bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of microbial populations. Mathematical modeling, laboratory exercises, and model‐based data analysis
Authors: Juška Alfonsas , Gedminienė Genovaitė , Ivanec Rūta 
Published: January 2007

AbstractThis paper has arisen as a result of teaching Models in Biology to undergraduates of Bioengineering at the Gediminas Technical University of Vilnius. The aim is to teach the students to use a fresh approach to the problems they are familiar with, to come up with an articulate verbal model after a mental effort, to express it in rigorous mathematical terms, to solve (with the aid of computers) corresponding equations, and finally, to analyze and interpret experimental data in terms of their (mathematical) models. Investigation of microbial growth provides excellent possibilities to combine laboratory exercises, mathematical modeling, and model‐based data analysis. Application of mathematics in this field proved to be very fruitful in getting deeper insight into the processes of microbial growth. The step‐by‐step modeling resulted in an extended model of the growth covering conventional “lag,” “exponential,” and “stationary” phases. In contrast to known models (differential equations that can be solved only numerically), the present model is expressed symbolically as a finite combination of elementary functions. The approach can be applied in other areas of modern biology, such as dynamics of various cellular processes, enzyme and receptor kinetics, and others.
Time, the forgotten dimension of ligand binding teaching
Authors: Corzo Javier 
Published: January 2007

AbstractLigand binding is generally explained in terms of the equilibrium constant Kd for the protein‐ligand complex dissociation. However, both theoretical considerations and experimental data point to the life span of the protein‐ligand complex as an important, but generally overlooked, aspect of ligand binding by macromolecules. Short‐lived protein‐ligand complexes may be unable to trigger further biological processes as signal transduction or internalization if such processes are relatively slow with respect to dissociation of the complex that initiated them. Protein‐ligand complex life span depends on the first‐order rate constant for the dissociation of the complex, Koff, but this constant and its implications are generally not treated in textbooks. This report presents a brief discussion and some examples useful for teaching the importance of time in ligand binding by macromolecules in the context of a general biochemistry course.
Databases of metabolic pathways
Authors: Likić Vladimir A. 
Published: January 2007

AbstractStudies of metabolism usually evoke memories of densely written wall charts of metabolic pathways of enormous complexity, such as the IUBMB‐Nicholson metabolic pathways map or the Roche metabolic pathways wall chart. Advances in bioinformatics in the past decade have brought about a revolution in the way the information in metabolic pathways is viewed and managed. Today, metabolic pathways are stored in knowledge bases that can be queried, modified, copied, and extended with ease, precision, and speed. Moreover, the flexibility of the digital medium for the presentation of metabolic pathways surpasses the traditional printed form used in classical pathway maps. In digital presentations, the separation of the content from the visual presentation is the norm, implying that metabolic pathway maps can be generated dynamically from the information stored in the knowledge base. The most advanced metabolic pathways databases are freely available over the Internet, and this has important implications for modern studies of metabolic pathways in biochemistry and molecular biology. This study reviews two such databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the BioCyc collection of pathway/genome databases. The background information and the structure of these databases are presented, with the emphasis on BioCyc, which represents a global multicollaborative effort to unify the representation of metabolic pathways.
Microarrays for undergraduate classes
Authors: Hancock Dale , Nguyen Lisa L. , Denyer Gareth S. , Johnston Jill M. 
Published: January 2007

AbstractA microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by erythropoietic agents such as DMSO over a 72‐h time period. Students isolate total RNA from control (0 h) and 72‐h DMSO‐treated murine erythroleukemia cells. From this, they synthesize a cDNA copy incorporating amino‐allyl dUTP, which is then coupled to either a Cy5 or a Cy3 dye. Equal amounts of the two labeled cDNA samples are then applied to a standard cDNA microarray, which is then hybridized, washed, and scanned. Up‐ and down‐regulated genes are selected using an “in‐house” user‐friendly data base program. Quality control checks are included at various stages throughout the procedure and, as the process of erythropoiesis is well characterized, a number of erythroid sequences serve as internal controls on the validity of the array data. Through this experiment, students gain experience in a wide range of molecular biology techniques, the use of controls to check a multistep process, validation of results, and strategies to manage the large amount of data generated. Most importantly, it provides undergraduate students with an opportunity to carry out experiments using cutting edge techniques normally found only in research laboratories.
Exploring the ubiquitin‐proteasome protein degradation pathway in yeast
Authors: Will Tamara J. , McWatters Melissa K. , McQuade Kristi L. 
Published: January 2007

AbstractThis article describes an undergraduate biochemistry laboratory investigating the ubiquitin‐proteasome pathway in yeast. In this exercise, the enzyme β‐galactosidase (β‐gal) is expressed in yeast under the control of a stress response promoter. Following exposure to heat stress to induce β‐gal expression, cycloheximide is added to halt translation, and β‐gal degradation is monitored by measuring enzyme activity as a function of time. Students observe that an N‐Ile‐β‐gal variant with an N‐terminal isoleucine has a significantly lower stability than wild‐type β‐gal, whose N‐terminal residue is methionine. This strong dependence of protein stability on the N‐terminal residue is known as the “N‐end rule.” To corroborate the enzyme activity assay results, students perform denaturing protein electrophoresis and immunoblotting of lysates, observing that the time‐dependent loss of enzyme activity is coincident with the disappearance of the β‐gal protein.
Vectorial Transport in intestinal epithelial cells
Authors: Szeberenyi Jozsef 
Published: January 2007

AbstractTerms to be familiar with before you start to solve the test: polarized cells, vectorial transport, apical and basolateral membrane, tight junction, occludin, transmembrane proteins, passive and active transport, glucose transporter, Na+/glucose symporter, Na+/K+ ATPase, uniporter, antiporter, facilitated diffusion, lateral diffusion.
Three New Triterpenoids from Potentilla multicaulis
Authors: Li Ping‐Lin , Lin Chang‐Jun , Zhang Zhan‐Xin , Jia Zhong‐Jian 
Published: January 2007

AbstractThree new triterpenoids, 19‐hydroxy‐2,3‐secours‐12‐ene‐2,3,28‐trioic acid 3‐ methyl ester (1), 19‐hydroxy‐1‐oxo‐2‐nor‐2,3‐secours‐12‐ene‐3,28‐dioic acid (2), and (3β,18α,19α)‐3,28‐dihydroxy‐20,28‐epoxyursan‐24‐oic acid (3), were isolated from the roots of Potentilla multicaulis. Their structures were elucidated on the basis of spectroscopic methods (IR, HR‐ESI‐MS, and 1D‐ and 2D‐NMR). Compound 2b exhibited moderate cytotoxic activity against human promyelocytic leukemia (HL‐60) cells.
Isolation and Enzyme‐Inhibition Studies of the Chemical Constituents from Ajuga bracteosa
Authors: Riaz Naheed , Nawaz Sarfraz A. , Mukhtar Naveen , Malik Abdul , Afza Nighat , Ali Samar , Ullah Shafi , Muhammad Pir , Choudhary M. Iqbal 
Published: January 2007

AbstractBractin A (=(2S,3S,4R,5E)‐2‐{[(2R)‐2‐hydroxydodecanoyl]amino}triacont‐5‐ene‐1,3,4‐triol; 1) and bractin B (=(2S,3S,4R,5E,8E)‐2‐{[(2R)‐2‐hydroxyhexacosanoyl]amino}pentadeca‐5,8‐diene‐3,4,15‐triol 1‐O‐β‐D‐glucopyranoside; 2), new sphingolipids, and bractic acid (=(5Z,10Z,15Z)‐2‐decyl‐4,7,8,12,13,17,18‐heptahydroxy‐20,23‐dioxopentacosa‐5,10,15‐trienoic acid; 3), a long‐chain polyhydroxy acid, were isolated from the whole plant Ajuga bracteosa along with four known diterpenoids 4–7. Their structures were deduced by spectral studies including 1D‐ and 2D‐NMR spectroscopy. Compounds 1–3 displayed inhibitory potential against enzyme lipoxygenase, while compounds 4–7 inhibited cholinesterase enzymes in a concentration‐dependent manner with IC50 values in the range 10.0–33.0, 14.0–35.2, and 10.0–19.0 μM for lipoxygenase, acetylcholinesterase, and butyrylcholinesterase, respectively. Lineweaver–Burk, and Dixon plots, and their secondary replots indicated that all compounds exhibit non‐competitive type of inhibition with Ki values in the range of 9.5–35.2, 15.2–36.0, and 11.6–20.5 μM, for lipoxygenase, acetylcholinesterase, and butyrylcholinesterase, respectively.
A New Metabolite with a New Substitution Pattern from the Seeds of the Chinese Yew, Taxus mairei
Authors: Huo Chang‐Hong , Wang Yu‐Fang , Zhang Xi‐Ping , Li Cun‐Fang , Shi Qing‐Wen , Kiyota Hiromasa 
Published: January 2007

AbstractA new taxoid metabolite with a new substitution pattern was isolated from the methanol extract of the seeds of Taxus mairei, and its structure was established as 5α,15‐dihydroxy‐7β,9α‐diacetoxy‐11(15→1)abeo‐taxa‐4(20),11‐dien‐13‐one (1) on the basis of spectral analysis including 1H‐ and 13C‐NMR, HMQC, HMBC, NOESY, and confirmed by HR‐FAB mass spectrometry.
Conjugate Additions of Cyclic Oxygen‐Bound Nickel Enolates to α,β‐Unsaturated Ketones
Authors: Maya Celia M. , Cámpora Juan , Carmona Ernesto , Matas Inmaculada , Palma Pilar , Gutiérrez‐Puebla Enrique , Monge Angeles 
Published: January 2007

AbstractThe reaction of nickel enolates displaying a metallacyclic structure with the α,β‐unsaturated ketones methyl vinyl ketone (MVK) or methyl propenyl ketone (MPK) takes place in two stages, affording initially bicyclic adducts, which subsequently isomerize to the corresponding open‐chain products. The former are generated with high stereoselectivity and can be considered as the products of the [2+4] cycloaddition of the enolate to the enone. The ring opening process involves a prototropic rearrangement that can be catalyzed by water. In the case of the reaction of the parent nickel enolate complex 1 (which displays an unsubstituted NiOC(R)CH2 arrangement) with MVK, a double‐addition process has been observed, consisting of two successive cycloaddition/isomerization reactions. The carbonylation of the different cyclic and noncyclic products affords the corresponding lactones that retain the stereochemistry of the organometallic precursors. This methodology allowed trapping the primary product of the reaction of 1 with MPK as the corresponding organic lactone, demonstrating that the cycloaddition process takes place with exo selectivity. DFT modeling of the latter reaction provides further support for a quasi‐concerted cycloaddition mechanism, displaying a nonsymmetric transition state in which the CC and the CO bond are formed in an asynchronous manner.
Molecular Aggregation within Self‐Ordered Monolayers
Authors: Gross Leo , Rieder Karl‐Heinz , Gourdon André , Joachim Christian , Moresco Francesca 
Published: January 2007

AbstractThe monolayer growth of pyrimido‐pentaphenylbenzene (NPB) on Cu(111) is investigated by means of low‐temperature scanning tunneling microscopy (LT‐STM). The pyrimidine side group gives rise to a pronounced resonant tunneling state and, furthermore, affects molecular self‐ordering. Different molecular aggregates are formed inside the hexagonal closed packed monolayer. A structure model for the monolayer is proposed and the temperature dependence of this self‐ordering process is investigated by varying the preparation temperature between 270 and 370 K. The intermolecular bonding of the aggregates is demonstrated by STM manipulation experiments. Moreover, different aggregations of the molecules induce characteristic energy shifts in the resonant tunneling state, as revealed by means of scanning tunneling spectroscopy.
Tubular sprouting as a mode of vascular formation in a colonial ascidian (tunicata)
Authors: Gasparini Fabio , Longo Fabrizio , Manni Lucia , Burighel Paolo , Zaniolo Giovanna 
Published: January 2007

AbstractAlthough phylogenetically related to vertebrates, invertebrate chordate tunicates possess an open circulatory system, with blood flowing in lacunae among organs. However, the colonial circulatory system (CCS) of the ascidian Botryllus schlosseri runs in the common tunic and forms an anastomized network of vessels, defined by simple epithelium, connected to the open circulatory system of the zooids. The CCS originates from epidermal evagination, grows, and increases its network accompanying colony propagation. New vessels are formed by means of mechanisms of tubular sprouting which, in their morphogenesis and molecular regulation, are very similar to those occurring in other metazoans, particularly during vertebrate angiogenesis. From the apex of new vessels, epithelial cells detach and migrate into the tunic, while exploring filopodia extend toward the tunic and possibly guide vessel growth. Immunohistology showed that growth factors fibroblast growth factor‐2 and vascular endothelial growth factor and the receptor vascular endothelial growth factor receptor‐1 participate in sprouting, associated with cell proliferation. As in vertebrates, these factors may regulate cell migration, proliferation, sprouting, and tube formation. Our data indicate that similar, conserved signals were co‐opted in the sprouting processes of two nonhomologous circulatory systems, that of ascidian CCS, and vertebrate circulatory systems, by recruitment of the same signaling pathway. Developmental Dynamics 236:719–731, 2007. © 2007 Wiley‐Liss, Inc.
Aberrant Bmp signaling and notochord delamination in the pathogenesis of esophageal atresia
Authors: Li Yina , Litingtung Ying , Ten Dijke Peter , Chiang Chin 
Published: January 2007

AbstractHuman foregut malformation known as esophageal atresia with tracheoesophageal fistula (EA/TEF) occurs in 1 in 4,000 live births with unknown etiology. We found that mice lacking Noggin (Nog−/−) displayed Type C EA/TEF, the most common form in humans, and notochordal defects strikingly similar to the adriamycin‐induced rat EA/TEF model. In accord with esophageal atresia, Nog−/− embryos displayed reduction in the dorsal foregut endoderm, which was associated with reduced adhesion and disrupted basement membrane. However, significant apoptosis in the Nog−/− dorsal foregut was not observed. Instead, non‐notochordal, likely endodermal, cells were found in Nog−/− notochord, suggesting that Noggin function is required in the notochordal plate for its proper delamination from the dorsal foregut. Notably, ablating Bmp7 function in Nog−/− embryos rescued EA/TEF and notochord branching defects, establishing a critical role of Noggin‐mediated Bmp7 antagonism in EA/TEF pathogenesis. Developmental Dynamics 236:746–754, 2007. © 2007 Wiley‐Liss, Inc.
Vascular dysfunction in human and rat cirrhosis: Role of receptor-desensitizing and calcium-sensitizing proteins
Authors: Hennenberg Martin , Trebicka Jonel , Biecker Erwin , Schepke Michael , Sauerbruch Tilman , Heller Jörg 
Published: January 2007

In cirrhosis, vascular hypocontractility leads to vasodilation and contributes to portal hypertension. Impaired activation of contractile pathways contributes to vascular hypocontractility. Angiotensin II type 1 receptors (AT1-Rs) are coupled to the contraction-mediating RhoA/Rho-kinase pathway and may be desensitized by phosphorylation through G-protein-coupled receptor kinases (GRKs) and binding of β-arrestin-2. In the present study, we analyzed vascular hypocontractility to angiotensin II in cirrhosis. Human hepatic arteries were obtained during liver transplantation. In rats, cirrhosis was induced by bile duct ligation (BDL). Contractility of rat aortic rings was measured myographically. Protein expression and phosphorylation were analyzed by Western blot analysis. Immunoprecipitation was performed with protein A–coupled Sepharose beads. Myosin light chain (MLC) phosphatase activity was assessed as dephosphorylation of MLCs. Aortas from BDL rats were hyporeactive to angiotensin II and extracellular Ca2+. Expression of AT1-R and Gαq/11,12,13 remained unchanged in hypocontractile rat and human vessels, whereas GRK-2 and β-arrestin-2 were up-regulated. The binding of β-arrestin-2 to the AT1-R was increased in hypocontractile rat and human vessels. Inhibition of angiotensin II–induced aortic contraction by the Rho-kinase inhibitor Y-27632 was pronounced in BDL rats. Basal phosphorylation of the ROK-2 substrate moesin was reduced in vessels from rats and patients with cirrhosis. Analysis of the expression and phosphorylation of Ca2+-sensitizing proteins (MYPT1 and CPI-17) in vessels from rats and patients with cirrhosis suggested decreased Ca2+ sensitivity. Angiotensin II–stimulated moesin phosphorylation was decreased in aortas from BDL rats. MLC phosphatase activity was elevated in aortas from BDL rats.Conclusion :Vascular hypocontractility to angiotensin II in cirrhosis does not result from changes in expression of AT1-Rs or G-proteins. Our data suggest that in cirrhosis-induced vasodilation, the AT1-R is desensitized by GRK-2 and β-arrestin-2 and that changed patterns of phosphorylated Ca2+-sensitizing proteins decrease Ca2+ sensitivity.
Mutual changes of thioredoxin and nitrosothiols during biliary cirrhosis: Results from humans and cholestatic rats
Authors: Grattagliano Ignazio , Portincasa Piero , Palmieri Vincenzo O. , Palasciano Giuseppe 
Published: January 2007

Cholestasis is associated with changes in NO metabolism and thiol oxidation. Thioredoxin contributes to regulate vascular tone and intracellular redox status by cleaving nitrosothiols and maintaining −SH groups. This study investigated the changes in circulating thioredoxin and nitrosothiols and the relationship with protein sulfhydryls (PSH), hepatic concentrations, hyaluronate, and histology in patients with primary biliary cirrhosis (PBC) and in rats with bile duct ligation (BDL). PSH in erythrocytes were significantly decreased in stage III and IV PBC and at day 10 after BDL. Compared with controls, erythrocyte thioredoxin levels were higher in stage I through III PBC and lower in stage IV patients. Serum thioredoxin levels were significantly higher in PBC stages I and II and lower in stages III and IV. Serum nitrosothiols were higher in all PBC patients and inversely related to thioredoxin and hyaluronate. In rats, serum, hepatic, and mitochondrial thioredoxin had initially increased after BDL (day 1-3) and then decreased. After day 7 BDL, nitrosothiols were 10-fold increased in serum and liver, and even higher in mitochondria. In the liver, thioredoxin was inversely related to both nitrosothiols and PSH. In rats, the difference in time average changes from baseline among serum, hepatic, and erythrocyte thioredoxin suggests that most of circulating thioredoxin originates from the liver.Conclusion:Our findings indicate that cholestasis is associated with significant mutual and interrelated changes between circulating and hepatic thioredoxin and nitrosothiols. The increase of hepatic, mitochondrial, and circulating nitrosothiols with ongoing cholestasis suggests an active participation of NO in both liver injury and extrahepatic changes.
Iridoid Glycosides from Lamiophlomis rotata
Authors: Tan Jun‐Jie , Tan Chang‐Heng , Li Mu , Jiang Shan‐Hao , Zhu Da‐Yuan 
Published: January 2007

AbstractThe seven new iridoid diglycosides 1–7, together with eleven known iridoid and phenylpropanoid glycosides, were isolated from the 50% EtOH extract of the roots of Lamiophlomis rotata. Their structures were elucidated by chemical and spectroscopic methods.
Lycopodium Alkaloids from Huperzia serrata
Authors: Wang Heng‐Bin , Tan Chang‐Heng , Tan Jun‐Jie , Gao Ming‐Yao , Li Yi‐Ming , Jiang Shan‐Hao , Zhu Da‐Yuan 
Published: January 2007

AbstractThree new Lycopodium alkaloids, 2‐chlorohuperzine E (1), huperzines E′ (2), and F′ (3), along with two known compounds, huperzines E and F, were isolated from Huperzia serrata (Thunb.) Trev. Their structures were elucidated by spectroscopic methods.
Chemical Constituents of Ligusticum sinensisOliv.
Authors: Ma Jian‐Ping , Tan Chang‐Heng , Zhu Da‐Yuan 
Published: January 2007

AbstractThe new phenylpropanoid diglycoside ligusinenoside A (1), and the two new 8,4′‐oxyneolignan(‘8‐O‐4′‐neolignan’) diglycosides ligusinenosides B (2) and C (3), together with nine known compounds, were isolated from the rhizomes of Ligusticum sinensis Oliv. The structures of 1–3 were elucidated on the basis of spectroscopic analyses.
Sesquiterpene Lactones from Anthemis melanolepis
Authors: Saroglou Vasiliki , Karioti Anastasia , Heilmann Jörg , Kypriotakis Zacharias , Skaltsa Helen 
Published: January 2007

AbstractFrom the aerial parts of A. melanolepis, two new sesquiterpene lactones, melanolepin B ( = 1α,4β,8α‐trihydroxyeudesm‐11(13)‐en‐12,6α‐olide; 1) and melanolepin C (= 1α,10β‐epoxy‐8β‐hydroxygermacra‐4(15),11(13)‐dien‐12,6α‐olide; 2), were isolated, together with four known compounds, desacetyllaurenobiolide, dentatin A, taraxasterol, and (3S,5R)‐loliolide. Compound 1 was found to have the rare cis‐fused eudesmane skeleton. The structures of the isolated compounds were established by means of NMR (1H, 1H‐COSY, 1H,13C‐HSQC, HMBC, NOESY) and MS analyses.
Benzofuran Derivatives from Gerbera saxatilis
Authors: Chen Yan‐Jun , Li Ya , Chen Jian‐Jun , Gao Kun 
Published: January 2007

AbstractThree new substituted 2,3‐dihydro‐1‐benzofuran derivatives, compounds 1–3, were isolated from two extracts of Gerbera saxatilis, together with twelve known constituents. The structures of the new compounds were established by means of detailed spectroscopic analysis and by comparison of analytical data with those reported for structurally related compounds.
Total Synthesis of (2Z)‐[(4R,5R,6S)‐6‐(β‐D‐Glucopyranosyloxy)‐4,5‐dihydroxycyclohex‐2‐en‐1‐ylidene]ethanenitrile, a Cyanoglucoside from Ilex warburgii
Authors: Josien‐Lefebvre Delphine , Le Drian Claude 
Published: January 2007

AbstractThe total synthesis of the noncyanogenic cyanoglucoside 1, originally isolated from Ilex warburgii, was achieved in nine steps (9% overall yield), starting from an optically pure Diels–Alder adduct ((+)‐3). The key step of the synthesis, the glycosidation, was carried out under Koenigs–Knorr conditions closely related to those developed for the total syntheses of (−)‐lithospermoside and (−)‐bauhinin. We had to tune the protecting groups used for the two free cis‐configured OH groups of the aglycone, which afforded the desired β‐d‐glucoside intermediate 15 in very good yield (62%).
Secoleuconoxine and Oxopericine Derivatives from Kopsia
Authors: Lim Kuan‐Hon , Kam Toh‐Seok 
Published: January 2007

AbstractTwo new indole alkaloids, viz., arboloscine (1), the first example of a secoleuconoxine, and pericidine (5), an oxidized derivative of pericine (6), were obtained as minor alkaloids from the stem‐bark extract of the Malayan Kopsia species, K. arborea. Their structures were established by spectroscopic analysis.
Rearranged Calamenene and Eudesmane Sesquiterpenoids from two Chinese Liverworts
Authors: Ma Bin , Lu Zhi‐Qiang , Guo Huai‐Fang , Lou Hong‐Xiang 
Published: January 2007

AbstractFour novel rearranged calamenene sesquiterpenoids, 1–4, and two eudesmane sesquiterpenoids, 5 and 6, were isolated from the Chinese liverworts Chiloscyphus polyanthus (L.) and Bazzania japonica S. (Lac.) Lindb. Their structures and relative configurations were determined by chemical derivatization and in‐depth spectroscopic methods, especially 1D‐ and 2D‐NMR as well as HR‐MS analyses.