Genome scale metabolic modelling of Phaeodactylum tricornutum

Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable and diverse marine phytoplankton. Their ability to synthesise lipid as a storage compound (20%-50% dry cell weight) makes them a potential sources of biofuel and high-value commodities such as ω fatty acids. However, diatoms have unique features in their biochemistry as compared to higher plants and hence, there is a prior need to understand diatom metabolism to enable physiological and genetic manipulation, and improve their strains. The present work involves construction and analysis of genome scale metabolic models (GSMs) of Phaeodactylum tricornutum, a model diatom, the characterisation of physiological properties and the identification of the potential strategies to optimise the lipid production. GSMs were constructed based on a previously published model and metabolic databases, and were analysed using structural modelling techniques to understand the metabolic responses at different environmental and physiological conditions. The model results suggest change in metabolic responses, mainly associated with the Calvin cycle, reductant transfer, photorespiration, TCA cycle, glyoxylate cycle, lipid metabolism, carbohydrate metabolism and energy dissipation mechanisms under changing environmental and physiological conditions. Carbon xation and triose-phosphate production can take place solely in the chloroplast, despite of differences in the localisation and regulation of the Calvin cycle enzymes as compared to higher plants. Further, model analysis suggests that lipid production in P. tricornutum increases both when exposed to high light and with the availability of glycerol. The potential metabolic routes for lipid production involves phosphoketolase pathway, threonine metabolism, recycling of glycolate and HCO3 fixation. Based on the model analysis, experiments were designed where cultures were exposed to high light, supplemented with HCO3 , under phototrophic and mixotrophic conditions. This resulted to an increase in biomass and lipid productivity. In addition, by revealing the potential metabolic routes involved with lipid production, our work also suggests possible targets for metabolic engineering that could divert carbon towards lipid production

An Overview of Computational Approaches in Structure Based Drug Design

Drug design is a costly and difficult process. Drug must fulfill several criteria of being active, nontoxic and bioavailable. The conventional way of synthesizing drugs is a monotonous process. But computer aided drug design is a proficient way to overcome the tedious process of conventional method. Drugs can be designed computationally by structure or target based drug designing (SBDD). This review summarizes the methods of structure based drug design, usage of related softwares and a case study that explores to find a suitable drug (lead) molecule for the mutated state of H-Ras protein in order to prevent complex formation with Raf protein.Keywords: computer aided drug design; structure based drug design; Ras-proteinDOI: http://dx.doi.org/10.3126/njb.v2i1.5680Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 53-6

Successful pregnancy outcome in a patient with Robertsonian translocation (13; 14) (Q10:Q10) with recurrent pregnancy loss

Robertsonian translocations are unique type of whole-arm translocation that result from ‘centric fusion’ of the long arms of two acrocentric chromosomes with loss of the short arms, thus reducing the number of chromosomes by one. RT’s are present in 0.1% of the general population and 1% of the infertile population. Most frequent type of RT includes translocation rob (13; 14), whereas translocation rob (13; 15) and rob (14; 15) are rare. In the present report, RT in a female with spontaneous repeated abortions and infertility is reported. Cytogenetic analysis of a couple with repeated abortions revealed the presence of 45, XX, rob (13; 14) (q10; q10) chromosomal constitution in the female partner. The patient conceived after diagnostic laparoscopy followed by ovulation induction and intra uterine insemination and with proper antenatal care and support she delivered a healthy male baby with normal karyotype. The history of repeated abortions and infertility could be the outcome of unbalanced gametes (either monosomy or trisomy) resulting during the meiotic segregation of the balanced heterozygote female carrier. Cytogenetic analysis should be offered to all couples with unexplained recurrent abortions to evaluate the probable presence of any chromosomal aberrations

Role of levonorgestrel releasing intrauterine device in management of heavy menstrual bleeding: a conservative approach

Background: Heavy menstrual bleeding (HMB) is defined as prolonged (>7 days) or excessive menstrual blood loss greater than or equal to 80 ml per menstrual cycle. The objective of the study was to assess the efficacy, acceptability and side effects of LUS IUS in women with heavy menstrual bleeding.Methods: 42 women with heavy menstrual bleeding with or without associated dysmenorrhoea or chronic pelvic pain and had no contraindication to IUS insertion were included in the study. Patients having active genital tract infection, suspicion of pregnancy, uterine fibroids >2.5 cm in size or sub mucosal distorting the uterine cavity, uterine size >12 weeks, atypical endometrial hyperplasia or malignancy, abnormal cervical cytology, coagulopathy or liver disease were excluded from the study. Preliminary endometrial biopsy was done to rule out malignancy and LNG IUS was inserted under anaesthesia. Women were followed for 3,6,12 and 24 months post insertion.Results: In first 3 months, 20% patients achieved normal menstrual cycle, and at 6 months 44.44% had scanty menstrual flow and after 1 year of use 81.5% achieved amenorrhoea. In initial 3 months 37.5% patients had irregular heavy bleeding, which reduced to 13.89% at 6 months and 0% at 1 year follow up. Irregular spotting was second most complaint in 32.5% patients in initial 3 months that persisted in 7.4% patients at 1year follow up. In 5.0% patients, there was spontaneous expulsion of the device in first 3 menstrual cycles. After 3 months of use 57.5% patients were satisfied with the device and at the end of 1 year 92.5% were satisfied.Conclusions: LNG IUS is highly effective in controlling blood loss, well tolerated and better alternative for hysterectomy with higher user satisfaction in all age group of women

Molecular Characterization of Nepali Potato Cultivars Using Randomly Amplified Polymorphic DNA (Rapd) Markers

Randomly amplified polymorphic DNA (RAPD) was used to study the genetic diversity of four local cultivars of potato. Amplification with ten arbitrary decamer primers produced 29 different marker bands of which 69.0% were polymorphic. The size range of the amplified DNAs ranged between 370 bp and 2500 bp. On average, 17.5 alleles per genotype were amplified using the RAPD primers. With the selected primers sufficient polymorphism could be detected to allow identification of individual genotypes. A dendrogram displaying the relative genetic similarities between the genotypes showed a range of 55.2-69.0% similarity

Physico-chemical and microbiological characterization of the ground water across the city Bareilly (U.P.), India

The drinking water quality (underground water) of Bareilly city has been assessed by estimating physicochemical parameters and calculating Water Quality Index (WQI). Water Quality Index plays an important role in interpreting the information on water quality. The WQI of different sites shows that drinking water is of good quality. The correlation between different parameters was also estimated. During course of study the average value of physico-chemical parameters studied were observed as temperature 20.17 o C, turbidity 2.17 NTU, pH 8.13, electrical conductivity 1360 mmhos/cm, total dissolved solids 1218.9 mg/l, total hardness 515.0 mg/l chlorides 106.34 mg/l, alkalinity 342.15, fluorides 0.44 mg/l, sulphates 84.68 mg/l, nitrates 22.83 mg/l, DO 2.44 mg/l, BOD 1.26 mg/l. While average MPN were observed as 5.66 and average WQI as 21.48

A novel algorithm to calculate elementary modes : analysis of Campylobacter jejuni metabolism

We describe a novel algorithm, ‘LPEM’, that given a steady-state flux vector from a (possibly genome-scale) metabolic model, decomposes that vector into a set of weighted elementary modes such that the sum of these elementary modes is equal to the original flux vector. We apply the algorithm to a genome scale metabolic model of the human pathogen Campylobacter jejuni. This organism is unusual in that it has an absolute growth requirement for oxygen, despite being able to operate the electron transport chain anaerobically. We conclude that (1) Microaerophilly in C. jejuni can be explained by the dependence of pyridoxine 5′- phosphate oxidase for the synthesis of pyridoxal 5′- phosphate (the biologically active form of vitamin B6), (2) The LPEM algorithm is capable of determining the elementary modes of a linear programming solution describing the simultaneous production of 51 biomass precursors, (3) Elementary modes for the production of individual biomass precursors are significantly more complex when all others are produced simultaneously than those for the same product in isolation and (4) The sum of elementary modes for the production of all precursors in isolation requires a greater number of reactions and overall total flux than the simultaneous production of all precursors.peer-reviewe

Molecular Characterization of Nepali Potato Cultivars using Randomly Amplified Polymorphic DNA (RAPD) Markers

Randomly amplified polymorphic DNA (RAPD) was used to study the genetic diversity of four local cultivars of potato. Amplification with ten arbitrary decamer primers produced 29 different marker bands of which 69.0% were polymorphic. The size range of the amplified DNAs ranged between 370 bp and 2500 bp. On average, 17.5 alleles per genotype were amplified using the RAPD primers. With the selected primers sufficient polymorphism could be detected to allow identification of individual genotypes. A dendrogram displaying the relative genetic similarities between the genotypes showed a range of 55.2-69.0% similarity

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Antibacterial Evaluation of Plant Extracts: an insight into Phytomedicine

This study was carried out to evaluate the antibacterial activity of petroleum ether, methanol and aqueous extract of the two plant Ocimum sanctum and pepper nigrum extract using agar well diffusion and broth dilution method against gram-positive bacterial strains (B. firmus, B. megaterium and B. cereus) and gram-negative bacterial strains (Escherichia coli, Enterobacter sp. and Klebsiella pneumoniae). The results indicate that petroleum ether extract compare to methanol and aqueous extract of O. sanctum and P. nigrum exhibited significant antibacterial activity against gram-positive bacteria with minimum inhibitory concentration (MIC) ranging from 0.13 to 0.21x 10-4 mg/well concentration. Moreover, gram-negative bacteria were less susceptible against petroleum ether, methanol and aqueous extract of O. sanctum and P. nigrum and their MIC ranging from 0.13 to 0.21x 10-2. The most susceptible organism to the organic extracts from both studied plants was B. firmus and the most resistant organism was Enterobacter sp. The result obtained with B. cereus and K. pneumoniae were particularly interesting, since it was inhibited by antibiotic ampicillin used and susceptibility was observed with the individual extracts, where higher antibacterial activity with petroleum ether and aqueous extracts of O. sanctum and P. nigrum respectively.  The presence of phytochemicals such as alkaloids, tannins, saponin, triterpenoids, steroids and glycosides in the extracts of these plants supports their traditional uses as medicinal plants for the treatment of various ailments. The present study reveals potential use of these plants for developing new antibacterial herbal drugs against pathogenic microorganisms