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Open Access journal
ISSN (Print) 2190-572X - ISSN (Online) 2190-5738
Published by SpringerOpen [188 journals]
- Extraction and bioactive profile of the compounds produced by Rhodococcus
Abstract: Abstract A potent actinobacterial strain isolated from the marine samples of Bheemunipatnam beach, Visakhapatnam, India, was identified as Rhodococcus sp. VLD-10 using the conventional and genomic (16S rRNA) approaches. Bioactive compounds responsible for the antimicrobial activity of the strain were elucidated by cultivating the strain VLD-10 in a modified yeast extract-malt extract-lactose broth followed by subsequent chromatographic and spectroscopic analyses. Extraction, purification, and structural confirmation of five compounds, viz., benzoic acid, 2-nitrobenzaldehyde, 4-chlorobenzaldehyde, nonadeconoic acid, and 3-isopropylhexahydro-1H-pyrido[1,2-a] pyrazine-1,4(6H)-dione, from Rhodococcus sp. VLD-10 were fruitfully described. The bioactivity of the compounds isolated from the strain VLD-10 against Gram-positive as well as Gram-negative bacteria, yeast, and molds was tested and their minimum inhibition concentration was reported. Antibacterial activity of 3-isopropylhexahydro-1H-pyrido[1,2-a] pyrazine-1,4(6H)-dione is more prominent against Bacillus subtilis, B. cereus, B. megaterium, Corynebacterium diphtheriae, and Escherichia coli, whereas its antifungal spectrum showed less potency against yeast and fungi. This is the first report on the natural occurrence and bioactivity of 3-isopropylhexahydro-1H-pyrido[1,2-a] pyrazine-1,4(6H)-dione from Rhodococcus sp. VLD-10.
- Response surface methodology-based optimization of production media and
purification of α-galactosidase in solid-state fermentation by Fusarium
moniliforme NCIM 1099
Abstract: Abstract Response surface methodology was used to enhance the production of α-galactosidase from Fusarium moniliforme NCIM 1099 in solid-state fermentation. Plackett–Burman design was employed for selection of critical media constituents which were optimized by central composite rotatable design. Wheat bran, peptone and FeSO4·7H2O were identified as significant medium components using PB design. Further CCRD optimized medium components as wheat bran; 4.62 μg, peptone; 315.42 μg, FeSO4·7H2O; 9.04 μg. RSM methodological optimization increased the enzyme production from 13.17 to 207.33 U/g showing 15.74-fold enhancement. The α-galactosidase was purified by 70% fractionation followed by DEAE anion exchange column chromatography which yields 23.33% with 28.68-fold purification. The molecular weight of α-galactosidase was 57 kDa which was determined by SDS-PAGE analysis. Purified enzyme has optimum pH of 4.0 and was found to be stable in wide pH range of 3.0–9.0. Its optimum temperature was 50 °C, whereas its activity remains above 50% up to 2 h at 75 °C. Hg2+ was found to be a potent inhibitor and Mg2+ acted as an activator of enzyme. No significant change was observed in enzyme activity for galactose concentration, ranging from 1 to 100 mM. The K m values of enzyme for substrates p-nitrophenyl-α-d-galactopyranoside, melibiose and raffinose were 0.20, 1.36, and 3.66 mM, respectively. Low K m and stability to various physiological conditions of enzyme represents its potential which can be exploited in various industrial applications.
- Identification and quantification of novel RNA isoforms in horn cancer of
Bos indicus by comprehensive RNA-Seq
Abstract: Abstract Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions. Based on pathway clustering and in silico verification, 102 novel splice isoforms were selected and further analysed with respect to change in protein sequence using Blastp. Finally, fourteen novel splicing events supported both by Cufflinks and UCSC genome browser were selected and confirmed expression by RT-qPCR. Future studies targeted at in-depth characterization of these potential candidate splice isoforms might be helpful in the development of relevant biomarkers for early diagnosis of HC. The results reported in this study refine the available information on transcriptome repertoire of bovine species and boost the research in the line of development of relevant biomarkers for early diagnosis of HC.
- A combined chloroplast atpB – rbcL and trnL - F phylogeny unveils the
ancestry of balsams ( Impatiens spp.) in the Western Ghats of India
Abstract: Abstract Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB–rbcL and trnL-F intergenic spacer-specific forward and reverse primers. Thirteen sequences of Impatiens species from three centers of diversity were obtained from GenBank for reconstructing the evolutionary relationships within the genus Impatiens. Bayesian inference analysis was carried out in MrBayes v.3.2.2. This analysis supported Southeast Asia as the ancestral place of origin of extant Impatiens species. Molecular phylogeny of South Indian Impatiens spp. based on combined chloroplast sequences showed the same association as that of morphological taxonomy. Sections Scapigerae, Tomentosae, Sub-Umbellatae, and Racemosae showed Southeast Asian relationship, while sections Annuae and Microsepalae showed African affinity.
- Optimization of phytase production from potato waste using Aspergillus
Abstract: Abstract Solid-state fermentation (SSF) can divert food waste from landfills and produce high-value products. This study was aimed to investigate the feasibility of using SSF and optimize the conditions of production of phytase by Aspergillus ficuum from potato waste. Different parameters including pH of the potato waste, inoculum level, moisture content, incubation period, temperature, and supplementary nitrogen and carbon sources were evaluated. The results indicated that pH, inoculum level, and moisture content did not significantly vary phytase production. However, different incubation periods, incubation temperatures, nitrogen sources, and carbon sources changed the phytase production significantly. The ideal and economic conditions for phytase production consisted of a normal moisture content (79%) of potato waste, 1.0 ml inoculum size, and normal pH 6.1 at room temperature for 144 h incubation time. The highest phytase activity (5.17 ± 0.82 U/g ds) was obtained under the aforementioned optimized conditions. When (NH4)2SO4 was used as a nitrogen source in the substrate, the phytase activity increased to 12.93 ± 0.47 U/g ds, which was a 2.5-fold increase compared to the control treatment. This study proposed a novel and economical way to convert food processing waste to highly valuable products and investigated the optimal conditions of the production of phytase during SSF in potato waste.
- Role of GNB3 , NET , KCNJ11 , TCF7L2 and GRL genes single nucleotide
polymorphism in the risk prediction of type 2 diabetes mellitus
Abstract: Abstract Type 2 diabetes (T2DM) is a polygenic metabolic disorder characterized by hyperglycemia occurring as a result of impaired insulin secretion or insulin resistance. Various environmental and genetic factors interact and increase the risk of T2DM and its complications. Among the various genetic factors associated with T2DM, single nucleotide polymorphism in different candidate genes have been studied intensively and the resulting genetic variants have been found to have either positive or negative association with T2DM thereby increasing or decreasing the risk of T2DM, respectively. In this review, we will focus on Guanine nucleotide-binding protein subunit beta 3 (GNB3), Norepinephrine Transporter (NET), Potassium Channel gene (KCNJ11), Transcription Factor 7-Like 2 (TCF7L2) and Glucocorticoid receptor (GRL) genes and their association with T2DM studied in different ethnic groups. The products of these genes are involved in the biochemical pathway leading to T2DM. Polymorphisms in these genes have been intensively studied in individuals of different ethnic origins. Results show that genetic variants of TCF7L2 and KCNJ11 genes have potential to emerge as a risk biomarker for T2DM whereas results of GNB3, GRL and NET genes have been controversial when studied in individuals of different ethnicities. We have tried to summarize the results generated globally in context to the selected genes which could possibly help researchers working in this field and would eventually help in understanding the mechanistic pathways of T2DM leading early diagnosis and prevention.
- Diversity of bacteria and archaea in the rhizosphere of bioenergy crop
Abstract: Abstract Plant-microbial interaction in rhizosphere plays vital role in shaping plant’s growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties. Diversity was estimated by terminal restriction fragment length polymorphism (TRFLP) targeting 16S rRNA gene of bacteria and archaea. Fifteen bacterial and 17 archaeal terminal restriction fragments (TRFs) were retrieved from J. curcas rhizosphere. Bacterial indicative TRFs were Actinobacteria, Firmicutes, Acidobacteria, Verrumicrobiaceae, and Chlroflexi. Major archaeal TRFs were crenarchaeota, and euryarchaeota. In case of bacteria, relative fluorescence was low for TRF160 and high for TRF51, TRF 420. Similarly, for archaea relative fluorescence of TRF 218, and TRF 282 was low and high for TRF 278, TRF468 and TRF93. Principal component analysis (PCA) of bacterial TRFs designated PC 1 with 46.83% of variation and PC2 with 31.07% variation. Archaeal TRFs designated 90.94% of variation by PC1 and 9.05% by PC2. Simpson index varied from 0.530 to 0.880 and Shannon index from 1.462 to 3.139 for bacteria. For archaea, Simpson index varied from 0.855 to 0.897 and Shannon index varied from 3.027 to 3.155. Study concluded that rhizosphere of J. curcas constituted of diverse set of both bacteria and archaea, which might have promising plant growth promoting activities.
- Acknowledgement to Referees
- Impact assessment of silver nanoparticles on plant growth and soil
Abstract: Abstract The present study was carried out to investigate the impact of silver nanoparticles (AgNPs) on the growth of three different crop species, wheat (Triticum aestivum, var. UP2338), cowpea (Vigna sinensis, var. Pusa Komal), and Brassica (Brassica juncea, var. Pusa Jai Kisan), along with their impact on the rhizospheric bacterial diversity. Three different concentrations (0, 50 and 75 ppm) of AgNPs were applied through foliar spray. After harvesting, shoot and root parameters were compared, and it was observed that wheat was relatively unaffected by all AgNP treatments. The optimum growth promotion and increased root nodulation were observed at 50 ppm treatment in cowpea, while improved shoot parameters were recorded at 75 ppm in Brassica. To observe the impact of AgNPs on soil bacterial community, sampling was carried out from the rhizosphere of these crops at 20 and 40 days after the spraying of AgNPS. The bacterial diversity of these samples was analyzed by both cultural and molecular techniques (denaturing gradient gel electrophoresis). It is clearly evident from the results that application of AgNPs changes the soil bacterial diversity and this is further influenced by the plant species grown in that soil. Also, the functional bacterial diversity differed with different concentrations of AgNPs.
- Erratum to: Molecular characterization of phytoplasmas of ‘Clover
proliferation’ group associated with three ornamental plant species in
- Modification of Sargassum angustifolium by molybdate during a facile
cultivation for high-rate phosphate removal from wastewater: structural
characterization and adsorptive behavior
Abstract: Abstract In this paper, a new and facile approach for molybdate loading in the brown algae of Sargassum angustifolium is introduced. The molybdate ions were entered into the algae body during a short cultivation to produce algae–Mo as a novel adsorbent for eliminating phosphate ions from synthetic and real wastewaters. Results of the surface analysis showed that molybdate loading onto the algae was successfully performed. Herein, basic variables, such as initial solution pH, adsorbent dosage, contact time, phosphate concentration, and temperature, were investigated in detail to assess the phosphate adsorption performance of algae–Mo. The pseudo-second-order kinetic model fitted our acquired experimental kinetic data most appropriately, in comparison to the use of a pseudo-first-order model. The Langmuir model appeared to fit the adsorption data more desirably than that of Freundlich and Dubnin–Radushkevich models, with a maximum phosphate adsorption capacity of 149.25 mg/g at 25 °C. The finding of the thermodynamic study revealed that the phosphate adsorption onto algae–Mo was spontaneous, feasible, and endothermic in nature. The study on Mo2+ ions leaching strongly suggested that the risk of Mo2+ leakage during phosphate adsorption was negligible at a wide pH range of 3–9. The adsorption efficiency attained was 53.4% at the sixth cycle of reusability. Two real wastewaters with different qualities were successfully treated by the algae–Mo, suggesting that the algae–Mo could be ordered for practical wastewater treatment.
- De novo transcriptome sequencing in Monsonia burkeana revealed putative
genes for key metabolic pathways involved in tea quality and medicinal
Abstract: Abstract Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts. Annotation of these transcripts revealed best hits for homology to discover more than 17,800 functional genes and conserved domains. A total of 93 KEGG pathways and associated genes encoded by more than 90% of the coding transcripts are responsible for the biosynthesis of these life-saving metabolites. We validated and enriched the genes by GO annotation and linked this to enzyme-powered pathways through interactive network map. Caffeine metabolism, flavonoid, phenylpropanoid and terpenoids biosynthesis and xenobiotics degradation were typical in tea quality and drug therapy. The relatedness of more than 80 gene families encoding key enzymes was shown using unrooted phylogenetic tree. In conclusion, the M. burkeana leaf transcriptome gives insight into tea and drug-specific products, therefore representing basis in further investigation of the plant.
- Antimicrobial, antibiofilm, and microbial barrier properties of poly
(ε-caprolactone)/cloisite 30B thin films
Abstract: Abstract Development of antibacterial and antibiofilm surfaces is in high demand. In this study, nanocomposite of Poly (ε-caprolactone)/Cloisite 30B was prepared by the solvent casting method. The membranes were characterised by SEM, AFM, and FTIR. Evaluation of water uptake, antimicrobial, antibiofilm, and microbial barrier properties demonstrated a significant antimicrobial and antibiofilm activity against MTCC strain of Staphylococcus haemolyticus and strong biofilm positive Staphylococcus epidermidis of clinical origin at low clay concentrations. These membranes acted as an excellent barrier to the penetration of microorganism. These nanocomposites can have promising applications in various fields including packaging.
- Xanthine oxidase inhibitory and antioxidant potential of Indian Muscodor
Abstract: Abstract Xanthine oxidase is a key enzyme responsible for hyperuricemia, a pre-disposing factor for Gout and oxidative stress-related diseases. Only two clinically approved xanthine oxidase inhibitors Allopurinol and Febuxostat are currently used for treatment of hyperuricemia. However, owing to their side effects there is a need for new non-purine-based selective inhibitors of xanthine oxidase. In the process of exploring novel xanthine oxidase inhibitors and anti-oxidants, we screened the culture filtrate of 07 novel species of Muscodor, a sterile endophytic fungi isolated from Cinnamomum and Aegle marmelos. Chloroform extract of M. darjeelingensis exhibited the maximum xanthine oxidase inhibition in the qualitative and quantitative assays. The IC50 of chloroform extract of M. darjeelingensis was 0.54 µg/ml which was much lower to Allopurinol but higher when compared to Febuxostat. 88% reduction in uric acid production was recorded by M. darjeelingensis chloroform extract which was similar to allopurinol. The maximum anti-oxidant activity was exhibited by M. indica against the gallic acid standard in the DPPH-free radical assay. Anti-oxidant activity index of M. indica was 7.7, which was followed by M. kashayum with 5.4. M. darjeelingensis exhibited a moderate anti-oxidant activity with anti-oxidant activity index of 1.63 in the DPPH assay. The present study is the very first report of Muscodor species exhibiting xanthine oxidase inhibitory and anti-oxidant activity together. Chloroform extract of M. darjeelingensis and M. indica stand out as potential candidates for isolation and characterization of the xanthine oxidase inhibitor and anti-oxidant compound, respectively.
- Roles of plant hormones and anti-apoptosis genes during drought stress in
rice ( Oryza sativa L.)
Abstract: Abstract We previously identified the rice (Oryza sativa) senescence-associated gene OsSAP which encodes a highly conserved protein involved in anti-apoptotic activity. This novel Bax suppressor-related gene regulates tolerance to multiple stresses in yeast. Here, we show the effects of drought stress on leaf and root tissues of plants over-expressing OsSAP in relation to the levels of phytohormones, abscisic acid (ABA), jasmonic acid (JA), indole-3-carboxylic acid (ICA), gibberellic acid (GA3), and zeatin. Results showed that rice plants over-expressing SAP were tolerant to drought stress compared to wild type and the plants over-expressing AtBI-1, which is a homolog of the human Bax inhibitor-1 in Arabidopsis. ABA and JA levels in OsSAP and AtBI-1 transgenic plants consistently increased up to at least 3 days after drought treatment, whereas lower GA3 levels were recorded during early drought period. Comparison between control and transgenic plants overexpressing anti-apoptosis genes OsSAP and AtBI-1 resulted in different patterns of hormone levels, indicating that these genes are involved in the plant responses to drought stress and present an opportunity for further study on drought stress tolerance in rice and other plant species.
- Brevibacillus borstelensis and Streptomyces albogriseolus have roles to
play in degradation of herbicide, sulfosulfuron
Abstract: Abstract Use of herbicides, in particular sulfosulfuron, at more than recommended doses has raised major concerns about the health hazards for animals and humans. In the present study, isolation of sulfosulfuron-degrading Brevibacillus borstelensis and Streptomyces albogriseolus from the field soils in the northwestern region of India was carried out where the use of sulfosulfuron is predominant, and further assessed for their potential to degrade sulfosulfuron individually and together in a consortium form under lab conditions. Concentration of sulfosulfuron was reduced from 10 to 7.72 µg/ml in 12 h to 5.13 µg/ml in 20 h by B. borstelensis and the metabolites detected by LCMS–MS were aminopyrimidine and a rearranged amine in 12 and 20 h of growth. Similarly, S. albogriseolus reduced the concentration of sulfosulfuron from 10 to 6.74 µg/ml in 12 h to 6.62 µg/ml in 20 h with aminopyrimidine and a rearranged amine as metabolites. B. borstelensis and S. albogriseolus together also reduced the concentration of sulfosulfuron from 10 µg/ml in initial hour to 8.34 µg/ml in 12 h to 6.66 µg/ml in 20 h. Hence, B. borstelensis and S. albogriseolus provide a safer, inexpensive and effective way to bio-remediate the harmful and toxic sulfosulfuron from the environment if further explored at a larger field scale in near future.
- Molecular detection and pathogenicity of a nucleopolyhedrovirus isolated
from looper caterpillar ( Hyposidra talaca ), a tea pest
Abstract: Abstract Hyposidra talaca is a major defoliating pest of tea plants in north-eastern part of India. In this study, we look for variations (if any) in the attacking virus. Viral samples were collected from different regions of the northern part of West Bengal in India and were analyzed by PCR technique to study the variations across the region. The partial segment of the HytaNPV polyhedrin gene was cloned and sequenced. A 527 bp nucleotide sequence containing highly conserved region from polyhedrin gene of HytaNPV was observed. The blast homology search for studied polyhedrin gene showed 98% sequence identity with the sequence of previous reported NPV of H. talaca, H. infixaria and Buzura suppressaria. Pathogenicity study against second instar H. talaca indicated that the LC50 values ranged from 4.61 × 105 to 7.57 × 105 polyhedral occlusion bodies per ml (POBs/ml) and the LT50 values ranged from 4.2 to 6.66 days. Sequencing result reveals that the same HytaNPV strain dominates across this area and the pathogenicity indicates its potential as an alternative to chemical insecticides to control H. talaca.
- Phytotoxicity and oxidative stress perspective of two selected
nanoparticles in Brassica juncea
Abstract: Abstract This study elaborates the consequences of oxidative stress caused by copper oxide (CuO) and titanium dioxide (TiO2) nanoparticles (NPs) in Brassica juncea. Effect of these two NPs on plant physiology, reactive oxygen scavenging enzyme system (ascorbate peroxidase, catalase, superoxide dismutase), proline content and lipid peroxidation has been estimated in leaves as well as root tissues. Bioaccumulation of NPs has also been evaluated in the current study and the interrelated cascade of the enzymatic system with H2O2 production was identified. The uptake of NPs in plant leaves was confirmed by scanning electron microscopy, X-ray diffraction, and Fourier Transform Infrared Spectroscopy. Plant growth was found to be diminished with elevated levels of CuO NPs whereas TiO2 NPs had shown an opposite effect. The plant species accumulated lower concentration of NPs and displayed considerable tolerance against stress, probably due to well-organized and coordinated defense system at the root and shoot level by the intonation of antioxidative enzymes.
- Characterization and development of EST-SSR markers in sweet potato (
Ipomoea batatas (L.) Lam)
Abstract: Abstract In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag–simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.
- Isolation and screening of l -asparaginase free of glutaminase and urease
from fungal sp.
Abstract: Abstract l-Asparaginase is a chemotherapeutic drug used in the treatment of acute lymphoblastic leukaemia (ALL), a malignant disorder in children. l-Asparaginase helps in removing acrylamide found in fried and baked foods that is carcinogenic in nature. l-Asparaginase is present in plants, animals and microbes. Various microorganisms such as bacteria, yeast and fungi are generally used for the production of l-asparaginase as it is difficult to obtain the same from plants and animals. l-Asparaginase from bacteria causes anaphylaxis and other abnormal sensitive reactions due to low specificity to asparagine. Toxicity and repression caused by bacterial l-asparaginase shifted focus to eukaryotic microorganisms such as fungi to improve the efficacy of l-asparaginase. Clinically available l-asparaginase has glutaminase and urease that may lead to side effects during treatment of ALL. Current work tested 45 fungal strains isolated from soil and agricultural residues. Isolated fungi were tested using conventional plate assay method with two indicator dyes, phenol red and bromothymol blue (BTB), and results were compared. l-Asparaginase activity was measured by cultivating in modified Czapek–Dox medium. Four strains have shown positive result for l-asparaginase production with no urease or glutaminase activity, among these C7 has high enzyme index of 1.57 and l-asparaginase activity of 33.59 U/mL. l-Asparaginase production by C7 was higher with glucose as carbon source and asparagine as nitrogen source. This is the first report focussing on fungi that can synthesize l-asparaginase of the desired specificity. Since the clinical toxicity of l-asparaginase is attributed to glutaminase and urease activity, available evidence indicates variants negative for glutaminase and urease would provide higher therapeutic index than variants positive for glutaminase and urease.