Biotechnology and Bioinformatics

In current study isolates of two native microalgae species were screened on the basis of growth kinetics and lipid accumulation potential. On the basis of data obtained on growth parameters and lipid accumulation, it is concluded that Scenedesmus dimorphus has better potential as biofuel feedstock. Two of the isolates of Scenedesmus dimorphus performed better than other isolates with respect to important growth parameters with lipid content of ~30% of dry biomass. Scenedesmus dimorphus was found to be more suitable as biodiesel feedstock candidate on the basis of cumulative occurrence of five important biodiesel fatty acids, relative occurrence of SFA (53.04%), MUFA (23.81%) and PUFA (19.69%), and more importantly that of oleic acid in its total lipids. The morphological observations using light and Scanning Electron Microscope and molecular characterization using amplified 18S rRNA gene sequences of microalgae species under study were also performed. Amplified 18S rRNA gene fragments of the microalgae species were sequenced, annotated at the NCBI website and phylogenetic analysis was done. We have published eight 18S rRNA gene sequences of microalgae species in NCBI GenBank.

Recently micro algae are increasingly being recognized as a promising feedstock for biofuel
production, but success in this area requires rapid strain characterization from vast unexplored
biodiversity, continuous strain improvements apart from development of scalable production
technologies. In present study a survey, isolation and characterization of dominant local
microalgae from H.P. was done with a perspective of exploration and to upsurge bioresources for
future research and strain development. Chlorella sp. was dominant in most of the sample
collections followed by Scenedesmus quadricauda and Scenedesmus dimorphus. The uni-algal
cultures were established and characterized mophplogically as well as by 18s RNA partial gene
sequences. The morphological behavior of the cultures was examined under a light microscope,
Scenedesmus quadricauda, Scenedesmus dimorphus formed the typical colonies of eight, and
four cells whereas the cells of Chlorella sp. were solitary. The 18S rRNA gene segment of each
micro algal species was amplified using green algae specific primers, amplified fragments
sequenced and resultant sequences submitted to NCBI database (KC790428- KC790435).
Longest fragment was subsequently annotated using BLAST at the NCBI website, however
microalgae under study could not be assigned to species level on the basis of 18s RNA sequence
analysis as more representative sequences of algae are needed in public databases to make
identification straightforward. The sequences from database showing the highest scores with 18s
RNA sequences of isolated micro algae species were retrieved from Gen Bank and phylogenetic
analysis was done using software Mega 5.0.2. Nile red staining followed by fluorescent
microscopy images revealed that size of lipid bodies was largest in Scenedesmus dimorphus and
least in Scenedesmus quadricauda. The total lipid content as percentage of dry biomass of three
algal species was also found in same order.

Recently micro algae are increasingly being recognized as a promising feedstock for biofuel production, but success in this area requires rapid strain characterization from vast unexplored biodiversity, continuous strain improvements apart from development of scalable production technologies. In present study selected isolates of three important microalgae species collected from Himachal Pradesh were characterized with a perspective to upsurge bio resources for future research and strain development. The microalgae species Scenedesmus quadricauda and Scenedesmus dimorphus were observed to form typical colonies of four and eight cells under light microscope whereas Chlorella species cells were solitary. The 18S rRNA gene segment of each micro algae species was amplified using green algae specific primers, amplified fragments sequenced and resultant sequences submitted to NCBI database (KC790428-KC790435). Longest fragment was annotated using BLAST at the NCBI website; still microalgae under study could not be assigned to species level on the basis of 18S rRNA sequence analysis as more representative sequences of algae are needed in public databases to make identification straightforward. The sequences from database showing the highest scores with 18s rRNA sequences of isolated micro algae species were retrieved from Gen Bank and phylogenetic analysis was done using software Mega 5.0.2. The micro algae species were also characterized for growth and lipid production. Although the three species did not differ significantly for growth rate as revealed by specific growth rate and doubling time but difference with respect to lipid content and biomass and lipid productivity were significant. Highest lipid content and productivity was recorded for Scenedesmus dimorphus (29.286%, 14.889 mg/l/day) followed by of Scenedesmus quadricauda and least for Chlorella species. The results indicate further studies on Scenedesmus dimorphus is required in order to exploit its potential.

Microalgae are the eukaryotic photosynthetic micro-organisms that are found in marine and freshwater environment. These naturally produce many different and unusual fats, sugars, phenols, flavonoids, bioactive compounds and hence constitute important biological resources with wide range of  applications. This study focus on evaluating the nutritional and antioxidant attributes of selected isolates of Scenedesmus quadricauda, Scenedesmus dimorphus and Chlorella sp isolated from Himachal Pradesh. The maximum carbohydrate and protein content was found in Scenedesmus dimorphus. Total phenolic and flavonoid content was observed to be highest in Chlorella sp. among the three species under study. The reports on evaluation of Scenedesmus sp are very scarce in literature and this preliminary study indicates that these species could also be exploited as food and feed supplement.

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility ofthese primers offers opportunities for phylogenetic and population research.

Gene expression studies revealed a large degree of variability in gene expression patterns particularly in tissues even in genetically identical individuals. It helps to reveal the components majorly fluctuating during the disease condition. With the advent of gene expression studies many microarray studies have been conducted in prostate cancer, but the results have varied across different studies. To better understand the genetic and biological regulatory mechanisms of prostate cancer, we conducted a meta-analysis of three major pathways i.e. androgen receptor (AR), mechanistic target of rapamycin (mTOR) and Mitogen-Activated Protein Kinase (MAPK) on prostate cancer. Meta-analysis has been performed for the gene expression data for the human species that are exposed to prostate cancer. Twelve datasets comprising AR, mTOR, and MAPK pathways were taken for analysis, out of which thirteen potential biomarkers were identified through meta-analysis. These findings were compiled based u...

The ecdB is a transcription factor, located in the echinocandin B biosynthetic gene cluster of Emericella rugulosa NRRL11440. Here, we validated the ecdB mRNA sequence for functional expression and to explore the role of EcdB protein in the echinocandin B regulation. The sequence alignment study revealed that the ecdB coding sequence was found 75 bp shorter than the reference mRNA sequence. This coding sequence encodes for EcdB protein and comprises three conserved domains; DNA binding domain (DBD), coiled-coil domain, and signature middle homology region. The full-length and DBD (truncated) DNA sequences were expressed in Escherichia coli BL21(DE3) under different tested conditions. The expression of EcdB protein was found to be toxic, which curbs the cell growth. In contrast to truncated protein (GST:EcdB1-54), the full-length (GST:EcdB) protein was expressed at very low titer and not detectable in SDS-PAGE under the varying isopropyl β-D-1-thiogalactopyranoside (IPTG), temperature, and media conditions. However, GST:EcdB1-54 was successfully purified under standard conditions (0.5 mM IPTG at 0.5OD) with 33 kDa expected size. The functionality of GST:EcdB1-54 was attained by electrophoretic mobility shift assay study as a clear band shifting showed with ecdA promoter. Taken together, we conclude that EcdB interacts with the ecdA promoter that reflected to require for echinocandin B regulation. C

Background: Indiscriminate use of synthetic insecticides to eradicate mosquitoes has caused physiological resistance. Plants provide a reservoir of biochemical compounds; among these compounds some have inhibitory effect on mosquitoes. In the present study the larvicidal, adulticidal and genotoxic activity of essential oil of Psoralea corylifolia Linn. against Culex quinquefasciatus Say was explored. Methods: Essential oil was isolated from the seeds of P. corylifolia Linn. Larvicidal and adulticidal bioassay of Cx. quinquefasciatus was carried out by WHO method. Genotoxic activity of samples was determined by comet assay. Identification of different compounds was carried out by gas chromatography-mass spectrometry analysis. Results: LC 50 and LC 90 values of essential oil were 63.38±6.30 and 99.02±16.63 ppm, respectively against Cx. quinquefasciatus larvae. The LD 50 and LD 90 values were 0.057±0.007 and 0.109±0.014 mg/cm 2 respectively against adult Cx. quinquefasciatus,. Genotoxicity of adults was determined at 0.034 and 0.069 mg/cm 2. The mean comet tail length was 6.2548±0.754 μm and 8.47±0.931 μm and the respective DNA damage was significant i.e. 6.713% and 8.864% in comparison to controls. GCMS analysis of essential oil revealed 20 compounds. The major eight compounds were caryophyllene oxide (40.79%), phenol,4-(3,7-dimethyl-3-ethenylocta-1,6-dienyl) (20.78%), caryophyllene (17.84%), α-humulene (2.15%), (+)-aromadendrene (1.57%), naphthalene, 1,2,3,4-tetra hydro-1,6dimethyle-4-(1-methyl)-, (1S-cis) (1.53%), trans-caryophyllene (0.75%), and methyl hexadecanoate (0.67%). Conclusion: Essential oil obtained from the seeds of P. corylifolia showed potent toxicity against larvae and adult Cx. quinquefasciatus. The present work revealed that the essential oil of P. corylifolia could be used as environmentally sound larvicidal and adulticidal agent for mosquito control.

Artemisia which produces a large number of secondary metabolites is naturally found in cold deserthigh altitude environment of India. Secondary metabolites such as alkaloids, flavonoids, phenols,polysaccharides and terpenes represent a significant barrier to the extraction of pure genomic DNA.
Thus, in this study, the DNA extraction protocol to extract pure genomic DNA from different Artemisiaspecies was tailored. The protocol was based on the CTAB method with slight modifications. In thestudy, 1.6 M NaCl, 2% cetyltrimethyl ammonium bromide (CTAB), 3% polyvinylpyrrolidone (PVP) and
0.5% β-mercaptoethanol was used in the extraction buffer. The incubation period was kept for 1 h at65°C with one-tenth of the volume of warm (55°C) 10% CTAB solution during the extraction process.This study described a reliable protocol for extracting good quality and optimum amount of DNA from
Artemisia species suitable for PCR analysis.

Artemisia annua is an important medicinal plant valued all over the world. Genetic characterization of 20 genotypes of A. annua collected from two valleys viz. Nubra (9,600 ft) and Leh (11,500 ft) of the Trans-Himalayan (Ladakh, India) region were analyzed using 37 polymerase chain reaction (PCR) markers (20 random amplification of polymorphic deoxyribonucleic acid. (RAPDs) and 17 inter simple sequence repeats) (ISSRs). RAPD analysis yielded 124 polymorphic fragments (96.9%), with an average of 6.2 polymorphic fragments per primer. ISSR analysis produced 85 bands, of which 78 were polymorphic (86.1%), with an average of 4.58 polymorphic fragments per primer. The primers based on (CT) n produced maximum number of bands (nine) while, (AT) n and many other motifs gave no
amplification. The genetic diversity was high among the genotypes (Nei’s genetic diversity = 0.336 and Shannon’s information index = 0.495) as measured by combination of both RAPD and ISSR markers. The mean coefficient of gene differentiation (Gst) was 0.145, indicating 85.5% of the genetic diversity resided within the genotypes. RAPD markers were found more efficient with respect to polymorphism detection, as they detected 96.9% in comparison to 86.1% for ISSR markers. It was found that the
genetic diversity among genotypes from Nubra valley was narrow than that of Leh valley, suggesting the importance and feasibility of introducing elite genotypes from different origins for Artemisia germplasm conservation and breeding programs.

The phylogenetic relationships of 36 locally grown Prunus armeniaca genotypes which are collected from nine sampling sites from two valleys viz. Nubra (9,600 ft) and Leh (11,500 ft) of trans-Himalayan region were analyzed using 31 PCR markers (20 RAPDs and 11 ISSRs). This is the first report of molecular genetic diversity studies in apricot from this region of the world. RAPD analysis yielded 139 fragments, of which 136 were polymorphic, with an average of 6.8 polymorphic fragments per primer. ISSR analysis produced 58 bands, of which 56 were polymorphic, with an average of 5.09 polymorphic fragments per primer. The primers based on (CT)n produced maximum number of bands (nine) while, (AT)n and many other motifs gave no amplification. RAPD markers were found more efficient with regards to polymorphism detection, as they detected 97.84 % as compared to 96.5 % for ISSR markers. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in RAPD and combined data of RAPD + ISSR. The results of PCA analysis were comparable to the cluster analysis. These analyses, allowed us to identify the groups corresponding to the two apricot collection sites.

Artemisia which produces a large number of secondary metabolites is naturally found in cold desert high altitude environment of India. Secondary metabolites such as alkaloids, flavonoids, phenols, polysaccharides and terpenes represent a significant barrier to the extraction of pure genomic DNA. Thus, in this study, the DNA extraction protocol to extract pure genomic DNA from different Artemisia species was tailored. The protocol was based on the CTAB method with slight modifications. In the study, 1.6 M NaCl, 2% cetyltrimethyl ammonium bromide (CTAB), 3% polyvinylpyrrolidone (PVP) and 0.5% β-mercaptoethanol was used in the extraction buffer. The incubation period was kept for 1 h at 65°C with one-tenth of the volume of warm (55°C) 10% CTAB solution during the extraction process. This study described a reliable protocol for extracting good quality and optimum amount of DNA from Artemisia species suitable for PCR analysis.

... India. Chaurasia, OP, Ballabh, B., Janifer, R., Saurav, K., Diwakar, S. and Amol, T. (2008). In: Advances in Agriculture, Environment and Health.(eds. Chaurasia, OP, Yadav, A., Rimando, AM and Terrill, TH) Satish Serial Publishing House, Delhi. pp. 512 ...

Progression through the cell cycle involves the coordinated activities of a suite of cyclin/cyclin-dependent kinase (CDK) complexes. The activities of the complexes are regulated by CDK inhibitors (CDKIs). Apart from its role as cell cycle regulators, CDKIs are involved in apoptosis, transcriptional regulation, cell fate determination, cell migration and cytoskeletal dynamics. As the complexes perform crucial and diverse functions, these are important drug targets for tumour and stem cell therapeutic interventions. However, CDKIs are represented by proteins with considerable sequence heterogeneity and may fail to be identified by simple similarity search methods. In this work we have evaluated and developed machine learning methods for identification of CDKIs. We used different compositional features and evolutionary information in the form of PSSMs, from CDKIs and non-CDKIs for generating SVM and ANN classifiers. In the first stage, both the ANN and SVM models were evaluated using Leave-One-Out Cross-Validation and in the second stage these were tested on independent data sets. The PSSM-based SVM model emerged as the best classifier in both the stages and is publicly available through a user-friendly web interface at

Background: Functional annotation of rapidly amassing nucleotide and protein sequences presents a challenging task for modern bioinformatics. This is particularly true for protein families sharing extremely low sequence identity, as for lipocalins, a family of proteins with varied functions and great diversity at the sequence level, yet conserved structures.