bluuebunny/crossref_metadata_2025 huggingface dataset:
SUMO
ylation
Authors: Schimmel Joost , Vertegaal Alfred CO
Published: December 2009

SUMOs
are Small
Ubiquitin
‐like MOdifier proteins that are covalently attached to hundreds of known target proteins to regulate their function. SUMOylation is the process of conjugating
SUMOs
to target proteins via
E1
,
E2
and
E3
enzymes and occurs mostly at specific SUMOylation consensus sites in targets. SUMOylation is a reversible process;
SUMO‐specific proteases
remove
SUMOs
from target proteins. It has been established that reversible protein SUMOylation is critical for eukaryotic life. A wide variety of cellular processes are regulated by SUMOylation including
deoxyribonucleic acid
(DNA) metabolism, transport, ribosome biogenesis and translation. Proteins can also associate with
SUMO
noncovalently via
SUMO
interaction motifs (SIMs). This affects target protein function and can also affect the subcellular localization of target proteins. Similar to
ubiquitin
,
SUMOs
can form polymers via internal SUMOylation sites. Crosstalk between SUMOylation and other posttranslational modifications such as phosphorylation, acetylation and ubiquitination is required for appropriate control of target protein activity.

Key concepts:

SUMOs are Small Ubiquitin‐like MOdifiers that are covalently attached to lysines in target proteins.

SUMOylation, the process of SUMO conjugation to a target protein, frequently occurs on a lysine situated in a SUMOylation consensus site.

Conjugated SUMOs can be removed from target proteins by SUMO‐specific proteases.

Vertebrates express three different SUMO isoforms, SUMO‐1, SUMO‐2 and SUMO‐3, encoded by three different genes.

SUMOs can form polymers via internal SUMOylation sites in SUMO‐2 and SUMO‐3.

Several proteins can bind noncovalently to SUMOs via SUMO interaction motifs (SIMs).

A finely balanced SUMOylation/deSUMOylation system is required for eukaryotic life.

Crosstalk between SUMOylation and other posttranslational modifications like acetylation, phosphorylation and ubiquitination, is important for full control of target protein activity.
Purifying and Analysing Cytosolic Protein Complexes
Authors: Phillips Theresa M
Published: December 2009

The study of cytosolic protein complexes, called systems or functional proteomics, is complicated by the challenges associated with purifying unadulterated, functional complexes, and with developing analytical methods for studying protein structure that can accommodate high molecular masses, or weak and transient protein–protein interactions. Development of new analytical techniques has progressed considerably in recent years, with the adaptation of mass spectrometry (MS) and nuclear magnetic resonance (NMR) for large complexes, in particular, adaptations using the popular electrospray ionization (ESI) coupled with a ToF (time‐of‐flight) analyser. Purification methods that have been adapted for the study of protein–protein interactions include electromobility shift assays, formaldehyde crosslinking, tandem affinity purification (TAP) and coexpression purification techniques, whereas flow field‐flow fractionation (F4) has been cited as having many significant advantages over all of these. New approaches to study posttranslational modifications, and adaptation of detection methods for quantitative analyses, are also being used to advance the study of protein complexes.

Key Concepts:

Functional proteomics aims to identify how proteins interact with each other and other macromolecules.

Purification of protein complexes is more difficult than that of individual proteins.

Techniques for protein complex purification include methods such as formaldehyde crosslinking and tandem affinity purification.

The introduction of electrospray ionization made it possible to create aerosols of proteins that could be analysed by mass spectrometry.

Methods for isolation of a complex for study include
in vitro
reconstitution, coexpression and endogenous complex purification.

Protein complexes with transient interactions can be studied using nuclear magnetic resonance.

Formaldehyde crosslinking stabilizes protein interactions during purification.

The yeast two‐hybrid technique is usually used to isolate transcriptional proteins from the nucleus.

A modification of the Western blot, called a gel overlay assay, is used to detect proteins with binding affinity for one another.
EM
Analysis of Protein Structure
Authors: Ohi Melanie D
Published: December 2009

Proteins carry out most cellular processes in the context of dynamic multiprotein assemblies. Although mapping the large number of protein interactions found within cells is progressing rapidly, we still lack knowledge about how proteins assemble into macromolecular machines to perform their functions. Electron microscopy can be used to determine the shape and structures of biological molecules that are difficult to study by more traditional structural approaches, such as X‐ray crystallography and NMR analysis. However, since biological molecules are composed mainly of low electron scattering atoms and contain large amounts of water, it is necessary to use special preparation techniques to protect the structural integrity of biological specimens in the vacuum of the electron microscope and improve the amount of contrast created by the sample. Negative staining, rotary shadowing and cryo‐EM are all powerful techniques that are useful for examining the structures and molecular organization of biological complexes by EM.

Key concepts:

Negative staining is a valuable approach to characterizing the structural homogeneity of a sample.

Negative staining can be used to quantify major conformational shifts of proteins and complexes in response to the addition of inhibitors, activators or ligands.

Rotary shadowing provides information about the surface topology of a specimen.

Cryo‐EM preserves specimens in a near‐native environment and is used to generate high‐resolution 3D structures of large macromolecular complexes.
Positive Interspecific Interactions
Authors: Hacker Sally D
Published: December 2009

Cooperative relationships between species have been recognized for centuries but, until recently, their acceptance as important forces in community ecology has lagged behind that of antagonistic interactions. Interspecific positive interactions are defined as relationships between different species that result in better growth, reproduction and/or survival for at least one species involved in the interaction without negatively affecting the other species. They may be trophic or nontrophic and act directly or indirectly (through a third species). Positive interactions are not static but vary in their strength and symmetry depending on the context under which they occur. They can act to promote species coexistence especially under harsh physical or biological stress and thus are important to species diversity, species invasions and the conservation and management of highly impacted systems.

Key concepts:

Recent attention to the cooperative relationships among species shows that they are important forces in shaping community structure.

Positive interspecific interactions are defined as cooperative relationships between different species that result in better growth, reproduction and/or survival for at least one species involved in the interaction without negatively affecting the other species.

Positive interactions can be trophic and nontrophic, can act directly or indirectly (mediated by a third species) and can be symmetric (species have equal effects) or asymmetric (species have unequal effects).

Positive species interactions are not static but vary in their outcome depending on the context under which they occur.

Theory and experiments show that positive interactions are more likely to occur under stressful physical or biological contexts.

Studies demonstrate that succession in any community is driven by a complex array of species interactions but that positive interactions are important forces especially early when physical and biological conditions may be harsh.

Positive interactions should promote species coexistence and thus increase species diversity.

Species invasions are facilitated by other species although positive feedbacks between multiple non‐native species have rarely been shown.

Restoration of degraded communities can involve reintroducing dominant species that promote the colonization and maintenance of rare species by providing basic habitat and/or favourable physical modifications to the environment.
Biodegradation of 2,4‐dinitrophenol under denitrification conditions
Authors: Zhu Jian‐Hang , Yan X.i‐Luan
Published: December 2009

Nitrophenols are often found in industrial wastewaters for a wide range of processes; they are highly toxic and potentially carcinogenic. Anaerobic biodegradation of nitrophenols has advantages of relatively low cost, less sludge produced, and high efficiency, when compared with aerobic biodegradation and physical/chemical treatments, although available published results are often contradictory. This paper reports on 2,4‐dinitrophenol biodegradation in an anaerobic bioreactor operated in a continuous mode in order to determine optimal operating conditions, and the effects of the main operating parameters such as hydraulic retention time and chemical oxygen demand (COD) loading on the process efficiency.

In this study, an 80‐day gradual enrichment of an anaerobic culture has been carried out at 25 °C in an anaerobic bioreactor for continuously treating a synthetic wastewater containing 210 mg/l 2,4‐dinitrophenol and 100 mg/l nitrate. The results showed that the enriched culture could utilize 2,4‐dinitrophenol as a sole electron donor and nitrate as an electron acceptor at the end of the enrichment (on Day 80). Almost all nitrate and 95.5% 2,4‐dinitrophenol could be simultaneously removed at a hydraulic retention time of 12 h in the anaerobic bioreactor. The removal of 1 g of the added nitrate required about 4.60 g COD (as provided by the 2,4‐dinitrophenol) as the electron donor, and the removal of 2,4‐dinitrophenol by this enriched culture was strongly dependent on the presence of nitrate. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd.
Effect of different thermal treatments on the mechanical performance of poly(L‐lactic acid) based eco‐composites
Authors: Dobreva T. , Benavente R. , Pereña J. M. , Pérez E. , Avella M. , García M. , Bogoeva‐Gaceva G.
Published: December 2009

PLLA‐based eco‐composites reinforced with kenaf fiber and rice straw and containing red or yellow pigments have been studied. The mechanical behavior of the composites was tested by DMTA at two different annealing temperatures (65°C and 85°C) and times (15 min and 120 min) as well as at two preparation conditions: vacuum drying and long time at room temperature. A decrease of microhardness was observed during the water absorption tests. Moreover, the rice straw‐based composites absorbed more water than the kenaf‐ones. Generally, the dyed NFs composites presented better water resistance than undyed ones. The pigments improved the adhesion and led to better mechanical performance. The natural fibers favored the cold crystallization process of PLLA and shifted the cold crystallization peak temperature to lower values, as it was confirmed by DSC measurements. The values of tensile storage modulus obtained after different preparation condition were strongly affected by the process of physical ageing. According to, tan δ parameter, the samples stored at room temperature for a long time showed the highest amorphous content. The PLLA eco‐composite reinforced with kenaf fibers, dyed with the red pigment, and annealed at 85°C for 2 h displays the best mechanical properties. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Effect of nucleation agents on the crystallization of poly(3‐hydroxybutyrate‐co‐4‐hydroxybutyrate) (P3/4HB)
Authors: Wang Liang , Wang Xiaojuan , Zhu Wenfu , Chen Zhifei , Pan Jueyu , Xu Kaitian
Published: December 2009

Boron nitride (BN), talc, hydroxyapatite (HA), and zinc stearate (ZnSt) were investigated as nucleation agents (NA) for nonfossil‐based poly(3‐hydroxybutyrate‐co‐4‐hydroxybutyrate) (P3/4HB) plastics. Nonisothermal crystallization behaviors of the P3/4HB/NA blends were examined by DSC. It revealed that BN is the most efficient nucleation agent to promote the crystallization rate, however, but not the crystallization degree. The lasting crystallization of P3/4HB was also removed. The nucleation effect was strengthened with increase of BN content up to 1% and then slackened deeply when further BN was added. Isothermal crystallization analysis revealed that the addition of nucleation agent BN does not alter the crystal growth mode of P3/4HB, with maintaining the Avrami parameter n value around 2.40. Talc did enhance the crystallization of P3/4HB with however milder crystal growth rate. HA and ZnSt did not promote, but depressed the crystallization of P3/4HB plastics. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Synthesis and characterization of polyaniline/graphite composites and study of their electrical and electrochemical properties
Authors: Konwer S. , Pokhrel B. , Dolui S. K.
Published: December 2009

Polyaniline/graphite (PA/G) composites were prepared by the incorporation of graphite in various proportions (0.2, 0.5, and 1.0%) into polyaniline (PA) through the in situ polymerization of aniline. The polymer composites were characterized by Fourier transform infrared (FTIR) spectroscopy, ultraviolet–visible (UV–vis) spectroscopy, X‐ray diffraction, scanning electron microscopy, thermogravimetric analysis, differential scanning calorimetry, a four‐probe method, current–voltage characteristics, and cyclic voltammetry (CV). FTIR and UV–vis spectroscopy revealed interaction between graphite and the imine groups of PA. The polymer composites showed a crystalline nature with a hexagonal primitive structure. The uniform distribution of graphite particles was observed within the polymer matrix. The composites were found to possess good thermal stability up to 573 K. The conductivity of the composites was in the range 4.53–238.08 S/cm, and the conductivity varied with temperature. The band gap of the composites was found in the range 1.2–1.6 eV. The PA/G composites also displayed a reversible electrochemical response, as revealed by the CV study. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Life writing in the shadow of the Shoah: fathers and sons in the memoirs of Elie Wiesel and Leon Weliczker Wells
Authors: Cohler Bertram J.
Published: December 2009

This paper contrasts the accounts of mourning and the resolution of grief in the aftermath of the Shoah as portrayed in the memoirs of two men Elie Wiesel (1928–) and Leon Weliczker Wells (1925–). Each life writer grew up in an Eastern European shtetl, a traditional community, in which he was immersed in Hasidic culture, and was incarcerated during adolescence in an extermination camp. This paper explores the impact of each life writer's experienced childhood relationship with his father in coping with his losses over the post‐war period. Wells' memoir is a factual account of the perfidy of the regime that he witnessed as a member of a Sonderkommando or death brigade in the Janowska extermination camp and kept a journal, later used as evidence for the indictment of the regime at the Eichman trial. Wiesel's acclaimed text Night, and his memoirs, reflect his continuing guilt regarding his father's death while they were together in Auschwitz and Buchenwald. Copyright © 2009 John Wiley & Sons, Ltd.
Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity
Authors: Snell‐Rood Emilie C. , Van Dyken James David , Cruickshank Tami , Wade Michael J. , Moczek Armin P.
Published: December 2009

Adaptive phenotypic plasticity allows organisms to cope with environmental variability, and yet, despite its adaptive significance, phenotypic plasticity is neither ubiquitous nor infinite. In this review, we merge developmental and population genetic perspectives to explore costs and limits on the evolution of plasticity. Specifically, we focus on the role of modularity in developmental genetic networks as a mechanism underlying phenotypic plasticity, and apply to it lessons learned from population genetic theory on the interplay between relaxed selection and mutation accumulation. We argue that the environmental specificity of gene expression and the associated reduction in pleiotropic constraints drive a fundamental tradeoff between the range of plasticity that can be accommodated and mutation accumulation in alternative developmental networks. This tradeoff has broad implications for understanding the origin and maintenance of plasticity and may contribute to a better understanding of the role of plasticity in the origin, diversification, and loss of phenotypic diversity.
Variability in Foliar Essential Oils among Different Morphotypes of Lantana Species Complexes, and Its Taxonomic and Ecological Significance
Authors: Love Amit , Naik Dattatraya , Basak Sandip K. , Babu Suresh , Pathak Namrata , Babu Cherukuri R.
Published: December 2009

The genus Lantana has many species complexes, and L. camara is one of the aggressive alien weedy species complexes; species delimitation in these complexes is a nightmare for taxonomists. We examined the diversity in the chemical composition of foliar essential oils among morphotypes of Lantana species complexes inhabiting the same ecological gradient, and its taxonomic and ecological significance. The yields of essential oils varied from 0.1 to 0.79% in foliar hydrodistillates of eleven morphotypes, and a total of 39 chemical constituents were detected by GC/MS. The quantitative and qualitative variability in the composition of essential oils among morphotypes was very high, and hence they represent chemotypes. The diversity observed in the composition of essential oils appears to be of genetic origin and thus of taxonomic value. The formation of distinct clusters and sub‐clusters at high distance cluster combine values also substantiates that the patterns of distribution of chemical constituents among morphotypes can be used in delimiting species and infraspecific taxa within the species complexes. The presence of β‐caryophyllene and other such compounds, which are known to prevent herbivory, in morphotypes of Lantana species complexes suggest that these compounds may provide selective advantage to Lantana over native species in the invasion of new and disturbed habitats.
Chemical Composition of Hydrodistilled Essential Oil of Artemisia incana (L.) Druce and Antimicrobial Activity against Foodborne Microorganisms
Authors: Çetin Bülent , Özer Hakan , Çakir Ahmet , Mete Ebru , Tosun Murat , Öztürk Erdoğan , Polat Taşkın , Kandemir Ali
Published: December 2009

The oil obtained by hydrodistillation from the aerial parts of Artemisia incana (L.) Druce from Turkey was analyzed by GC and GC/MS. Sixty‐three compounds were characterized, representing 97.2% of the total components detected, and camphor (19.0%), borneol (18.9%), 1,8‐cineole (14.5%), bornyl acetate (7.8%), camphene (4.9%), and α‐thujone (4.8%) were identified as predominant components. The essential oil was also tested for its antimicrobial activity against 44 different foodborne microorganisms, including 26 bacteria, 15 fungi, and 3 yeast species. The essential oil of A. incana exhibited considerable inhibitory effects against all bacteria, fungi, and yeast species tested. However, the oil showed lower inhibitory activity against the tested bacteria than the reference antibiotics.
Ethical dimensions of the open‐door admissions policy
Authors: Ingram William G. , Morrissey Sharon E.
Published: December 2009

Ethical dilemmas at the community college often pose a choice between options equally grounded in the core values of the institution. These dilemmas often emerge from disputes that are complex, dynamic, and politically volatile. We review the development of one such dispute to show how our understanding of institutional core values is often only clarified through reflection and consultation with appropriate advisors, authorities, and constituencies.
Reprogramming of a Malonic N‐Heterocyclic Carbene: A Simple Backbone Modification with Dramatic Consequences on the Ligand's Donor Properties
Authors: César Vincent , Lugan Noël , Lavigne Guy
Published: December 2009

Reaction of N,N′‐dimesitylformamidine with dimethylmalonyl dichloride in dichloromethane in the presence of an excess of triethylamine gives the 2‐chloro‐4,5‐dioxohexahydropyrimidine 1. The corresponding diamidocarbene 3 is generated in situ by further deprotonation with KHMDS at –40 °C and identified by trapping with S8 to give the fully characterized (including X‐ray structure) sulfur adduct 4. It also reacts with [RhCl(cod)]2 to yield the NHC complex [RhCl(3)(cod)] (5) (characterized also by X‐ray structure). The donor properties of 3 were evaluated against the established IR [ν(CO)] scale from [RhCl(3)(CO)2] (6). The average value of ν(CO) = 2045 cm–1 indicates that the diamidocarbene 3 is much less nucleophilic than structurally relevant six‐membered NHCs including the anionic diaminocarbenes previously reported in our group.
A mathematical technique for estimating the melting points of triacylglycerols from the component fatty acid melting points
Authors: Maruzeni Shoji
Published: December 2009

A method of correlating the value of the melting point of triacylglycerol (tag) with the values of the melting points of the three fatty acids constituting the tag as its acyl radicals was studied by applying the least squares method. The method was applied to the sets of values of the melting points of the α, β', and β forms of crystals of tag with saturated acyl radicals comprising decanoyl, lauroyl, myristoyl, palmitoyl, and stearoyl. The value of the melting point of the crystal form of the tag is expressed by prediction equations that comprise the values of the melting points of the three fatty acids above as variables. The best‐fit equation can be fixed by satisfying the criterion of least squares to the prediction equations. The method enables us to estimate the values of the melting points of possible molecular species of tag consisting of the acyl radicals above. The correlation coefficient relevant to the correlation between the values of the melting points of the particular crystal form and the corresponding values of the best‐fit equation is obtained. The more thermodynamically stable the crystal form, the larger is the value of the correlation coefficient.
A Decade of Advancements in Pauson–Khand‐Type Reactions
Authors: Lee Hang‐Wai , Kwong Fuk‐Yee
Published: December 2009

This Microreview illustrates the conceptual evolution ofPauson–Khand‐type reactions and the recent advancements in catalyst design and applications. Intra‐ and intermolecular Pauson–Khand‐type reactions, as well as their enantioselective versions, are reviewed. In addition to previous reviews, this article mainly covers literature references on the developments between the late 1990s and early 2009.
Palladium‐Catalyzed C2 or C5 Direct Arylation of 3‐Formylthiophene Derivatives with Aryl Bromides
Authors: Dong Jia Jia , Doucet Henri
Published: December 2009

The system Pd(OAc)2/dppb was found to be an efficient catalyst precursor for the direct arylation of 3‐formylthiophene derivatives. When using 3‐formylthiophene, the 2‐arylated thiophenes were obtained with regioselectivities of 76–86 %, whereas the arylation of 3‐formylthiophene diethyl acetal gave the 5‐arylated thiophenes with regioselectivities of 64–88 %. These reactions were performed by using only 0.1 mol‐% of the catalyst. Moreover, this procedure has been found to be tolerant to a variety of functional groups on the aryl bromide such as formyl, propionyl, benzoyl, nitrile, or nitro.
Recovery of polyhydroxybutyrate (PHB) from Cupriavidus necator biomass by solvent extraction with 1,2‐propylene carbonate
Authors: Fiorese Mônica Lady , Freitas Filomena , Pais Joana , Ramos Ana Maria , de Aragão Gláucia M. F. , Reis Maria A. M.
Published: December 2009

An integrated procedure for the recovery of polyhydroxybutyrate (PHB) produced by Cupriavidus necator based on the extraction with 1,2‐propylene carbonate was evaluated. The effect of temperature (100–145°C) and contact time (15–45 min), precipitation period, and biomass pretreatments (pH shock and/or thermal treatments) on PHB extraction efficiency and polymer properties was evaluated. The highest yield (95%) and purity (84%) were obtained with the combination of a temperature of 130°C and a contact time of 30 min, with a precipitation period of 48 h. Under these conditions, PHB had a molecular weight of 7.4×105, which was the highest value obtained. Lower values (2.2×105) were obtained for higher temperatures (145°C), while lower temperatures resulted in incomplete extraction yields (45–54%). No further yield improvement was achieved with the pH/heat pretreatments, but the polymer's molecular weight was increased to 1.3×106. The PHB physical properties were not significantly affected by any of the tested procedures, as shown by the narrow ranges obtained for the glass transition temperature (4.8–5.0°C), melting temperature (170.1–180.1°C), melting enthalpy (77.8–88.5 J/g) and crystallinity (55–62%). 1,2‐Propylene carbonate was shown to be an efficient solvent for the extraction of PHB from biomass. The precipitation procedure was found to highly influence the polymer recovery and its molecular weight. Although polymer molecular weight and purity were improved by applying pH/heat pretreatment to the biomass, the procedure involves the use of large amounts of chemicals, which increases the recovery costs and makes the process environmentally unfriendly.
Proteomics reveal rat hippocampal lateral asymmetry
Authors: Samara A. , Vougas K. , Papadopoulou A. , Anastasiadou E. , Baloyanni N. , Paronis E. , Chrousos G.P. , Tsangaris G.Th.
Published: December 2009

Brain laterality has been observed in animals and humans structurally, functionally, and behaviorally. MRI and CT scans have revealed pathological and normal brain asymmetry. A coarse assessment of rat or human brain fails to expose profound left/right differences, while a finer examination of its structure reveals an array of asymmetric features. This lateralization may be derived from evolutionary, genetic, developmental, epigenetic, and pathologic factors. However, brain structure and function is complex and macroscopic or microscopic asymmetries may be hard to discern from random fluctuations. This study concentrated on the hippocampus and we explored laterization employing a molecular high‐throughput approach. Using proteomic analysis based on a combined approach of 2‐D PAGE and MS, we examined differential protein expression in the hippocampi (left vs. right) of young adult male rats. Initial proteomic analysis demonstrated quantitative differences of approximately eighty proteins between the right (RH) and left hippocampus (LH). These were primarily energy‐, cell metabolism‐, stress‐inducible chaperone proteins and cytoskeleton‐ proteins. Analysis revealed higher abundance of metabolic enzymes related to cellular energy metabolism, in the RH than the LH. In contrast, higher concentrations of proteins which are located mainly in astrocytes were shown in the LH than the RH. Immunoblotting of brain‐specific proteins, on single animal hippocampal lysates confirmed the expression of Dynamin‐1, DRP2, synapsin‐1 and others, to be higher in the RH than LH lysates. These findings demonstrate major laterality in the expression of protein molecules between the two hippocampi providing a fertile field for mapping studies relating molecular, neuroimaging and functional data. Undoubtedly, asymmetries found at the animal level are hard to extrapolate to humans; however, studies in animal models will increase our understanding of the developing and adult brain and the healthy and diseased brain. © 2009 Wiley‐Liss, Inc.
Synthesis of 15‐Cyano‐12‐oxopentadecano‐15‐lactone and 15‐Cyano‐ 12‐oxopentadecano‐15‐lactam
Authors: Wu Peng , Liang Xiao‐Mei , Zhang Jian‐Jun , Jia Yue‐Mei , Dong Yan‐Hong , Huang Jia‐Xing , Chen Fu‐Heng , Wang Dao‐Quan
Published: December 2009

15‐Cyano‐12‐oxopentadecano‐15‐lactone was synthesized in 59% total yield starting from 2‐nitrocyclododecanone by Michael addition to acrylaldehyde, followed by reaction with trimethylsilylcyanide, hydrolysis, ring‐expansion, and Nef reaction. A two‐step, one‐pot synthesis of intermediate 2‐hydroxy‐4‐(1‐nitro‐2‐oxycyclododecyl)butanenitrile from 3‐(1‐nitro‐2‐oxocyclododecyl)propanal was developed and the conditions for the Nef reaction were studied. 15‐Cyano‐12‐oxopentadecano‐15‐lactam was synthesized in 40% total yield starting from 2‐nitrocyclododecanone by Michael addition to acrylaldehyde, followed by Strecker reaction, ring‐expansion, and Nef reaction. The conditions for the Strecker and Nef reactions were studied. The structures of the target compounds, intermediates, and by‐product were characterized by IR, 1H‐ and 13C‐NMR, and elemental analysis or MS.
Two New Diterpenoid Glucosides from Clerodendrathus spicatus
Authors: Chen Yi‐Lei , Tan Chang‐Heng , Tan Jun‐Jie , Zhao Xue‐Mei , Jiang Shan‐Hao , Zhu Da‐Yuan
Published: December 2009

Two new diterpenoid glucosides, clerodendranthusides B and C (1 and 2, resp.), together with 16 known compounds, comprising four lignans, five miscellaneous phenylpropanoids, two flavonoids, one sesquiterpenoid glycoside, two triterpenoid glycosides, one megastigmane, as well as one anthraquinone, were isolated from the 50% EtOH extract of the whole plants of Clerodendrathus spicatus. Their structures were elucidated by chemical and spectroscopic methods.
Oligonucleotide Analogues with Integrated Bases and Backbone. Part 22
Authors: Bernet Bruno , Johar Zeena , Ritter Anne , Jaun Bernhard , Vasella Andrea
Published: December 2009

The tritylated and silylated self‐complementary A*[s]U*[s]A*[s]U* and U*[s]A*[s]U*[s]A* tetramers 18 and 24, linked by thiomethylene groups (abbreviated as [s]) between a nucleobase and C(5′) of the neighbouring nucleoside unit were prepared by a linear synthesis based on S‐alkylation of 5′‐thionucleosides by 6‐(chloromethyl)uridines, 7 or 10, or 8‐(chloromethyl)adenosines, 12 or 15. The tetramers 18 and 24 were detritylated to the monoalcohols 19 and 25, and these were desilylated to the diols 20 and 26, respectively. The association of the tetramers 18–21 and 24–26 in CDCl3 or in CDCl3/(D6)DMSO 95 : 5 was investigated by the concentration dependence of the chemical shifts for HN(3) or H2NC(6). The formation of cyclic duplexes connected by four base pairs is favoured by the presence of one and especially of two OH groups. The diol 20 with the AUAU sequence prefers reverse‐Hoogsteen, and diol 26 with the UAUA sequence Watson–Crick base pairing. The structure of the cyclic duplex of 26 in CDCl3 at 2° was derived by a combination of AMBER* modeling and simulated annealing with NMR‐derived distance and torsion‐angle restraints resulting in a Watson–Crick base‐paired right‐handed antiparallel helix showing large roll angles, especially between the centre base pairs, leading to a bent helix axis.
β‐Peptide Conjugates: Syntheses and CD and NMR Investigations of β/α‐Chimeric Peptides, of a DPA‐β‐Decapeptide, and of a PEGylated β‐Heptapeptide
Authors: Gardiner James , Mathad Raveendra I. , Jaun Berhard , Schreiber Jürg V. , Flögel Oliver , Seebach Dieter
Published: December 2009

β3‐Peptides consisting of six, seven, and ten homologated proteinogenic amino acid residues have been attached to an α‐heptapeptide (all d‐amino acid residues; 4), to a hexaethylene glycol chain (PEGylation; 5c), and to dipicolinic acid (DPA derivative 6), respectively. The conjugation of the β‐peptides with the second component was carried out through the N‐termini in all three cases. According to NMR analysis (CD3OH solutions), the (M)‐314‐helical structure of the β‐peptidic segments was unscathed in all three chimeric compounds (Figs. 2, 4, and 5). The α‐peptidic section of the α/β‐peptide was unstructured, and so was the oligoethylene glycol chain in the PEGylated compound. Thus, neither does the appendage influence the β‐peptidic secondary structure, nor does the latter cause any order in the attached oligomers to be observed by this method of analysis. A similar conclusion may be drawn from CD spectra (Figs. 1, 3, and 5). These results bode well for the development of delivery systems involving β‐peptides.
Electron localizability indicators ELI–D and ELIA for highly correlated wavefunctions of homonuclear dimers. I. Li2, Be2, B2, and C2
Authors: Bezugly Viktor , Wielgus Pawel , Kohout Miroslav , Wagner Frank R.
Published: December 2009

Electron localizability indicators based on the parallel‐spin electron pair density (ELI–D) and the antiparallel‐spin electron pair density (ELIA) are studied for the correlated ground‐state wavefunctions of Li2, Be2, B2, and C2 diatomic molecules. Different basis sets and reference spaces are used for the multireference configuration interaction method following the complete active space calculations to investigate the local effect of electron correlation on the extent of electron localizability in position space determined by the two functionals. The results are complemented by calculations of effective bond order, vibrational frequency, and Laplacian of the electron density at the bond midpoint. It turns out that for Li2, B2, and C2 the reliable topology of ELI–D is obtained only at the correlated level of theory. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
A molecular mechanics model for imatinib and imatinib:kinase binding
Authors: Aleksandrov Alexey , Simonson Thomas
Published: December 2009

Imatinib is an important anticancer drug, which binds specifically to the Abl kinase and blocks its signalling activity. To model imatinib:protein interactions, we have developed a molecular mechanics force field for imatinib and four close analogues, which is consistent with the CHARMM force field for proteins and nucleic acids. Atomic charges and Lennard‐Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with imatinib fragments at 32 different positions. We considered both a neutral and a protonated imatinib. The final RMS deviation between the ab initio and force field energies, averaged over both forms, was 0.2 kcal/mol. The model also reproduces the ab initio geometry and flexibility of imatinib. To apply the force field to imatinib:Abl simulations, it is also necessary to determine the most likely imatinib protonation state when it binds to Abl. This was done using molecular dynamics free energy simulations, where imatinib is reversibly protonated during a series of MD simulations, both in solution and in complex with Abl. The simulations indicate that imatinib binds to Abl in its protonated, positively‐charged form. To help test the force field and the protonation prediction, we did MD free energy simulations that compare the Abl binding affinities of two imatinib analogs, obtaining good agreement with experiment. Finally, two new imatinib variants were considered, one of which is predicted to have improved Abl binding. This variant could be of interest as a potential drug. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
A first principle study of the structural, vibrational and electronic properties of tetrathiafulvalene adsorbed on Ag(110) and Au(110) surfaces
Authors: Martorell Benjamí , Clotet Anna , Fraxedas Jordi
Published: December 2009

We have studied the adsorption properties of a charge donor organic molecule, tetrathiafulvalene (TTF), on the (110) surfaces of silver and gold by means of the generalized gradient approach of the density functional theory using periodic slab models. This molecule is the core building block of a host of molecular materials exhibiting extremely reach phase diagrams with a variety of ground states. The interfaces formed with metallic surfaces have received only limited attention, despite of their relevance. We have determined the stable adsorption sites for two unit cells representing high and low coverage, which are determinant for the adsorption properties of TTF on the surface. The preferential chemisorption is via the direct interaction of sulfur atoms with the Ag or Au atoms on top sites. All adsorbed TTF are more stable than gas phase TTF. The simulation of the vibrational spectra has permitted us to find the fingerprints of these structures to characterize them on this surface. The donor nature of TTF induces charge transfer to the metallic surfaces. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution
Authors: Kritayakornupong Chinapong , Vchirawongkwin Viwat , Rode Bernd M.
Published: December 2009

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree‐Fock level in conjunction with Dunning double‐ζ plus polarization function basis sets. The simulation predicts an average HCl bond distance of 1.28 Å, which is in good agreement with the experimental value. The HHCl···Ow and ClHCl···Hw distances of 1.84 and 3.51 Å were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure‐making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
An ecological examination of rural mozambican women's attainment of postwar wellbeing
Authors: Deacon Zermarie , Sullivan Cris
Published: December 2009

Women's experiences of warfare and postwar recovery are qualitatively different from those of men. However, to date, the processes whereby women recover from the gendered impacts of war have not been sufficiently explored. In order to address this gap in the literature and to inform policies and services aimed at women recovering from warfare, a qualitative investigation was conducted of the process whereby women in one rural community in northern Mozambique attained wellbeing in the wake of war. Findings indicate that factors at all levels of the socio‐ecological system were significant in supporting women's attainment of postwar wellbeing. © 2009 Wiley Periodicals, Inc.
Defining the heterogeneity of skeletal muscle‐derived side and main population cells isolated immediately ex vivo
Authors: Kallestad Kristen M. , McLoon Linda K.
Published: December 2009

Myoblast transfer therapy for Duchenne muscular dystrophy (DMD) largely fails due to cell death and inability of transplanted cells to engraft in diseased muscles. One method attempting to enrich for cell subpopulations is the Hoechst 33342 dye exclusion assay, yielding a side population (SP) thought to be progenitor enriched and a main population (MP). However, in vitro and transplant studies yielded inconsistent results relative to downstream progeny. Cell surface markers expressed by skeletal muscle‐derived MP and SP cells have not been fully characterized directly ex vivo. Using flow cytometry, MP and SP cells were characterized based on their expression of several well‐accepted progenitor cell antigens. Both the MP and SP populations are heterogeneous and overlapping in the cells they contain. The percentages of cells in each population vary with species and specific muscle examined. MP and SP populations contain both satellite and multipotent progenitor cells, based on expression of CD34, Sca‐1, Pax7, and M‐cadherin. Thus, isolation using this procedure cannot be used to predict downstream differentiation outcomes, and explains the conflicting literature on these cells. Hoechst dye also results in significant mortality of sorted cells. As defined subpopulations are easily obtained using flow cytometry, sorting immediately ex vivo based on accepted myogenic precursor cell markers will yield superior results in terms of cell homogeneity for transplantation therapy. J. Cell. Physiol. 222: 676–684, 2010. © 2009 Wiley‐Liss, Inc.
Fully automated liquid extraction‐based surface sampling and ionization using a chip‐based robotic nanoelectrospray platform
Authors: Kertesz Vilmos , Van Berkel Gary J.
Published: December 2009

A fully automated liquid extraction‐based surface sampling device utilizing an Advion NanoMate chip‐based infusion nanoelectrospray ionization system is reported. Analyses were enabled for discrete spot sampling by using the Advanced User Interface of the current commercial control software. This software interface provided the parameter control necessary for the NanoMate robotic pipettor to both form and withdraw a liquid microjunction for sampling from a surface. The system was tested with three types of analytically important sample surface types, viz., spotted sample arrays on a MALDI plate, dried blood spots on paper, and whole‐body thin tissue sections from drug dosed mice. The qualitative and quantitative data were consistent with previous studies employing other liquid extraction‐based surface sampling techniques. Published in 2009 by John Wiley & Sons, Ltd.
Nonalcoholic fatty liver disease after liver transplantation for cryptogenic cirrhosis or nonalcoholic fatty liver disease
Authors: Yalamanchili Kanthi , Saadeh Sherif , Klintmalm Göran B. , Jennings Linda W. , Davis Gary L.
Published: December 2009

Nonalcoholic steatohepatitis (NASH) may account for many cases of cryptogenic cirrhosis. If so, then steatosis might recur after liver transplantation. Two thousand fifty-two patients underwent primary liver transplantation for chronic liver disease between 1986 and 2004. Serial liver biopsy samples were assessed for steatosis and fibrosis. Two hundred fifty-seven patients (12%) had a pretransplant diagnosis of cryptogenic cirrhosis (239) or NASH (18). Fatty liver developed in 31% and was more common when the pretransplant diagnosis was NASH (45% at 5 years versus 23% for cryptogenic cirrhosis, P = 0.007). NASH developed in only 4% and occurred exclusively when steatosis had already occurred. Steatosis after liver transplantation was associated with the baseline body weight and body mass index by univariate analyses, but no pretransplant or posttransplant characteristic independently predicted steatosis after liver transplantation because obesity was so common in all groups. Five percent and 10% developed bridging fibrosis or cirrhosis after 5 and 10 years, respectively, and this was more common after NASH (31%) than in those who developed steatosis alone (6%) or had no fat (3%, P = 0.002). One-, 5-, and 10-year survival was the same in patients who underwent transplantation for cryptogenic cirrhosis or NASH (86%, 71%, and 56%) and in patients who underwent transplantation for other indications (86%, 71%, and 53%; not significant), but death was more often due to cardiovascular disease and less likely from recurrent liver disease. In conclusion, fatty liver is common after liver transplantation for cryptogenic cirrhosis or NASH but is twice as common in the latter group; this suggests that some cryptogenic cirrhosis, but perhaps not all, is caused by NASH. Posttransplant NASH is unusual, and steatosis appears to be a prerequisite. Advanced fibrosis is uncommon, and survival is the same as that of patients who undergo transplantation for other causes. Liver Transpl 16:431-439, 2010. © 2010 AASLD.
Synthesis of Amphiphilic and Double‐Hydrophilic Block Copolymers Containing Poly(vinyl amine) Segments by RAFT Polymerization of N‐Vinylphthalimide
Authors: Maki Yuya , Mori Hideharu , Endo Takeshi
Published: December 2009

We report on the controlled synthesis of amphiphilic and double‐hydrophilic block copolymers having poly(vinyl amine) segments by the reversible addition–fragmentation chain transfer (RAFT) polymerization of N‐vinylphthalimide (NVPI), followed by deprotection. The block copolymer poly(NVPI)‐b‐poly(N‐isopropylacrylamide) with a controlled molecular weight and low molecular mass distribution was obtained by the polymerization of N‐isopropylacrylamide (NIPAAm) using dithiocarbamate‐terminated poly(NVPI). The chain extension from the dithiocarbamate‐terminated polystyrene to NVPI could be controlled well under suitable conditions, and provided the block copolymer, polystyrene‐b‐poly(NVPI). We also investigated the thermoresponsive and optoelectronic properties and the aggregation behavior of double hydrophilic and amphiphilic block copolymers obtained after deprotection.

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HPLC fingerprints combined with principal component analysis, hierarchical cluster analysis and linear discriminant analysis for the classification and differentiation of Peganum sp. indigenous to China
Authors: Cheng Xue‐mei , Zhao Ting , Yang Tao , Wang Chang‐hong , Bligh S. W. Annie , Wang Zheng‐tao
Published: December 2009

Introduction – Seeds of wild Peganum harmala Linn., P. multisectum (Maxim) Bobr., P. nigellastrum Bunge and a probable indeterminate species, herein referred to as P. variety, are commonly used in Chinese medicine. These seeds cannot be differentiated based on morphology.

Objective – Seeds of P. harmala Linn., P. multisectum (Maxim) Bobr., P. nigellastrum Bunge and P. variety were collected in different provinces in China and their HPLC profiles were recorded for statistical analysis and pattern recognition.

Methodology – HPLC chromatograms of seed extracts were recorded under the same conditions. Individual HPLC chromatograms for each species were evaluated against the mean chromatogram for the same species generated using a similarity evaluation computer program. Data from chromatographic fingerprints were also processed using principal component analysis (PCA), hierarchical cluster analysis (HCA) and linear discriminant analysis (LDA).

Results – The Peganum sp. seed extracts had similar HPLC fingerprints but with some inter‐specific differences. The chromatographic fingerprints combined with PCA, HCA and LDA could distinguish the seeds of the different species of Peganum investigated.

Conclusion – HPLC fingerprints can be used to authenticate and differentiate the seeds of three different species of genus Peganum indigenous to China. The results indicated that the unidentified P. variety might indeed be a new species or variety. Copyright © 2009 John Wiley & Sons, Ltd.