bluuebunny/crossref_metadata_2025 huggingface dataset:
Year‐round high arachidonic acid levels in herbivorous rabbit fish Siganus fuscescens tissues
Authors: Osako Kazufumi , Saito Hiroaki , Kuwahara Koichi , Okamoto Akira
Published: February 2007

To identify a stable resource of 20∶4 n−6 (arachidonic acid, AA) in marine fish tissues, the lipid profiles of Siganus fuscescens organs (muscle, liver, and other viscera) and stomach contents were examined throughout the year. Crude total lipid (TL) contents in respective organs showed seasonal variations and were high in winter and low in summer. The main FA in TL were 16∶0, 18∶0, 16∶1n−7, 18∶1n−9, AA, and 22∶6n−3 (DHA). These FA were those generally observed in marine fish lipids, except for comparatively high levels of AA. In TL of muscle and liver, AA showed relatively high values during the period from late May to August (muscle, 4.6–13.1%; liver, 4.5–9.1%), compared with other seasons (muscle, 4.3–9.5%; liver, 3.6–8.4%). The AA levels in TL of other viscera and stomach contents fluctuated (other viscera, 2.0–10.7%; stomach contents, 7.6–26.7%). Regardless of the fishing season, each organ contained a higher level of AA in polar lipids (PL) than in neutral lipids. It was concluded that the fish contain comparatively high levels of AA in their TL throughout the year, and they accumulate AA characteristically in their tissue PL, probably from dietary food sources. Moreover, it was suggested that S. fuscescens has potential utility as a natural marine source of nutritional lipids, because the fish contain comparatively high levels of DHA and AA.
cis‐4,7,10,trans‐13–22∶4 fatty acid distribution in phospholipids of pectinid species Aequipecten opercularis and Pecten maximus
Authors: Kraffe Edouard , Soudant Philippe , Marty Yanic
Published: February 2007

The distribution of cis‐4,7,10,trans‐13‐docosate‐traenoic (c4,7,10,t13–22∶4), a peculiar FA previously isolated in the glycerophospholipids of some pectinid bivalves, was investigated in glycerophospholipid classes and subclasses of separated organs (gills, mantle, gonads, and muscle) of the queen scallop Aequipecten opercularis and the king scallop Pecten maximus. Plasmalogen (Pls) and diacyl + alkyl (Ptd) forms of serine, ethanolamine, and choline glycerophospholipids were isolated by HPLC and their FA compositions analyzed by GC‐FID. Pls and Ptd forms of serine glycerophospholipids (PlsSer and PtdSer), and to a lesser extend the Pls form of ethanolamine glycerophospholipids (PlsEtn), were found to be specifically enriched with c4,7,10,t13–22∶4. This specificity was found to decrease in the tested organs in the following order: gills, mantle, gonad, and muscle. In gills, c4,7,10,t13–22∶4 was shown to be the main unsaturated FA of serine glycerophospholipids in both Pls and Ptd forms (23.8 and 19.4 mol%, respectively, for A. opercularis, and 21.0 and 26.2 mol% for P. maximus). These results represent the first comprehensive report on the FA composition of plasmalogen serine subclass isolated from pectinid bivalves. The specific association of the PlsSer with the c4,7,10,t13–22∶4 for the two pectinid species can be paralleled to the specific association of the PlsSer with the non‐methylene interrupted (NMI) FA and 20∶1(n−11) observed in mussels, clams, and oysters (Kraffe, E., Soudant, P., and Marty, Y. (2004) Fatty Acids of Serine, Ethanolamine and Choline Plasmalogens in Some Marine Bivalves, Lipids 39, 59–66.) This, led us to hypothesize a similar functional significance for c4,7,10,t13–22∶4, NMI FA, and 20∶1(n−11) associated with PlsSer subclass of bivalves.
Synthesis of 3‐oxalinolenic acid and β‐oxidation‐resistant 3‐oxa‐oxylipins
Authors: Hamberg Mats , Chechetkin Ivan R. , Grechkin Alexander N. , de León Inés Ponce , Castresana Carmen , Bannenberg Gerard
Published: February 2007

3‐Oxalinolenic acid (3‐oxa‐9(Z), 12(Z), 15(Z)‐octadecatrienoic acid or (6(Z), 9(Z), 12(Z)‐pentadecatrienyloxy)acetic acid) was synthesized from 5(Z), 8(Z), 11(Z), 14(Z), 17(Z)‐eicosapentaenoic acid by a sequence involving the C15 aldehyde 3(Z), 6(Z), 9(Z), 12(Z)‐pentadecatetraenal as a key intermediate. Conversion of the aldehyde by isomerization and two steps of reduction afforded 6(Z), 9(Z), 12(Z)‐pentadecatrienol, which was coupled to bromoacetate to afford after purification by HPLC >99%‐pure 3‐oxalinolenic acid in 10–15% overall yield. 3‐Oxalinolenic acid was efficiently oxygenated by soybean lipoxygenase‐1 into 3‐oxa‐13(S)‐hydroperoxy‐9(Z), 11(E), 15(Z)‐octadecatrienoic acid, and this hydroperoxide could be further converted chemically into 3‐oxa‐13(S)‐hydroxy‐9(Z), 11(E), 15(Z)‐octadecatrienoic acid and 3‐oxa‐13‐oxo‐9(Z), 11(E), 15(Z)‐octadecatrienoic acid. The 3‐oxa‐hydroperoxide also served as the substrate for the plant enzymes allene oxide synthase, divinyl ether synthase, and hydroperoxide lyase to produce 3‐oxa‐12‐oxo‐10, 15(Z)‐phytodienoic acid and other 3‐oxa‐oxylipins that were characterized by MS, 3‐Oxalinolenic acid was not oxygenated by 9‐lipoxygenase from tomato but was converted at a slow rate into 3‐oxa‐9(S)‐hydroperoxy‐10(E), 12(Z), 15(Z)‐octadecatrienoic acid by recombinant maize 9‐lipoxygenase. Recombinant α‐dioxygenase‐1 from Arabidopsis thaliana catalyzed the conversion of 3‐oxalinolenic acid into a 2‐hydroperoxide, which underwent spontaneous degradation into a mixture of 6,9,12‐pentadecatrienol and 6,9,12‐pentadecatrienyl formate. A novel α‐dioxygenase from the moss Physcomitrella patens was cloned and expressed and was found to display the same activity with 3‐oxalinolenic acid as Arabidopsis thaliana α‐dioxygenase‐1. Lipoxygenase‐generated 3‐oxa‐oxylipins are resistant toward β‐oxidation and have the potential for displaying enhanced biological activity in situations where activity is limited by metabolic degradation.
2,6‐hexadecadiynoic acid and 2,6‐nonadecadiynoic acid: Novel synthesized acetylenic fatty acids as potent antifungal agents
Authors: Carballeira Néstor M. , Sanabria David , Cruz Clarisa , Parang Keykavous , Wan Baojie , Franzblau Scott
Published: February 2007

The hitherto unknown 2,6‐hexadecadiynoic acid, 2,6‐nonadecadiynoic acid, and 2,9‐hexadecadiynoic acid were synthesized in two steps and in 11–18% overall yields starting from either 1,5‐hexadiyne or 1,8‐nonadiyne. Among all the compounds 2,6‐hexadecadiynoic acid displayed the best overall antifungal activity against both the fluconazole‐resistant Candida albicans strains ATCC 14053 and ATCC 60193, with a minimum inhibitory concentration (MIC of 11 μM), and against Cryptococcus neoformans ATCC 66031 (MIC<5.7 μM). 2,9‐Hexadecadiynoic acid did not display any significant cytotoxicity against the fluconazole‐resistant C. albicans strains, but it showed fungitoxicity against C. neoformans ATCC 66031 with a MIC value of <5.8 μM. Other FA, such as 2‐hexadecynoic acid, 5‐hexadecynoic acid, 9‐hexadecynoic acid, and 6‐nonadecynoic acid were also synthesized and their antifungal activities compared with those of the novel acetylenic FA, 2‐Hexadecynoic acid, a known antifungal FA, exhibited the best antifungal activity (MIC=9.4 μM) against the fluconazole‐resistant C, albicans ATCC 14053 strain, but it showed a MIC value of only 100 μM against C. albicans ATCC 60193. 2,6‐Hexadecadiynoic acid and 2‐hexadecynoic acid also displayed a MIC of 140–145 μM toward Mycobacterium tuberculosis H37Rv in Middlebrook 7H12 medium. In conclusion, 2,6‐hexadecadiynoic acid exhibited the best fungitoxicity profile compared with other analogues. This diynoic FA has the potential to be further evaluated for use in topical antifungal formulations.
Differential biohydrogenation and isomerization of [U‐13C]Oleic and [1‐13C]Oleic acids by mixed ruminal microbes
Authors: Mosley Erin E. , Nudda Anna , Corato Adolfo , Rossi Erica , Jenkins Tom , McGuire Mark A.
Published: February 2007

The additional mass associated with 13C in metabolic tracers may interfere with their metabolism. The comparative isomerization and biohydrogenation of oleic, [1‐13C]oleic, and [U‐13C]oleic acids by mixed ruminal microbes was used to evaluate this effect. The percent of stearic, cis‐14 and‐ 15, and trans‐9 to‐16 18∶1 originating from oleic acid was decreased for [U‐13C]oleic acid compared with [1‐13C]oleic acid. Conversely, microbial utilization of [U‐13C]oleic acid resulted in more of the 13C label in cis‐9 18∶1 compared with [1‐13C]oleic acid (53.7 vs. 40.1%). The isomerization and biohydrogenation of oleic acid by ruminal microbes is affected by the mass of the labeled tracer.
Virus membrane fusion
Authors: Weissenhorn Winfried , Hinz Andreas , Gaudin Yves
Published: February 2007

Membrane fusion of enveloped viruses with cellular membranes is mediated by viral glycoproteins (GP). Interaction of GP with cellular receptors alone or coupled to exposure to the acidic environment of endosomes induces extensive conformational changes in the fusion protein which pull two membranes into close enough proximity to trigger bilayer fusion. The refolding process provides the energy for fusion and repositions both membrane anchors, the transmembrane and the fusion peptide regions, at the same end of an elongated hairpin structure in all fusion protein structures known to date. The fusion process follows several lipidic intermediate states, which are generated by the refolding process. Although the major principles of viral fusion are understood, the structures of fusion protein intermediates and their mode of lipid bilayer interaction, the structures and functions of the membrane anchors and the number of fusion proteins required for fusion, necessitate further investigations.
Cyclic nucleotide‐gated channels in plants
Authors: Kaplan Boaz , Sherman Tal , Fromm Hillel
Published: February 2007

Until recently the role of cyclic nucleotide monophosphates (cNMPs) in plants had been controversial, with equivocal data about their concentrations, biosynthetic and degrading enzymes, and cellular targets. This review discusses the current knowledge in this field, with focus on the largest class of cNMP targets in plant cells, the cyclic nucleotide‐gated channels (CNGCs). Aspects of structure and function are addressed, with reference to studies in heterologous systems and in planta. The picture emerging, albeit still fragmented, is of proteins with diverse functions in the control of ion homeostasis, development, and defense against biotic and abiotic threats.
Proteasomal degradation of the KLF5 transcription factor through a ubiquitin‐independent pathway
Authors: Chen Ceshi , Zhou Zhongmei , Guo Peng , Dong Jin-Tang
Published: February 2007

KLF5 is a Kruppel‐like zinc finger transcription factor modulating cell proliferation, differentiation, cell cycle, apoptosis, and angiogenesis. The KLF5 protein undergoes multiple posttranslational modifications including phosphorylation, acetylation and ubiquitination. We have demonstrated that the KLF5 protein can be ubiquitinated by the WWP1 E3 ubiquitin ligase and degraded by the proteasome. In this study, we found that KLF5 protein degradation is blocked by an N‐terminal FLAG tag or a small N‐terminal deletion without reducing ubiquitination and degradation mediated by WWP1. Interestingly, the N‐terminal fragments of KLF5 containing the first 237 or 171 amino acids are as unstable as the full length KLF5 protein. The N‐terminal FLAG tag or 19 amino acid deletion also delayed the degradation of the C‐terminal truncated KLF5 proteins. To further understand the mechanism, we generated a lysine‐less mutant KLF5(1–171). This mutant is efficiently degraded by the proteasome without ubiquitination in vitro and in vivo. These findings suggest that KLF5 protein degradation by the proteasome could be regulated in a ubiquitin‐independent manner.
Central administration of melanocortin agonist increased insulin sensitivity in diet‐induced obese rats
Authors: Banno Ryoichi , Arima Hiroshi , Hayashi Masayuki , Goto Motomitsu , Watanabe Minemori , Sato Ikuko , Ozaki Nobuaki , Nagasaki Hiroshi , Ozaki Noriyuki , Oiso Yutaka
Published: February 2007

In this study, we examined the effects of intracerebroventricular administration of melanotan II (MTII), a melanocortin agonist, on insulin sensitivity in diet‐induced obese (DIO) rats. Although MTII treatment significantly decreased food intake and body weight for 10 days, there was no significant difference in body weight between MTII and pair‐fed groups. The insulin tolerance test showed that insulin sensitivity was significantly improved in the MTII group compared to the pair‐fed group. Furthermore, MTII treatment increased the number of small‐sized adipocytes in epididymal white adipose tissues, suggesting that MTII increased insulin sensitivity through action on the white adipose tissues in DIO rats.
Abuse during pregnancy in Mexico City
Authors: Díaz‐Olavarrieta C. , Paz F. , Abuabara K. , Martínez Ayala H.B. , Kolstad K. , Palermo T.
Published: February 2007

Objective: Measure the prevalence of physical and sexual abuse during pregnancy, determine the nature and severity of abuse, and assess correlates with abuse. Method: A total of 1314 women seeking prenatal care between July 2000 and January 2003 were approached at three public hospitals in Mexico City. An original composite case record form was created to measure physical and sexual abuse before and during pregnancy. Result: Forty‐one percent of respondents had a history of physical or sexual abuse, with current abuse reported by 11.1%, and abuse during pregnancy by 7.6%. Among abused women, 71% reported an increase in the severity of abuse since becoming pregnant. Logistic regression revealed physically fighting with a partner and a history of abuse best predict violence during pregnancy. Conclusion: The severity of abuse among abused women appears to increase during pregnancy. Prenatal care visits in Mexico are an important opportunity for violence screening and intervention.
Peatland development at the arctic tree line (Québec, Canada) influenced by flooding and permafrost
Authors: Bhiry Najat , Payette Serge , Robert Élisabeth C.
Published: February 2007

In this study, we documented the Holocene history of a peat plateau at the arctic tree line in northern Québec using stratigraphic and macrofossil analyses to highlight the effects of geomorphic setting in peatland development. Paludification of the site began about 6800 cal yr BP. From 6390 to 4120 cal yr BP, the peatland experienced a series of flooding events. The location of the peatland in a depression bounded by two small lakes likely explains its sensitivity to runoff. The proximity of a large hill bordering the peatland to the south possibly favored the inflow of mineral-laden water. The onset of permafrost aggradation in several parts of the peatland occurred after 3670 cal yr BP. Uplifting of the peatland surface caused by permafrost stopped the flooding. According to radiocarbon dating of the uppermost peat layers, permafrost distribution progressed from the east to the west of the peatland, indicating differential timing for the initiation of permafrost throughout the peatland. Most of the peatland was affected by permafrost growth during the Little Ice Age.Picea marianamacroremains at 6450 cal yr BP indicate that the species was present during the early stages of peatland development, which occurred soon after the sea regression.
The Würm in NW Iberia, A pollen record from Area Longa (Galicia)
Authors: Gómez-Orellana Luis , Ramil-Rego Pablo , Muñoz Sobrino Castor
Published: February 2007

The pollen record at Area Longa is the westernmost sequence available for investigation of the last glaciation in continental Europe. It is located in a region, NW Iberia, for which data from times earlier than the late glacial period are scarce. It comprises a series of exposed limnetic levels that lie above an Eemian (Oxygen Isotope Stage [OIS] 5e) beach and are separated by inorganic layers. The oldest limnetic level (Level I), attributed to the early glacial period (OIS 5a to OIS 5d), shows a dominance of woodland with high proportions of Fagus pollen and is tentatively identified with St. Germain I. The lower pleniglacial (OIS 4) Level II records a stadial landscape of grassland and shrub. Level III, from the pleniglacial interstade (OIS 3), reflects a complex period in which three warmer woodland phases alternated with periods of more open vegetation. This cyclical behavior correlates with the ice core isotope record and with the general tendencies observed in other Würmian pollen records, but the composition of our pollen profiles differs from those observed in these other records. In NW Iberia, the dominant trees were deciduous taxa, not conifers. Of particular note is the presence of lowland Fagus woodlands during the pre-Würm, and the occurrence of Carpinus considerably farther west than the boundary of its current distribution in the Iberian Peninsula.
Alternative Drying Processes for the Industrial Preservation of Lactic Acid Starter Cultures
Authors: Santivarangkna Chalat , Kulozik Ulrich , Foerst Petra
Published: February 2007

The preservation of lactic acid starter cultures by alternative drying processes has attracted increasing attention due to the high costs and energy consumption of freezing and freeze drying. This review thus aims to provide a survey regarding the state of knowledge of starter culture production at high levels of viability. The results from numerous studies on various drying processes and lactic acid bacteria are summarized. The alternative drying processes considered, such as spray drying, fluidized bed drying, and vacuum drying, are mainly of industrial interest. The features, advantages, and disadvantages of these drying processes are described. In conclusion, the important factors that need to be considered, standardized, or optimized to achieve high levels of viability include intrinsic tolerance of cultures, growth media and conditions, stress induction, cell harvesting conditions, protective agents, rehydration conditions, enumeration of cells, and storage conditions.
Promoter targeting sequence mediates enhancer interference in the
Drosophila
embryo
Authors: Lin Qing , Chen Qi , Lin Lan , Smith Sheryl , Zhou Jumin
Published: February 2007

Gene transcription can be regulated by promoter competition when multiple promoters are available for a single enhancer. The converse, however, is largely undescribed. Here we report an occurrence of several enhancers competing for one promoter (enhancer interference) and propose its underlying mechanism. The promoter targeting sequence from the
Abdominal-B
locus of the
Drosophila
bithorax complex overcomes the enhancer-blocking activity of insulators in transgenic embryos. It may facilitate the long-range enhancer–promoter communication in
Abdominal-B
by bypassing insulator elements such as
Frontabdominal-7
and
Frontabdominal-8
. In transgenic embryos, the anti-insulator activity allowed both an insulator-blocked enhancer and a nonblocked enhancer to contact the same promoter. We found that these two enhancers exhibited mutual inhibition or mutual exclusion in cells where both are transcriptionally active. This enhancer interference occurred at the level of enhancer–promoter communication. It occurred only between enhancers on opposite sides of an insulator and depended on enhancer activity. We hypothesize that enhancer interference limits the interaction of the
Abdominal-B
promoter to the enhancer(s) from only one regulatory domain in a specific abdominal segment.
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
Authors: Shedlock Andrew M. , Botka Christopher W. , Zhao Shaying , Shetty Jyoti , Zhang Tingting , Liu Jun S. , Deschavanne Patrick J. , Edwards Scott V.
Published: February 2007

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in
Anolis
. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.
Determining the stoichiometry of protein heterocomplexes in living cells with fluorescence fluctuation spectroscopy
Authors: Chen Yan , Müller Joachim D.
Published: February 2007

The brightness of fluorescence fluctuations provides information about protein interactions in the intercellular environment under equilibrium conditions. Here we demonstrate that the stoichiometry of a protein complex containing two proteins labeled with CFP and YFP can be determined by brightness analysis. The brightness profile, which characterizes the brightness as a function of the labeled protein coexpression ratio, together with brightness titration experiments, provides sufficient information to quantify the composition of a protein complex under stoichiometric binding conditions. The selective and simultaneous excitation of proteins labeled with CFP and YFP by choosing different excitation wavelengths is used to identify the composition of the protein complex. Interactions between nuclear receptors and their coactivators play a crucial role in the regulation of gene expression. We choose the ligand-binding domain of retinoic X receptor and the nuclear receptor interacting domain of the steroid receptor coactivator-1 as a model for exploring the formation of a hetero-oligomer by brightness analysis directly in living cells. Our results show the formation of a heterotetramer with three nuclear receptors binding to the coactivator domain. Elimination of one of the nuclear receptor binding sites through a truncation mutant changed the interaction between both proteins significantly and led to a nuclear receptor-induced oligomerization of the truncated coactivator. Quantifying protein interactions in a cell is an important step in understanding cellular function on a molecular level. This study provides proof-of-principle experiments that illustrate the potential of brightness analysis as a powerful tool for quantifying protein interactions in living cells.
A stochastic, cantilever approach to the evaluation of solution phase thermodynamic quantities
Authors: Snyder Phillip W. , Lee Gwangrog , Marszalek Piotr E. , Clark Robert L. , Toone Eric J.
Published: February 2007

A cantilever device based on competitive binding of an immobilized receptor to immobilized and soluble ligand and capable of measuring solution-phase thermodynamic quantities is described. Through multiple binary queries, the device stochastically measures the probability of the formation of a bound complex between immobilized protein and immobilized ligand as a function of soluble ligand concentration. The resulting binding isotherm is described by a binding polynomial consisting of the activities of soluble and immobilized ligand and binding constants for the association of immobilized protein with free and immobilized ligand. Evaluation of the polynomial reveals an association constant for the formation of a complex between immobilized ligand and immobilized protein close to that for the formation of complex between soluble protein and soluble ligand. The methodology lays the foundation for construction of practical portable sensing devices.
Moonlight shifts the endogenous clock of
Drosophila melanogaster
Authors: Bachleitner Wolfgang , Kempinger Lena , Wülbeck Corinna , Rieger Dirk , Helfrich-Förster Charlotte
Published: February 2007

The ability to be synchronized by light–dark cycles is a fundamental property of circadian clocks. Although there are indications that circadian clocks are extremely light-sensitive and that they can be set by the low irradiances that occur at dawn and dusk, this has not been shown on the cellular level. Here, we demonstrate that a subset of
Drosophila
's pacemaker neurons responds to nocturnal dim light. At a nighttime illumination comparable to quarter-moonlight intensity, the flies increase activity levels and shift their typical morning and evening activity peaks into the night. In parallel, clock protein levels are reduced, and clock protein rhythms shift in opposed direction in subsets of the previously identified morning and evening pacemaker cells. No effect was observed on the peripheral clock in the eye. Our results demonstrate that the neurons driving rhythmic behavior are extremely light-sensitive and capable of shifting activity in response to the very low light intensities that regularly occur in nature. This sensitivity may be instrumental in adaptation to different photoperiods, as was proposed by the morning and evening oscillator model of Pittendrigh and Daan. We also show that this adaptation depends on retinal input but is independent of cryptochrome.
Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes
Authors: Reinhard Björn M. , Sheikholeslami Sassan , Mastroianni Alexander , Alivisatos A. Paul , Liphardt Jan
Published: February 2007

Pairs of Au nanoparticles have recently been proposed as “plasmon rulers” based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.
Tetramer visualization of gut-homing gluten-specific T cells in the peripheral blood of celiac disease patients
Authors: Ráki Melinda , Fallang Lars-Egil , Brottveit Margit , Bergseng Elin , Quarsten Hanne , Lundin Knut E. A. , Sollid Ludvig M.
Published: February 2007

Tetramers of MHC–peptide complexes are used for detection and characterization of antigen-specific T cell responses, but they require knowledge about both antigenic peptide and the MHC restriction element. The successful application of these reagents in human diseases involving CD4+T cells is limited. Celiac disease, an intestinal inflammation driven by mucosal CD4+T cells recognizing wheat gluten peptides in the context of disease-associated HLA-DQ molecules, is an ideal model to test the potential clinical use of these reagents. We investigated whether gluten-specific T cells can be detected in the peripheral blood of celiac disease patients using DQ2 tetramers. Nine DQ2+patients and six control individuals on a gluten-free diet were recruited to the study. Participants consumed 160 g of gluten-containing bread daily for 3 days. After bread-challenge, gluten-specific T cells were detectable in the peripheral blood of celiac patients but not controls both directly by tetramer staining and indirectly by enzyme-linked immunospot. These T cells expressed the β7integrin indicative of gut-homing properties. Most of the cells had a memory phenotype, but many other phenotypic markers showed a heterogeneous pattern. Tetramer staining of gluten-specific T cells has the potential to be used for diagnosis of celiac disease.
Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization
Authors: García-Álvarez Begoña , de Cárcer Guillermo , Ibañez Sonia , Bragado-Nilsson Elisabeth , Montoya Guillermo
Published: February 2007

Polo-like kinase (Plk1) is crucial for cell cycle progression through mitosis. Here we present the molecular and structural mechanisms that regulate the substrate recognition of Plk1 and influence its centrosomal localization and activity. Our work shows that Plk1 localization is controlled not only by the polo box domain (PBD); remarkably, the kinase domain is also involved in Plk1 targeting mechanism to the centrosome. The crystal structures of the PBD in complex with Cdc25C and Cdc25C-P target peptides reveal that Trp-414 is fundamental in their recognition regardless of its phosphorylation status. Binding measurements demonstrate that W414F mutation abolishes molecular recognition and diminishes centrosomal localization. Therefore, Plk1 centrosomal localization is not controlled by His-538 and Lys-540, the residues involved in phosphorylated target binding. The different conformations of the loop, which connects the polo boxes in the apo and the PBD-Cdc25C and PBD-Cdc25C-P complex structures, together with changes in the proline adjacent to the phosphothreonine in the target peptide, suggest a regulatory mechanism to detect binding of unphosphorylated or phosphorylated target substrates. Altogether, these data propose a model for the interaction between Plk1 and Cdc25C.
Electrostatics at the oil–water interface, stability, and order in emulsions and colloids
Authors: Leunissen Mirjam E. , van Blaaderen Alfons , Hollingsworth Andrew D. , Sullivan Matthew T. , Chaikin Paul M.
Published: February 2007

Oil–water mixtures are ubiquitous in nature and are particularly important in biology and industry. Usually additives are used to prevent the liquid droplets from coalescing. Here, we show that stabilization can also be obtained from electrostatics, because of the well known remarkable properties of water. Preferential ion uptake leads to a tunable droplet charge and surprisingly stable, additive-free, water-in-oil emulsions that can crystallize. For particle-stabilized (“Pickering”) emulsions we find that even extremely hydrophobic, nonwetting particles can be strongly bound to (like-charged) oil–water interfaces because of image charge effects. These basic insights are important for emulsion production, encapsulation, and (self-)assembly, as we demonstrate by fabricating a diversity of structures in bulk, on surfaces, and in confined geometries.
Conformational entropy of alanine versus glycine in protein denatured states
Authors: Scott Kathryn A. , Alonso Darwin O. V. , Sato Satoshi , Fersht Alan R. , Daggett Valerie
Published: February 2007

The presence of a solvent-exposed alanine residue stabilizes a helix by 0.4–2 kcal·mol
−1
relative to glycine. Various factors have been suggested to account for the differences in helical propensity, from the higher conformational freedom of glycine sequences in the unfolded state to hydrophobic and van der Waals' stabilization of the alanine side chain in the helical state. We have performed all-atom molecular dynamics simulations with explicit solvent and exhaustive sampling of model peptides to address the backbone conformational entropy difference between Ala and Gly in the denatured state. The mutation of Ala to Gly leads to an increase in conformational entropy equivalent to ≈0.4 kcal·mol
−1
in a fully flexible denatured, that is, unfolded, state. But, this energy is closely counterbalanced by the (measured) difference in free energy of transfer of the glycine and alanine side chains from the vapor phase to water so that the unfolded alanine- and glycine-containing peptides are approximately isoenergetic. The helix-stabilizing propensity of Ala relative to Gly thus mainly results from more favorable interactions of Ala in the folded helical structure. The small difference in energetics in the denatured states means that the Φ-values derived from Ala → Gly scanning of helices are a very good measure of the extent of formation of structure in proteins with little residual structure in the denatured state.
Night eating and obesity in the EP3R-deficient mouse
Authors: Sanchez-Alavez Manuel , Klein Izabella , Brownell Sara E. , Tabarean Iustin V. , Davis Christopher N. , Conti Bruno , Bartfai Tamas
Published: February 2007

Adult mice carrying a null mutation of the prostanoid receptor EP3R (EP3R−/−mice) exhibit increased frequency of feeding during the light cycle of the day and develop an obese phenotype under a normal fat diet fed ad libitum. EP3R−/−mice show increased motor activity, which is not sufficient to offset the increased feeding leading to increased body weight. Altered “nocturnal” activity and feeding behavior is present from a very early age and does not seem to require age-dependent factors for the development of obesity. Obesity in EP3R−/−mice is characterized by elevated leptin and insulin levels and >20% higher body weight compared with WT littermates. Abdominal and subcutaneous fat and increased liver weight account for the weight increase in EP3R−/−mice. These observations expand the roles of prostaglandin E2signaling in metabolic regulation beyond the reported stimulation of leptin release from adipose tissue to involve actions mediated by EP3R in the regulation of sleep architecture and feeding behavior. The findings add to the growing literature on links between inflammatory signaling and obesity.
Requirements for DNA hairpin formation by RAG1/2
Authors: Grundy Gabrielle J. , Hesse Joanne E. , Gellert Martin
Published: February 2007

The rearrangement of antigen receptor genes is initiated by double-strand breaks catalyzed by the RAG1/2 complex at the junctions of recombination signal sequences and coding segments. As with some “cut-and-paste” transposases, such as Tn5 and Hermes, a DNA hairpin is formed at one end of the break via a nicked intermediate. By using abasic DNA substrates, we show that different base positions are important for the two steps of cleavage. Removal of one base in the coding flank enhances hairpin formation, bypassing a requirement for a paired complex of two signal sequences. Rescue by abasic substrates is consistent with a base-flip mechanism seen in the crystal structure of the Tn5 postcleavage complex and may mimic the DNA changes on paired complex formation. We have searched for a tryptophan residue in RAG1 that would be the functional equivalent of W298 in Tn5, which stabilizes the DNA interaction by stacking the flipped base on the indole ring. A W956A mutation in RAG1 had an inhibitory effect on both nicking and hairpin stages that could be rescued by abasic substrates. W956 is therefore a likely candidate for interacting with this base during hairpin formation.
Genome-wide transcription map of an archaeal cell cycle
Authors: Lundgren Magnus , Bernander Rolf
Published: February 2007

Relative RNA abundance was measured at different cell-cycle stages in synchronized cultures of the hyperthermophilic archaeon
Sulfolobus acidocaldarius
. Cyclic induction was observed for >160 genes, demonstrating central roles for transcriptional regulation and cell-cycle-specific gene expression in archaeal cell-cycle progression. Many replication genes were induced in a cell-cycle-specific manner, and novel replisome components are likely to be among the genes of unknown function with similar induction patterns. Candidate genes for the unknown genome segregation and cell division machineries were also identified, as well as seven transcription factors likely to be involved in cell-cycle control. Two serine-threonine protein kinases showed distinct cell-cycle-specific induction, suggesting regulation of the archaeal cell cycle also through protein modification. Two candidate recognition elements, CCR boxes, for transcription factors in control of cell-cycle regulons were identified among gene sets with similar induction kinetics. The results allow detailed characterization of the genome segregation, division, and replication processes and may, because of the extensive homologies between the archaeal and eukaryotic information machineries, also be applicable to core features of the eukaryotic cell cycle.
Dendritic cells with TGF-β1 differentiate naïve CD4+CD25−T cells into islet-protective Foxp3+regulatory T cells
Authors: Luo Xunrong , Tarbell Kristin V. , Yang Hua , Pothoven Kathryn , Bailey Samantha L. , Ding Ruchuang , Steinman Ralph M. , Suthanthiran Manikkam
Published: February 2007

CD4+CD25+Foxp3+regulatory T cells (T regs) are important for preventing autoimmune diabetes and are either thymic-derived (natural) or differentiated in the periphery outside the thymus (induced). Here we show that β-cell peptide-pulsed dendritic cells (DCs) from nonobese diabetic (NOD) mice can effectively induce CD4+CD25+Foxp3+T cells from naïve islet-specific CD4+CD25−T cells in the presence of TGF-β1. These induced, antigen-specific T regs maintain high levels of clonotype-specific T cell receptor expression and exert islet-specific suppressionin vitro. When cotransferred with diabetogenic cells into NOD scid recipients, T regs induced with DCs and TGF-β1 prevent the development of diabetes. Furthermore, in overtly NOD mice, these cells are able to significantly protect syngeneic islet grafts from established destructive autoimmunity. These results indicate a role for DCs in the induction of antigen-specific CD4+CD25+Foxp3+T cells that can inhibit fully developed autoimmunity in a nonlymphopoenic host, providing an important potential strategy for immunotherapy in patients with autoimmune diabetes.
Improvement of cancer-targeting therapy, using nanocarriers for intractable solid tumors by inhibition of TGF-β signaling
Authors: Kano Mitsunobu R. , Bae Younsoo , Iwata Caname , Morishita Yasuyuki , Yashiro Masakazu , Oka Masako , Fujii Tomoko , Komuro Akiyoshi , Kiyono Kunihiko , Kaminishi Michio , Hirakawa Kosei , Ouchi Yasuyoshi , Nishiyama Nobuhiro , Kataoka Kazunori , Miyazono Kohei
Published: February 2007

Transforming growth factor (TGF)-β plays a pivotal role in regulation of progression of cancer through effects on tumor microenvironment as well as on cancer cells. TGF-β inhibitors have recently been shown to prevent the growth and metastasis of certain cancers. However, there may be adverse effects caused by TGF-β signaling inhibition, including the induction of cancers by the repression of TGF-β-mediated growth inhibition. Here, we present an application of a short-acting, small-molecule TGF-β type I receptor (TβR-I) inhibitor at a low dose in treating several experimental intractable solid tumors, including pancreatic adenocarcinoma and diffuse-type gastric cancer, characterized by hypovascularity and thick fibrosis in tumor microenvironments. Low-dose TβR-I inhibitor altered neither TGF-β signaling in cancer cells nor the amount of fibrotic components. However, it decreased pericyte coverage of the endothelium without reducing endothelial area specifically in tumor neovasculature and promoted accumulation of macromolecules, including anticancer nanocarriers, in the tumors. Compared with the absence of TβR-I inhibitor, anticancer nanocarriers exhibited potent growth-inhibitory effects on these cancers in the presence of TβR-I inhibitor. The use of TβR-I inhibitor combined with nanocarriers may thus be of significant clinical and practical importance in treating intractable solid cancers.
Transcription factor T-bet regulates skin sclerosis through its function in innate immunity and via IL-13
Authors: Aliprantis Antonios O. , Wang Jingsong , Fathman John W. , Lemaire Raphael , Dorfman David M. , Lafyatis Robert , Glimcher Laurie H.
Published: February 2007

Tissue remodeling with fibrosis is a predominant pathophysiological mechanism of many human diseases. Systemic sclerosis is a rare, often lethal, disorder of unknown etiology manifested by dermal fibrosis (scleroderma) and excessive connective tissue deposition in internal organs. Currently, there are no available antifibrotic therapeutics, a reflection of our lack of understanding of this process. Animal models of scleroderma are useful tools to dissect the transcription factors and cytokines that govern fibrosis. A disproportionate increase of type 2 cytokines, like TGF-β and IL-4, more than type 1 cytokines, like IFN-γ, is thought to underlie the pathogenesis of scleroderma. In this study, we show that mice deficient in the transcription factor T-box expressed in T cells (T-bet), a master regulator of type 1 immunity, display increased sensitivity to bleomycin-induced dermal sclerosis. Despite the well-established role of T-bet in adaptive immunity, we also show that RAG2
−/−
mice, which lack T and B cells, are vulnerable to bleomycin-induced scleroderma and that RAG2/T-bet double-deficient mice maintain the increased sensitivity to bleomycin observed in T-bet
−/−
mice. Furthermore, overexpression of T-bet in T cells does not affect the induction of skin sclerosis in this model. Lastly, we show that IL-13 is the profibrotic cytokine regulated by T-bet in this model. Together, we conclude that T-bet serves as a repressor of dermal sclerosis through an IL-13-dependent pathway in innate immune cells. T-bet, and its transcriptional network, represent an attractive target for the treatment of systemic sclerosis and other fibrosing disorders.
An intronic element contributes to splicing repression in spinal muscular atrophy
Authors: Kashima Tsuyoshi , Rao Nishta , Manley James L.
Published: February 2007

The neurodegenerative disease spinal muscular atrophy is caused by mutation of the
survival motor neuron 1
(
SMN1
) gene.
SMN2
is a nearly identical copy of
SMN1
that is unable to prevent disease, because most
SMN2
transcripts lack exon 7 and thus produce a nonfunctional protein. A key cause of inefficient
SMN2
exon 7 splicing is a single nucleotide difference between
SMN1
and
SMN2
within exon 7. We previously provided evidence that this base change suppresses exon 7 splicing by creating an inhibitory element, a heterogeneous nuclear ribonucleoprotein (hnRNP) A1-dependent exonic splicing silencer. We now find that another rare nucleotide difference between
SMN1
and
SMN2
, in intron 7, potentially creates a second
SMN2
-specific hnRNP A1 binding site. Remarkably, this single base change does indeed create a high-affinity hnRNP A1 binding site, and base substitutions that disrupt it restore exon 7 inclusion
in vivo
and prevent hnRNP A1 binding
in vitro
. We propose that interactions between hnRNP A1 molecules bound to the exonic and intronic sites cooperate to exclude exon 7 and discuss the significance of this exclusion with respect to
SMN
expression and splicing control more generally.
Far-Infrared Spectroscopy and the Physics and Chemistry of Interstellar Clouds
Authors: Dan M Watson
Published: February 2007

A review is presented of observations of, and interpretation of the intensities of, ionic and atomic fine structure lines and molecular rotational lines arising in interstellar clouds at far-infrared and submillimeter wavelengths (30-1000 μm). Included is a discussion of the nature of high-resolution spectroscopic instrumentation for these wavelengths and a summary of the instruments in use, particularly those on the NASA Kuiper Airborne Observatory.
The homophilic adhesion molecule sidekick‐1 contributes to augmented podocyte aggregation in HIV‐associated nephropathy
Authors: Kaufman Lewis , Yang Guozhe , Hayashi Kayo , Ashby James R. , Huang Li , Ross Michael J. , Klotman Mary E. , Klotman Paul E.
Published: February 2007

The collapsing glomerulopathy of HIV‐associated nephropathy (HIVAN) is characterized by podocyte dedifferentiation and proliferation. In affected glomeruli, proliferating podocytes adhere in aggregates to form glomerular pseudocrescents and fill an enlarged Bowman's space. Previously, we reported that sidekick‐1 (sdk‐1), an adhesion molecule of the immunoglobulin superfamily, was highly up‐regulated in HIV‐1 transgenic podocytes. In the current work, we explore how sdk‐1 overexpression contributes to HIVAN pathogenesis. Murine podocytes infected with HIV‐1 virus expressed significantly more sdk‐1 than control‐infected cells. Podocytes stably transfected with an sdk‐1 expression construct grew in large aggregates with a simplified morphology characterized by a disorganized actin cytoskeleton, changes similar to podocytes in HIVAN. In contrast to controls, HIV‐1 infected podocytes adhered to stably transfected sdk‐1 podocyte aggregates in mixing studies. Furthermore, substrate‐released cell sheets of wild‐type podocytes were readily dissociated by mechanical stress, whereas HIV‐1 podocytes remained in aggregates. The number of HIV‐1 podocyte aggregates was significantly reduced in cells expressing a short hairpin RNA (shRNA) construct specific for sdk‐1 compared with cells expressing control shRNA. Finally, in a HIVAN mouse model, sdk‐1 protein was detected in podocytes in collapsed glomerular tufts and in glomerular pseudocrescents. These findings suggest that sdk‐1 is an important mediator of cellular adhesion in HIV‐infected podocytes and may contribute to podocyte clustering that is characteristic of pseudocrescent formation in HIVAN.—Kaufman, L., Yang, G., Hayashi, K., Ashby, J.R., Huang, L., Ross, M.J., Klotman, M.E., Klotman, P.E. The homophilic adhesion molecule sidekick‐1 contributes to augmented podocyte aggregation in HIV‐associated nephropathy. FASEB J. 21, 1367–1375 (2007)
Reduced Content of Homogalacturonan Does Not Alter the Ion-Mediated Increase in Xylem Hydraulic Conductivity in Tobacco
Authors: Nardini Andrea , Gascó Antonio , Cervone Felice , Salleo Sebastiano
Published: February 2007

Xylem hydraulic conductivity (K  s) in stems of tobacco (Nicotiana tabacum) wild-type SR1 was compared to that of PG7 and PG16, two transgenic lines with increased levels of expression of the gene encoding the Aspergillus niger endopolygalacturonase (AnPGII). Activity of AnPGII removes in planta blocks of homogalacturonan (HG) with deesterified carboxyls, thus increasing the degree of neutrality of pectins. The effect of K+ was tested in increasing stem K  s using model plants with more neutral polysaccharides in primary walls and, hence, in intervessel pit membranes. K  s measured with deionized water was compared to that with KCl solutions at increasing concentrations (ΔK  s, %). Plants transformed for HG degree of neutrality showed a dwarfed phenotype, but ΔK  s did not differ among the three experimental groups. The ion-mediated hydraulic effect saturated at a KCl concentration of 25 mm in SR1 plants. All the three tobacco lines showed ΔK  s of around +12.5% and +17.0% when perfused with 10 and 25 mm KCl, respectively. Because modification of HG content did not influence ion-mediated hydraulic enhancement, we suggest that pectin components other than HG, like rhamnogalacturonan-I and/or rhamnogalacturonan-II, might play important roles in the hydrogel behavior of pit membranes.