monitoring of the respiration using single-lead ECG.

Molecular insights into the functional role of nitric oxide (NO) as a signal for plant responses in chickpea

The molecular mechanisms and targets of nitric oxide (NO) are not fully known in plants. Our study reports the first large-scale quantitative proteomic analysis of NO donor responsive proteins in chickpea. Dose response studies carried out using NO donors, sodium nitroprusside (SNP), diethylamine NONOate (DETA) and S-nitrosoglutathione (GSNO) in chickpea genotype ICCV1882, revealed a dose dependent positive impact on seed germination and seedling growth. SNP at 0.1mM concentration proved to be most appropriate following confirmation using four different chickpea genotypes. while SNP treatment enhanced the percentage of germination, chlorophyll and nitrogen contents in chickpea, addition of NO scavenger, cPTIO reverted its impact under abiotic stresses. Proteome profiling revealed 172 downregulated and 76 upregulated proteins, of which majority were involved in metabolic processes (118) by virtue of their catalytic (145) and binding (106) activity. A few crucial proteins such as S-adenosylmethionine synthase, dehydroascorbate reductase, pyruvate kinase fragment, 1-aminocyclopropane-1-carboxylic acid oxidase, 1-pyrroline-5-carboxylate synthetase were less abundant whereas Bowman-Birk type protease inhibitor, non-specific lipid transfer protein, chalcone synthase, ribulose-1-5-bisphosphate carboxylase oxygenase large subunit, PSII D2 protein were highly abundant in SNP treated samples. This study highlights the protein networks for a better understanding of possible NO induced regulatory mechanisms in plants.

Molecular cloning and expression analysis of Aquaporin genes in pearl millet [Pennisetum glaucum (L) R. Br.] genotypes contrasting in their transpiration response to high vapour pressure deficits

Pearl millet is a crop of the semi-arid tropics having high degree of genetic diversity and variable tolerance to drought stress. To investigate drought tolerance mechanism that possibly accounts for differences in drought tolerance, four recombinant inbred lines from a high resolution cross (HRC) were selected for variability in their transpiration rate (Tr) response to vapour pressure deficit (VPD) conditions. The differential Tr response of the genotypes to increased VPD conditions was used to classify the genotypes as sensitive or insensitive to high VPD. Aquaporin (AQP) genes PgPIP1;1, PgPIP1;2, PgPIP2;1, PgPIP2;3, PgPIP2;6, PgTIP1;1 and PgTIP2;2 were cloned. Phylogenetic analysis revealed that the cloned PgAQPs were evolutionarily closer to maize AQPs than to rice. PgAQP genes, including PgPIP1;1 and PgPIP2;6 in root tissue showed a significant expression pattern with higher expression in VPD-insensitive genotypes than VPD-sensitive genotypes under low VPD conditions (1.2kPa) i.e when there is no high evaporative demand from the atmosphere. PgAQP genes (PgPIP2;1 in leaf and root tissues; PgPIP1;2 and PgTIP2;2 in leaf and PgPIP2;6 in root) followed a diurnal rhythm in leaves and roots that have either higher or lower expression levels at different time intervals. Under high VPD conditions (4.21kPa), PgPIP2;3 showed higher transcript abundance in VPD-insensitive genotypes, and PgPIP2;1 in VPD-sensitive genotypes, while rest of the PgAQPs showed differential expression. Our current hypothesis is that these differences in the expression of AQP genes under different VPDs suggests a role of the AQPs in tuning the water transport pathways with variation between genotypes.

Nitric Oxide (NO) in Plant Heat Stress Tolerance: Current Knowledge and Perspectives

High temperature is one of the biggest abiotic stress challenges for agriculture. While, Nitric oxide (NO) is gaining increasing attention from plant science community due to its involvement in resistance to various plant stress conditions, its implications on heat stress tolerance is still unclear. Several lines of evidence indicate NO as a key signaling molecule in mediating various plant responses such as photosynthesis, oxidative defense, osmolyte accumulation, gene expression, and protein modifications under heat stress. Furthermore, the interactions of NO with other signaling molecules and phytohormones to attain heat tolerance have also been building up in recent years. Nevertheless, deep insights into the functional intermediaries or signal transduction components associated with NO-mediated heat stress signaling are imperative to uncover their involvement in plant hormone induced feed-back regulations, ROS/NO balance, and stress induced gene transcription. Although, progress is underway, much work remains to define the functional relevance of this molecule in plant heat tolerance. This review provides an overview on current status and discuss knowledge gaps in exploiting NO, thereby enhancing our understanding of the role of NO in plant heat tolerance.

Multilocation field trials for risk assessment of a combination fungicide Fluopicolide + Propamocarb in tomato

Dissipation kinetics of two systemic fungicides, namely fluopicolide and propamocarb used as a combination formulation (Infinito 68.75 SC), were studied on tomato at four different locations by the All India Network Project on Pesticide Residues to recommend their pre-harvest interval (PHI) and to propose the maximum residue limits (MRL) for the two fungicides based on chronic hazard exposure assessment. The combination fungicide was sprayed thrice at the recommended dosage of 93.75 g a.i./ha fluopicolide and 937.50 g a.i./ha propamocarb as well as at double the recommended dosage of 187.50 g a.i./ha fluopicolide and 1875.0 g a.i./ha propamocarb on tomato crops and the residues were monitored periodically by GC-MS. The fungicides dissipated to below the limit of quantification (LOQ) within 10 to 15 days, with a half-life of 2-4 days for fluopicolide and 1-2 days for propamocarb. Taking into consideration the MRLs of codex and calculations made using the method of MRL fixation of the Food Safety and Standard Authority of India (FSSAI) as well as the Organization for Economic Co-operation and Development (OECD) calculator, MRL of 5 mg/kg is proposed for fluopicolide and 15 mg/kg for propamocarb, following critical exposure of the commodity considering PHI of 1 day.

Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization

Accurate and reliable gene expression data from qPCR depends on stable reference gene expression for potential gene functional analyses. In this study, 15 reference genes were selected and analyzed in various sample sets including abiotic stress treatments (salt, cold, water stress, heat, and abscisic acid) and tissues (leaves, roots, seedlings, panicle, and mature seeds). Statistical tools, including geNorm, NormFinder and RefFinder, were utilized to assess the suitability of reference genes based on their stability rankings for various sample groups. For abiotic stress, PP2A and CYP were identified as the most stable genes. In contrast, EIF4α was the most stable in the tissue sample set, followed by PP2A; PP2A was the most stable in all the sample set, followed by EIF4α. GAPDH, and UBC1 were the least stably expressed in the tissue and all the sample sets. These results also indicated that the use of two candidate reference genes would be sufficient for the optimization of normalization studies. To further verify the suitability of these genes for use as reference genes, SbHSF5 and SbHSF13 gene expression levels were normalized using the most and least stable sorghum reference genes in root and water stressed-leaf tissues of five sorghum varieties. This is the first systematic study of the selection of the most stable reference genes for qPCR-related assays in Sorghum bicolor that will potentially benefit future gene expression studies in sorghum and other closely related species.

Behavior and bioefficacy of tribenuron-methyl in wheat (Triticum astevum L.) under irrigated agro-ecosystem in India

Possible bioaccumulation of pesticides in crop produce may cause ill effects on animals and humans. Tribenuron-methyl is a new post-emergence herbicide and is highly efficient to control the broad-leaf weeds in cereals, pasture, and plantation crops. There are scarce studies on its bioefficacy, sensitivity to weeds, tolerance to wheat, and persistence in crop produce, which are important information required before recommending an herbicide for use by the farmers. Weed control efficiency of an herbicide is dose-sensitive and site/soil-specific. Tribenuron-methyl (75% DF) was applied at 22.5 and 45.0 g a.i./ha along with the surfactant 300.12 mL/ha as a tank mixes after 30 days of sowing in wheat as post-emergence herbicide. The samples of wheat foliage, soil, and grains at harvest were processed and analyzed for residues by high-performance liquid chromatography using a UV detector at 240 nm. The study revealed that there was a significant reduction in weed population and dry matter accumulation due to tribenuron-methyl application at a higher dose (45.0 g/ha) compared to a lower dose (of 22.5 g/ha). The weed density was found to be from 16.1 to 44.3 no/m(2) for application rate of 22.5 g/ha while at the 45.0 g/ha application, the weed density was 5.3-5.9 as compared to untreated control, where 184.3-120.5 no/m(2) was observed. The yield varied from 4.30 to 4.80 t/ha as compared to 2.25-3.55 t/ha in unweeded control with the LSD value being 21.5-16.3 to 0.27-0.19. Residues were below detectable level (BDL, <0.005 mg/kg) of tribenuron-methyl since they were detected in wheat grains at 22.5 g a.i./ha rates. However, 0.012 μg/g residues were detected in wheat foliage at an application rate of 45.0 g a.i./ha. It can be concluded that it is safe to use tribenuron-methyl at 22.5 g a.i./ha on wheat crop as post-emergence herbicide.

NO to drought-multifunctional role of nitric oxide in plant drought: Do we have all the answers?

Nitric oxide (NO) is a versatile gaseous signaling molecule with increasing significance in plant research due to its association with various stress responses. Although, improved drought tolerance by NO is associated greatly with its ability to reduce stomatal opening and oxidative stress, it can immensely influence other physiological processes such as photosynthesis, proline accumulation and seed germination under water deficit. NO as a free radical can directly alter proteins, enzyme activities, gene transcription, and post-translational modifications that benefit functional recovery from drought. The present drought-mitigating strategies have focused on exogenous application of NO donors for exploring the associated physiological and molecular events, transgenic and mutant studies, but are inadequate. Considering the biphasic effects of NO, a cautious deployment is necessary along with a systematic approach for deciphering positively regulated responses to avoid any cytotoxic effects. Identification of NO target molecules and in-depth analysis of its effects under realistic field drought conditions should be an upmost priority. This detailed synthesis on the role of NO offers new insights on its functions, signaling, regulation, interactions and co-existence with different drought-related events providing future directions for exploiting this molecule towards improving drought tolerance in crop plants.

Reverse Transcriptase in Action: FRET-Based Assay for Monitoring Flipping and Polymerase Activity in Real Time

Reverse transcriptase (RT) of human immunodeficiency virus-1 (HIV-1) is a multifunctional enzyme that catalyzes the conversion of the single stranded viral RNA genome into double-stranded DNA, competent for host-cell integration. RT is endowed with RNA- and DNA-dependent DNA polymerase activity and DNA-directed RNA hydrolysis (RNase H activity). As a key enzyme of reverse transcription, RT is a key target of currently used highly active antiretroviral therapy (HAART), though RT inhibitors offer generally a poor resistance profile, urging new RT inhibitors to be developed. Using single molecule fluorescence approaches, it has been recently shown that RT binding orientation and dynamics on its substrate play a critical role in its activity. Currently, most in vitro RT activity assays, inherently end-point measurements, are based on the detection of reaction products by using radio-labeled or chemically modified nucleotides. Here, we propose a simple and continuous real-time Förster resonance energy transfer (FRET) based-assay for the direct measurement of RT's binding orientation and polymerase activity, with the use of conventional steady-state fluorescence spectroscopy. Under our working conditions, the change in binding orientation and the primer elongation step can be visualized separately on the basis of their opposite fluorescence changes and their different kinetics. The assay presented can easily discriminate non-nucleoside RT inhibitors from nucleoside RT inhibitors and determine reliably their potency. This one-step and one-pot assay constitutes an improved alternative to the currently used screening assays to disclose new anti-RT drugs and identify at the same time the class to which they belong.

Dissipation pattern and risk assessment of flubendiamide on chili at different agro-climatic conditions in India

Dissipation pattern and risk assessment of flubendiamide and its metabolite (desiodo flubendiamide) on chili were studied at four different agro-climatic locations of India at the standard and double dose at 60 and 120 g a.i. ha(-1) at 10 days interval. Quantification of residues was done on a high-performance liquid chromatograph (HPLC) with a photo diode array detector. The limit of quantification (LOQ) of this method was found to be 0.01 mg kg(-1) while limit of detection (LOD) being 0.003 mg kg(-1). Residues of flubendiamide were found to be below the determination limit in 15 days at both the dosages in all locations. Half-life of flubendiamide when applied at 60 and 120 g a.i. ha(-1) ranged from 0.85 to 1.80 and from 0.95 to 2.79 days, respectively. On the basis of data generated under the All India Network Project on Pesticide Residues, a preharvest interval (PHI) of 1 day has been recommended and the flubendiamide 480 SC has been registered for use on chili in India by the Central Insecticide Board and Registration Committee, Ministry of Agriculture, Government of India. The maximum residue limit (MRL) of flubendiamide on chili has been fixed by the Food Safety Standard Authority of India, Ministry of Health and Family Welfare, Government of India, as 0.02 μg g(-1) after its risk assessment.

Molecular Cloning and Differential Expression of Cytosolic Class I Small Hsp Gene Family in Pennisetum glaucum (L.)

Small heat shock protein (Hsp) family genes have been reported in several plant species that function as molecular chaperones to protect proteins from being denatured in extreme conditions. As a first step towards the isolation and characterization of genes that contribute to combating abiotic stresses particularly heat stress, construction and screening of the subtracted complementary DNA (cDNA) library is reported here. In this study, a subtractive heat stress cDNA library was constructed that was used to isolate members of small Hsps (sHsps) using PgsHsp17.9A gene as a probe. As a result, a total of 150 cDNA clones were isolated from the subtracted cDNA library screening, leading to 121 high-quality expressed sequence tags (ESTs), with an average size of 450 bp, comprising of 15 contigs, and majority of these isolated sHsp genes belong to cytosolic class I (CI) family. In silico sequence analysis of CI-sHsp family genes revealed that the length of sHsp proteins varied from 151 to 159 amino acids and showed large variation in isoelectric point value (5.03 to 10.05) and a narrow range of molecular weight (16.09 to 17.94 kDa). The real-time PCR results demonstrated that CI-sHsp genes are differentially expressed in Pennisetum leaves under different abiotic stress conditions particularly at high temperature. The results presented in this study provide basic information on PgCI-sHsp family genes and form the foundation for future functional studies of these genes.

DREB1A overexpression in transgenic chickpea alters key traits influencing plant water budget across water regimes

We demonstrate the role of DREB1A transcription factor in better root and shoot partitioning and higher transpiration efficiency in transgenic chickpea under drought stress Chickpea (Cicer arietinum L.) is mostly exposed to terminal drought stress which adversely influences its yield. Development of cultivars for suitable drought environments can offer sustainable solutions. We genetically engineered a desi-type chickpea variety to ectopically overexpress AtDREB1A, a transcription factor known to be involved in abiotic stress response, driven by the stress-inducible Atrd29A promoter. From several transgenic events of chickpea developed by Agrobacterium-mediated genetic transformation, four single copy events (RD2, RD7, RD9 and RD10) were characterized for DREB1A gene overexpression and evaluated under water stress in a biosafety greenhouse at T6 generation. Under progressive water stress, all transgenic events showed increased DREB1A gene expression before 50 % of soil moisture was lost (50 % FTSW or fraction of transpirable soil water), with a faster DREB1A transcript accumulation in RD2 at 85 % FTSW. Compared to the untransformed control, RD2 reduced its transpiration in drier soil and higher vapor pressure deficit (VPD) range (2.0-3.4 kPa). The assessment of terminal water stress response using lysimetric system that closely mimics the soil conditions in the field, showed that transgenic events RD7 and RD10 had increased biomass partitioning into shoot, denser rooting in deeper layers of soil profile and higher transpiration efficiency than the untransformed control. Also, RD9 with deeper roots and RD10 with higher root diameter showed that the transgenic events had altered rooting pattern compared to the untransformed control. These results indicate the implicit influence of rd29A::DREB1A on mechanisms underlying water uptake, stomatal response, transpiration efficiency and rooting architecture in water-stressed plants.

Persistence and risk assessment of spiromesifen on tomato in India: a multilocational study

Supervised field trials were conducted at four different agro-climatic locations of India to evaluate the dissipation pattern and risk assessment of spiromesifen on tomato. Spiromesifen 240 SC was sprayed on tomato at 150 and 300 g a.i. ha(-1). Samples of tomato fruits were drawn at 0, 1, 3, 5, 7, 10 and 15 days after treatment and soil at 15 days after treatment. Quantification of residues was done on gas chromatograph-mass spectrophotometer in selective ion monitoring mode in the mass range of 271-274 (m/z). The limit of quantification of the method was found to be 0.05 mg kg(-1), while the limit of determination was 0.015 mg kg(-1). Residues were found below the LOQ of 0.05 mg kg(-1) in 10 days at both the doses of application at all the locations. Spiromesifen dissipated with a half-life of 0.93-1.38 days at the recommended rate of application and 1.04-1.34 days at the double the rate of application. Residues of spiromesifen in soil were detectable level (<0.05 mg kg(-1)) after 15 days of treatment. A preharvest interval (PHI) of 1 day has been recommended on tomato on the basis of data generated under All India Network Project on Pesticide Residues. Spiromesifen 240 SC has been registered for its use on tomato by Central Insecticide Board and Registration Committee, Ministry of Agriculture, Government of India. The maximum residue limit (MRL) of spiromesifen on tomato has been fixed by Food Safety Standard Authority of India, Ministry of Health and Family Welfare, Government of India as 0.3 μg/g after its risk assessment.

Residual behavior and risk assessment of flubendiamide on tomato at different agro-climatic conditions in India

Supervised field trials were conducted at four different agro-climatic zones in India to evaluate the dissipation pattern and risk assessment of flubendiamide on tomato. Flubendiamide 480 SC was sprayed on tomato at 48 and 96 g active ingredient (a.i.) ha(-1). Samples of tomato fruits were drawn at 0, 1, 3, 5, 7, 10, 15, and 20 days after treatment. Quantification of residues was done on a high-performance liquid chromatography (HPLC) device with a photo diode array detector. The limit of quantification (LOQ) of this method was found to be 0.01 mg kg(-1) while limit of detection (LOD) being 0.003 mg kg(-1). Residues of flubendiamide were found below the determination limit of 0.01 mg kg(-1) in 20 days at both the dosages in all the locations. The half-life of flubendiamide at an application rate of 48 g a.i. ha(-1) varied from 0.33 to 3.28 days and at 48-g a.i. ranged from 1.21 to 3.00 days. On the basis of data generated under the All India Network Project on Pesticide Residues, a preharvest interval (PHI) of 1 day has been recommended, and the flubendiamide 480 SC has been registered for its use on tomato by the Central Insecticide Board and Registration Committee, Ministry of Agriculture, Government of India. The maximum residue limit (MRL) of flubendiamide on tomato has been fixed by the Ministry of Health and Family Welfare, Government of India under Food Safety Standard Authority of India, as 0.07 μg g(-1) after its risk assessment.

Safety evaluation of flubendiamide and its metabolites on cabbage and persistence in soil in different agroclimatic zones of India

Supervised field trials following good agricultural practices were conducted at the research farms of four agricultural universities located at four different agroclimatic zones of India to evaluate the persistence and dissipation of flubendiamide and its metabolite, des-iodo flubendiamide, on cabbage. Two spray applications of flubendiamide 480 SC of standard and double dose at the rate of 24 and 48 g a.i. ha(-1) were given to the crop at a 15-day interval, and the residues of flubendiamide 2 h after spray were found in the range of 0.107-0.33 and 0.20-0.49 mg kg(-1) at respective doses. Residue of des-iodo flubendiamide was not detected in any cabbage sample during study period. No residues were found in the soil samples collected from all treated fields after 15 days of application. On the basis of data generated under All India Network Project on Pesticide Residues, a preharvest interval (PHI) of 10 days has been recommended, and the flubendiamide 480 SC has been registered for its use on cabbage by Central Insecticide Board and Registration Committee, Ministry of Agriculture, Government of India. The maximum residue limit (MRL) of flubendiamide on cabbage has been fixed by the Ministry of Health and Family Welfare, Government of India, under Food Safety Standard Authority of India as 0.05 μg/g after its risk assessment.

Changes in timing of water uptake and phenology favours yield gain in terminal water stressed chickpea AtDREB1A transgenics

Terminal drought causes major yield loss in chickpea, so it is imperative to identify genotypes with best suited adaptive traits to secure yield in terminal drought-prone environments. Here, we evaluated chickpea (At) rd29A:: (At) DREB1A transgenic events (RD2, RD7, RD9 and RD10) and their untransformed C235 genotype for growth, water use and yield under terminal water-stress (WS) and well-watered (WW) conditions. The assessment was made across three lysimetric trials conducted in contained environments in the greenhouse (2009GH and 2010GH) and the field (2010F). Results from the greenhouse trials showed genotypic variation for harvest index (HI), yield, temporal pattern of flowering and seed filling, temporal pattern of water uptake across crop cycle, and transpiration efficiency (TE) under terminal WS conditions. The mechanisms underlying the yield gain in the WS transgenic events under 2009GH trial was related to conserving water for the reproductive stage in RD7, and setting seeds early in RD10. Water conservation also led to a lower percentage of flower and pod abortion in both RD7 and RD10. Similarly, in the 2010GH trial, reduced water extraction during vegetative stage in events RD2, RD7 and RD9 was critical for better seed filling in the pods produced from late flowers in RD2, and reduced percentage of flower and pod abortion in RD2 and RD9. However, in the 2010F trial, the increased seed yield and HI in RD9 compared with C235 came along only with small changes in water uptake and podding pattern, probably not causal. Events RD2 (2010GH), RD7 (2010GH) and RD10 (2009GH) with higher seed yield also had higher TE than C235. The results suggest that DREB1A, a transcription factor involved in the regulation of several genes of abiotic stress response cascade, influenced the pattern of water uptake and flowering across the crop cycle, leading to reduction in the percentage of flower and pod abortion in the glasshouse trials.

An efficient and economical method for extraction of DNA amenable to biotechnological manipulations, from diverse soils and sediments

AIMS

An attempt was made to optimize a new protocol for isolation of pure metagenomic DNA from soil samples.

METHODS AND RESULTS

Various chemicals (FeCl3 , MgCl2 , CaCl2 and activated charcoal) were tested for their efficacy in isolation of metagenomic DNA from different soil and compost samples. Among these trials, charcoal and MgCl2 when used in combination yielded highly pure DNA free from humic acids and other contaminants. The DNA extracted with the optimized protocol was readily digested, amplified and cloned. Moreover, compared with a well-established commercial DNA isolation kit (UltraClean™ Soil DNA Isolation Kit), our method for DNA isolation was found to be economical. This demonstrated that the method developed can be applied to a wide variety of soil samples and allows handling of multiple samples at a given time.

CONCLUSIONS

The optimized protocol developed has successfully yielded pure metagenomic DNA amenable to biotechnological manipulations.

SIGNIFICANCE AND IMPACT OF THE STUDY

A user-friendly and economical protocol for isolation of DNA from soil and compost samples has been developed.

Three new species of Kerria (Hemiptera: Coccoidea: Tachardiidae) from India

Three new species of Kerria Targioni-Tozzetti from India, namely Kerria pennyae Ahmad & Ramamurthy sp. nov. on Schleichera oleosa from Orissa, Kerria dubeyi Ahmad & Ramamurthy sp. nov. on Ficus bengalensis from Bangalore and Kerria varshneyi Ahmad & Ramamurthy sp. nov. on Ziziphus mauritiana from Punjab are described and illustrated, and a key is provided to species of Kerria known from India.

Evaluation and validation of reference genes for normalization of quantitative real-time PCR based gene expression studies in peanut

The quantitative real-time PCR (qPCR) based techniques have become essential for gene expression studies and high-throughput molecular characterization of transgenic events. Normalizing to reference gene in relative quantification make results from qPCR more reliable when compared to absolute quantification, but requires robust reference genes. Since, ideal reference gene should be species specific, no single internal control gene is universal for use as a reference gene across various plant developmental stages and diverse growth conditions. Here, we present validation studies of multiple stably expressed reference genes in cultivated peanut with minimal variations in temporal and spatial expression when subjected to various biotic and abiotic stresses. Stability in the expression of eight candidate reference genes including ADH3, ACT11, ATPsyn, CYP2, ELF1B, G6PD, LEC and UBC1 was compared in diverse peanut plant samples. The samples were categorized into distinct experimental sets to check the suitability of candidate genes for accurate and reliable normalization of gene expression using qPCR. Stability in expression of the references genes in eight sets of samples was determined by geNorm and NormFinder methods. While three candidate reference genes including ADH3, G6PD and ELF1B were identified to be stably expressed across experiments, LEC was observed to be the least stable, and hence must be avoided for gene expression studies in peanut. Inclusion of the former two genes gave sufficiently reliable results; nonetheless, the addition of the third reference gene ELF1B may be potentially better in a diverse set of tissue samples of peanut.

Three new species of Kerria (Hemiptera: Sternorrhyncha: Coccoidea: Tachardiidae), a redesciption of K. yunnanensis Ou & Hong, and a revised key to species of Kerria

Three new species of lac insect, Kerria Targioni-Tozzetti viz., Kerria manipurensis Ahmad & Ramamurthy sp. nov., Kerria maduraiensis Ahmad & Ramamurthy sp. nov., and Kerria thrissurensis Ahmad & Ramamurthy sp. nov. are described and illustrated. Kerria yunnanensis Ou & Hong is illustrated and redescribed, and a key to the known species of Kerria is provided. The usefulness of star pores as a diagnostic character in the subgeneric divisions of Kerria is also discussed.

DREB1A promotes root development in deep soil layers and increases water extraction under water stress in groundnut

Water deficit is a major yield-limiting factor for many crops, and improving the root system has been proposed as a promising breeding strategy, although not in groundnut (Arachis hypogaea L.). The present work was carried out mainly to assess how root traits are influenced under water stress in groundnut, whether transgenics can alter root traits, and whether putative changes lead to water extraction differences. Several transgenic events, transformed with DREB1A driven by the rd29 promoter, along with wild-type JL24, were tested in a lysimeter system that mimics field conditions under both water stress (WS) and well-watered (WW) conditions. The WS treatment increased the maximum rooting depth, although the increase was limited to about 20% in JL24, compared to 50% in RD11. The root dry weight followed a similar trend. Consequently, the root dry weight and length density of transgenics was higher in layers below 100-cm depth (Exp. 1) and below 30 cm (Exp. 2). The root diameter was unchanged under WS treatment, except a slight increase in the 60-90-cm layer. The root diameter increased below 60 cm in both treatments. In the WW treatment, total water extraction of RD33 was higher than in JL24 and other transgenic events, and somewhat lower in RD11 than in JL24. In the WS treatment, water extraction of RD2, RD11 and RD33 was higher than in JL24. These water extraction differences were mostly apparent in the initial 21 days after treatment imposition and were well related to root length density in the 30-60-cm layer (R(2) = 0.68), but not to average root length density. In conclusion, water stress promotes rooting growth more strongly in transgenic events than in the wild type, especially in deep soil layers, and this leads to increased water extraction. This opens an avenue for tapping these characteristics toward the improvement of drought adaptation in deep soil conditions, and toward a better understanding of genes involved in rooting in groundnut.