bluuebunny/crossref_metadata_2025 huggingface dataset:
Disparities in the availability of fruits and vegetables between racially segregated urban neighbourhoods
Authors: Morland Kimberly , Filomena Susan
Published: June 2007

Objective

Public health professionals continue to see the benefits of fruit and vegetable consumption on population health. While studies that evaluate the availability of produce are sparse in the medical literature, disparities in availability may explain the disproportional intake of produce for some people. Therefore, the purpose of this study was to evaluate the availability and variety of produce located in two racially and economically diverse urban neighbourhoods.

Design

A cross-sectional study was conducted in which 50% of the supermarkets, small grocery stores, delicatessens, and fruit and vegetable markets located in specific neighbourhoods were randomly sampled and surveyed between September 2004 and July 2005. Food stores were evaluated for the availability of 20 types of fresh fruits and 19 types of fresh vegetables, as well as their varieties and whether they were canned, frozen or previously prepared. 2000 US Census information was used to determine characteristics of the geo-coded census tracts where the food stores were located.

Setting

Brooklyn, New York.

Results

A supermarket was located in approximately every third census tract in predominantly white areas (prevalence = 0.33) and every fourth census tract in racially mixed areas (prevalence = 0.27). There were no supermarkets located in the predominantly black areas. With the exception of bananas, potatoes, okra and yucca, a lower proportion of predominantly black area stores carried fresh produce, while supermarkets carried the largest variety of produce types. Canned and frozen fruits and vegetables were found in the majority of stores, whereas prepared and organic produce was limited to predominantly white area stores.

Conclusions

These data demonstrate that the availability and variety of fresh produce is associated with neighbourhood racial composition and may be a factor contributing to differences in intake among residents.
Eating out of home and its correlates in 10 European countries. The European Prospective Investigation into Cancer and Nutrition (EPIC) study
Authors: Orfanos Philippos , Naska Androniki , Trichopoulos Dimitrios , Slimani Nadia , Ferrari Pietro , van Bakel Marit , Deharveng Genevieve , Overvad Kim , Tjønneland Anne , Halkjær Jytte , Santucci de Magistris Maria , Tumino Rosario , Pala Valeria , Sacerdote Carlotta , Masala Giovanna , Skeie Guri , Engeset Dagrun , Lund Eiliv , Jakszyn Paula , Barricarte Aurelio , Chirlaque Maria-Dolores , Martinez-Garcia Carmen , Amiano Pilar , Quirós J Ramon , Bingham Sheila , Welch Ailsa , Spencer Elizabeth A , Key Timothy J , Rohrmann Sabine , Linseisen Jakob , Ray Jennifer , Boeing Heiner , Peeters Petra H , Bueno-de-Mesquita H Bas , Ocke Marga , Johansson Ingegerd , Johansson Gerd , Berglund Göran , Manjer Jonas , Boutron-Ruault Marie-Christine , Touvier Mathilde , Clavel-Chapelon Françoise , Trichopoulou Antonia
Published: June 2007

Objective

To compare the average out-of-home (OH) consumption of foods and beverages, as well as energy intake, among populations from 10 European countries and to describe the characteristics of substantial OH eaters, as defined for the purpose of the present study, in comparison to other individuals.

Design

Cross-sectional study. Dietary data were collected through single 24-hour dietary recalls, in which the place of consumption was recorded. For the present study, substantial OH eaters were defined as those who consumed more than 25% of total daily energy intake at locations other than the household premises. Mean dietary intakes and the proportion of substantial OH eaters are presented by food group and country. Logistic regression analyses were used to estimate the odds of being a substantial OH eater in comparison to not being one, using mutually adjusted possible non-dietary determinants.

Setting

Ten European countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC).

Subjects

The subjects were 34 270 individuals, 12 537 men and 21 733 women, aged 35–74 years.

Results

The fraction of energy intake during OH eating was generally higher in northern European countries than in the southern ones. Among the food and beverage groups, those selectively consumed outside the home were coffee/tea/waters and sweets and, to a lesser extent, cereals, meats, added lipids and vegetables. Substantial OH eating was positively associated with energy intake and inversely associated with age and physical activity. Substantial OH eating was less common among the less educated compared with the more educated, and more common during weekdays in central and north Europe and during the weekend in south Europe.

Conclusions

Eating outside the home was associated with sedentary lifestyle and increased energy intake; it was more common among the young and concerned in particular coffee/tea/waters and sweets.
Deformation method for electromagnetic magnetospheric fields: 1. Theory
Authors: Toivanen P. K.
Published: June 2007

In this paper the deformation method for magnetospheric magnetic fields is generalized to electric fields. It has been previously shown that an initial magnetic field configuration can be deformed to another configuration given in original coordinates by expressing the initial field in terms of the deformed coordinates and by multiplying this field by a deformation matrix. The method introduced here can be used in constructing model three‐dimensional electric fields consistent with model magnetic fields, and, most importantly, the electric field contributions induced by temporal variations of the magnetic field are globally modeled. The generalization is done by introducing a deformation matrix (M) of the vector potential consistent with the deformation matrix (T) of the magnetic field. These two types of deformations termed as M‐type and T‐type have different properties. Most importantly, the M‐type deformation conserves the curl‐free properties of an initial potential field, whereas the T‐type deformation introduces a curl to an initial potential field. It is shown that as previously shown for the magnetic field, no explicit Euler potentials are required for the deformation of the electric field that corresponds to frozen‐in plasma convection. This is a result of central importance for electromagnetic field modeling when only fields are initially known. Presently, the method assumes a gauge of zero magnetic helicity, and it is valid only for simply connected magnetic fields.
Consequences of the force‐free model of magnetic clouds for their heliospheric evolution
Authors: Leitner M. , Farrugia C. J. , Möstl C. , Ogilvie K. W. , Galvin A. B. , Schwenn R. , Biernat H. K.
Published: June 2007

We examine the implications of the widely used, force‐free, constant‐αflux rope model of interplanetary magnetic clouds for the evolution of these mesoscale (fraction 1 AU) structures in the heliosphere, with special emphasis on the inner (≤1 AU) heliosphere. We employ primarily events observed by the Helios 1 and 2 probes between 0.3 and 1 AU in the ascending and maximum phases of solar cycle 21 and by Wind at 1 AU in a similar phase of solar activity cycle. We supplement these data by observations from other spacecraft (e.g., Voyagers 1 and 2, Pioneers 10 and 11, and others). Our data set consists of 130 events. We explore three different approaches. In the first, we work with ensemble averages, binning the results into radial segments of width 0.1 AU in the range 0.3 ≤rh≤ 1 AU. Doing this, we find that in the inner heliosphere the modeled average central axial field strength, 〈B0〉, varies with heliospheric distancerhas 〈B0〉 [nT] = 18.1 ·rh−1.64[AU], and the average diameter increases quasi‐linearly as 〈D〉 [AU] = 0.23rh1.14. The orientation of the axis of the underlying magnetic flux tube in our data set is generally found to lie along the east–west direction and in the ecliptic plane at all values ofrh, but there is considerable scatter about these average directions. In the second, we monitor the evolution of magnetic clouds in snapshot fashion, using seven spacecraft alignments. The results are in broad agreement with the statistics reported under step 1. In the final approach, we obtain the functional dependence ofB0andDpredicted by an analytic expression for a freely expanding Lundquist flux tube. We findDto vary linearly withrh, broadly similar to that obtained under approach 1. The maximum field strength scales asrh−2compared to arh−1.3dependence obtained from statistics. We compare our findings with those of Bothmer and Schwenn (1998), who used a different methodology. The results obtained form a good background to the forthcoming Solar Terrestrial Relations Observatory (STEREO) and Sentinels missions and to multispacecraft studies of magnetic clouds.
Geology and hydrothermal evolution of the Mothra Hydrothermal Field, Endeavour Segment, Juan de Fuca Ridge
Authors: Glickson Deborah A. , Kelley Deborah S. , Delaney John R.
Published: June 2007

Detailed characterization of the Mothra Hydrothermal Field, the most southern and spatially extensive field on the Endeavour Segment of the Juan de Fuca Ridge, provides new insights into its geologic and hydrothermal development. Meter‐scale bathymetry, side‐scan sonar imagery, and direct dive observations show that Mothra is composed of six actively venting sulfide clusters spaced 40–200 m apart. Chimneys within each cluster have similar morphology and venting characteristics, and all clusters host a combination of active and extinct sulfide structures. Black smoker chimneys venting fluids above 300°C are rare, while more common lower‐temperature, diffusely venting chimneys support dense colonies of macrofauna and bacterial mat. Hydrothermal sediment and extinct sulfide debris cover 10–15 m of the seafloor surrounding each vent cluster, obscuring the underlying basaltic substrate of light to moderately sedimented pillow, lobate, sheet, and chaotic flows, basalt talus, and collapse terrain. Extinct sulfide chimneys and debris between the clusters indicate that hydrothermal flow was once more widespread and that it has shifted spatially over time. The most prominent structural features in the axial valley at Mothra are regional (020°) trending faults and fissures and north‐south trending collapse basins. The location of actively venting clusters within the field is controlled by (1) localization of fluid upflow along the western boundary fault zone, and diversion of these fluids by antithetic faults to feed vent clusters near the western valley wall, and (2) tapping of residual magmatic heat in the central part of the axial valley, which drives flow beneath vent clusters directly adjacent to the collapse basins 70–90 m east of the western valley wall. These processes form the basis for a model of axial valley and hydrothermal system development at Mothra, in which the field is initiated by an eruptive‐diking episode and sustained through intense microseismicity and non‐eruptive diking events.
Effects of sub‐seasonal variability on seasonal‐to‐interannual Indian Ocean meridional heat transport
Authors: Halkides D. J. , Han Weiqing , Lee Tong , Masumoto Yukio
Published: June 2007

Numerical experiments using the Hybrid Coordinate Ocean Model are performed to examine atmospheric intraseasonal oscillation (ISO) effects on seasonal‐to‐interannual meridional heat transport (Qv) in the tropical Indian Ocean. Analysis focuses on the equator and 14.5°S, latitudes associated with the cross‐equatorial and southern subtropical meridional cells. ISOs alter seasonal Qv anomaly (Qv*) at these latitudes by a‐few‐hundredths PW up to 2–3 tenths PW. On interannual timescales, heat transport anomaly (Q′v) induced by ISOs tends to reinforce (correlates positively with) the total Q′v signal. ISO winds can induce interannual Q′v up to 0.15 PW, comparable to the maximum amplitude of the Q′v signal. Net effects of atmospheric ISOs can account for ∼30% of Q′v in some years; in others, ISO contributions are insignificant. Wind stress (via momentum flux) and wind speed (via turbulent heat fluxes and vertical mixing) play notable roles in ISO effects on Qv* and in some years on Q′v.
First continuous GPS soundings of temperature structure over Antarctic winter from FORMOSAT‐3/COSMIC constellation
Authors: Wang Kuo‐Ying , Lin Song‐Chin
Published: June 2007

The FORMOSAT‐3/COSMIC mission provides unprecedented spatial coverage of daily sounding profiles of the Antarctic atmosphere. Our analysis shows that temperature profiles from these global positioning system (GPS) soundings agree well with the radiosondes over the South Pole and Neumayer stations during the 2006 Southern Hemisphere (SH) winter season. These GPS soundings reveal a vertical domain of low temperature (e.g., T ≤ −78°C at 28‐km altitude) that is not clearly defined by the Antarctic radiosondes. Latitudinal analysis of the GPS soundings shows that regions with T ≤ −78°C occur from about 10‐km to 28‐km altitudes, indicating an 18‐km thick of the cold vertical layer. The extremely cold regions are found at latitudes between 71°S and 87°S and in altitudes between 15 and 25 km, not coinciding with the geographical South Pole. These results demonstrate the potential of the FORMOSAT‐3/COSMIC data for polar studies.
Reasons why some solar wind changes do not trigger substorms
Authors: Lee D.‐Y. , Lyons L. R. , Weygand James M. , Wang C.‐P.
Published: June 2007

Previous studies have shown that a northward turning of the interplanetary magnetic field (IMF) or a reduction in the magnitude of IMF By component can trigger a substorm. Also a solar wind dynamic pressure enhancement has been found to trigger a substorm under strongly southward IMF conditions. Solar wind changes directed opposite to those of, or not satisfying the conditions of, these known triggers may be considered as inherently nontriggers. In the present paper we have examined 12 events where more than one solar wind quantity change simultaneously and no substorm is triggered. We suggest that nontriggering by the solar wind changes studied in the present work can be explained by the following three reasons: (1) there is a lack of, or insufficient, substorm growth phase development prior to the potential triggering change; (2) the solar wind change is an inherently nontriggering change; (3) the nullifying effect occurs, where one quantity changes in the direction of a substorm trigger and simultaneously another quantity changes in the direction opposite to that of a trigger. The nontriggering types found in this study are consistent with the suggestion that variations of the solar wind that do not reduce the convection strength within the inner plasma sheet do not trigger substorms, which is opposite to what is expected from a triggering solar wind variation.
Plants at risk from climate change
Authors: Yesson Chris , Culham Alastair
Published: June 2007

The popular garden flower Cyclamen grows natively in the Mediterranean. Climate change could make the region unsuitable for 18/21 species in 50 years time. Ant-dispersed Cyclamen can’t hope to migrate to suitable new areas without assistance.

Background:

The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants?

Results:

We demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters. Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species re considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective.

Conclusion:

Examining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.
Revolutionizing scientific communication and collaboration
Authors: Foerstner Konrad
Published: June 2007

This presentation introduces new web-based ways of scientific communication and collaboration. It focuses on wikis and the First Online EMBL PhD Symposium as an example of an online conference.
Using optical tweezers for measuring the interaction forces between human bone cells and implant surfaces: System design and force calibration
Authors: Andersson Martin , Madgavkar Ashwin , Stjerndahl Maria , Wu Yanrong , Tan Weihong , Duran Randy , Niehren Stefan , Mustafa Kamal , Arvidson Kristina , Wennerberg Ann
Published: July 2007

Optical tweezers were used to study the interaction and attachment of human bone cells to various types of medical implant materials. Ideally, the implant should facilitate cell attachment and promote migration of the progenitor cells in order to decrease the healing time. It is therefore of interest, in a controlled manner, to be able to monitor the cell adhesion process. Results from such studies would help foresee the clinical outcome of integrating medical implants. The interactions between two primary cell culture models, human gingival fibroblasts and bone forming human osteoblast cells, and three different implant materials, glass, titanium, and hydroxyapatite, were studied. A novel type of optical tweezers, which has a newly designed quadrant detector and a powerful 3W laser was constructed and force calibrated using two different methods: one method in which the stiffness of the optical trap was obtained by monitoring the phase lag between the trap and the moved object when imposing a forced oscillation on the trapped object and another method in which the maximum trapping force was derived from the critical velocity at which the object escapes the trap. Polystyrene beads as well as cells were utilized for the calibrations. This is the first time that cells have been used directly for these types of force calibrations and, hence, direct measurements of forces exerted on cells can be performed, thus avoiding the difficulties often encountered when translating the results obtained from cell measurements to the calibrations obtained with reference materials. This more straightforward approach represents an advantage in comparison to established methods.
Recovery of infectious murine norovirus using pol II-driven expression of full-length cDNA
Authors: Ward Vernon K. , McCormick Christopher J. , Clarke Ian N. , Salim Omar , Wobus Christiane E. , Thackray Larissa B. , Virgin Herbert W. , Lambden Paul R.
Published: June 2007

Noroviruses are the major cause of nonbacterial gastroenteritis in humans. These viruses have remained refractory to detailed molecular studies because of the lack of a reverse genetics system coupled to a permissive cell line for targeted genetic manipulation. There is no permissive cell line in which to grow infectious human noroviruses nor an authentic animal model that supports their replication. In contrast, murine norovirus (MNV) offers a tractable system for the study of noroviruses with the recent discovery of permissive cells and a mouse model. The lack of a reverse genetic system for MNV has been a significant block to understanding the biology of noroviruses. We report recovery of infectious MNV after baculovirus delivery of viral cDNA to human hepatoma cells under the control of an inducible DNA polymerase (pol) II promoter. Recovered virus replicated in murine macrophage (RAW264.7) cells, and the recovery of MNV from DNA was confirmed through recovery of virus containing a marker mutation. This pol II promoter driven expression of viral cDNA also generated infectious virus after transfection of HEK293T cells, thus providing both transduction and transfection systems for norovirus reverse genetics. We used norovirus reverse genetics to demonstrate by mutagenesis of the protease–polymerase (pro–pol) cleavage site that processing of pro–pol is essential for the recovery of infectious MNV. This represents the first infectious reverse genetics system for a norovirus, and should provide approaches to address fundamental questions in norovirus molecular biology and replication.
Structures of the thermophilic F
1
-ATPase ε subunit suggesting ATP-regulated arm motion of its C-terminal domain in F
1
Authors: Yagi Hiromasa , Kajiwara Nobumoto , Tanaka Hideaki , Tsukihara Tomitake , Kato-Yamada Yasuyuki , Yoshida Masasuke , Akutsu Hideo
Published: June 2007

The ε subunit of bacterial and chloroplast F
o
F
1
-ATP synthases modulates their ATP hydrolysis activity. Here, we report the crystal structure of the ATP-bound ε subunit from a thermophilic
Bacillus
PS3 at 1.9-Å resolution. The C-terminal two α-helices were folded into a hairpin, sitting on the β sandwich structure, as reported for
Escherichia coli
. A previously undescribed ATP binding motif, I(L)DXXRA, recognizes ATP together with three arginine and one glutamate residues. The
E. coli
ε subunit binds ATP in a similar manner, as judged on NMR. We also determined solution structures of the C-terminal domain of the PS3 ε subunit and relaxation parameters of the whole molecule by NMR. The two helices fold into a hairpin in the presence of ATP but extend in the absence of ATP. The latter structure has more helical regions and is much more flexible than the former. These results suggest that the ε C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F
o
F
1
-ATP synthase.
Sir2p-dependent protein segregation gives rise to a superior reactive oxygen species management in the progeny of
Saccharomyces cerevisiae
Authors: Erjavec Nika , Nyström Thomas
Published: June 2007

Yeast cytokinesis entails a rejuvenation process by which the aged mother cell generates daughter cells enjoying full replicative potential. Here we show that this process includes a precipitous reduction in the levels of reactive oxygen species in the progeny immediately after completion of cytokinesis. The reduction in hydrogen peroxide is the result of a Sir2p and actin cytoskeleton-dependent segregation of the cytosolic catalase Ctt1p such that the daughter cell receives a higher load of undamaged and active Ctt1p than the progenitor cell. Such spatial quality control provides the daughter cells with a superior capacity to combat external oxidative stress and delays self-inflicted oxidative damage to their cellular proteins.
Dynamics around solutes and solute–solvent complexes in mixed solvents
Authors: Kwak Kyungwon , Park Sungnam , Fayer M. D.
Published: June 2007

Ultrafast 2D-IR vibrational echo experiments, IR pump-probe experiments, and FT-IR spectroscopy of the hydroxyl stretch of phenol-OD in three solvents, CCl
4
, mesitylene (1, 3, 5 trimethylbenzene), and the mixed solvent of mesitylene and CCl
4
(0.83 mole fraction CCl
4
), are used to study solute-solvent dynamics via observation of spectral diffusion. Phenol forms a complex with Mesitylene. In the mesitylene solution, there is only complexed phenol; in the CCl
4
solution, there is only uncomplexed phenol; and in the mixed solvent, both phenol species are present. Dynamics of the free phenol in CCl
4
or the mixed solvent are very similar, and dynamics of the complex in mesitylene and in the mixed solvent are very similar. However, there are differences in the slowest time scale dynamics between the pure solvents and the mixed solvents. The mixed solvent produces slower dynamics that are attributed to first solvent shell solvent composition variations. The composition variations require a longer time to randomize than is required in the pure solvents, where only density variations occur. The experimental results and recent MD simulations indicate that the solvent structure around the solute may be different from the mixed solvent's mole fraction.
Consumer versus resource control of producer diversity depends on ecosystem type and producer community structure
Authors: Hillebrand Helmut , Gruner Daniel S. , Borer Elizabeth T. , Bracken Matthew E. S. , Cleland Elsa E. , Elser James J. , Harpole W. Stanley , Ngai Jacqueline T. , Seabloom Eric W. , Shurin Jonathan B. , Smith Jennifer E.
Published: June 2007

Consumer and resource control of diversity in plant communities have long been treated as alternative hypotheses. However, experimental and theoretical evidence suggests that herbivores and nutrient resources interactively regulate the number and relative abundance of coexisting plant species. Experiments have yielded divergent and often contradictory responses within and among ecosystems, and no effort has to date reconciled this empirical variation within a general framework. Using data from 274 experiments from marine, freshwater, and terrestrial ecosystems, we present a cross-system analysis of producer diversity responses to local manipulations of resource supply and/or herbivory. Effects of herbivory and fertilization on producer richness differed substantially between systems: (
i
) herbivores reduced species richness in freshwater but tended to increase richness in terrestrial systems; (
ii
) fertilization increased richness in freshwater systems but reduced richness on land. Fertilization consistently reduced evenness, whereas herbivores increased evenness only in marine and terrestrial ecosystems. Producer community evenness and ecosystem productivity mediated fertilization and herbivore effects on diversity across ecosystems. Herbivores increased producer richness in more productive habitats and in producer assemblages with low evenness. These same assemblages also showed the strongest reduction in richness with fertilization, whereas fertilization increased (and herbivory decreased) richness in producer assemblages with high evenness. Our study indicates that system productivity and producer evenness determine the direction and magnitude of top-down and bottom-up control of diversity and may reconcile divergent empirical results within and among ecosystems.
Selective control of cortical axonal spikes by a slowly inactivating K+current
Authors: Shu Yousheng , Yu Yuguo , Yang Jing , McCormick David A.
Published: June 2007

Neurons are flexible electrophysiological entities in which the distribution and properties of ionic channels control their behaviors. Through simultaneous somatic and axonal whole-cell recording of layer 5 pyramidal cells, we demonstrate a remarkable differential expression of slowly inactivating K+currents. Depolarizing the axon, but not the soma, rapidly activated a low-threshold, slowly inactivating, outward current that was potently blocked by low doses of 4-aminopyridine, α-dendrotoxin, and rTityustoxin-Kα. Block of this slowly inactivating current caused a large increase in spike duration in the axon but only a small increase in the soma and could result in distal axons generating repetitive discharge in response to local current injection. Importantly, this current was also responsible for slow changes in the axonal spike duration that are observed after somatic membrane potential change. These data indicate that low-threshold, slowly inactivating K+currents, containing Kv1.2 α subunits, play a key role in the flexible properties of intracortical axons and may contribute significantly to intracortical processing.
Hyaluronic acid hydrogel for controlled self-renewal and differentiation of human embryonic stem cells
Authors: Gerecht Sharon , Burdick Jason A. , Ferreira Lino S. , Townsend Seth A. , Langer Robert , Vunjak-Novakovic Gordana
Published: June 2007

Control of self-renewal and differentiation of human ES cells (hESCs) remains a challenge. This is largely due to the use of culture systems that involve poorly defined animal products and do not mimic the normal developmental milieu. Routine protocols involve the propagation of hESCs on mouse fibroblast or human feeder layers, enzymatic cell removal, and spontaneous differentiation in cultures of embryoid bodies, and each of these steps involves significant variability of culture conditions. We report that a completely synthetic hydrogel matrix can support (
i
) long-term self-renewal of hESCs in the presence of conditioned medium from mouse embryonic fibroblast feeder layers, and (
ii
) direct cell differentiation. Hyaluronic acid (HA) hydrogels were selected because of the role of HA in early development and feeder layer cultures of hESCs and the controllability of hydrogel architecture, mechanics, and degradation. When encapsulated in 3D HA hydrogels (but not within other hydrogels or in monolayer cultures on HA), hESCs maintained their undifferentiated state, preserved their normal karyotype, and maintained their full differentiation capacity as indicated by embryoid body formation. Differentiation could be induced within the same hydrogel by simply altering soluble factors. We therefore propose that HA hydrogels, with their developmentally relevant composition and tunable physical properties, provide a unique microenvironment for the self-renewal and differentiation of hESCs.
Identification of a retroviral receptor used by an Envelope protein derived by peptide library screening
Authors: Sarangi Anindita , Bupp Keith , Roth Monica J.
Published: June 2007

This study demonstrates the power of a genetic selection to identify a variant virus that uses a new retroviral receptor protein. We screened a random peptide library within the receptor-binding domain of a feline leukemia virus retroviral Envelope (FeLV Env) protein for productive infection of feline AH927 cells. One variant, A5, obtained with altered tropic properties acquired the ability to use the solute carrier protein family 35 member F2 (SLC35F2) as a receptor. The SLC35F2 protein is a presumed transporter of unknown function predicted to encode 8 to 10 transmembrane-spanning regions and is not homologous to any identified retroviral receptor. Expression of the feline SLC35F2 cDNA in nonpermissive cells renders the cells susceptible to infection by A5 virus, with remarkably high titers in the range of 105infectious units per ml. The human SLC35F2 ORF also functioned as the retroviral receptor, albeit at lower efficiency than the feline homologue. The successful selection of a novel molecule, the SLC35F2 transporter/channel-type protein, as a receptor by the FeLV Env backbone suggests that multipass transmembrane proteins may be particularly suited for use in productive viral entry and fusion. The analysis of retroviral Env libraries randomized in the receptor-binding domain offers a viable means to develop viral vectors targeted to specific cell types in the absence of known targeting ligands.
Oncogenic All1 fusion proteins target Drosha-mediated microRNA processing
Authors: Nakamura Tatsuya , Canaani Eli , Croce Carlo M.
Published: June 2007

MicroRNAs (miRNAs) are noncoding small RNA of ≈22 bases, which suppress expression of target genes through translational block or degradation of a target's transcript. Recent studies uncovered specific miRNA expression profiles in human malignancies. Nevertheless, the mechanisms underlying cancer-specific miRNA expression are largely unknown. miRNA biogenesis consists of a series of steps beginning with generation of a primary transcript, termed pri-miRNA, and continuing into excision of a stem-loop hairpin structure within pri-miRNA by the nuclear RNaseIII enzyme Drosha, transportation to the cytoplasm, and further processing by a second RNaseIII enzyme Dicer, into a 22-base mature duplex RNA. In principle, alteration in any step during this maturation process could affect miRNA production. The
ALL-1
(also termed
MLL
) gene was originally isolated by virtue of its involvement in recurrent chromosome translocations associated with acute leukemias, particularly in infant and therapy-related leukemias. These translocations result in the fusion of
ALL-1
with partner genes and the consequent production of chimeric leukemogenic proteins. Here, we identify specific miRNAs up-regulated in leukemias triggered by All1 fusions. Further, we demonstrate coimmunoprecipitation of the All1/Af4 and All1/Af9 fusions with Drosha, disrupted by treatment with DNase I. Finally, we present evidence from ChIP experiments for All1 fusion protein-mediated recruitment of Drosha to target genes encoding miRNAs. Such recruitment may underlie the enhanced expression of the relevant miRNAs.
Nasir al-Din Shah and the Dar al-Funun: The Evolution of an Institution
Authors: Ekhtiar Maryam
Published: July 2007

Nasir al-Din Shah uttered the following words in the presence of his trusted physician, Dr. Jakob Eduard Polak.

“If only no European had ever set foot in my country, we would have been spared all of these tortures. But since these aliens have penetrated, I intend to take as good and as much advantage of them as possible.”

Such words of despair reflect the court's ambivalent attitude toward European reform as well as the underlying motives for founding the Dar al-Funun, Iran's first modern European-style institution of higher learning (figs. 1 and 2).

The driving force behind the creation of the Dar al-Funun was Nasir al-Din Shah's first premier, Mirza Muhammad Taqi Khan Farahani, better known as Amir Kabir. He founded the institution with the intention of ensuring that a new generation of Iranian youth, primarily military officers, was trained in the “useful sciences.”
Reflections on The Social and Economic Structure of Safavid Persia at Its Zenith
Authors: Banani Amin
Published: July 2007

It is generally agreed that the rise of the Safavids in the sixteenth century marks a new period in the history of Persia. Hegemony of one dynasty over nearly all the Persian-speaking world, accompanied by the swift forced conversion of the overwhelming majority of the Persians into Twelver Shi'ism, resulted in the emergence of the first Persian state in the modern era. Such a signal event could not but invest the Persian state and society with major, fundamental institutions. The same institutions have continued to characterize and to influence Persia down to the Constitutionalist Revolution of 1905-1911. It is these institutions that constitute the “traditional” features of the society against which the forces of “modernization” have been operating since the adoption of the Constitution and the Supplementary Fundamental Law of 1907.
Tribe and State in Revolutionary Iran: The Return of the Qashqa'i Khans
Authors: Beck Lois
Published: July 2007

This paper discusses the attempted resumption of paramount Qashqa'i leadership upon the fall of the Pahlavi regime in 1979. Paramount Qashqa'i leaders had been exiled from Iran following their support of Prime Minister Mosaddeq in the early 1950s and had, since then, either remained in exile or returned to Iran to live under political restrictions. In early 1979, those in exile returned to Iran and joined the others in resuming positions of regional and national political power.

These questions are central to the discussion and analysis: What was the nature of Qashqa'i leadership both before and during Pahlavi rule, and how and why had it changed under the Islamic Republic of Iran? How had changes in Iran affecting the Qashqa'i people between 1953 and 1979 affected the attempted resumption of paramount leadership? How had the nature of the Iranian state changed during these periods? How are Qashqa'i leaders best characterized? Are they “tribal” or national-minority leaders, or are they better seen as regional and national powers? How is Qashqa'i leadership different from other kinds of political leadership in Iran, in particular that of other tribes and national minorities, and why?
Al-Khwarazmi's Historical-Cultural Synthesis
Authors: Asimov M. S.
Published: July 2007

In 1983, the 1,200th anniversary of the death of Abu Abd Allah Mohammad ibn Musa al-Khwarazmi was celebrated in recognition of his profound impact on the history of human civilization.

Among his best-known achievements were major developments in the fields of arithmetic and algebra. Through his works the Indian decimal system was eventually transmitted to Europe. And the name “algebra” itself comes from the title of one of his books, Al-Jabr wa'l -muqābalah.

Besides his unparalleled contributions in the field of mathematics, al-Khwarazmi's life and works provide us with a broader insight into the aspects of the formation and progress of human civilization. The history of human civilization is marked by migratory processes, by the movements of peoples and ideas from region to region. For historical reasons, centers of civilization arose, flourished, and declined in various parts of the world; but although those centers themselves disappeared, their achievements did not. Instead, these contributions to human knowledge were adopted and developed in new centers under new conditions.
The Politics of Passions: Growing Up Shia
Authors: Fazel Mohammed K.
Published: July 2007

And youth is cruel, and has no remorse

And smiles at situations which it cannot see.

I smile, of course,

And go on drinking tea.

T. S. Eliot

My mother's mother Kaukab Khanum (Madam Dahlia) was convinced that our family was accursed. Along with her sister, uncles, and a handful of cousins, she had left her native city of Kirman in southern Iran in the 1890s, plodded through deserts, crossed mountains, and reached the Persian Gulf port of Lengeh, whence an Arab dhow provided a tortuous trip to Bombay, India. They were running away from famine, endemic in southern Iran at the turn of the century.

Kaukab Khanum believed that our family was accursed because in their eagerness to leave and for expediency, they had abandoned a blind cousin barely fifteen years old. Times were bad, the destination vague, the trip arduous and tricky.
Crystallizing and Emancipating Identities in Post-Communist Estonia
Authors: Vihalemm Triin
Published: July 2007

This article concerns collective identities in the context of EU enlargement and the post-Soviet transition of Estonian society, particularly of the two main ethno-linguistic groups: ethnic Estonians and the Russian-speaking population in Estonia. The empirical basis of the study is formed by factor structures of self-identification. The data were obtained from nationally representative surveys carried out in 2002, before Estonia joined the EU, and in 2005. The thinking patterns behind the structures of self-categorization are discussed mainly on the basis of theoretical concepts of individualization and transition culture. For background information, comparative data collected in Latvia (2006) and in Sweden (2003) are used. The survey results reveal that in the post-communist transformation, EU integration and spread of global mass culture have homogenized the mental patterns of the Estonians and the Russians. It is characteristic of post-communist Estonia that both minority and majority groups have utilized trans-national and civic identity and individualistic patterns of self-identification in terms of (sub)culture and social and material achievement, extracted from social norms and existing structures. Surveys confirm that for political actors in both Estonia and Russia it is hardly possible any more to create a common umbrella identity for the Russians in Estonia—the self-designation patterns of the Estonian Russians have been emancipated during the transition period.
Magnesium depletion impairs myocardial carbohydrate and lipid metabolism and cardiac bioenergetics and raises myocardial calcium content in‐vivo: Relationship to etiology of cardiac diseases
Authors: Altura Burton M. , Gebrewold Asefa , Altura Bella T. , Brautbar Nachman
Published: July 2007

This study examines the effects of Mg depletion on myocardial bioenergetic, carbohydrate, lipid and phospholipid metabolism. Rats were studied after long‐term (12 week) selective dietary restriction of Mg (20% normal dietary intake). Myocardial biopsy samples were examined for glucose 6‐phosphate and glycogen to evaluate carbohydrate pathways and for glycerol phosphate and mitochondrial fatty acid oxidation and phospholipid contents to evaluate lipid and phospholipid turnover. Dietary Mg deficiency resulted in falls in myocardial glycogen, glucose‐6‐phosphate, glycerol phosphate, as well as the contents of phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidyl glycerol (DPG), phosphatidyl inositol (PI) and total phospholipid phosphorus. These observations demonstrate impaired phospholipid metabolism, probably at the biosynthetic level. The mitochondrial oxidation of long‐chain fatty acids was also impaired after Mg depletion. Mg depletion (serum Mg fell 60%) also resulted in significant falls in myocardial [ATP], phosphocreatine (PCr), and Mg with a concomitant rise in myocardial Ca content. These observations are consistent with the tenet that prolonged low [Mg2+]. can result in marked reduction in oxygen and substrate delivery to the cardiac myocytes, with concomitant changes in membrane phospholipids (potentially resulting in a pro‐oxidant state) probably as a result of coronary vasoconstriction.
Synergistic stimulation of fibrinogen gelation by casein kinase II and polycationic compounds
Authors: Suk Kyoungho , Lee Jin‐Young , Kim Seung‐Ho
Published: July 2007

The processes of thrombin‐induced gelation of the fibrinogen may be influenced by a variety of factors including phosphorylational state of the fibrinogen. Casein kinase II (CKII) has been shown to phosphorylate fibrinogen in vitro and accelerate gelation of the fibrinogen. In this work, we have demonstrated that CKII and polycationic compounds such as polylysine, spermine, and spermidine synergistically stimulate thrombin‐induced gelation of the fibrinogen. These polycationic compounds were also found to increase the stimulatory effects of CKII on the platelet aggregation. Current findings suggest potential role of CKII and polycationic compounds in the process of hemostasis.
Distinct Domains of Yeast Cortical Tag Proteins Bud8p and Bud9p Confer Polar Localization and Functionality
Authors: Krappmann Anne-Brit , Taheri Naimeh , Heinrich Melanie , Mösch Hans-Ulrich
Published: June 2007

In Saccharomyces cerevisiae, diploid yeast cells follow a bipolar budding program, which depends on the two transmembrane glycoproteins Bud8p and Bud9p that potentially act as cortical tags to mark the cell poles. Here, we have performed systematic structure-function analyses of Bud8p and Bud9p to identify functional domains. We find that polar transport of Bud8p and Bud9p does not depend on N-terminal sequences but instead on sequences in the median part of the proteins and on the C-terminal parts that contain the transmembrane domains. We show that the guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange factor Bud5p, which is essential for bud site selection and physically interacts with Bud8p, also interacts with Bud9p. Regions of Bud8p and Bud9p predicted to reside in the extracellular space are likely to confer interaction with the N-terminal region of Bud5p, implicating indirect interactions between the cortical tags and the GDP/GTP exchange factor. Finally, we have identified regions of Bud8p and Bud9p that are required for interaction with the cortical tag protein Rax1p. In summary, our study suggests that Bud8p and Bud9p carry distinct domains for delivery of the proteins to the cell poles, for interaction with the general budding machinery and for association with other cortical tag proteins.
The Concentration of Nuf, a Rab11 Effector, at the Microtubule-organizing Center Is Cell Cycle–regulated, Dynein-dependent, and Coincides with Furrow Formation
Authors: Riggs Blake , Fasulo Barbara , Royou Anne , Mische Sarah , Cao Jian , Hays Thomas S. , Sullivan William
Published: June 2007

Animal cytokinesis relies on membrane addition as well as acto-myosin–based constriction. Recycling endosome (RE)-derived vesicles are a key source of this membrane. Rab11, a small GTPase associated with the RE and involved in vesicle targeting, is required for elongation of the cytokinetic furrow. In the early Drosophila embryo, Nuclear-fallout (Nuf), a Rab11 effector, promotes vesicle-mediated membrane delivery and actin organization at the invaginating furrow. Although Rab11 maintains a relatively constant localization at the microtubule-organizing center (MTOC), Nuf is present at the MTOC only during the phases of the cell cycle in which furrow invagination occurs. We demonstrate that Nuf protein levels remain relatively constant throughout the cell cycle, suggesting that Nuf is undergoing cycles of concentration and dispersion from the MTOC. Microtubules, but not microfilaments, are required for proper MTOC localization of Nuf and Rab11. The MTOC localization of Nuf also relies on Dynein. Immunoprecipitation experiments demonstrate that Nuf and Dynein physically interact. In accord with these findings, and in contrast to previous reports, we demonstrate that microtubules are required for proper metaphase furrow formation. We propose that the cell cycle–regulated, Dynein-dependent recruitment of Nuf to the MTOC influences the timing of RE-based vesicle delivery to the invaginating furrows.
The Mitochondrial Transcription Factor TFAM Coordinates the Assembly of Multiple DNA Molecules into Nucleoid-like Structures
Authors: Kaufman Brett A. , Durisic Nela , Mativetsky Jeffrey M. , Costantino Santiago , Hancock Mark A. , Grutter Peter , Shoubridge Eric A.
Published: June 2007

Packaging DNA into condensed structures is integral to the transmission of genomes. The mammalian mitochondrial genome (mtDNA) is a high copy, maternally inherited genome in which mutations cause a variety of multisystem disorders. In all eukaryotic cells, multiple mtDNAs are packaged with protein into spheroid bodies called nucleoids, which are the fundamental units of mtDNA segregation. The mechanism of nucleoid formation, however, remains unknown. Here, we show that the mitochondrial transcription factor TFAM, an abundant and highly conserved High Mobility Group box protein, binds DNA cooperatively with nanomolar affinity as a homodimer and that it is capable of coordinating and fully compacting several DNA molecules together to form spheroid structures. We use noncontact atomic force microscopy, which achieves near cryo-electron microscope resolution, to reveal the structural details of protein–DNA compaction intermediates. The formation of these complexes involves the bending of the DNA backbone, and DNA loop formation, followed by the filling in of proximal available DNA sites until the DNA is compacted. These results indicate that TFAM alone is sufficient to organize mitochondrial chromatin and provide a mechanism for nucleoid formation.