This study characterizes three strains of Gram-negative bacteria MTD10B, MTD10C and MTD10D isolated from soil collected from tea plantations of Darjeeling hills, exhibiting extreme tolerance towards mercury. The minimum inhibitory concentration of mercury against these strains sits at a high level of 0.2 mg/mL of HgCl2. The isolates also display an expansive pattern of resistance to known clinically relevant synthetic antibiotics and a host of other potent heavy metals such as lead, cadmium, arsenic, chromium, silver, nickel etc. Biochemical and molecular characterization via 16S rRNA sequencing identified MTD10B and MTD10C as strains of Brevundimonas diminuta and MTD10D as Alcaligenes faecalis respectively. This study also explores the plant growth promoting abilities of these strains and their respective growth trends under normal conditions in comparison to when they are under mercury stress. This work attempts to cultivate an understanding of their potential for use as candidates for the bioremediation of mercury contamination in diverse environments.
{"title":"Emergence of Highly Mercury Tolerant Plant Growth promoting Bacteria in Tea Plantation Soil of Darjeeling Hills","authors":"S. Acharyya, S. Saha, M. Bhattacharya","doi":"10.25303/1904rjbt014023","DOIUrl":"https://doi.org/10.25303/1904rjbt014023","url":null,"abstract":"This study characterizes three strains of Gram-negative bacteria MTD10B, MTD10C and MTD10D isolated from soil collected from tea plantations of Darjeeling hills, exhibiting extreme tolerance towards mercury. The minimum inhibitory concentration of mercury against these strains sits at a high level of 0.2 mg/mL of HgCl2. The isolates also display an expansive pattern of resistance to known clinically relevant synthetic antibiotics and a host of other potent heavy metals such as lead, cadmium, arsenic, chromium, silver, nickel etc. Biochemical and molecular characterization via 16S rRNA sequencing identified MTD10B and MTD10C as strains of Brevundimonas diminuta and MTD10D as Alcaligenes faecalis respectively. This study also explores the plant growth promoting abilities of these strains and their respective growth trends under normal conditions in comparison to when they are under mercury stress. This work attempts to cultivate an understanding of their potential for use as candidates for the bioremediation of mercury contamination in diverse environments.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140414524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rim Song-guk, Hong Chol, Ri Yong-jin, Nam Kyong-ryong, Kim Hui-won
A strain was isolated from the digestive organs of Walleye pollack residing in the East Sea of the DPR Korea, which not only produces cryophilic protease, organic acid but also has intestinal adhesion property and bacteriostatic activity against pathogens. The strain was classified and identified as Pseudomonas fragi by genetic system classification methods and registered as KCCC 10110 at the Korean Centre for Culture Collection (KCCC) of the State Academy of Sciences, DPR KOREA. In vivo and in vitro toxicity of Pseudomonas fragi KCCC 10110 was evaluated using Paramecium caudatum. In the treatments with P. fragi KCCC 10110, Bacillus subtilis KCCC 11214 and Lactobacillus lactis KCCC 13208, all of these being well known as non-toxic and probiotic for animals and fishes, higher microbial counts and normal movement of P.caudatum were observed while significant lower cell numbers and abnormal movement of P.caudatum were shown in the treatments with pathogenic strains Clostridium tetani 473, Salmonella typhosa 901 and Aeromonas punctata 823. These results suggest that probiotic and pathogenic bacteria have different influence on Paramecium caudatum and that the strain isolated from Walleye pollack digestive tract is non-toxic.
{"title":"Toxicity evaluation of a strain isolated from pollack digestive tract using Paramecium caudatum","authors":"Rim Song-guk, Hong Chol, Ri Yong-jin, Nam Kyong-ryong, Kim Hui-won","doi":"10.25303/1904rjbt096099","DOIUrl":"https://doi.org/10.25303/1904rjbt096099","url":null,"abstract":"A strain was isolated from the digestive organs of Walleye pollack residing in the East Sea of the DPR Korea, which not only produces cryophilic protease, organic acid but also has intestinal adhesion property and bacteriostatic activity against pathogens. The strain was classified and identified as Pseudomonas fragi by genetic system classification methods and registered as KCCC 10110 at the Korean Centre for Culture Collection (KCCC) of the State Academy of Sciences, DPR KOREA. In vivo and in vitro toxicity of Pseudomonas fragi KCCC 10110 was evaluated using Paramecium caudatum. In the treatments with P. fragi KCCC 10110, Bacillus subtilis KCCC 11214 and Lactobacillus lactis KCCC 13208, all of these being well known as non-toxic and probiotic for animals and fishes, higher microbial counts and normal movement of P.caudatum were observed while significant lower cell numbers and abnormal movement of P.caudatum were shown in the treatments with pathogenic strains Clostridium tetani 473, Salmonella typhosa 901 and Aeromonas punctata 823. These results suggest that probiotic and pathogenic bacteria have different influence on Paramecium caudatum and that the strain isolated from Walleye pollack digestive tract is non-toxic.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140415804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-29DOI: 10.25303/1904rjbt1420145
S. Krupa, Gnanesh Rao, N. Laksmikanth, N. Mohan
Samanea saman belongs to the Leguminosae family commonly known as rain tree. The phytochemical screening of S. saman revealed the presence of many secondary metabolites such as alkaloids, pithecolobine and saponin (Samarin) which have been used for the treatment of different diseases. Natural products from plants have been used as therapeutic drugs throughout the world. This review is mainly focused on the morphology, distribution and phytochemicals contributing to the pharmacological properties of S.saman.
{"title":"A comprehensive review of the ecological significance, pharmacological potential and economic importance of Samanea saman","authors":"S. Krupa, Gnanesh Rao, N. Laksmikanth, N. Mohan","doi":"10.25303/1904rjbt1420145","DOIUrl":"https://doi.org/10.25303/1904rjbt1420145","url":null,"abstract":"Samanea saman belongs to the Leguminosae family commonly known as rain tree. The phytochemical screening of S. saman revealed the presence of many secondary metabolites such as alkaloids, pithecolobine and saponin (Samarin) which have been used for the treatment of different diseases. Natural products from plants have been used as therapeutic drugs throughout the world. This review is mainly focused on the morphology, distribution and phytochemicals contributing to the pharmacological properties of S.saman.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140412761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Ambawade, D. D. Patil, G. R. Pathade, Gajanan V. Mali
We have screened 23 endophytic isolates to estimate the production of indole acetic acid (IAA) from the root of the banana (Musa spp) by using Salkowski’s reagent spectrophotometric method with and without L- tryptophan supplement. Amongst 23 isolates only eight isolates, showed the ability to produce IAA. It is observed that one isolates out of eight produced maximum amount of IAA supplemented with and without L-tryptophan in medium. Based on morphological, cultural, biochemical and 16s rRNA gene sequencing method, this promising endophytic bacterial isolate (BE 1) was identified as Agrobacterium tumefaciens. IAA production of BE-1 was further confirmed by Thin-layer chromatography as well as by High-Performance Liquid Chromatography with and without L-tryptophan in medium. Statistical analysis was carried out using paired t-test to test whether the production of IAA significantly increased by using L-tryptophan in medium.
{"title":"Indole acetic acid (IAA) production by endophytic bacterial isolate Agrobacterium tumefaciens BE-1 from roots of Musa acuminata","authors":"M. Ambawade, D. D. Patil, G. R. Pathade, Gajanan V. Mali","doi":"10.25303/1904rjbt032039","DOIUrl":"https://doi.org/10.25303/1904rjbt032039","url":null,"abstract":"We have screened 23 endophytic isolates to estimate the production of indole acetic acid (IAA) from the root of the banana (Musa spp) by using Salkowski’s reagent spectrophotometric method with and without L- tryptophan supplement. Amongst 23 isolates only eight isolates, showed the ability to produce IAA. It is observed that one isolates out of eight produced maximum amount of IAA supplemented with and without L-tryptophan in medium. Based on morphological, cultural, biochemical and 16s rRNA gene sequencing method, this promising endophytic bacterial isolate (BE 1) was identified as Agrobacterium tumefaciens. IAA production of BE-1 was further confirmed by Thin-layer chromatography as well as by High-Performance Liquid Chromatography with and without L-tryptophan in medium. Statistical analysis was carried out using paired t-test to test whether the production of IAA significantly increased by using L-tryptophan in medium.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140416117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-29DOI: 10.25303/1904rjbt1000106
Veda Sai Kalavalapalli, Meghana Kolati, Aishwarya Bandaru, P. R. Gyana
The use of fertilizers is a common practice to improve soil fertility and increase crop yields. Chemical fertilizers have played a significant role in increasing crop yields, but their widespread use has led to environmental degradation and soil depletion. The continuing challenges in agro-ecosystem and environment require more sustainable solutions than chemical fertilizers. In recent years, there has been a growing interest in the use of biofertilizers as a sustainable alternative to chemical fertilizers. Biofertilizers are natural substances that improve soil fertility, modify soil microbiota and enhance plant growth. Cyanobacteria are one of the well-known bio inoculants for paddy crops. However, the use of cyanobacteria for other plants has not been very well documented. We screened certain cyanobacteria isolated from different natural environments as biofertilizers for certain aromatic plants. Artemisia pallens and Origanum majorana are two plants with aromatic compound productions. The aim of this study was to screen for enhancement in the growth and propagation of the plants for their yield using bio inoculants. Further air-dried, powdered plant materials of the aerial parts of A pallens and O. majorana were extracted using solvents ranging in polarity from non-polar (n-hexane), semi-polar (chloroform) and polar (acetone, methanol). These extracts were tested for antioxidant activity, several plant extracts showed antioxidant activity, with water exhibiting the greatest levels. The purpose of the experiment was to investigate the effects of bioinoculants on the growth of the test plant. Our observation showed that all the tested cyanobacterial strains i.e. KM1, KM2 and VM1, VM2, the bioinoculants, enhanced plant growth to various levels. KM1 and KM2 exhibited a greater ability to increase plant growth. This demonstrates that Artemisia's and Origanum’s growth and herbage output may be successfully enhanced by the use of cyanobacterial bioinoculants.
使用化肥是改善土壤肥力和提高作物产量的普遍做法。化肥在提高作物产量方面发挥了重要作用，但化肥的广泛使用导致了环境退化和土壤流失。农业生态系统和环境面临的持续挑战需要比化肥更可持续的解决方案。近年来，人们对使用生物肥料作为化肥的可持续替代品越来越感兴趣。生物肥料是一种天然物质，可以提高土壤肥力、改变土壤微生物群和促进植物生长。蓝藻是著名的水稻作物生物接种剂之一。然而，蓝藻在其他植物上的应用还没有很好的记录。我们筛选了从不同自然环境中分离出来的某些蓝藻，将其作为生物肥料用于某些芳香植物。苍术和牛至是两种可产生芳香化合物的植物。本研究的目的是利用生物接种剂筛选出能促进植物生长和繁殖的生物肥料。研究人员使用极性不同的溶剂（非极性溶剂（正己烷）、半极性溶剂（氯仿）和极性溶剂（丙酮、甲醇）），进一步萃取风干的 A pallens 和 O. majorana 气生部分粉末状植物材料。对这些提取物进行了抗氧化活性测试，几种植物提取物都显示出抗氧化活性，其中水的抗氧化活性最高。实验的目的是研究生物熏蒸剂对测试植物生长的影响。我们的观察结果表明，所有测试的蓝藻菌株，即 KM1、KM2 和 VM1、VM2，作为生物接种剂，都在不同程度上促进了植物的生长。其中，KM1 和 KM2 对植物生长的促进作用更大。这表明，使用蓝藻生物驯化剂可以成功地提高青蒿和牛至的生长和草料产量。
{"title":"Bioinoculants for growth enhancement of aromatic plants: Artemisia pallens and Origanum majorana","authors":"Veda Sai Kalavalapalli, Meghana Kolati, Aishwarya Bandaru, P. R. Gyana","doi":"10.25303/1904rjbt1000106","DOIUrl":"https://doi.org/10.25303/1904rjbt1000106","url":null,"abstract":"The use of fertilizers is a common practice to improve soil fertility and increase crop yields. Chemical fertilizers have played a significant role in increasing crop yields, but their widespread use has led to environmental degradation and soil depletion. The continuing challenges in agro-ecosystem and environment require more sustainable solutions than chemical fertilizers. In recent years, there has been a growing interest in the use of biofertilizers as a sustainable alternative to chemical fertilizers. Biofertilizers are natural substances that improve soil fertility, modify soil microbiota and enhance plant growth. Cyanobacteria are one of the well-known bio inoculants for paddy crops. However, the use of cyanobacteria for other plants has not been very well documented. We screened certain cyanobacteria isolated from different natural environments as biofertilizers for certain aromatic plants. Artemisia pallens and Origanum majorana are two plants with aromatic compound productions. The aim of this study was to screen for enhancement in the growth and propagation of the plants for their yield using bio inoculants. Further air-dried, powdered plant materials of the aerial parts of A pallens and O. majorana were extracted using solvents ranging in polarity from non-polar (n-hexane), semi-polar (chloroform) and polar (acetone, methanol). These extracts were tested for antioxidant activity, several plant extracts showed antioxidant activity, with water exhibiting the greatest levels. The purpose of the experiment was to investigate the effects of bioinoculants on the growth of the test plant. Our observation showed that all the tested cyanobacterial strains i.e. KM1, KM2 and VM1, VM2, the bioinoculants, enhanced plant growth to various levels. KM1 and KM2 exhibited a greater ability to increase plant growth. This demonstrates that Artemisia's and Origanum’s growth and herbage output may be successfully enhanced by the use of cyanobacterial bioinoculants.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140413906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The objective of this study was to examine the phytochemical properties of the baobab tree (Adansonia digitata) stems and leaves. The dried powder of leaves and stem extract were analyzed for the presence or absence of different phytochemicals, flavonoids, terpenoids, saponins, tannins, alkaloids etc. The quantitative analysis revealed that the leaves and stem of A. digitata are rich in total phenols, alkaloids, terpenoids, flavonoids and saponins. The presence of these compounds was known to show medicinal potential as well as antioxidant activity and this justifies the use of baobab leaves as one of the major sources of soup in Africa. Chlorophyll (chl.) estimation was also studied by two different methods in fresh leaves and dried leaves. Fresh leaves have high chlorophyll content of 2.0 mg/g while shade and sun-dried leaves have content 1.664 mg/g and 1.047 mg/g respectively. With DMSO, high chlorophyll content of fresh leaves is 2.240 mg/g and for shade and sun-dried leaves, it is 1.695 mg/g and 1.526 mg/g respectively. This represents that high chlorophyll and phytochemicals present in plants show high antioxidant properties. Subsequently, antioxidant activity at different concentrations 62.5, 125, 250, 500, 750 μg/ml of the extract was established using FRAP assay and DPPH action radical scavenging activity methods respectively. Ethanolic extract shows higher antioxidant activity than hydroethanolic extract.
{"title":"Quantitative Phytochemicals and Antioxidant Potential of Adansonia digitata leaves and stem extract","authors":"Chhavi Goel, R. Dutta","doi":"10.25303/1904rjbt05013","DOIUrl":"https://doi.org/10.25303/1904rjbt05013","url":null,"abstract":"The objective of this study was to examine the phytochemical properties of the baobab tree (Adansonia digitata) stems and leaves. The dried powder of leaves and stem extract were analyzed for the presence or absence of different phytochemicals, flavonoids, terpenoids, saponins, tannins, alkaloids etc. The quantitative analysis revealed that the leaves and stem of A. digitata are rich in total phenols, alkaloids, terpenoids, flavonoids and saponins. The presence of these compounds was known to show medicinal potential as well as antioxidant activity and this justifies the use of baobab leaves as one of the major sources of soup in Africa. Chlorophyll (chl.) estimation was also studied by two different methods in fresh leaves and dried leaves. Fresh leaves have high chlorophyll content of 2.0 mg/g while shade and sun-dried leaves have content 1.664 mg/g and 1.047 mg/g respectively. With DMSO, high chlorophyll content of fresh leaves is 2.240 mg/g and for shade and sun-dried leaves, it is 1.695 mg/g and 1.526 mg/g respectively. This represents that high chlorophyll and phytochemicals present in plants show high antioxidant properties. Subsequently, antioxidant activity at different concentrations 62.5, 125, 250, 500, 750 μg/ml of the extract was established using FRAP assay and DPPH action radical scavenging activity methods respectively. Ethanolic extract shows higher antioxidant activity than hydroethanolic extract.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140414229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-29DOI: 10.25303/1904rjbt1350141
S.A. Raj, S. Adithya, A. Shanker, F. Ahmad
Cerebral palsy (CP) is a neuromuscular condition caused by deficits in the developmental trajectory of the brain or due to physical injury to the developing brain. It affects many school-going and newly born children and is indicated by exaggerated movements and reflexes and unusual movements of the limbs, digits and posture. The present review article discusses the therapeutic potential of botulinum toxin (BoNT) for the treatment of CP. BoNT is a well-known commercially available neurotoxin which blocks the release of neurotransmitters (e.g. acetylcholine), thereby decreasing the undesirable muscle movement of the voluntary muscles in the case of CP. The review also discusses the effectiveness of the therapy, rehabilitation of the patients after treatment and various scales used to measure the movement before and after therapy.
{"title":"Botulinum toxin as a therapy for cerebral palsy","authors":"S.A. Raj, S. Adithya, A. Shanker, F. Ahmad","doi":"10.25303/1904rjbt1350141","DOIUrl":"https://doi.org/10.25303/1904rjbt1350141","url":null,"abstract":"Cerebral palsy (CP) is a neuromuscular condition caused by deficits in the developmental trajectory of the brain or due to physical injury to the developing brain. It affects many school-going and newly born children and is indicated by exaggerated movements and reflexes and unusual movements of the limbs, digits and posture. The present review article discusses the therapeutic potential of botulinum toxin (BoNT) for the treatment of CP. BoNT is a well-known commercially available neurotoxin which blocks the release of neurotransmitters (e.g. acetylcholine), thereby decreasing the undesirable muscle movement of the voluntary muscles in the case of CP. The review also discusses the effectiveness of the therapy, rehabilitation of the patients after treatment and various scales used to measure the movement before and after therapy.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140417277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Triple negative breast cancer (TNBC) is still considered a medical challenge as it is an aggressive cancer characterized by poor prognosis, frequent metastasis, distinct clinical and pathological features and lack of proper treatment options. In TNBC, estrogen, progesterone and Her2 neu receptors are absent, which are usually present in otherwise breast cancers. So, hormonal therapy cannot be given in case of TNBC, leaving chemotherapy as the mainstay for treatment. However, chemotherapy is an infamous therapeutic option due to several aweful side effects like loss of appetite, extreme weight loss, hair loss, vomiting, fatigue etc. Several reports have highlighted role of Peroxisome Proliferated Activated Receptor gamma (PPAR-γ) in ameliorating breast cancer, but it is still less explored receptor for TNBC. Moreover, synthetic PPAR gamma agonists like thiazolidinediones, have good capability of activating PPAR-γ receptor, but these are also gloomy therapeutic agent due to their dreadful side effects like hepatotoxicity, bladder cancer, congestive heart failure etc. So, there is serious urge among researchers to find safer therapeutic option for TNBC. Phytochemicals are nowadays grabbing attention worldwide to treat several diseases due to their fewer or no side effects. This in silico study was performed after thorough review to select a natural, potent PPAR-γ agonist Gallotanin, as a query compound for ligand based similarity searching in PubChem database with 80% filter. Top 10 obtained compounds having highest similarity index were chosen for molecular docking in AutoDock Vina, with PPAR-γ receptor (3V9T) to know their binding patterns. Further, top 5 compounds having highest dock scores underwent ADME studies in SwissADME to assess pharmacokinetic profile of these compounds. Finally, this in silico study resulted in discovery of compound called Chamuvaritin which is still not known as a PPAR-γ agonist, efficient enough to act as potent therapeutic agent against TNBC.
{"title":"Identification of novel PPAR-γ agonist ameliorating triple negative breast cancer by in silico methods","authors":"A. Laxmi, Jeena Gupta, Pawan Gupta","doi":"10.25303/1903rjbt058069","DOIUrl":"https://doi.org/10.25303/1903rjbt058069","url":null,"abstract":"Triple negative breast cancer (TNBC) is still considered a medical challenge as it is an aggressive cancer characterized by poor prognosis, frequent metastasis, distinct clinical and pathological features and lack of proper treatment options. In TNBC, estrogen, progesterone and Her2 neu receptors are absent, which are usually present in otherwise breast cancers. So, hormonal therapy cannot be given in case of TNBC, leaving chemotherapy as the mainstay for treatment. However, chemotherapy is an infamous therapeutic option due to several aweful side effects like loss of appetite, extreme weight loss, hair loss, vomiting, fatigue etc. Several reports have highlighted role of Peroxisome Proliferated Activated Receptor gamma (PPAR-γ) in ameliorating breast cancer, but it is still less explored receptor for TNBC. Moreover, synthetic PPAR gamma agonists like thiazolidinediones, have good capability of activating PPAR-γ receptor, but these are also gloomy therapeutic agent due to their dreadful side effects like hepatotoxicity, bladder cancer, congestive heart failure etc. So, there is serious urge among researchers to find safer therapeutic option for TNBC. Phytochemicals are nowadays grabbing attention worldwide to treat several diseases due to their fewer or no side effects. This in silico study was performed after thorough review to select a natural, potent PPAR-γ agonist Gallotanin, as a query compound for ligand based similarity searching in PubChem database with 80% filter. Top 10 obtained compounds having highest similarity index were chosen for molecular docking in AutoDock Vina, with PPAR-γ receptor (3V9T) to know their binding patterns. Further, top 5 compounds having highest dock scores underwent ADME studies in SwissADME to assess pharmacokinetic profile of these compounds. Finally, this in silico study resulted in discovery of compound called Chamuvaritin which is still not known as a PPAR-γ agonist, efficient enough to act as potent therapeutic agent against TNBC.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140476936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Argemone mexicana (family: Papaveraceae) is an important medicinal plant that produces a wide range of secondary metabolites. In this study, the RNA-seq data of Argemone mexicana plant stem was retrieved from the NCBI SRA database (SRR287649). The quality checking and trimming of the raw data were performed by using FastQC, Cutadapt and Trimmomatic 0.39 software. Further, de-novo sequence assembly by Trinity software package generated a total 29591 number of contig sequences. As subsequent work, BLASTX and annotation of all the contig by using Blast2GO and WEGO2 tool produced 19780 annotated genes with 44440 gene ontology (GO) terms. Further, the genes involved in secondary metabolite production of the Argemone mexicana plant were predicted by functional assignment of the contig sequences.
{"title":"De novo transcriptome analysis of Argemone mexicana plant (SRR287649) and annotation for secondary metabolite producing genes","authors":"Raghunath Satpathy","doi":"10.25303/1903rjbt086092","DOIUrl":"https://doi.org/10.25303/1903rjbt086092","url":null,"abstract":"Argemone mexicana (family: Papaveraceae) is an important medicinal plant that produces a wide range of secondary metabolites. In this study, the RNA-seq data of Argemone mexicana plant stem was retrieved from the NCBI SRA database (SRR287649). The quality checking and trimming of the raw data were performed by using FastQC, Cutadapt and Trimmomatic 0.39 software. Further, de-novo sequence assembly by Trinity software package generated a total 29591 number of contig sequences. As subsequent work, BLASTX and annotation of all the contig by using Blast2GO and WEGO2 tool produced 19780 annotated genes with 44440 gene ontology (GO) terms. Further, the genes involved in secondary metabolite production of the Argemone mexicana plant were predicted by functional assignment of the contig sequences.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140478122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shwetha Karaningannavar, Rajat Hegde, Ramesh Babu Yarajarla
Wild fruit fly larvae can be distinguished at the family level such as Drosophilidae and Tephritidae larvae are based on size or spiracles arrangement, but such visual distinction is more intricate between Drosophilid species. In the present study, to identify the Drosophila immigrans and Drosophila suzukii species at the larval stage, we employed a simple, rapid PCR-RFLP experiment. Wild suspected larvae from Drosophila immigrans and Drosophila suzukii species were collected from 3 different geographical regions. DNA was isolated and a PCR-RFLP profile was developed using the XmnI restriction enzyme. Sequencing of the mitochondrial COI gene from larvae was performed to evaluate the species. PCR-RFLP analysis from Drosophila suzukii wild larvae generated three distinct bands with 120bp, 210bp and 250bp. Similarly, Drosophila immigrans generated 2 distinct bands with 270bp and 310bp. Restriction digestion products from both the larvae and adult flies were the same, hence the accuracy of the PCR-RFLP profile developed from both suspected wild larvae and adult flies was 100%. Sequencing analysis confirms that wild field collected larvae belong to Drosophila suzukii and Drosophila immigrans. Present study clearly shows that PCR‐RFLP is a fast, simple, inexpensive and accurate molecular method and it can be successfully used for species identification at the early stages of the life cycle of Drosophila species.
{"title":"Simple and Rapid PCR-RFLP based species identification in Drosophila suzukii and Drosophila immigrans larvae","authors":"Shwetha Karaningannavar, Rajat Hegde, Ramesh Babu Yarajarla","doi":"10.25303/1903rjbt048050","DOIUrl":"https://doi.org/10.25303/1903rjbt048050","url":null,"abstract":"Wild fruit fly larvae can be distinguished at the family level such as Drosophilidae and Tephritidae larvae are based on size or spiracles arrangement, but such visual distinction is more intricate between Drosophilid species. In the present study, to identify the Drosophila immigrans and Drosophila suzukii species at the larval stage, we employed a simple, rapid PCR-RFLP experiment. Wild suspected larvae from Drosophila immigrans and Drosophila suzukii species were collected from 3 different geographical regions. DNA was isolated and a PCR-RFLP profile was developed using the XmnI restriction enzyme. Sequencing of the mitochondrial COI gene from larvae was performed to evaluate the species. PCR-RFLP analysis from Drosophila suzukii wild larvae generated three distinct bands with 120bp, 210bp and 250bp. Similarly, Drosophila immigrans generated 2 distinct bands with 270bp and 310bp. Restriction digestion products from both the larvae and adult flies were the same, hence the accuracy of the PCR-RFLP profile developed from both suspected wild larvae and adult flies was 100%. Sequencing analysis confirms that wild field collected larvae belong to Drosophila suzukii and Drosophila immigrans. Present study clearly shows that PCR‐RFLP is a fast, simple, inexpensive and accurate molecular method and it can be successfully used for species identification at the early stages of the life cycle of Drosophila species.","PeriodicalId":48695,"journal":{"name":"Research Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.2,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140474830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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