De-novo Hybrid Protein Design for Biodegradation of Organophosphate Pesticides

Garima Awasthi,Ruchi Yadav,Prachi Srivastava 한국미생물·생명공학회 2019 한국미생물·생명공학회지 Vol.47 No.2

In the present investigation, we attempted to design a protocol to develop a hybrid protein with better bioremediation capacity. Using in silico approaches, a Hybrid Open Reading Frame (Hybrid ORF) is developed targeting the genes of microorganisms known for degradation of organophosphates. Out of 21 genes identified through BLAST search, 8 structurally similar genes (opdA, opd, opaA, pte RO, pdeA, parC, mpd and phnE) involved in biodegradation were screened. Gene conservational analysis categorizes these organophosphates degrading 8 genes into 4 super families i.e., Metallo-dependent hydrolases, Lactamase B, MPP and TM_PBP2 superfamily. Hybrid protein structure was modeled using multi-template homology modeling (3S07_A; 99%, 1P9E_A; 98%, 2ZO9_B; 33%, 2DXL_A; 33%) by Schrödinger software suit version 10.4.018. Structural verification of protein models was done using Ramachandran plot, it was showing 96.0% residue in the favored region, which was verified using RAMPAGE. The phosphotriesterase protein was showing the highest structural similarity with hybrid protein having raw score 984. The 5 binding sites of hybrid protein were identified through binding site prediction. The docking study shows that hybrid protein potentially interacts with 10 different organophosphates. The study results indicate that the hybrid protein designed has the capability of degrading a wide range of organophosphate compounds.

VARIOUS TYPES OF WELL-POSEDNESS FOR MIXED VECTOR QUASIVARIATIONAL-LIKE INEQUALITY USING BIFUNCTIONS

Garima Virmani,Manjari Srivastava 한국전산응용수학회 2014 Journal of applied mathematics & informatics Vol.32 No.3

In this paper, we investigate the α-well-posedness and α-L- well-posedness for a mixed vector quasivariational-like inequality using bifunctions. Some characterizations are derived for the above mentioned well-posedness concepts. The concepts of α-well-posedness and α-L-well- posedness in the generalized sense are also given and similar characteriza- tions are derived.. In this paper, we investigate the α-well-posedness and α-L- well-posedness for a mixed vector quasivariational-like inequality using bifunctions. Some characterizations are derived for the above mentioned well-posedness concepts. The concepts of α-well-posedness and α-L-well- posedness in the generalized sense are also given and similar characteriza- tions are derived.

Wine Quality Classification with Multilayer Perceptron

Garima Agrawal,Dae-Ki Kang 한국인터넷방송통신학회 2018 International Journal of Internet, Broadcasting an Vol.10 No.2

This paper is about wine quality classification with multilayer perceptron using the deep neural network. Wine complexity is an issue when predicting the quality. And the deep neural network is considered when using complex dataset. Wine Producers always aim high to get the highest possible quality. They are working on how to achieve the best results with minimum cost and efforts. Deep learning is the possible solution for them. It can help them to understand the pattern and predictions. Although there have been past researchers, which shows how artificial neural network or data mining can be used with different techniques, in this paper, rather not focusing on various techniques, we evaluate how a deep learning model predicts for the quality using two different activation functions. It will help wine producers to decide, how to lead their business with deep learning. Prediction performance could change tremendously with different models and techniques used. There are many factors, which, impact the quality of the wine. Therefore, it is a good idea to use best features for prediction. However, it could also be a good idea to test this dataset without separating these features. It means we use all features so that the system can consider all the feature. In the experiment, due to the limited data set and limited features provided, it was not possible for a system to choose the effective features.

RNAi-based transgene conferred extreme resistance to the geminivirus causing apical leaf curl disease in potato

Garima Tomar,S. K. Chakrabarti,Nitya Nanda Sharma,A. Jeevalatha,S. Sundaresha,Kanika Vyas,Wamik Azmi 한국식물생명공학회 2018 Plant biotechnology reports Vol.12 No.3

Potato apical leaf curl disease is an emerging geminiviral disease in tropics and subtropics. It was reported for the first time in the year 1999 in northern plains of India but quickly spread to almost all potato growing regions of the country largely due to prevalence of warmer weather during early crop growth, thereby favoring whitefly vector. The problem of apical leaf curl disease in India became more severe due to lack of seed indexing for this virus in conventional seed production scheme. Although it accounts for major yield loss, there is no conventional source of resistance available in potato against Tomato Leaf Curl New Delhi Virus-Potato (ToLCNDV-Potato) that causes this disease in potato. In the present study, we have investigated the potential use of RNAi for obtaining resistance against this DNA virus in potato. The replication-associated protein gene (AC1) of the virus was used to obtain pathogen-derived resistance. The AC1 gene was PCR amplified from field-infected potato leaves, cloned and sequenced (JN393309). It showed 93% sequence similarity with the AC1 gene of Tomato Leaf Curl Virus-New Delhi (TOLCV-NDe; DQ169056) virus. Transgenic plants encoding the AC1 gene in three different orientations, viz. sense, antisense and hairpin loop, were raised. Transgenic lines when challenge inoculated with ToLCNDV-Potato showed different levels of resistance for all three constructs. Transgene integration and copy number in selected transgenic lines were determined by qPCR and further confirmed by Southern blot analysis. Though a reduction in viral titer was observed in transgenic lines encoding either antisense or hairpin loop constructs of AC1 gene, the latter transgenics showed most significant results as shown by reduction in the level of symptom expression in glasshouse screening as well as real-time data of in vivo virus concentration. In fact, we obtained a few totally asymptomatic transgenic lines with hairpin loop strategy.

Detection of nerve fibers in the eutopic endometrium of women with endometriosis, uterine fibroids and adenomyosis

( Garima Yadav ),( Meenakshi Rao ),( Meenakshi Gothwal ),( Pratibha Singh ),( Priyanka Kathuria ),( Prem Prakash Sharma ) 대한산부인과학회 2021 Obstetrics & Gynecology Science Vol.64 No.5

Objective The primary objective of this study was to establish the presence of nerve fibers in the eutopic endometrium of women with endometriosis and to determine whether these nerve fibers are exclusive to endometriosis or are also found in other pelvic pathologies associated with dysmenorrhea. Methods Endometrial tissue was obtained by aspiration (Pipelle), endometrial curettage, or following hysterectomy in women with endometriosis confirmed through histopathological examination, leiomyomas, and adenomyosis. The eutopic endometrium was subjected to immunohistochemical staining to detect PGP 9.5, which is a highly specific pan-neuronal marker. The nerve fiber density was correlated with the patient’s pain score, as indicated by the Visual Analog Scale. A control group was formed by staining the endometrium of women presenting with dysmenorrhea but without the above-mentioned disorders. Results Nerve fibers were observed in sections of the endo-myometrium (in the deep endometrium) in 68% of patients with endometriosis who underwent hysterectomy or a deep endometrial biopsy. Nerve fibers were not observed in the aspirated endometrium of women with endometriosis. Only 13.7% of women with adenomyosis and 3.3% of women with fibroids had nerve fibers in their endometrium. Nerve fiber density was correlated with pain score in women with endometriosis. Conclusion Nerve fibers were found in the functional layer of eutopic endometrium in women with endometriosis; hence, we concluded that the presence of nerve fibers in the eutopic endometrium could diagnose endometriosis with a fairly good specificity of 92.7%. However, the absence of nerve fibers does not always exclude the disease.

Synthesis of Quercetin-loaded Oil-in-water Pickering Emulsion Using Dialdehyde Laminarin-stabilized Ultrafine Silver Nanoparticles

Garima SHARMA,Kwanjira WANGPIMOOL,Jin-Chul KIM 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.9

Aphicidal effects of terpenoids present in Citrus limon on Macrosiphum roseiformis and two generalist insect predators

Garima Gupta,Uday Agarwal,Harneet Kaur,Neelima R. Kumar,Pawan Gupta 한국응용곤충학회 2017 Journal of Asia-Pacific Entomology Vol.20 No.4

The current study is the first report that revealed insecticidal effects of lemon (Citrus limon) peel aqueous extract (LFPAE) against common insect pest of rose, aphids (Macrosiphum roseiformis) and for its influence on useful nontarget predators viz., Coccinella septempunctata and Orius laevigatus on rose plants. Effects of LFPAE seemed promising concerning pest and predators of Rosa spp. The LC ESI Q-TOF MS/MS analysis of extract revealed the presence of (L-pipecolic acid, scopoletin, pulegone, γ-terpinene, carvone, menthone, myrcene, limonene, (−)-trans-isopiperitenol, geranial and linalool as active components that may be ascribed to observed effects. Also, some major terpenoids α-pinene, β-pinene, γ-terpinene, menthone, linalool, limonene which are known to be present in lemon were tested for their efficacy. LFPAE did not show any toxicity towards C. septempunctata. However, it was moderately toxic to O. laevigatus. Food choice assays and odor choice assay revealed that there was no significant difference obtained between the percentage of pests/predators that reached a particular choice (LFPAE treated, or untreated rose leaves). According to LC50 values of LFPAE for aphids, the highest toxicity and least value (6.68 mg/ml), was obtained at 72 h which was almost similar to the lowest concentration tested (×6 =6.25 mg/ml). Besides at 24 and 48 h LC50 values were somewhere around ×2 (100 mg/ml) and ×3 (50 mg/ml) concentrations. Among all the terpenoids tested at 24–72 h, γ-terpinene was most toxic with LC50 value ranging from 0.18 to 0.004 mg/ml followed by menthone (0.8–0.008), β-pinene (5.8–0.004), limonene (5.8–0.009), mixture (8.5–0.003), linalool (12.3–0.13) and α-pinene (17.8–0.02), respectively. Field data showed that LFPAE at ×1 (200 mg/ml), ×2 and ×3 concentration was effective until nine days after treatment (DAT) and lowest concentration ×4 did not show affectivity beyond seven days. However, terpenoids mixture at ×1 (10 mg/ml each) showed affectivity till 11DAT and lower two concentrations (×2 and ×3) caused significant mortality up to 7DAT.

Conceptual mechanism and kinetic studies of chelating agent assisted metal extraction process from spent catalyst

Garima Chauhan,K.D.P. Nigam,K.K. Pant 한국공업화학회 2015 Journal of Industrial and Engineering Chemistry Vol.27 No.-

Metal extraction from spent catalysts using chelation technology is an acknowledged concept, howeveran underlying mechanism and kinetics associated with the process is still inexplicable. Therefore, effortshave been made to propose a generalized framework for extraction process and rate determining stepwas identified. Various empirical models were analyzed to choose the optimum one regarding theirrelative accuracy of fitting experimental data. Peleg model was considered the best fitted model withlowest root mean square error ( 2.33%) and highest linear regression coefficient (0.9937). Thermodynamicanalysis suggests activation energy of 24.8 kJ/mol and 12.07 kJ/mol for cobalt and molybdenum, respectively.

Harmonicity of almost Norden submersions between almost Norden manifolds

Garima Gupta,Rakesh Kumar,Rachna Rani,Rashmi Sachdeva 대한수학회 2022 대한수학회보 Vol.59 No.2

We define an almost Norden submersion (holomorphic and semi-Riemannian submersion) between almost Norden manifolds and \linebreak show that, in most of the cases, the base manifold has the similar kind of structure as that of total manifold. We obtain necessary and sufficient conditions for almost Norden submersion to be a totally geodesic map. We also derive decomposition theorems for the total manifold of such submersions. Moreover, we study the harmonicity of almost Norden submersions between almost Norden manifolds and between Kaehler-Norden manifolds. Finally, we derive conditions for an almost Norden submersion to be a harmonic morphism.

Growth and development of ladybird beetle Coccinella septempunctata L. (Coleoptera: Coccinellidae), on plant and animal based protein diets

Garima Gupta,Neelima R. Kumar 한국응용곤충학회 2017 Journal of Asia-Pacific Entomology Vol.20 No.3

Different protein sources from plant and animal origin viz., soybean flour (SF-AD) and soaked soybean (SS-AD), bee pollen (BP-AD), honey bee drone larvae (DL-AD) and frozen aphids (AF-AD) were assessed as an artificial diet of C. septempunctata in comparison to their natural diet live aphids. Highest growth index was obtained with SS-AD (4.05) diet almost similar to control (4.0), followed by SF-AD, BP-AD, DL-AD and AF-AD as 3.8, 2.4, 1.98 and 1.94 respectively. Similarly, data showed that success index of the adults fed on an artificial diet containing soybean (SS-AD =1.03, SF-AD =0.98) was almost similar to control (1.0), whereas the diets containing bee pollen, drone larvae, and frozen aphids was lower than control as 0.83, 0.84 and 0.78, respectively. Protein concentration was highest in live aphid (5.9 μg/ml) diet followed by SS-AD (5.6), SF-AD (5.2), BP-AD (3.4), AFAD (2.2) and DL AD (1.3). The results indicated that soybean based diets were more or equivalently suitable to beetles for their growth and development likewise their natural prey and the efficiency of artificial diets was related to its protein concentration.