RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis

The Panax genus has been a source of natural medicine, benefitting human health over the ages, among which the Panax japonicus represents an important species. Our understanding of several key pathways and enzymes involved in the biosynthesis of ginsenosides, a pharmacologically active class of metabolites and a major chemical constituents of the rhizome extracts from the Panax species, are limited. Limited genomic information, and lack of studies on comparative transcriptomics across the Panax species have restricted our understanding of the biosynthetic mechanisms of these and many other important classes of phytochemicals. Herein, we describe Illumina based RNA sequencing analysis to characterize the transcriptome and expression profiles of genes expressed in the five tissues of P. japonicus, and its comparison with other Panax species. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profiling, and gene ontology enrichment analysis for five tissues of P. japonicus showed that although overall processes were evenly conserved across all tissues. However, each tissue was characterized by several unique unigenes with the leaves showing the most unique unigenes among the tissues studied. A comparative analysis of the P. japonicus transcriptome assembly with publically available transcripts from other Panax species, namely, P. ginseng, P. notoginseng, and P. quinquefolius also displayed high sequence similarity across all Panax species, with P. japonicus showing highest similarity with P. ginseng. Annotation of P. japonicus transcriptome resulted in the identification of putative genes encoding all enzymes from the triterpene backbone biosynthetic pathways, and identified 24 and 48 unigenes annotated as cytochrome P450 (CYP) and glycosyltransferases (GT), respectively. These CYPs and GTs annotated unigenes were conserved across all Panax species and co-expressed with other the transcripts involved in the triterpenoid backbone biosynthesis pathways. Unigenes identified in this study represent strong candidates for being involved in the triterpenoid saponins biosynthesis, and can serve as a basis for future validation studies.

P14: DOXYCYCLINE: A RARE CAUSE OF DRUG INDUCED PANCREATITIS

Purpose of Study

Drug-induced pancreatitis (DIP) is a rare clinicopathologic entity. We report a 58-year-old female who developed DIP secondary to administration of doxycycline.

Methods Used

A 48 year old female with a history of hypertension presented to the hospital with complains of nausea/vomiting, right upper-quadrant gnawing abdominal pain, 8/10 in intensity with radiation to the back. She denied exacerbating factors, use of alcohol, tobacco and drug. Patient also denied diarrhea, constipation and changes in skin or stool color. On examination patient was hypertensive (155/95) with a heart rate of 102. She had epigastric/right upper quadrant tenderness on superficial palpation, hypoactive bowel sounds without any palpable organs, rebound tenderness or rigidity. Serum lipase was elevated at 2508 IU/L, negative pregnancy and insignificant urinalysis findings. Liver function tests, lipid panel, chemistry panel and hematologic panel were within normal limits. Radiologic investigations with abdominal ultrasound depicted mild proximal dilatation of the common bile duct with smooth tapering of the duct distally indicating status post-cholecystectomy. Contrast enhanced computed tomography scan revealed mild enlargement of the body of the pancreas with adjacent peripancreatic fatty infiltration consistent with acute pancreatitis. Upon further questioning patient explains recent diagnosis (7 days) of tibial orthopedic hardware infection as she was prescribed doxycycline 200 mg twice a day in anticipation of irrigation of infected site. After confirmation, and discontinuation of doxycycline, our patient recovered and has been disease-free for over a month.

Summary of Results

Drug-induced pancreatitis is uncommon etiology of acute pancreatitis, which is responsible for 0.1%–2% of all the acute pancreatitis cases. Among adverse drug reactions, pancreatitis is often-ignored because of the difficulty in implicating a drug as its cause.

Conclusions

In our vastly evolving pharmacotherapy world, DIP should be included in the differential of idiopathic pancreatitis, especially after other common causes have been ruled out.

Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics

The hairy roots (HR) of Ophiorrhiza pumila produce camptothecin (CPT), a monoterpenoid indole alkaloid used as a precursor in the synthesis of chemotherapeutic drugs. O. pumila HR culture is considered as a promising alternative source of CPT, however, the knowledge about the biosynthetic pathway and regulatory mechanism is still limited. In this study, five genes that encode AP2/ERF transcription factors, namely OpERF1-OpERF5, were isolated from HR of O. pumila. Phylogenetic analysis of AP2/ERF protein sequences suggested the close evolutionary relationship of OpERF1 with stress-responsive ERF factors in Arabidopsis and of OpERF2 with ERF factors reported to regulate alkaloid production, such as ORCA3 in Catharanthus roseus, NIC2 locus ERF in tobacco, and JRE4 in tomato. We generated the transgenic HR lines of O. pumila, ERF1i and ERF2i, in which the expression of OpERF1 and OpERF2, respectively, was suppressed using RNA interference technique. The transcriptome and metabolome of these suppressed HR were analyzed for functional characterization of OpERF1 and OpERF2. Although significant changes were not observed in the metabolome, including CPT and related compounds, the suppression of OpERF2 resulted in reduced expression of genes in the 2-C-methyl-d-erythritol 4-phosphate and secologanin-strictosidine pathways, which supply a precursor, strictosidine, for CPT biosynthesis. Furthermore, while it was not conclusive for OpERF1, enrichment analysis of differentially expressed genes in the suppressed HR showed that the gene ontology terms for oxidation-reduction, presumably involved in secondary metabolite pathways, were enriched in the ERF2i downregulated gene set. These results suggest a positive role of OpERF2 in regulating specialized metabolism in O. pumila.

Omics data input for metabolic modeling

Recent advancements in high-throughput large-scale analytical methods to sequence genomes of organisms, and to quantify gene expression, proteins, lipids and metabolites have changed the paradigm of metabolic modeling. The cost of data generation and analysis has decreased significantly, which has allowed exponential increase in the amount of omics data being generated for an organism in a very short time. Compared to progress made in microbial metabolic modeling, plant metabolic modeling still remains limited due to its complex genomes and compartmentalization of metabolic reactions. Herein, we review and discuss different omics-datasets with potential application in the functional genomics. In particular, this review focuses on the application of omics-datasets towards construction and reconstruction of plant metabolic models.

Risk Factors and Outcome of Neonates Born through Meconium Stained Amniotic Fluid in a Tertiary Hospital of Nepal

Introduction: The incidence of meconium aspiration syndrome is still high in the developing world contributing significantly to the neonatal mortality. The study was aimed to know the risk factors contributing to meconium aspiration syndrome and neonatal outcome in a tertiary government hospital of the country.Materials and Methods: It was a hospital based cross sectional study done over a period of three months. All live newborns born through meconium stained liquor were enrolled and all the details regarding mother, neonate were recorded. Odd’s ratio and bivariate analysis was done to assess the risk factors for meconium aspiration syndrome.Result: Out of all the deliveries 14.6% were meconium stained amniotic fluid and meconium aspiration syndrome developed in 6.6% of the neonates. Low Apgar score and premature rupture of membranes was significantly associated with the risk of occurrence of meconium aspiration syndrome. Neonates who developed meconium aspiration syndrome had mortality of 11.3%.Conclusion: Perinatal asphyxia and premature rupture of membranes were significantly associated with the development of meconium aspiration syndrome and neonates who developed meconium aspiration syndrome had high mortality.J Nepal Paediatr Soc 2015;35(1):44-48

Supercritical extraction of sunflower oil: A central composite design for extraction variables

Supercritical carbon dioxide (SC-CO2) extraction of sunflower seed for the production of vegetable oil is investigated and compared to conventional methods. The effects of extracting variables, namely pressure, temperatures, particle size, SC-CO2 flow rate and co-solvent, on SC-CO2 extraction are investigated. The maximum yield for sunflower oil is found to be about 54.37 wt%, and is obtained when SC-CO2 extraction is carried out at 80 °C, 400 bar, 0.75 mm particle and 10 g/min solvent flow with 5% co-solvent. A central composite design is used to develop the model and also to predict the optimum conditions. At optimum conditions obtained based on desirability function, 80.54 °C, 345 bar, 1.00 mm, 10.50 g/min and 7.58% ethanol, SC-CO2 extraction has performed and found that extraction yield dropped by 2.88% from the predicted value. Fatty acid composition of SC-CO2 and hexane extracted oil shows negligible difference and found high source of linoleic acid.

Alterations in lipid and fatty acid composition of the cyanobacterium Scytonema geitleri bharadwaja under water stress

The composition of the glycerolipids [monogalactosyl diacylglycerol (MGDG), digalactosyl diacylglycerol (DGDG), sulfoquinovosyl diacylglycerol (SQDG) and phosphatidylglycerol (PG)] and alterations in their saturation and unsaturation levels in response to osmotic and matric water potential have been investigated in the cyanobacterium Scytonema geitleri Bharadwaja. The level of MGDG in S. geitleri was high followed by PG, DGDG and SQDG. Whereas, the amount of fatty acids namely palmitic, stearic, oleic, linoleic and linolenic acid were high, arachidic and behenic acid were, however, present in traces in the four glycerolipids. A significant reduction in the level of total lipid as well as individual class lipid was observed in S. geitleri in response to matric water potential to that of its total lipid and individual class lipid in response to osmotic water potential. The levels of polyunsaturated and unsaturated fatty acids also increased in response to matric water potential to that of osmotic water potential.

Locus minimization in breed prediction using artificial neural network approach

Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.

Assessment of the oral health status of healthcare-seeking adults living with HIV in Kathmandu Valley, Nepal

AIMS

This study looks to assess the oral health status in the study subjects and to quantify the prevalence of WHO defined HIV-related oral stage 3 and 4 lesions (HIV-OL) as those conditions are indicating need for treatment independently of CD4 count.

METHODS

This quantitative screening study used both structured questionnaire and clinical examination to determine the prevalence of HIV-OL in 83 adults living with HIV randomly selected from a list of service users at a community based HIV organization.

RESULTS

The screening revealed a 40 % (95%-CI: 30-51%) prevalence of HIV-OL in this population where 71 are under Antiretroviral Therapy (ART). Most frequent HIV-OL found were persistent oral candidiasis (19% prevalence), and acute necrotizing gingivitis/stomatitis (18% prevalence) Prevalence of HIV-OL was correlating with CD4 count. Patients with multiple HIV-OL have a mean of 133 CD4 cells/μl, patients with a single HIV-OL have 327 CD4 cells/μl and patients without HIV-OL do have a mean of 457CD4 cells/μl (ANOVA-p=0.002). 6 of 12 patients not taking ART yet were found to have stage 3 or 4 HIV-OL. 46 (55%) of the study population had poor or very poor oral hygiene and 29 (35%) had never had an oral examination, 36 (43%) had attended only for extraction. Only 4 of 54 patients who had previously accessed oral health care have revealed their HIV status to the dentist at that time.

CONCLUSIONS

Wider access to oral healthcare is required for people living with HIV in Kathmandu Valley/Nepal. In this setting HIV-OL are still an important consideration in assessing patients living with HIV, which can have decisive therapeutic implications. Stage 3 and 4 conditions are, independently of CD4 count, indication to start ART without delay in people living with HIV.

Sevoflurane and thoracic epidural anesthesia for trans-sternal thymectomy in a child with juvenile myasthenia gravis

Literature on anesthetic management of juvenile myasthenia gravis (JMG) for thymectomy is limited. Recently, use of inhalational agents and total intravenous anesthesia with propofol and remifentanyl has been reported. All these techniques individually or in combination have been tried to avoid the use of muscle relaxant. We report successful use of sevoflurane as sole anesthetic agent for intubation and in combination with thoracic epidural anesthesia for intraoperative anesthetic management in a 5-year-old child with JMG.

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice

In pathogenic bacteria, identification of essential proteins which are non-homologous to the host plants represents potential antimicrobial targets. We applied subtractive genomics approach for the identification of novel antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A, the causative agent of bacterial blight in rice. Comparative analysis was performed through BLAST available with the NCBI. The analysis revealed that 27 essential protein sequences out of 4,988 sequences of X. oryzae pv. oryzae PXO99A are non-homologous to Oryza sativa. Subsequent analysis of 27 essential proteins revealed their involvement in different metabolic activities such as transport activity, DNA binding, structural constituent of ribosome, cell division, translation, and plasma membrane. These 27 proteins were analyzed for virulence and novelty and out of 27, three essential non-homologous proteins were found to be the novel antimicrobial targets.

Characterization and functional analysis of eugenol O-methyltransferase gene reveal metabolite shifts, chemotype specific differential expression and developmental regulation in Ocimum tenuiflorum L

Eugenol-O-methyltransferase (EOMT) catalyzes the conversion of eugenol to methyleugenol in one of the final steps of phenylpropanoid pathway. There are no comprehensive reports on comparative EOMT gene expression and developmental stage specific accumulation of phenylpropenes in Ocimum tenuiflorum. Seven chemotypes, rich in eugenol and methyleugenol, were selected by assessment of volatile metabolites through multivariate data analysis. Isoeugenol accumulated in higher levels during juvenile stage (36.86 ng g(-1)), but reduced sharply during preflowering (8.04 ng g(-1)), flowering (2.29 ng g(-1)) and postflowering stages (0.17 ng g(-1)), whereas methyleugenol content gradually increased from juvenile (12.25 ng g(-1)) up to preflowering (16.35 ng g(-1)) and then decreased at flowering (7.13 ng g(-1)) and post flowering (5.95 ng g(-1)) from fresh tissue. Extreme variations of free intracellular and alkali hydrolysable cell wall released phenylpropanoid compounds were observed at different developmental stages. Analyses of EOMT genomic and cDNA sequences revealed a 843 bp open reading frame and the presence of a 90 bp intron. The translated proteins had eight catalytic domains, the major two being dimerisation superfamily and methyltransferase_2 superfamily. A validated 3D structure of EOMT protein was also determined. The chemotype Ot7 had a reduced reading frame that lacked both dimerisation domains and one of the two protein-kinase-phosphorylation sites; this was also reflected in reduced accumulation of methyleugenol compared to other chemotypes. EOMT transcripts showed enhanced expression in juvenile stage that increased further during preflowering but decreased at flowering and further at postflowering. The expression patterns may possibly be compared and correlated to the amounts of eugenol/isoeugenol and methyleugenol in different developmental stages of all chemotypes.

A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in Arabidopsis

Metabolic perturbations by a gain-of-function approach provide a means to alter steady states of metabolites and query network properties, while keeping enzyme complexes intact. A combination of genetic and targeted metabolomics approach was used to understand the network properties of phenylpropanoid secondary metabolism pathways. A novel quercetin oxidoreductase, QuoA, from Pseudomonas putida, which converts quercetin to naringenin, thus effectively reversing the biosynthesis of quercetin through a de novo pathway, was expressed in Arabidopsis thaliana. QuoA transgenic lines selected for low, medium, and high expression levels of QuoA RNA had corresponding levels of QuoA activity and hypocotyl coloration resulting from increased anthocyanin accumulation. Stems of all three QuoA lines had increased tensile strength resulting from increased lignification. Sixteen metabolic intermediates from anthocyanin, lignin, and shikimate pathways had increased accumulation, of which 11 paralleled QuoA expression levels in the transgenic lines. The concomitant upregulation of the above pathways was explained by a significant downregulation of the phenolamide pathway and its precursor, spermidine. In a tt6 mutant line, lignifications as well as levels of the lignin pathway metabolites were much lower than those of QuoA transgenic lines. Unlike QuoA lines, phenolamides and spermidine were not affected in the tt6 line. Taken together, these results suggest that phenolamide pathway plays a major role in directing metabolic intermediates into the lignin pathway. Metabolic perturbations were accompanied by downregulation of five genes associated with branch-point enzymes and upregulation of their corresponding products. These results suggest that gene-metabolite pairs are likely to be co-ordinately regulated at critical branch points. Thus, these perturbations by a gain-of-function approach have uncovered novel properties of the phenylpropanoid metabolic network.

The effect of (NH4)2Sx passivation on the (311)A GaAs surface and its use in AlGaAs/GaAs heterostructure devices

We have studied the efficacy of (NH4)2Sx surface passivation on the (311)A GaAs surface. We report XPS studies of simultaneously-grown (311)A and (100) heterostructures showing that the (NH4)2Sx solution removes surface oxide and sulfidizes both surfaces. Passivation is often characterized using photoluminescence measurements; we show that while (NH4)2Sx treatment gives a 40-60 ×  increase in photoluminescence intensity for the (100) surface, an increase of only 2-3 ×  is obtained for the (311)A surface. A corresponding lack of reproducible improvement in the gate hysteresis of (311)A heterostructure transistor devices made with the passivation treatment performed immediately prior to gate deposition is also found. We discuss possible reasons why sulfur passivation is ineffective for (311)A GaAs, and propose alternative strategies for passivation of this surface.

Desflurane versus opioid anesthesia for cardiac shunt procedures in infants with cyantoic congential heart disease

BACKGROUND

Placement of a Blalock-Taussig (BT) shunt is frequently performed for palliation of cyanotic congenital heart disease (CCHD).

OBJECTIVES

Inhalational anesthetics, when used in adult heart surgery, offer advantages of myocardial protection and decrease in use of inotropes, duration of ventilation, ICU and hospital length of stay (LOS).There is little literature, however, in the comparative use of inhalational and narcotic anesthesia in CCHD.

PATIENTS AND METHODS

Following Institutional Ethical Review Board approval and parental consent, 35 patients presenting for BT shunt were prospectively randomized to receive either a desflurane anesthetic or a narcotic anesthetic. Institutional practice for all patients undergoing BT shunt is to undergo cardiopulmonary bypass (CPB) following median sternotomy. Induction was accomplished with 5-7% sevoflurane in 100% oxygen, 2ug/kg fentanyl, 0.05mg/kg midazolam and 0.1mg/kg vecuronium. After intubation, patients in the narcotic group (n=16) received an additional 5-10ug/kg fentanyl, 0.1mg/kg midazolam, 100% oxygen and vecuronium. Patients in the inhalational group (n=19) received desflurane, 0.6-1 MAC, 100% oxygen, 0.05mg/kg midazolam, IV paracetamol 15mg/kg and vecuronium. At the end of surgery, patients were transferred to the ICU and received IV paracetamol and midazolam. Ventilation was weaned when the patient was hemodynamically stable. Demographics, baseline, intra and post-op heart rates, duration of inotrope use, ICU and hospital LOS, pre and post-op creatinine and serious adverse events (SAE) were recorded. Data were analyzed using Student, paired t, Mann-Whitney U and Chi square/Fisher exact tests, P < 0.05 significant.

RESULTS

Demographic data were similar, except for a modestly higher pre-op heart rate in the group receiving opioid anesthesia. Patients receiving desflurane had a significantly shorter duration of mechanical ventilation and length of ICU and hospital stay. Inotrope use was similar in both groups. The group receiving opioid anesthesia had an increase in creatinine post operatively which was not observed in the desflurane group. There was no difference in incidence of significant adverse events in either group.

CONCLUSIONS

Use of inhalational anesthesia has increased in adult cardiac surgery and has proved to reduce duration of elective ventilation, decrease ICU and hospital LOS, and mortality. Inhalational anesthetics are less well-studied in CCHD. In the current study, desflurane was chosen because of its low solubility, decreased recovery time and lack of metabolism or organ system toxicities. Although it is a popular belief that desflurane is associated with tachycardia and airway irritation, findings of the current study are consistent with those of the previous works demonstrating a lack of these side effects below 1 MAC3. No hemodynamic instability was encountered and there was no evidence that desflurane exerted a negative inotropic effect. Markers of cardio protection were not examined, although desflurane may have had a renal protective effect compared to narcotic technique. In the current study, a desflurane anesthetic for BT shunt decreased the duration of mechanical ventilation and ICU and hospital LOS by nearly three days, with no difference in perioperative morbidity or mortality. Larger studies are required to determine whether these changes result in overall decreased complication rate and morbidity/mortality and whether desflurane has a cardio or renal protective effect in the patient population.

Richard III -- the final act

On 4 February 2013 experts confirmed that the remains of the last English king to die in battle were found under a council car park in Leicester, England. Richard III, the last Plantagenet king, wore the crown from 1483 until his untimely death in 1485. There have been many myths published about him, even one with a dental reference. This paper explores what dentistry was like at the time of Richard III, reveals the truth behind the myths and sees how the University of Leicester's findings about his dentition and skull has provided an insight into his identification, lifestyle and final moments.