bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐scale metabolic model integrated with RNAseq data to identify metabolic states of Clostridium thermocellum
Authors: Gowen Christopher M. , Fong Stephen S. 
Published: July 2010

AbstractConstraint‐based genome‐scale metabolic models are becoming an established tool for using genomic and biochemical information to predict cellular phenotypes. While these models provide quantitative predictions for individual reactions and are readily scalable for any biological system, they have inherent limitations. Using current methods, it is difficult to computationally elucidate a specific network state that directly depicts an in vivo state, especially in the instances where the organism might be functionally in a suboptimal state. In this study, we generated RNA sequencing data to characterize the transcriptional state of the cellulolytic anaerobe, Clostridium thermocellum, and algorithmically integrated these data with a genome‐scale metabolic model. The phenotypes of each calculated metabolic flux state were compared to 13 experimentally determined physiological parameters to identify the flux mapping that best matched the in vitro growth of C. thermocellum. By this approach we found predicted fluxes for 88 reactions to be changed between the best solely computational prediction (flux balance analysis) and the best experimentally derived prediction. The alteration of these 88 reaction fluxes led to a detailed network‐wide flux mapping that was able to capture the suboptimal cellular state of C. thermocellum.
Metabolic systems analysis to advance algal biotechnology
Authors: Schmidt Brian J. , Lin‐Schmidt Xiefan , Chamberlin Austin , Salehi‐Ashtiani Kourosh , Papin Jason A. 
Published: July 2010

AbstractAlgal fuel sources promise unsurpassed yields in a carbon neutral manner that minimizes resource competition between agriculture and fuel crops. Many challenges must be addressed before algal biofuels can be accepted as a component of the fossil fuel replacement strategy. One significant challenge is that the cost of algal fuel production must become competitive with existing fuel alternatives. Algal biofuel production presents the opportunity to fine‐tune microbial metabolic machinery for an optimal blend of biomass constituents and desired fuel molecules. Genome‐scale model‐driven algal metabolic design promises to facilitate both goals by directing the utilization of metabolites in the complex, interconnected metabolic networks to optimize production of the compounds of interest. Network analysis can direct microbial development efforts towards successful strategies and enable quantitative fine‐tuning of the network for optimal product yields while maintaining the robustness of the production microbe. Metabolic modeling yields insights into microbial function, guides experiments by generating testable hypotheses, and enables the refinement of knowledge on the specific organism. While the application of such analytical approaches to algal systems is limited to date, metabolic network analysis can improve understanding of algal metabolic systems and play an important role in expediting the adoption of new biofuel technologies.
Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessing
Authors: Salimi Fahimeh , Zhuang Kai , Mahadevan Radhakrishnan 
Published: July 2010

AbstractAn alternative consolidated bioprocessing approach is the use of a co‐culture containing cellulolytic and solventogenic clostridia. It has been demonstrated that the rate of cellulose utilization in the co‐culture of Clostridium acetobutylicum and Clostridium cellulolyticum is improved compared to the mono‐culture of C. cellulolyticum, suggesting the presence of syntrophy between these two species. However, the metabolic interactions in the co‐culture are not well understood. To understand the metabolic interactions in the co‐culture, we developed a genome‐scale metabolic model of C. cellulolyticum comprising of 431 genes, 621 reactions, and 603 metabolites. The C. cellulolyticum model can successfully predict the chemostat growth and byproduct secretion with cellulose as the substrate. However, a growth arrest phenomenon, which occurs in batch cultures of C. cellulolyticum at cellulose concentrations higher than 6.7 g/L, cannot be predicted by dynamic flux balance analysis due to the lack of understanding of the underlying mechanism. These genome‐scale metabolic models of the pure cultures have also been integrated using a community modeling framework to develop a dynamic model of metabolic interactions in the co‐culture. Co‐culture simulations suggest that cellobiose inhibition cannot be the main factor that is responsible for improved cellulose utilization relative to mono‐culture of C. cellulolyticum.
Nociceptin and its natural and specifically‐modified fragments: Structural studies
Authors: Podstawka‐Proniewicz E. , Kosior M. , Kim Y. , Rolka K. , Proniewicz L. M. 
Published: July 2010

AbstractThe vibrational structures of Nociceptin (FQ), its short bioactive fragments, and specifically‐modified [Tyr1]FQ (1‐6), [His1]FQ (1‐6), and [His1,4]FQ (1‐6) fragments were characterized. We showed that in the solid state, all of the aforementioned peptides except FQ adopt mainly turn and disordered secondary structures with a small contribution from an antiparallel β‐sheet conformation. FQ (1‐11), FQ (7‐17) [His1]FQ (1‐6), and [His1,4]FQ (1‐6) have an α‐helical backbone arrangement that could also slightly influence their secondary structure. The adsorption behavior of these peptides on a colloidal silver surface in an aqueous solution (pH = ∼8.3) was investigated by means of surface‐enhanced Raman scattering (SERS). All of the peptides, excluding FQ (7‐17), chemisorbed on the colloidal silver surfaces through a Phe4residue, which for FQ, FQ (1‐11), FQ (1‐6), [Tyr1]FQ (1‐6), and [His1]FQ (1‐6) lies almost flat on this surface, while for FQ (1‐13) and FQ (1‐13)NH2adopts a slightly tilted orientation with respect to the surface. The Tyr1residue in [Tyr1]FQ (1‐6) does not interact with the colloidal silver surface, suggesting that the Tyr1and Phe4side chains are located on the opposite sides of the peptide backbone, which can be also true for His1and Phe4in [His1]FQ (1‐6). The lone pair of electrons on the oxygen atom of the ionized carbonyl group of FQ (1‐13) and FQ (7‐17) appears to be coordinated to the colloidal silver nanoparticles, whereas in the case of the remaining peptides, it only assists in the adsorption process, similar to the NH2group. We also showed that upon adsorption, the secondary structure of these peptides is altered. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1039–1054, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Structural investigations on the Nodal‐Cripto binding: A theoretical and experimental approach
Authors: Calvanese Luisa , Marasco Daniela , Doti Nunzianna , Saporito Angela , D'Auria Gabriella , Paolillo Livio , Ruvo Menotti , Falcigno Lucia 
Published: July 2010

AbstractNodal, a member of the transforming growth factor‐β superfamily, is a potent embryonic morphogen also implicated in tumor progression. Up to date structural information on the interaction of Nodal with its molecular partners are unknown. To deepen our understanding about mechanisms underlying both embryonic development and Nodal/Cripto‐dependent tumor progression, we present here a molecular model of activin receptor‐like kinase 4/Cripto/Nodal complex built by homology modeling as well as docking tests aimed at identifying potential binding epitopes. Starting from this model, we have predicted a large interaction surface on Nodal, which encompasses residues 43–69 and includes the prehelix loop and the H3 helix. This hypothesis has been subsequently assessed by surface plasmon resonance binding assays between the full‐length Cripto and synthetic peptides reproducing the selected Nodal regions. In addition, the binding affinity between the full‐length Nodal and Cripto proteins has been evaluated for the first time. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1011–1021, 2010.
Effect of the ΔPhe residue configuration on a didehydropeptides conformation: A combined CD and NMR study
Authors: Lisowski Marek , Jaremko Łukasz , Jaremko Mariusz , Mazur Adam , Latajka Rafał , Makowski Maciej 
Published: July 2010

AbstractConformations of two pairs of dehydropeptides with the opposite configuration of the ΔPhe residue, Boc‐Gly‐ΔZPhe‐Gly‐Phe‐OMe (Z‐OMe), Boc‐Gly‐ΔEPhe‐Gly‐Phe‐OMe (E‐OMe), Boc‐Gly‐ΔZPhe‐Gly‐Phe‐p‐NA (Z‐p‐NA), and Boc‐Gly‐ΔEPhe‐Gly‐Phe‐p‐NA (E‐p‐NA) were compared on the basis of CD and NMR studies in MeOH, trifluoroethanol (TFE), MeCN, chloroform, and dimethylsulfoxide (DMSO). The CD results were used as the additional input data for the NMR‐based determination of the detailed solution conformations of the peptides. It was found that E‐OMe is unordered and Z‐OMe, Z‐p‐NA, and E‐p‐NA adopt the β‐turn conformation. There are two overlapping β‐turns in each of those peptides: type II and type III′ in Z‐OMe and Z‐p‐NA, and two type III in E‐p‐NA. The ordered structure‐inducing properties of ΔZPhe and ΔEPhe in the peptides studied depend on the C‐terminal blocking group. In methyl esters, the ΔZPhe residue is a strong inducer of ordered conformations whereas the ΔEPhe one has no such properties. In p‐nitroanilides, both isomers of ΔPhe cause the peptides to adopt ordered structures to a similar extent. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1055–1064, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Nitrifying bacterial growth inhibition in the presence of algae and cyanobacteria
Authors: Choi Okkyoung , Das Atreyee , Yu Chang‐Ping , Hu Zhiqiang 
Published: July 2010

AbstractNitrifying bacteria, cyanobacteria, and algae are important microorganisms in open pond wastewater treatment systems. Nitrification involving the sequential oxidation of ammonia to nitrite and nitrate, mainly due to autotrophic nitrifying bacteria, is essential to biological nitrogen removal in wastewater and global nitrogen cycling. A continuous flow autotrophic bioreactor was initially designed for nitrifying bacterial growth only. In the presence of cyanobacteria and algae, we monitored both the microbial activity by measuring specific oxygen production rate (SOPR) for microalgae and cyanobacteria and specific oxygen uptake rate (SOUR) for nitrifying bacteria. The growth of cyanobacteria and algae inhibited the maximum nitrification rate by a factor of 4 although the ammonium nitrogen fed to the reactor was almost completely removed. Terminal restriction fragment length polymorphism (T‐RFLP) analysis indicated that the community structures of nitrifying bacteria remained unchanged, containing the dominant Nitrosospira, Nitrospira, and Nitrobacter species. PCR amplification coupled with cloning and sequencing analysis resulted in identifying Chlorella emersonii and an uncultured cyanobacterium as the dominant species in the autotrophic bioreactor. Notwithstanding their fast growth rate and their toxicity to nitrifiers, microalgae and cyanobacteria were more easily lost in effluent than nitrifying bacteria because of their poor settling characteristics. The microorganisms were able to grow together in the bioreactor with constant individual biomass fractions because of the uncoupled solids retention times for algae/cyanobacteria and nitrifiers. The results indicate that compared to conventional wastewater treatment systems, longer solids retention times (e.g., by a factor of 4) should be considered in phototrophic bioreactors for complete nitrification and nitrogen removal. Biotechnol. Bioeng. 2010;107: 1004–1011. © 2010 Wiley Periodicals, Inc.
Synthesis and utilization of E. coli‐encapsulated PEG‐based microdroplet using a microfluidic chip for biological application
Authors: Lee Kyoung G. , Park Tae Jung , Soo Song Young , Wang Kye Won , Kim Byeong I.I. , Park Jae Hong , Lee Chang‐Soo , Kim Do Hyun , Lee Seok Jae 
Published: July 2010

AbstractWe report herein an effective strategy for encapsulating Escherichia coli in polyethylene glycol diacrylate (PEGDA) microdroplets using a microfluidic device and chemical polymerization. PEGDA was employed as a reactant due to the biocompatibility, high porosity, and hydrophilic property. The uniform size and shape of microdroplets are obtained in a single‐step process using microfluidic device. The size of microdroplets can be controlled through the changing continuous flow rate. The combination of microdroplet generation and chemical polymerization techniques provide unique environment to produce non‐toxic ways of fabricating microorganism‐encapsulated hydrogel microbeads. Due to these unique properties of micro‐sized hydrogel microbeads, the encapsulated E. coli can maintain viability inside of microbeads and green fluorescent protein (GFP) and red fluorescent protein (RFP) genes are efficiently expressed inside of microbeads after isopropyl‐β‐D‐thiogalactopyranoside induction, suggesting that there is no low‐molecular weight substrate transfer limitation inside of microbeads. Furthermore, non‐toxic, gentle, and outstanding biocompatibility of microbeads, the encapsulated E. coli can be used in various applications including biotransformation, biosensing, bioremediation, and engineering of artificial cells. Biotechnol. Bioeng. 2010;107:747–751. © 2010 Wiley Periodicals, Inc.
Efficiency Optimization and Prediction in High‐Gradient Magnetic Centrifugation
Authors: Lindner J. , Wagner K. , Eichholz C. , Nirschl H. 
Published: July 2010

AbstractIn order to separate small magnetizable particles down to the micro‐ and nanometer scale, high‐gradient magnetic separation is a well‐established process. The superposition of magnetic filtration with centrifugation, called magnetic field‐enhanced centrifugation, permits continuous separation. The separation efficiency of magnetic filters and the prediction of the efficiency is described. The separation efficiency of one single stage could be enhanced from 51 to 78 % by increasing the wire number and improving the wire cross section. The separation efficiency on different particle sizes at different filter stage numbers and comparison to the prediction of separation efficiency based on magnetic forces and the fluid drag force is demonstrated.
Photochemistry and Reactivity of the Phenyl Radical–Water System: A Matrix Isolation and Computational Study
Authors: Mardyukov Artur , Crespo‐Otero Rachel , Sanchez‐Garcia Elsa , Sander Wolfram 
Published: July 2010

AbstractThe reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH⋅⋅⋅π interaction. This complex is photolabile, and visible‐light irradiation (λ>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with λ>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.
Do Trinuclear Triplesalen Complexes Exhibit Cooperative Effects? Synthesis, Characterization, and Enantioselective Catalytic Sulfoxidation by Chiral Trinuclear FeIII Triplesalen Complexes
Authors: Mukherjee Chandan , Stammler Anja , Bögge Hartmut , Glaser Thorsten 
Published: July 2010

AbstractThe chiral triplesalen ligand H6chand provides three chiral salen ligand compartments in a meta‐phenylene arrangement by a phloroglucinol backbone. The two diastereomeric versions H6chandRR and H6chandrac have been used to synthesize the enantiomerically pure chiral complex [(FeCl)3(chandRR)] (3RR) and the racemic complex [(FeCl)3(chandrac)] (3rac). The molecular structure of the free ligand H6chandrac exhibits at the terminal donor sides the O‐protonated phenol–imine tautomer and at the central donor sides the N‐protonated keto–enamine tautomer. The trinuclear complexes are comprised of five‐coordinate square‐pyramidal FeIII ions with a chloride at the axial positions. The crystal structure of 3rac exhibits collinear chiral channels of ∼11 Å in diameter making up 33.6 % of the volume of the crystals, whereas the crystal structure of 3RR exhibits voids of 560 Å3. Mössbauer spectroscopy demonstrates the presence of FeIII high‐spin ions. UV/Vis spectroscopy is in accordance with a large delocalized system in the central backbone evidenced by strong low‐energy shifts of the imine π–π* transitions relative to that of the terminal units. Magnetic measurements reveal weak intramolecular exchange interactions but strong magnetic anisotropies of the FeIII ions. Complexes 3rac and 3RR are good catalysts for the sulfoxidation of sulfides providing very good yields and high selectivities with 3RR being enantioselective. A comparison of 3RR and [FeCl(salen′)] provides higher yields and selectivities but lower enantiomeric excess values (ee values) for 3RR relative to [FeCl(salen′)]. The low ee values of 3RR appeared to be connected to a strong ligand folding in 3RR, opening access to the catalytically active high‐valent Fe–O species. The higher selectivity is assigned to a cooperative stabilization of the catalytically active high‐valent Fe–O species through the phloroglucinol backbone in the trinuclear complexes.
Gold Catalysis: Tandem Reactions of Diyne–Diols and External Nucleophiles as an Easy Access to Tricyclic Cage‐Like Structures
Authors: Hashmi A. Stephen K. , Bührle Miriam , Wölfle Michael , Rudolph Matthias , Wieteck Marcel , Rominger Frank , Frey Wolfgang 
Published: July 2010

AbstractDifferent diyne–diols composed of two terminal homopropargylic alcohol groups were prepared by bi‐directional synthesis. Subjection of the syn diastereomers to NAC–gold catalysts (NAC=nitrogen acyclic carbene) in the presence of external nucleophiles such as water or anilines provided substituted and highly rigid heterocyclic cages. The corresponding anti disastereomers polymerised. An intermediate of the reactions of the syn diastereomers could be isolated and even be characterised by crystal structure analysis. Overall, eight new bonds are formed in the reaction, which proceeds by a multistep sequence of highly selective hydroalkoxylations and hydrohydroxylation or hydroaminations. For furyl substituents and for internal alkynes competing reaction pathways could be identified. By the cross‐coupling of a product with an iodoaryl substituent, the use of these cage compounds as geometrically defined linking groups by using orthogonal transition‐metal‐catalysed methodology, namely, gold and palladium catalysis, could be demonstrated.
ChemInform Abstract: Synthesis of 5‐Aryl‐2‐[spiro‐(1,3‐dithiolane)‐2,4′‐(3′‐chloro‐2′‐azetidinone)‐1′‐yl] ‐1,3,4‐oxa(thia)diazoles and 5‐Aryl‐2‐[spiro‐(1,3‐dithiolane)‐2,2′‐(4′‐thiazolidinon)‐3′‐yl] ‐1,3,4‐oxa(thia)diazoles as Antimicrobial Agents.
Authors: KHAN M. H. , NIZAMUDDIN NIZAMUDDIN 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Acid‐Catalyzed Condensation of Azulenes with 9‐Anthracenecarbaldehyde and the Synthesis of (9‐Anthryl)di(1‐azulenyl)methyl and (1‐Azulenyl)[10‐(1‐azulenyl)‐9‐anthryl]methyl Hexafluorophosphates.
Authors: Ito Shunji , Fujita Miwako , Morita Noboru , Asao Toyonobu 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis of 1‐Amino‐ and 1‐Hydroxy‐9,10‐anthraquinone Derivatives Based on Reaction Sequences Between 2‐Acetyl‐1,4‐naphthoquinone and Enamines.
Authors: Kobayashi Kazuhiro , Uchida Masaharu , Watanabe Shinya , Takanohashi Atsushi , Tanmatsu Miyuki , Morikawa Osamu , Konishi Hisatoshi 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: 1‐Deamino‐1(15)‐carba and ‐dicarba Analogues of Endothelin‐1
Authors: Hlavacek Jan , Marcova Renata , Budesinsky Milos , Slaninova Jirina 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Arachno‐[Sn8]6‐ or closo‐[Li2Sn8]4‐? Synthesis and Characterization of A4Li2Sn8 (A: Rb, K).
Authors: Bobev Svilen , Sevov Slavi C. 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Structure of the FeIVO4‐4 Ion.
Authors: Weller Mark T. , Hector Andrew L. 
Published: July 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.