bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of starch synthesis results in overproduction of lipids in Chlamydomonas reinhardtii
Authors: Li Yantao , Han Danxiang , Hu Guangrong , Sommerfeld Milton , Hu Qiang
Published: May 2010

Starch and neutral lipids are two major carbon storage compounds in many microalgae and plants. Lipids are more energy rich and have often been used as food and fuel feedstocks. Genetic engineering of the lipid biosynthesis pathway to overproduce lipid has achieved only limited success. We hypothesize that through blocking the competing pathway to produce starch, overproduction of neutral lipid may be achieved. This hypothesis was tested using the green microalga Chlamydomonas reinhardtii and its low starch and starchless mutants. We discovered that a dramatic increase in neutral lipid content and the neutral lipid/total lipid ratio occurred among the mutants under high light and nitrogen starvation. BAFJ5, one of the mutants defective in the small subunit of ADP‐glucose pyrophosphorylase, accumulated neutral and total lipid of up to 32.6% and 46.4% of dry weight (DW) or 8‐ and 3.5‐fold higher, respectively, than the wild‐type. These results confirmed the feasibility of increasing lipid production through redirecting photosynthetically assimilated carbon away from starch synthesis to neutral lipid synthesis. However, some growth impairment was observed in the low starch and starchless mutants, possibly due to altered energy partitioning in PSII, with more excitation energy dissipated as heat and less to photochemical conversion. This study demonstrated that biomass and lipid production by the selected mutants can be improved by physiological manipulation. Biotechnol. Bioeng. 2010;107: 258–268. © 2010 Wiley Periodicals, Inc.
Effect of carbon source addition on toluene biodegradation by an Escherichia coli DH5α transconjugant harboring the TOL plasmid
Authors: Ikuma Kaoru , Gunsch Claudia
Published: May 2010

Horizontal gene transfer (HGT) of plasmids is a naturally occurring phenomenon which could be manipulated for bioremediation applications. Specifically, HGT may prove useful to enhance bioremediation through genetic bioaugmentation. However, because the transfer of a plasmid between donor and recipient cells does not always result in useful functional phenotypes, the conditions under which HGT events result in enhanced degradative capabilities must first be elucidated. The objective of this study was to determine if the addition of alternate carbon substrates could improve toluene degradation in Escherichia coli DH5α transconjugants. The addition of glucose (0.5–5 g/L) and Luria–Bertani (LB) broth (10–100%) resulted in enhanced toluene degradation. On average, the toluene degradation rate increased 14.1 (±2.1)‐fold in the presence of glucose while the maximum increase was 18.4 (±1.7)‐fold in the presence of 25% LB broth. Gene expression of xyl genes was upregulated in the presence of glucose but not LB broth, which implies different inducing mechanisms by the two types of alternate carbon source. The increased toluene degradation by the addition of glucose or LB broth was persistent over the short‐term, suggesting the pulse amendment of an alternative carbon source may be helpful in bioremediation. While the effects of recipient genome GC content and other conditions must still be examined, our results suggest that changes in environmental conditions such as alternate substrate availability may significantly improve the functionality of the transferred phenotypes in HGT and therefore may be an important parameter for genetic bioaugmentation optimization. Biotechnol. Bioeng. 2010;107: 269–277. © 2010 Wiley Periodicals, Inc.
Growth, lipid content, productivity, and fatty acid composition of tropical microalgae for scale‐up production
Authors: Huerlimann Roger , de Nys Rocky , Heimann Kirsten
Published: May 2010

Biomass and lipid productivity, lipid content, and quantitative and qualitative lipid composition are critical parameters in selecting microalgal species for commercial scale‐up production. This study compares lipid content and composition, and lipid and biomass productivity during logarithmic, late logarithmic, and stationary phase of Nannochloropsis sp., Isochrysis sp., Tetraselmis sp., and Rhodomonas sp. grown in L1‐, f/2‐, and K‐medium. Of the tested species, Tetraselmis sp. exhibited a lipid productivity of 3.9–4.8 g m−2 day−1 in any media type, with comparable lipid productivity by Nannochloropsis sp. and Isochrysis sp. when grown in L1‐medium. The dry biomass productivity of Tetraselmis sp. (33.1–45.0 g m−2 day−1) exceeded that of the other species by a factor 2–10. Of the organisms studied, Tetraselmis sp. had the best dry biomass and/or lipid production profile in large‐scale cultures. The present study provides a practical benchmark, which allows comparison of microalgal production systems with different footprints, as well as terrestrial systems. Biotechnol. Bioeng. 2010;107: 245–257. © 2010 Wiley Periodicals, Inc.
Disperse distribution of cationic amino acids on hydrophilic surface of helical wheel enhances antimicrobial peptide activity
Authors: Kim Young Soo , Cha Hyung Joon
Published: May 2010

The antimicrobial action of amphipathic antimicrobial peptides (AMPs) generally depends on perturbation of the bacterial membrane via electrostatic interactions promoting initial binding to the surface and hydrophobic interactions for pore formation into the membrane. Several studies have focused on the structure–activity relationship (SAR) of AMPs by modulation of structural parameters. However, modulation of one parameter commonly induces simultaneous changes in other parameters, making it difficult to investigate the specific influence of a single variable. In the present work, we investigated the distribution effect of cationic amino acids on the hydrophilic surface of the helical wheel using model AMPs composed of only lysine (K) and leucine (L) as representative cationic and hydrophobic residues, respectively, under conditions in which other parameters are fixed. Based on SAR analyses of α‐helical KL model AMPs displaying different cationic distributions, we propose that the dispersity of cationic amino acids on the hydrophilic surface is a factor that contributes to the antimicrobial activity of AMP. Moreover, antimicrobial activity is enhanced by rearrangement of cationic amino acids to promote dispersed distribution. We confirmed the cationic distribution effect using natural AMP‐derived α‐helical CRAMP18 and its analogs. Our data show that accumulation of lysine shifts in the CRAMP18 analog leads to higher dispersion, and subsequently to improved antimicrobial activity. Therefore, we propose that the cationic distribution effect can be applied for the rational redesign of amino acid sequences to improve the antimicrobial activities of natural α‐helical AMPs, in combination with regulation of other known structural parameters. Biotechnol. Bioeng. 2010;107: 216–223. © 2010 Wiley Periodicals, Inc.
Ethanol production from paper sludge by simultaneous saccharification and co‐fermentation using recombinant xylose‐fermenting microorganisms
Authors: Zhang Jiayi , Lynd Lee R.
Published: May 2010

Simultaneous saccharification and co‐fermentation (SSCF) of waste paper sludge to ethanol was investigated using two recombinant xylose‐fermenting microbes: Zymomonas mobilis 8b and Saccharomyces cerevisiae RWB222. S. cerevisiae RWB222 produced over 40 g/L ethanol with a yield of 0.39 g ethanol/g carbohydrate on paper sludge at 37°C, while similar titers and yields were achieved by Z. mobilis 8b at 30°C. Both S. cerevisiae RWB222 and Z. mobilis 8b exhibited decreasing cell viability at 37°C when producing over 40 g/L ethanol. A high ethanol concentration can account for S. cerevisiae RWB222 viability loss, but ethanol concentration was not the only factor influencing Z. mobilis 8b viability loss at 37°C. Over 3 g/L residual glucose was observed at the end of paper sludge SSCF by Z. mobilis 8b, and a statistical analysis revealed that a high calcium concentration originating from paper sludge, a high ethanol concentration, and a high temperature were the key interactive factors resulting in glucose accumulation. The highest ethanol yields were achieved by SSCF of paper sludge with S. cerevisiae RWB222 at 37°C and Z. mobilis 8b at 30°C. With good sugar consumption at 37°C, S. cerevisiae RWB222 was able to gain an improvement in the polysaccharide to sugar yield compared to that at 30°C, whereas Z. mobilis 8b at 30°C had a lower polysaccharide to sugar yield, but a higher sugar to ethanol yield than S. cerevisiae. Both organisms under optimal conditions achieved a 19% higher overall conversion of paper sludge to ethanol than the non‐xylose utilizing S. cerevisiae D5A at its optimal process temperature of 37°C. Biotechnol. Bioeng. 2010;107: 235–244. © 2010 Wiley Periodicals, Inc.
An investigation of intracellular glycosylation activities in CHO cells: Effects of nucleotide sugar precursor feeding
Authors: Wong Niki S.C. , Wati Lydia , Nissom Peter M. , Feng H.T. , Lee M.M. , Yap Miranda G.S.
Published: May 2010

Controlling glycosylation of recombinant proteins produced by CHO cells is highly desired as it can be directed towards maintaining or increasing product quality. To further our understanding of the different factors influencing glycosylation, a glycosylation sub‐array of 79 genes and a capillary electrophoresis method which simultaneously analyzes 12 nucleotides and 7 nucleotide sugars; were used to generate intracellular N‐glycosylation profiles. Specifically, the effects of nucleotide sugar precursor feeding on intracellular glycosylation activities were analyzed in CHO cells producing recombinant human interferon‐γ (IFN‐γ). Galactose (±uridine), glucosamine (±uridine), and N‐acetylmannosamine (ManNAc) (±cytidine) feeding resulted in 12%, 28%, and 32% increase in IFN‐γ sialylation as compared to the untreated control cultures. This could be directly attributed to increases in nucleotide sugar substrates, UDP‐Hex (∼20‐fold), UDP‐HexNAc (6‐ to 15‐fold) and CMP‐sialic acid (30‐ to 120‐fold), respectively. Up‐regulation of B4gal and St3gal could also have enhanced glycan addition onto the proteins, leading to more complete glycosylation (sialylation). Combined feeding of glucosamine + uridine and ManNAc + cytidine increased UDP‐HexNAc and CMP‐sialic acid by another two‐ to fourfold as compared to feeding sugar precursors alone. However, it did not lead to a synergistic increase in IFN‐γ sialylation. Other factors such as glycosyltransferase or glycan substrate levels could have become limiting. In addition, uridine feeding increased the levels of uridine‐ and cytidine‐activated nucleotide sugars simultaneously, which could imply that uridine is one of the limiting substrates for nucleotide sugar synthesis in the study. Hence, the characterization of intracellular glycosylation activities has increased our understanding of how nucleotide sugar precursor feeding influence glycosylation of recombinant proteins produced in CHO cells. It has also led to the optimization of more effective strategies for manipulating glycan quality. Biotechnol. Bioeng. 2010;107: 321–336. © 2010 Wiley Periodicals, Inc.
Rapid characterization and quality control of complex cell culture media solutions using raman spectroscopy and chemometrics
Authors: Li Boyan , Ryan Paul W. , Ray Bryan H. , Leister Kirk J. , Sirimuthu Narayana M.S. , Ryder Alan G.
Published: May 2010

The use of Raman spectroscopy coupled with chemometrics for the rapid identification, characterization, and quality assessment of complex cell culture media components used for industrial mammalian cell culture was investigated. Raman spectroscopy offers significant advantages for the analysis of complex, aqueous‐based materials used in biotechnology because there is no need for sample preparation and water is a weak Raman scatterer. We demonstrate the efficacy of the method for the routine analysis of dilute aqueous solution of five different chemically defined (CD) commercial media components used in a Chinese Hamster Ovary (CHO) cell manufacturing process for recombinant proteins.The chemometric processing of the Raman spectral data is the key factor in developing robust methods. Here, we discuss the optimum methods for eliminating baseline drift, background fluctuations, and other instrumentation artifacts to generate reproducible spectral data. Principal component analysis (PCA) and soft independent modeling of class analogy (SIMCA) were then employed in the development of a robust routine for both identification and quality evaluation of the five different media components. These methods have the potential to be extremely useful in an industrial context for “in‐house” sample handling, tracking, and quality control. Biotechnol. Bioeng. 2010;107: 290–301. © 2010 Wiley Periodicals, Inc.
Choreographing emotional facial expressions
Authors: Sloan Robin J.S. , Robinson Brian , Scott‐Brown Ken , Moore Fhionna , Cook Malcolm
Published: May 2010

While much is known about the appearance and human perception of emotional facial expressions, researchers and professionals experience difficulties when attempting to create believable animated characters. Methods for automating or capturing dynamic facial expressions have come on in leaps and bounds in recent years, resulting in increasingly realistic characters. However, accurate replication of naturalistic movement does not necessarily ensure authentic character performance. In this paper, the authors present a project which makes use of creative animation practices and artistic reflection as methods of research. The output of animation practice is tested experimentally by measuring observer perception and comparing the results with artistic observations and predictions. Ultimately, the authors aim to demonstrate that animation practice can generate new knowledge about dynamic character performance, and that arts‐based methods can and should be considered valuable tools in a field often dominated by technical methods of research. Copyright © 2010 John Wiley & Sons, Ltd.
Contribution of the Bees and Combs to Honey Volatiles: Blank‐Trial Probe for Chemical Profiling of Honey Biodiversity
Authors: Jerković Igor , Marijanović Zvonimir , Ljubičić I. , Gugić M.
Published: May 2010

This research is focused on the immediate contribution of the bees and combs to honey volatiles in order to exclude these compounds as botanical‐origin biomarkers for honey authentification. Therefore, the bees were closed in a hive containing empty combs under controlled food‐flow conditions (saccharose solution). The obtained ‘saccharose honey’ probe samples were subjected to ultrasonic solvent extraction (USE), followed by gas chromatography and mass spectrometry analyses (GC and GC/MS). A total of 66 compounds were identified. Higher alcohols made up ca. 50% of the total volatiles, mainly (Z)‐octadec‐9‐en‐1‐ol, hexadecan‐1‐ol, and octadecan‐1‐ol, with minor percentages of undecan‐1‐ol, dodecan‐1‐ol, tetradecan‐1‐ol, pentadecan‐1‐ol, and heptadecan‐1‐ol. Other abundant compounds were saturated long‐chain linear hydrocarbons, C10–C25, C27, and C28, particularly C23, C25, and C27). Identified chemical structures were related to the composition of combs and cuticular waxes, and less to the bee pheromones. In addition, the impact of two‐hour heat treatment at 80° and one‐year storage at room temperature on the same probe was investigated in order to identify thermal and storage artefacts. These findings can be considered as blank‐trial probe (no plant source) for honey chemical profiling and identification of reliable botanical origin biomarkers.
Composition and Biological Properties of the Volatile Oil of Artemisia gorgonumWebb
Authors: Ortet Risoleta , Thomas Olivier P. , Regalado Erik L. , Pino Jorge A. , Filippi Jean‐Jacques , Fernández Miguel D.
Published: May 2010

The chemical composition of Artemisia gorgonum Webb essential oil from Cape Verde was analyzed by GC and GC/MS. A total of 111 volatile compounds, accounting for 94.9% of the essential oil, were identified by GC and GC/MS. The major compounds were camphor (28.7%), chrysanthenone (10.8%), lavandulyl 2‐methylbutanoate (9.5%), α‐phellandrene (5.5%), lavandulyl propanoate (4.2%), camphene (4.0%), and p‐cymene (3.4%). The volatile oil of this endemic plant, which is used in Cape Verdean folk medicine against several ailments, was tested for its antioxidant and antimalarial properties, and was found to exhibit free‐radical scavenging on 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH), prevention of lipid peroxidation–in vitro by TBARS (thiobarbituric acid reactive species) assay, and antiplasmodial activity.
Influence of the Continental Climatic Conditions on the Essential‐Oil Composition of Salvia brachyodonVandas Transferred from Adriatic Coast
Authors: Vidic Danijela , Maksimović Milka , Ćavar Sanja , Siljak‐Yakovlev Sonja
Published: May 2010

Essential‐oil profile of Salvia brachyodon Vandas, an endemic Dinaric species transferred from Adriatic Coast to the continental climatic conditions, was determined. Hydrodistilled oils obtained from the plant material collected in three‐year field trial were subjected to the detailed GC/MS analysis. Hundred and fifty volatile compounds were identified in four samples. Comparison of the chemical composition of the isolated essential oils showed that population collected one year after transfer preserved sesquiterpene character of its oil (74.3%), while all subsequent samples gave the oils of monoterpene type with 1,8‐cineole as the principal constituent (22.2–42.3%). The high degree of variation in the qualitative and quantitative composition of the volatile constituents revealed the strong influence of environmental conditions on the nature of plant chemical composition that has an important role in a plant adaptation.
Comparative Analysis of Essential Oils of Six Anthemis Taxa from Serbia and Montenegro
Authors: Pavlović Milica , Lakušić Dmitar , Kovačević Nada , Tzakou Olga , Couladis Maria
Published: May 2010

The essential‐oil composition of six Anthemis taxa from several populations in Serbia and Montenegro, Anthemis triumfetti (L.) DC., A. tinctoria L., A. austriaca Jacq., A. ruthenica Bieb., A. cotula L., and A. cretica ssp. carpatica (Willd.) Grierson were analyzed by GC and GC/MS. The main constituents have been identified as follows: camphor (13.8–15.4%), α‐pinene (5.2–9.3%), β‐pinene (4.9–7.8%), and (E)‐caryophyllene (7.3–9.8%) in three populations, and cis‐chrysanthenol (27.0%) and 1,8‐cineole (8.4%) in one population of A. triumfetti; 1,8‐cineole (9.0–25.8%) in the oils of five populations, and borneol (16.0%) and spatulenol (16.0%) in the oil of one population of A. tinctoria; cis‐chrysanthenyl acetate (17.5–22.0%), β‐pinene (8.6–13.2%), and 1,8‐cineole (7.2–10.4%) in the oils of A. austriaca; germacrene D (8.3–11.3%) and terpinen‐4‐ol (6.3–7.3%) in A. ruthenica oils; β‐cedrene (10.3–19.0%), (E)‐β‐farnesene (7.8–13.5%), and germacrene D (5.2–9.1%) in the oils of A. cotula; cis‐thujone (39.0%), trans‐thujone (13.5%), and yomogi alcohol (7.1%) in the oil of A. cretica ssp. carpatica. The essential oil of A. austriaca was studied for the first time. A cluster analysis based on the relative percentages of all components of the essential oils was used to determine the distances between taxa and populations.
Four New Sesquiterpenes from Curcuma wenyujin and Their Inhibitory Effects on Nitric‐Oxide Production
Authors: Lou Yan , Zhao Feng , He Hao , Peng Kai‐Feng , Chen Li‐Xia , Qiu Feng
Published: May 2010

Four new sesquiterpenes including the novel sesquiterpene lactone (6R)‐dehydroxysipanolinolide (1), two new eudesmane‐type sesquiterpenes, curcolide (2) and curcodione (3), and a new xanthane‐type sesquiterpene, curcumadionol (4), were isolated from Curcuma wenyujin Y. H. Chen et C. Ling, together with five known ones, 5–9. The structures of the new compounds were elucidated by spectroscopic methods. The inhibitory effects of compounds 1–9 on nitric‐oxide production in lipopolysaccaride‐activated macrophages were evaluated.
Chemopreventive Properties of Phytosterols and Maslinic Acid Extracted from Coleus tuberosus in Inhibiting the Expression of EBV Early‐Antigen in Raji Cells
Authors: Mooi Lim Yang , Wahab Norhanom Abdul , Lajis Nordin Haji , Ali Abdul Manaf
Published: May 2010

Bioassay‐guided fractionation of a MeOH extract of tubers of Coleus tuberosus afforded the active anti‐tumor‐promoting compounds identified as the triterpenoid 2α,3β‐dihydroxyolean‐12‐en‐28‐oic acid (maslinic acid; CT2) and a phytosterol mixture (CT1). CT1 consists of stigmasterol (32%), β‐sitosterol (40.3%), and campesterol (27.7%) as determined by capillary gas chromatography. CT1 and CT2 showed very strong anti‐tumor‐promoting activities at IC50 0.7 μg/ml and 0.1 μg/ml, respectively, in a convenient, short‐term in vitro assay, i.e., the inhibition of Epstein–Barr virus (EBV) activation induced by phorbol 12‐myristate 13‐acetate (PMA) and sodium butyrate. We report for the first time the anti‐tumor‐promoting activity of 2α,3β‐dihydroxyolean‐12‐en‐28‐oic acid and show that a mixture of stigmasterol, β‐sitosterol, and campesterol is more potent than the individual components in inhibiting tumor‐promoting activity.
Leaf Essential Oil of Juniperus oxycedrus L. (Cupressaceae) Harvested in Northern Tunisia: Composition and Intra‐Specific Variability
Authors: Medini Hanen , Elaissi Ameur , Khouja Mohamed L. , Chraief Imed , Farhat Farhat , Hammami Mohamed , Chemli Rachid , Harzallah‐Skhiri Fethia
Published: May 2010

The essential oil composition of leaves of 60 individual trees of Juniperus oxycedrus L. growing in four locations in Tunisia harvested in three different seasons were investigated by GC and GC/MS. Seventy compounds were identified in the oils, and a relatively high variation in their contents were found. All the oils were dominated by terpenic hydrocarbons, with α‐pinene (27.35–58.03%) as the main component, followed by geranyl acetone (13; 1.96–7.14%), 13‐epimanoyl oxide (16; 1.35–6.95%), and eudesma‐4(15),7‐dien‐1‐ol (11; 1.39–4.18%). The 18 major oil components were processed by hierarchical clustering and principal component analysis (PCA) allowing to establish four groups, one divided into two subgroups, of populations according to the location and season of harvest. Their oils were differentiated by one compound or more, showing a clear seasonal and geographical polymorphism in their chemical composition allowing the identification of specific chemotypes. The pattern of geographic variation in the essential oil composition indicated that the oils of the populations from the continental site (Makthar) were clearly distinguished from those of the littoral localities (Tabarka, Hawaria, and Rimel).
Variation of the Chemical Composition of Essential Oils in Tunisian Populations of Thymus algeriensisBoiss. et Reut. (Lamiaceae) and Implication for Conservation
Authors: ElHadj Ali Imen Ben , Zaouali Yosr , Bejaoui Afef , Boussaid Mohamed
Published: May 2010

The variation of the essential‐oil composition among 14 Tunisian natural populations of Thymus algeriensis Boiss. et Reut. (=Thymus hirtus Willd. ssp. algeriensis Boiss. et Reut.) was assessed by GC (RI) and GC/MS. The populations were collected from different geographical regions belonging to the sub‐humid, upper semi‐arid, mean semi‐arid, lower semi‐arid, and upper‐arid bioclimates. A total of 47 constituents, representing 81.0 to 96.5% of the total oil, were identified. The main volatiles at the species level were 1,8‐cineole (17.7%), α‐pinene (15.5%), and camphor (8.2%). A high variation among populations for the majority of the compounds was shown. Camphor (0.2–14.0%), linalool (0.2–22.4%), borneol (<0.01–24.3%), caryophyllene oxide (<0.01–18.8%), thymol (<0.01–54.9%), γ‐terpinene (0.4–6.5%), α‐copaene (0.4–7.6%), linalyl acetate (<0.01–6.4%), and methyl eugenol (<0.01–6.9%) were the main constituents differentiating the populations. The chemical differentiation among populations, assessed by principal component analysis (PCA) and a UPGMA (unweighted pair‐group method with averaging) cluster analysis performed on all populations and compounds, was high. Six chemotypes according to the main compounds have been distinguished, i.e., caryophyllene oxide/1,8‐cineole/α‐pinene, 1,8‐cineole/α‐pinene, 1,8‐cineole/α‐pinene/camphor, borneol/1,8‐cineole/α‐pinene, linalool, and thymol chemotypes. The spatial chemotype distribution was linked to the geographic distance among populations rather than to bioclimates, indicating that local selective environmental factors act on the chemotype diversity.

The high chemical variation among populations according to their geographical and bioclimatic distribution imposes that conservation strategies of populations should be made appropriately, taking into account these factors. The in situ and ex situ conservation strategies should concern all populations representing the different chemotypes.
Essential Oil of Terminalia chebula Fruits as a Repellent for the Indian Honeybee Apis florea
Authors: Naik Dattatraya G. , Puntambekar Hemalata , Anantpure Priyanka
Published: May 2010

Plant‐based repellent formulations for honeybees play an important role in the bee management. For this purpose, the essential oil of an Indian medicinal plant, Terminalia chebula, commonly known as Myrobalan, was isolated for the first time. Hitherto unknown chemical constituents of the essential oil were determined by GC/MS. The repellent activity of formulations of the essential oil, tested towards the Indian honeybee Apis florea, was found to be dose dependent. The repellency (ΔR) increased with the concentration of essential oil in the formulations, reaching a maximum for the formulation containing 50 mg/ml of oil. A further increase in the oil concentration was found to reduce the ΔR. The screening of formulations of the major essential‐oil components identified indicated that formulations of furfural, 5‐methylfurfural, tetradecanoic acid, palmitic acid, and oleic acid elicited no response in honeybees. In contrast, the formulations of phenylacetaldehyde were repellent, while those of ethyl cinnamate were attractant. These findings might be an asset for beekeepers to improve the bee management. Attractant formulations are effective to attract bees to the desired areas, thus improving the efficiency of pollination. Repellent formulations are used to repel honeybees, especially when toxic insecticides are sprayed on the fields.
In vitro Ruthenation of Human Breast Cancer Suppressor Gene 1 (BRCA1) by the Antimetastasis Compound RAPTA‐C and Its Analogue CarboRAPTA‐C
Authors: Ratanaphan Adisorn , Temboot Pornvichai , Dyson Paul J.
Published: May 2010

The interaction of two ruthenium–arene–1,3,5‐triaza‐7‐phosphaadamantane compounds ([Ru(η6‐p‐cymene)Cl2(pta)] and [Ru(η6‐p‐cymene)(C6H6O4)(pta)], termed RAPTA‐C (3) and carboRAPTA‐C (4), resp.) with the DNA sequence of the human breast‐cancer suppressor gene 1 (BRCA1) has been studied using a range of techniques that probe conformation, cross‐linking, base specificity, restriction analysis, and in vitro inhibition of DNA polymerization. The study demonstrates that substitution of the two labile chloride ligands in 3 by the more stable cyclobutane‐1,1‐dicarboxylate ligand onto the RAPTA framework reduces the rate of reaction with DNA in a similar manner to the analogous Pt‐based drug pair cisplatin (1) and carboplatin (2), suggesting that hydrolysis may be a prerequisite to DNA binding with the Ru compounds. Moreover, the rate of DNA interaction for 3 is in a similar range to that of 2, despite the fact that these compounds have a different therapeutic profile. The similar rates of reaction contrasting with the different modes of activity suggests that the RAPTA compounds may be clinically useful against cancer cells that have developed resistance to Pt‐based therapies, particularly involving excision–repair mechanisms.
Computational Analysis of the Evolution of 1‐Deoxy‐D‐xylulose‐5‐phosphate Reductoisomerase, an Important Enzyme in Plant Terpene Biosynthesis
Authors: Fung Pui Kwan , Krushkal Julia , Weathers Pamela J.
Published: May 2010

Isoprenoids are a highly diverse and important group of natural compounds. The enzyme 1‐deoxy‐D‐xylulose‐5‐phosphate reductoisomerase (DXR) catalyzes a key regulatory step in the non‐mevalonate isoprenoid biosynthetic pathway in eubacteria and in plant plastids. For example, inArtemisia annuaDXR participates in regulation of the biosynthesis of artemisinin, an important antimalarial drug. We performed phylogenetic analysis using DXR protein sequences from a model prokaryote,Escherichia coli, a picoplanktonic alga,Ostreococcus lucimarinus, and higher plants. The functional domain of DXR was conserved, allowing molecular evolutionary comparisons of both prokaryotic and eukaryotic sequences of DXR. Despite this conservation, for some plant species such asCampthoteca acuminataandArabidopsis thaliana, phylogenetic relationships of their lineages were consistently violated. Our analysis revealed that plant DXR has an N‐terminal transit domain that is likely bipartite, consisting of a chloroplast transit peptide (cTP) and a lumen transit peptide (lTP). Several features observed in the lTP suggest that, while DXR is targeted to the chloroplast, it is localized to the thylakoid lumen. These features include a twin arginine motif, a hydrophobic region, and a proline‐rich region. The transit peptide also showed putative motifs for a 14‐3‐3 binding site with a chaperone phosphorylation site at Thr.
Exploring Biodiversity for Cellulosic Biofuel Production
Authors: Gowen Christopher M. , Fong Stephen S.
Published: May 2010

Industrial production of solvents such as EtOH and BuOH from cellulosic biomass has the potential to provide a sustainable energy source that is relatively cheap, abundant, and environmentally sound, but currently production costs are driven up by expensive enzymes, which are necessary to degrade cellulose into fermentable sugars. These costs could be significantly reduced if a microorganism could be engineered to efficiently and quickly convert cellulosic biomass directly to product in a one‐step process. There is a large amount of biodiversity in the number of existing microorganisms that naturally possess the enzymes necessary to convert cellulose to usable sugars, and many of these microorganisms can directly ferment sugars to EtOH or other solvents. Currently, the vast majority of cellulolytic organisms are poorly understood and have complex metabolic networks. In this review, we survey the current state of knowledge on different cellulases and metabolic capabilities found in various cellulolytic microorganisms. We also propose that the use of large‐scale metabolic models (and associated analyses) is potentially an ideal means for improving our understanding of basic metabolic network function and directing metabolic engineering efforts for cellulolytic microorganisms.
Fault Diagnosis Engineering in Molecular Signaling Networks: An Overview and Applications in Target Discovery
Authors: Abdi Ali , Emamian Effat S.
Published: May 2010

Fault diagnosis engineering is a key component of modern industrial facilities and complex systems, and has gone through considerable developments in the past few decades. In this paper, the principles and concepts of molecular fault diagnosis engineering are reviewed. In this area, molecular intracellular networks are considered as complex systems that may fail to function, due to the presence of some faulty molecules. Dysfunction of the system due to the presence of a single or multiple molecules can ultimately lead to the transition from the normal state to the disease state. It is the goal of molecular fault diagnosis engineering to identify the critical components of molecular networks, i.e., those whose dysfunction can interrupt the function of the entire network. The results of the fault analysis of several signaling networks are discussed, and possible connections of the findings with some complex human diseases are examined. Implications of molecular fault diagnosis engineering for target discovery and drug development are outlined as well.
Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned
Authors: Sullivan Daniel E. , Gabbard Joseph L. , Shukla Maulik , Sobral Bruno
Published: May 2010

Systems‐biology and infectious‐disease (host–pathogen–environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five‐year projects focused on pathosystems biology: thePathosystems Resource Integration Center(PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures‐development communities based on genomics data, and theResource Center for Biodefense Proteomics Research(RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include1) an approach for addressing discrepancies between experiment results and interpreted results, and2) expanding the range of data‐integration techniques to include usability engineering at the presentation level.
Network Analysis of EtOH‐Related Candidate Genes
Authors: Guo An‐Yuan , Sun Jingchun , Jia Peilin , Zhao Zhongming
Published: May 2010

Recently, we collected many large‐scale datasets for alcohol dependence and EtOH response in five organisms and deposited them in our EtOH‐related gene resource database (ERGR, http://bioinfo.mc.vanderbilt.edu/ERGR/). Based on multidimensional evidence among these datasets, we prioritized 57 EtOH‐related candidate genes. To explore their biological roles, and the molecular mechanisms of EtOH response and alcohol dependence, we examined the features of these genes by the Gene Ontology (GO) term‐enrichment test and network/pathway analysis. Our analysis revealed that these candidate genes were highly enriched in alcohol dependence/alcoholism and highly expressed in brain or liver tissues. All the significantly enriched GO terms were related to neurotransmitter systems or EtOH metabolic processes. Using the Ingenuity Pathway Analysis system, we found that these genes were involved in networks of neurological disease, cardiovascular disease, inflammatory response, and small molecular metabolism. Many key genes in signaling pathways were in the central position of these networks. Furthermore, our protein–protein interaction (PPI) network analysis suggested some novel candidate genes which also had evidence in the ERGR database. This study demonstrated that our candidate gene selection is effective and our network/pathway analysis is useful for uncovering the molecular mechanisms of EtOH response and alcohol dependence. This approach can be applied to study the features of candidate genes of other complex traits/phenotypes.
Functional Features, Biological Pathways, and Protein Interaction Networks of Addiction‐Related Genes
Authors: Sun Jingchun , Zhao Zhongming
Published: May 2010

Addictions are chronic and common brain disorders affected by many genetic, environmental, and behavioral factors. Recent genome‐wide linkage and association studies have revealed several promising genomic regions and multiple genes relating to addictions. To explore the underlying biological processes in the development of addictions, we used 62 genes recently reviewed by Li and Burmeister (2009) as representative addiction‐related genes, and then we investigated their features in gene function, pathways, and protein interaction networks. We performed enrichment tests of their Gene Ontology (GO) annotations and of their pathways in the Ingenuity Pathways Analysis (IPA) system. The tests revealed that these addiction‐related genes were highly enriched in neurodevelopment‐related processes. Interestingly, we found circadian rhythm signaling in one of the enriched pathways. Moreover, these addiction‐related genes tended to have higher connectivity and shorter characteristic shortest‐path distances compared to control genes in the protein–protein interaction (PPI) network. This investigation is the first of such kind in addiction studies, and it is useful for further addiction candidate‐gene prioritization and verification, thus helping us to better understand molecular mechanisms of addictions.
Gene Network Analysis during Early Infection of Human Coronary Artery Smooth Muscle Cells by Trypanosoma cruzi and Its gp83 Ligand
Authors: Nde Pius N. , Johnson Candice A. , Pratap Siddharth , Cardenas Tatiana C. , Kleshchenko Yuliya Y. , Furtak Vyacheslav A. , Simmons Kaneatra J. , Lima Maria F. , Villalta Fernando
Published: May 2010

Trypanosoma cruzi, the causative agent of Chagas' disease, infects heart and muscle cells leading to cardiac arrest, followed by death. The genetic architectures in the early T. cruzi infection process of human cells are unknown. To understand the genetic architectures of the early invasion process of T. cruzi, we conducted gene transcription microarray analysis, followed by gene network construction of the host cell response in primary human coronary artery smooth muscle (HCASM) cells infected with T. cruzi or exposed to T. cruzi gp83, a ligand used by the trypanosome to bind host cells. Using seven RT‐PCR verified up‐regulated genes (FOSB, ATF5, INPP1, CCND2, THBS1, LAMC1, and APLP2) as the seed for network construction, we built an interaction network of the early T. cruzi infection process containing 165 genes, connected by 598 biological interactions. This interactome network is centered on the BCL6 gene as a hub. Silencing the expression of two seed genes (THBS1 and LAMC1) by RNAi reduced T. cruzi infection. Overall, our results elucidate the significant and complex process involved in T. cruzi infection of HCASM cells at the transcriptome level. This is the first elucidation into the interactome network in human cells caused by T. cruzi and its gp83 ligand.
Analysis of Multitag Pyrosequence Data from Human Cervical Lavage Samples
Authors: Naqvi Ammar , Rangwala Huzefa , Spear Greg , Gillevet Patrick
Published: May 2010

We have been using the Roche GS‐FLX sequencing platform to produce tens of thousands of sequencing reads from samples of both bacterial communities (microbiome) and fungal communities (mycobiome) of stool, gut mucosa, vaginal washes, and oral washes from a large number of subjects. This vast volume of data from diverse sources has necessitated the development of an analysis pipeline in order to systematically and rapidly identify the taxa within the samples and to correlate the sample data with clinical and environmental features. Specifically, we have developed automated analytical tools for data tracking, taxonomical analysis, and feature clustering of bacteria in the human microbiome and demonstrate the pipeline using Cervical Vaginal Lavage (CVL) samples. This analysis pipeline will not only provide insight to our specific CVL dataset, but is applicable to other microbiome samples and will ultimately broaden our understanding of how the microbiome influences human health.
Quantitative Assessment of the Human Gut Microbiome Using Multitag Pyrosequencing
Authors: Gillevet Patrick , Sikaroodi Masoumeh , Keshavarzian Ali , Mutlu Ece A.
Published: May 2010

Recent advances in molecular techniques have now made it possible to interrogate the human microbiome in depth to better understand the interactions with the host organism and its role in diseases. We now report the utility of Length Heterogeneity Polymerase Chain Reaction (LH‐PCR) to survey samples and a proprietary Multitagged Pyrosequencing (MTPS) methodology to interrogate the gut microbiome in healthy and disease states. We present an overview of our studies demonstrating the application of these molecular‐biology techniques to an example disease state such as Inflammatory Bowel Disease (IBD). The findings show that there is a core mucosal bacterial microbiome (i.e., a mucosal biofilm) that is distinct from the luminal microbiome in health, and that the mucosal microbiome appears to be dysbiotic in IBD. We propose that the mucosal microbiome forms a synergistic and stable interaction with the host immune system, while the lumen microbiome varies based on diet or other environmental factors. We define this composite ecosystem of the human microbiome and human host as the Human Metabiome.
A Genome‐Scale Metabolic Model of Cryptosporidium hominis
Authors: Vanee Niti , Roberts Seth B. , Fong Stephen S. , Manque Patricio , Buck Gregory A.
Published: May 2010

The apicomplexan Cryptosporidium is a protozoan parasite of humans and other mammals. Cryptosporidium species cause acute gastroenteritis and diarrheal disease in healthy humans and animals, and cause life‐threatening infection in immunocompromised individuals such as people with AIDS. The parasite has a one‐host life cycle and commonly invades intestinal epithelial cells. The current genome annotation of C. hominis, the most serious human pathogen, predicts 3884 genes of which ca. 1581 have predicted functional annotations. Using a combination of bioinformatics analysis, biochemical evidence, and high‐throughput data, we have constructed a genome‐scale metabolic model of C. hominis. The model is comprised of 213 gene‐associated enzymes involved in 540 reactions among the major metabolic pathways and provides a link between the genotype and the phenotype of the organism, making it possible to study and predict behavior based upon genome content. This model was also used to analyze the two life stages of the parasite by integrating the stage‐specific proteomic data for oocyst and sporozoite stages. Overall, this model provides a computational framework to systematically study and analyze various functional behaviors of C. hominis with respect to its life cycle and pathogenicity.
Network‐Based Modeling of the Human Gut Microbiome
Authors: Naqvi Ammar , Rangwala Huzefa , Keshavarzian Ali , Gillevet Patrick
Published: May 2010

In this article, we used a network‐based approach to characterize the microflora abundance in colonic mucosal samples and correlate potential interactions between the identified species with respect to the healthy and diseased states. We analyzed the modelled network by computing several local and global network statistics, identified recurring patterns or motifs, fit the network models to a family of well‐studied graph models. This study has demonstrated, for the first time, an approach that differentiated the gut microbiota in alcoholic subjects and healthy subjects using topological network analysis of the gut microbiome.
Nitrooxymethyl‐Substituted Analogues of Rofecoxib: Synthesis and Pharmacological Characterization
Authors: Boschi Donatella , Cena Clara , Di Stilo Antonella , Rolando Barbara , Manzini Paola , Fruttero Roberta , Gasco Alberto
Published: May 2010

Nitrooxymethyl‐substituted derivatives of Rofecoxib were synthesized and tested for their cyclooxygenase (COX)‐inhibiting activity in whole human blood, vasodilator potency on rat aorta strips, and for their capacity of inhibiting platelet aggregation of human platelet‐rich plasma. The results show that their potency and selectivity in inhibiting COX isoforms, as well as their anti‐aggregatory properties, are closely dependent on the position at which the NO‐donor nitrooxymethyl function is introduced into the Rofecoxib scaffold. All the products were capable of dilating rat aorta strips precontracted with phenylephrine in a dose‐dependent manner, through a cGMP‐dependent mechanism. Compound10emerged as a quite potent COX‐2‐selective inhibitor endowed with good vasodilator activity. Interestingly, compound19behaved as a potent selective COX‐1 inhibitor, and displayed good vasodilator and anti‐aggregatory properties. The hydroxymethyl derivatives, potential metabolites of the nitrooxymethyl analogues, were similarly studied for a comparison.
Cellular Automata Modeling of FASL‐Initiated Apoptosis
Authors: Apte Advait , Bonchev Danail , Fong Stephen
Published: May 2010

Two strategies for fighting cancer by modulating FASL‐induced apoptosis were modeled by 2D‐cellular automata. Our models predict that cancer cells can be killed by maximizing the apoptosis via joint suppression of FLIP and IAP inhibitors by siRNA and SMAC proteins, respectively. It was also predicted that the presumed feedback loop CASP3→CASP9→|IAP in the intrinsic pathway accelerates the apoptosis, but does not change significantly the concentration of DFF40, the protein that decomposes DNA. The alternative strategy of preventing the killing of the immune system's T‐cells, via minimizing their tumor‐induced FAS‐L apoptosis by overexpression of FLIP and IAP, was also shown to be promising with a predicted considerable synergy action of the two inhibitors. Dual suppression or overexpression of apoptosis inhibitors emerges thus as promising approach in the fight against cancer. Our modeling has also brought some light on the process of turning type‐I cells into type‐II ones, which emerges as compensatory mechanism in case of damaged or silenced FASL pathway by preserving about the same self‐death level at only 10–12% lower performance rate.
How to Produce a Chemical Defense: Structural Elucidation and Anatomical Distribution of Aplysioviolin and Phycoerythrobilin in the Sea Hare Aplysia californica
Authors: Kamio Michiya , Nguyen Linh , Yaldiz Seymanur , Derby Charles D.
Published: May 2010

We previously used bioassay‐guided fractionation to identify phycoerythrobilin (1) and its monomethyl ester, aplysioviolin (2), as components in the ink secretion of a marine gastropod, the sea hare Aplysia californica, that act as chemical deterrents against predatory blue crabs. This was the first report of 1 as a natural product. Compound 2 was previously reported as a natural product from three species of Aplysia (A. fasciata, A. dactylomela, and A. parvula), but the reported structure and composition of stereoisomers of 2 are different among these species. Sea hares are thought to produce 2 from phycoerythrin, a photosynthetic pigment in their red‐algal diet composed of a phycobiliprotein covalently linked to the chromophore 1, by cleavage of the covalent bond and methylation of 1, but neither the sequence nor the anatomical location of the cleavage and methylation is known. In this study, we clarify the structure of 1 and 2 in ink secretion of A. californica, and describe the distribution of 1 and 2 in the tissues of sea hares. We conclude that cleavage of the covalent bond in phycoerythrin occurs first, forming 1 in the digestive gland, followed by methylation of 1 to yield 2 in the ink gland.
Antimicrobial and Cytotoxic Activities of Synthetically Derived Tambjamines C and E – J, BE‐18591, and a Related Alkaloid from the Marine Bacterium Pseudoalteromonas tunicata
Authors: Pinkerton David M. , Banwell Martin G. , Garson Mary J. , Kumar Naresh , de Moraes Manoel Odorico , Cavalcanti Bruno C. , Barros Francisco W. A. , Pessoa Cláudia
Published: May 2010

In the first comprehensive biological assessment of the tambjamine class of marine alkaloids, synthetically derived samples of compounds 1–9 have been subjected to evaluation as antimicrobial agents and screened for their cytotoxic effects on various human cancer cell lines. Most were strongly active against the fungus Malassezia furfur (>amphotericin B) and showed considerable, but non‐selective, antiproliferative activity against both human cancer and normal cell lines. Tambjamines I and J (6 and 7, resp.) displayed significant apoptosis‐inducing effects.