bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of Overweight Children's Fruit and Vegetable Intake Using Plasma Carotenoids
Authors: Burrows Tracy L. , Warren Janet M. , Colyvas Kim , Garg Manohar L. , Collins Clare E.
Published: November 2008

Assessing dietary intake in children is difficult and limited validated tools exist. Plasma carotenoids are nutritional biomarkers of fruit and vegetable intake and therefore suitable to validate reported dietary intakes. The aim of this study was to examine the comparative validity of a food frequency questionnaire (FFQ), completed by parents reporting child fruit and vegetable intake compared to plasma carotenoid concentrations. A sample of children aged 5–12 years (n = 93) from a range of weight categories were assessed. Dietary intake was measured using a 137‐item semi‐quantitative FFQ. Plasma carotenoids were measured using reverse phase high‐performance liquid chromatography. Pearson correlation coefficients between reported dietary intake of carotenoids and plasma carotenoid concentrations were strongest after adjustment for BMI (β‐carotene (r = 0.56, P < 0.05), α‐carotene (r = 0.51, P < 0.001), cryptoxanthin (r = 0.32, P < 0.001)). Significantly lower levels (P < 0.05) of all plasma carotenoids, except lutein, were found among overweight and obese children when compared to healthy weight children. Parental report of children's carotenoid intakes, using a FFQ can be used to provide a relative validation of fruit and vegetable intake. The lower plasma carotenoid concentrations found in overweight and obese children requires further investigation.
Anthropometric and Leptin Changes in Women Following Different Dietary Approaches to Weight Loss
Authors: Miller Larry E. , Volpe Joanne J. , Coleman‐Kelly Mary Dean , Gwazdauskas Francis C. , Nickols‐Richardson Sharon M.
Published: November 2008

Leptin may favorably respond to fat mass (FM) losses induced by a low‐carbohydrate (LC) diet, although this is unclear. We examined serum leptin concentrations in women in midlife undergoing different dietary approaches to body weight (BW) loss. Women followed either a LC, high‐protein (LCHP; n = 13) or high‐carbohydrate, low‐fat (HCLF; n = 12) diet for 12 weeks. Changes in anthropometric and soft‐tissue mass measurements and leptin concentrations were assessed. Women in both diet groups had reductions in BW, BMI, fat‐free soft‐tissue mass, FM, body fat percentage, and central abdominal fat (CAF) (P < 0.001 for all variables) over the 12‐week intervention. These changes were not significantly different between diet groups. Serum leptin concentrations decreased by 41.8% (P < 0.001) in the LCHP group and by 44.3% (P < 0.001) in the HCLF group from baseline to week 12, with no significant difference between groups. The association of CAF (r = 0.73) and FM (r = 0.83) change with leptin change was strong in the HCLF group. Leptin change did not relate to change in any variable in the LCHP group. Both LCHP and HCLF diets favorably lower FM, CAF, and leptin in women, suggesting that beneficial changes in leptin can be similarly achieved through different dietary approaches to BW loss.
Changes in the reciprocal position of the first polar body and oocyte chromosome set in golden hamsters
Authors: Wang Lingyan , Li Dexue , Li Ziyi
Published: November 2008

The golden hamster is an attractive model organism for studying reproductive physiology, oncology, genetics and virology. In an effort to establish experimental protocols necessary for cloning golden hamsters, we examined changes in the reciprocal position of the FPB (first polar body) and chromosome set of MII (the second meiotic metaphase) oocytes of golden hamsters. Oocytes were collected under three different conditions: (i) oocyte direct recovery from the oviduct of hormonally treated donor; (ii) oocyte recovery from the oviduct of hormonally treated donor followed by 5 h/10 h in vitro culture; and (iii) oocyte recovery from ovaries of hormonally treated donors and in vitro maturation. Then oocyte recovery was performed from the oviduct of hormonally treated donors, followed by 5 h in vitro culture with colchicine and/or CB (cytochalasin B). Denuded oocytes were stained with Hoechst 33342 and propidium iodide and evaluated under a microscope. Our results demonstrate that the change in FPB position in relation to the MII oocyte chromosome set increases with age of in vivo-matured oocytes. Cumulus cells can protect the FPB of in vitro-cultured oocytes from degeneration but do not significantly affect its repositioning, and in vitro-matured oocytes age slower. The colchicine has a stronger effect on cytoplasmic protrusions of golden hamster oocytes when compared with CB. These results define conditions for changes in FPB position relative to the MII oocyte chromosome set. Early ovulated oocytes, in vitro-matured oocytes and oocytes treated with colchicine should improve the effectiveness of the cloning procedure in golden hamsters as an animal model for human diseases.
The DGAT2 gene is a candidate for the dissociation between fatty liver and insulin resistance in humans
Authors: Kantartzis Konstantinos , Machicao Fausto , Machann Jürgen , Schick Fritz , Fritsche Andreas , Häring Hans-Ulrich , Stefan Norbert
Published: November 2008

The enzyme DGAT (acyl-CoA:diacylglycerol acyltransferase) catalyses the final step of triacylglycerol (triglyceride) synthesis. Mice overexpressing hepatic DGAT2 fed a high-fat diet develop fatty liver, but not insulin resistance, suggesting that DGAT2 induces a dissociation between fatty liver and insulin resistance. In the present study, we investigated whether such a phenotype also exists in humans. For this purpose, we determined the relationships between genetic variability in the DGAT2 gene with changes in liver fat and insulin sensitivity in 187 extensively phenotyped subjects during a lifestyle intervention programme with diet modification and an increase in physical activity. Changes in body fat composition [MR (magnetic resonance) tomography], liver fat and intramyocellular fat (1H-MR spectroscopy) and insulin sensitivity [OGTT (oral glucose tolerance test) and euglycaemic–hyperinsulinaemic clamp] were determined after 9 months of intervention. A change in insulin sensitivity correlated inversely with changes in total body fat, visceral fat, intramyocellular fat and liver fat (OGTT, all P<0.05; clamp, all P≤0.03). Changes in total body fat, visceral fat and intramyocellular fat were not different between the genotypes of the SNPs (single nucleotide polymorphisms) rs10899116 C>T and rs1944438 C>T (all P≥0.39) of the DGAT2 gene. However, individuals carrying two or one copies of the minor T allele of SNP rs1944438 had a smaller decrease in liver fat (−17±10 and −24±5%; values are means±S.E.M.) compared with subjects homozygous for the C allele (−39±7%; P=0.008). In contrast, changes in insulin sensitivity were not different among the genotypes (OGTT, P=0.76; clamp, P=0.53). In conclusion, our findings suggest that DGAT2 mediates the dissociation between fatty liver and insulin resistance in humans. This finding may be important in the prevention and treatment of insulin resistance and Type 2 diabetes in subjects with fatty liver.
Central Nervous System Air Embolism in Respiratory Distress Syndrome: Considerations for Patient Survival
Authors: Jordan Glenn D. , Jarrett Robert V. , Garcia Jose , Frank C. Gilbert , Pettett Philip G.
Published: November 2008

Neonatal pulmonary venous air embolism (arising as a consequence of ventilator therapy) remains at present an almost invariably fatal occurrence. We present a case that illustrates that it is possible for an infant to survive the immediate cardiovascular consequences of such an event; however, we demonstrate that embolic extension into the central nervous system (CNS) can occur as an associated sequela, and we offer the first published documentation (cranial ultrasonography) of this potentially pivotal complication. The temporal relationships between our patient's initial (but resolving) systemic embolism and his subsequent (and persistent) CNS event are documented and the implications discussed. Based on these observations, we caution that CNS involvement is difficult to recognize clinically and suggest that such involvement may contribute to a fatal outcome. Importantly, it appears that it may be possible to intervene in future cases to improve outcome, and we offer suggestions in this regard.
Image x-ray emission converters and microstrip porous dielectric x-ray detector
Authors: Lorikyan M. P.
Published: November 2008

The effective, fast, and accurate registration of x ray depends on the quality conversion of the X-quanta to photoelectrons. In this respect, of high interest are porous x-ray emission converters (PXECs). They are analogs of porous secondary electron emitters (PSEEs); the only difference is that active porous material should have high absorption properties for the X-quanta energies to be detected. Microstrip porous dielectric detector (MSPDD) is highly effective for x-ray registration without preliminary conversion of the X-quanta. Earlier it was shown that PSEE similar to PXEC has a high emission factor for 1–2 MeV β-particles and 5 MeV α-particles. It was shown that MSPDDs and PSEEs are very stable.
Interactions of silica nanoparticles in supercritical carbon dioxide
Authors: Vishnyakov Aleksey , Shen Yangyang , Tomassone M. Silvina
Published: November 2008

We report molecular simulation studies on the interaction forces between silica nanoparticles in supercritical carbon dioxide at 318K. Our goal is to find a better understanding of the interparticle solvation forces during rapid expansion of supercritical solutions. The parameters for interatomic potentials of fluid-fluid and solid-fluid interactions are obtained by fitting our simulations to (i) experimental bulk CO2 phase diagram at a given temperature and pressure and (ii) CO2 sorption isotherms on silica at normal boiling and critical temperatures. Our simulations show that the interaction forces between particles and supercritical CO2 at near-critical pressure of p=69atm (i.e., slightly below critical condition) reaches a minimum at distances of 0.5–0.8nm between the outer surfaces of the particles and practically vanishes at distances of approximately 3nm. The attraction is most prominent for densely hydroxylated particle surfaces that interact strongly with CO2 via hydrogen bonds. The effective attraction between silica and CO2 is significantly weaker for dehydroxylated particles. We also compared fluid sorption and interparticle forces between supercritical CO2 and subcritical nitrogen vapor, and our results showed qualitative similarities, suggesting that the CO2 configuration between the particles resembles a liquidlike junction.
Image reconstruction in segmented femtosecond laser-written waveguide arrays
Authors: Szameit Alexander , Dreisow Felix , Heinrich Matthias , Pertsch Thomas , Nolte Stefan , Tünnermann Andreas , Suran Eric , Louradour Frédéric , Barthélémy Alain , Longhi Stefano
Published: November 2008

We present the first experimental realization of image reconstruction in finite femtosecond laser-written waveguide arrays with segmentation. The results show that arbitrary field distributions can be imaged in one-dimensional as well as in two-dimensional geometries.
Nanomechanical behavior of single crystalline SiC nanotubes revealed by molecular dynamics simulations
Authors: Wang Zhiguo , Zu Xiaotao , Gao Fei , Weber William J.
Published: November 2008

Molecular dynamics simulations with Tersoff potentials were used to study the response of single crystalline SiC nanotubes under tensile, compressive, torsional, combined tension-torsional, and combined compression-torsional strains. The simulation results reveal that the nanotubes deform through bond-stretching and breaking and exhibit brittle properties under uniaxial tensile strain, except for the thinnest nanotube at high temperatures, which fails in a ductile manner. Under uniaxial compressive strain, the SiC nanotubes buckle with two modes, i.e., shell buckling and column buckling, depending on the length of the nanotubes. Under torsional strain, the nanotubes buckle either collapse in the middle region into a dumbbell-like structure for thinner wall thicknesses or fail by bond breakage for the largest wall thickness. Both the tensile failure stress and buckling stress decrease under combined tension-torsional and combined compression-torsional strain, and they decrease with increasing torsional rate under combined loading.
Thin water films grown at ambient conditions on BaF2(111) studied by scanning polarization force microscopy
Authors: Verdaguer A. , Cardellach M. , Fraxedas J.
Published: November 2008

The interaction of water with freshly cleaved BaF2(111) surfaces has been studied using scanning force microscopy operated in different modes at room temperature and under controlled humidity. The Kelvin probe microscopy (KPM) mode has been used to study the evolution of the surface potential differences (SPDs). In the 20%–50% relative humidity (RH) range, adsorbed water forms two-dimensional solidlike bilayers (islands). The SPD between water islands and the bare substrate surface exhibits a sign crossover from negative (∼−30 mV) at low RHs to positive (∼+50 mV) at higher RHs, evidencing a cooperative and irreversible flipping of the preferential orientation of water dipoles, from pointing toward the surface evolving into the opposite direction. The KPM results suggest that the classical hexagonal (Ih) bilayer configuration is not the most favorable structure.
Inactivation of spores using pulsed electric field in a pressurized flow system
Authors: Choi Jaegu , Wang Douyan , Namihira Takao , Katsuki Sunao , Akiyama Hidenori , Lin Xiaofei , Sato Hiroshi , Seta Harumichi , Matsubara Hitoshi , Saeki Takeshi
Published: November 2008

Pulsed electric field (PEF) inactivation is a very effective method to kill bacteria in liquid while avoiding thermal damage. However, only a limited inactivation effect on spores has been reported to date and the possible mechanisms are still unclear. Therefore, a study of inactivation of spores using PEF in a pressurized flow system is reported in this paper. PEF with a maximum magnitude higher than 110 kV/cm and a pulse width of 100 ns has been applied to a carefully designed treatment chamber through which a suspension fluid of 0.5 MPa continuously flows. Using the proposed PEF inactivation method, maximum 6.7 log reductions were achieved for B. subtilis spores that were investigated. These reductions were much greater than those obtained by a heat inactivation approach. Through frequency analysis using the frequency components of the applied pulses and the frequency response of the equivalent circuit of the spore, it was found that most voltage is applied to the outside of the core in the lower frequency and to the inside in the upper frequency. Also, transmission electron microscope micrographs of B. subtilis spores were taken in order to verify the effect of the PEF treatment.
Coarse-grained modeling of interactions of lipid bilayers with supports
Authors: Hoopes Matthew I. , Deserno Markus , Longo Margie L. , Faller Roland
Published: November 2008

We characterize the differences between supported and unsupported lipid bilayer membranes using a mesoscopic simulation model and a simple particle-based realization for a flat support on to which the lipids are adsorbed. We show that the nanometer roughness of the support affects membrane binding strength very little. We then compare the lipid distributions and pressure profiles of free and supported membranes. The surface localization of the proximal leaflet breaks the symmetry seen in a free bilayer, and we quantify the entropic penalty for binding and the increased lateral compression modulus.
High-performance millimeter-wave superlattice electronic devices
Authors: Eisele Heribert , Farrer Ian , Linfield Edmund H. , Ritchie David A.
Published: November 2008

Negative differential resistance devices, based on two similar AlAs/GaAs superlattice structures, were fabricated using a standard selective etching and integral heat sink technology and evaluated in a resonant-cap full-height WR-15 waveguide cavity. Devices from both superlattice structures generated comparable output powers in the fundamental mode at 59–71 GHz. The best devices yielded >80 mW (with corresponding dc-to-RF conversion efficiencies of >4.5%) around 63 GHz. In a second-harmonic mode, these devices yielded up to 14 mW (1%) at 133 GHz. Higher harmonic frequencies were also observed with powers of >0.4 mW at 190 GHz and >0.1 mW at 260 GHz. The highest observed dc-to-RF conversion efficiency was 5.1% at 62.8 GHz.
Strategies for control of the redlegged earth mite in Australia
Authors: Ridsdill-Smith T. J. , Hoffmann A. A. , Mangano G. P. , Gower J. M. , Pavri C. C. , Umina P. A.
Published: November 2008

The redlegged earth mite, Halotydeus destructor, continues to be an intractable pest causing damage to most crop and pasture species in southern Australia. H. destructor feed on all stages of plants, but particularly damage seedlings in autumn. Research has aimed to develop new controls based on a better understanding of the biology and ecology of this pest. Chemicals remain the key tool to control H. destructor, despite the recent appearance of resistance to synthetic pyrethroids. A control package, Timerite, has been developed by which a single well-timed spray in spring can prevent H. destructor from developing diapause eggs. Field trials show this strategy provides effective control of H. destructor the following autumn, and protects plant seedlings, although mite populations build up again during winter. Non-chemical control strategies include grazing, the use of tolerant plants such as cereals, resistant legume cultivars and avoiding rotations where favourable host plants are available in the year before growing susceptible crops such as canola. Natural enemies can assist in mite control, and their numbers can be enhanced by methods including increasing landscape features like shelterbelts. Interspecific competition can occur between H. destructor and other pest mites, but the extent to which these interactions influence the structure of pest communities under different management regimes remains to be investigated.
Photosynthetic water oxidation at elevated dioxygen partial pressure monitored by time-resolved X-ray absorption measurements
Authors: Haumann Michael , Grundmeier Alexander , Zaharieva Ivelina , Dau Holger
Published: November 2008

The atmospheric dioxygen (O
2
) is produced at a tetramanganese complex bound to the proteins of photosystem II (PSII). To investigate product inhibition at elevated oxygen partial pressure (
p
O
2
ranging from 0.2 to 16 bar), we monitored specifically the redox reactions of the Mn complex in its catalytic S-state cycle by rapid-scan and time-resolved X-ray absorption near-edge spectroscopy (XANES) at the Mn K-edge. By using a pressure cell for X-ray measurements after laser-flash excitation of PSII particles, we found a clear
p
O
2
influence on the redox reactions of the Mn complex, with a similar half-effect pressure as determined (2–3 bar). However, XANES spectra and the time courses of the X-ray fluorescence collected with microsecond resolution suggested that the O
2
evolution transition itself (S
3
⇒S
0
+O
2
) was not affected. Additional (nonstandard) oxidation of the Mn complex at high
p
O
2
explains our experimental findings more readily. Our results suggest that photosynthesis at ambient conditions is not limited by product inhibition of the O
2
formation step.
Isoprene interferes with the attraction of bodyguards by herbaceous plants
Authors: Loivamäki Maaria , Mumm Roland , Dicke Marcel , Schnitzler Jörg-Peter
Published: November 2008

Isoprene is the most abundant volatile compound emitted by vegetation. It influences air chemistry and is part of plant defense against abiotic stresses. However, whether isoprene influences biotic interactions between plants and other organisms has not been investigated to date. Here we show a new effect of isoprene, namely its influence on interactions between plants and insects. Herbivory induces the release of plant volatiles that attract the herbivore's enemies, such as parasitic wasps, as a kind of bodyguard. We used transgenic isoprene-emitting
Arabidopsis
plants in behavioral, chemical, and electrophysiological studies to investigate the effects of isoprene on ecological interactions in 2 tritrophic systems. We demonstrate that isoprene is perceived by the chemoreceptors of the parasitic wasp
Diadegma semiclausum
and interferes with the attraction of this parasitic wasp to volatiles from herbivore-infested plants. We verified this repellent effect on
D. semiclausum
female wasps by adding external isoprene to the volatile blend of wild-type plants. In contrast, the antennae of the parasitic wasp
Cotesia rubecula
do not perceive isoprene and the behavior of this wasp was not altered by isoprene emission. In addition, the performance of the 2 examined lepidopteran herbivores (
Pieris rapae
and
Plutella xylostella
) was not affected by isoprene emission. Therefore, attraction of parasitic wasps to host-infested herbaceous plants in the neighborhood of high isoprene emitters, such as poplar or willow, may be hampered by the isoprene emission that repels plant bodyguards.
Engineering antigen-specific primary human NK cells against HER-2 positive carcinomas
Authors: Kruschinski Anna , Moosmann Andreas , Poschke Isabel , Norell Håkan , Chmielewski Markus , Seliger Barbara , Kiessling Rolf , Blankenstein Thomas , Abken Hinrich , Charo Jehad
Published: November 2008

NK cells are promising effectors for tumor adoptive immunotherapy, particularly when considering the targeting of MHC class I low or negative tumors. Yet, NK cells cannot respond to many tumors, which is particularly the case for nonhematopoietic tumors such as carcinomas or melanoma even when these cells lose MHC class I surface expression. Therefore, we targeted primary human NK cells by gene transfer of an activating chimeric receptor specific for HER-2, which is frequently overexpressed on carcinomas. We found that these targeted NK cells were specifically activated upon recognition of all evaluated HER-2 positive tumor cells, including autologous targets, as indicated by high levels of cytokine secretion as well as degranulation. The magnitude of this specific response correlated with the level of HER-2 expression on the tumor cells. Finally, these receptor transduced NK cells, but not their mock transduced counterpart, efficiently eradicated tumor cells inRAG2knockout mice as visualized by in vivo imaging. Taken together, these results indicate that the expression of this activating receptor overrides inhibitory signals in primary human NK cells and directs them specifically toward HER-2 expressing tumor cells both in vitro and in vivo.
Discovery of drug-like inhibitors of an essential RNA-editing ligase in
Trypanosoma brucei
Authors: Amaro Rommie E. , Schnaufer Achim , Interthal Heidrun , Hol Wim , Stuart Kenneth D. , McCammon J. Andrew
Published: November 2008

Trypanosomatid RNA editing is a unique process and essential for these organisms. It therefore represents a drug target for a group of protozoa that includes the causative agents for African sleeping sickness and other devastating tropical and subtropical diseases. Here, we present drug-like inhibitors of a key enzyme in the editing machinery, RNA-editing ligase 1 (REL1). These inhibitors were identified through a strategy employing molecular dynamics to account for protein flexibility. A virtual screen of the REL1 crystal structure against the National Cancer Institute Diversity Set was performed by using AutoDock4. The top 30 compounds, predicted to interact with REL1's ATP-binding pocket, were further refined by using the relaxed complex scheme (RCS), which redocks the compounds to receptor structures extracted from an explicitly solvated molecular dynamics trajectory. The resulting reordering of the ligands and filtering based on drug-like properties resulted in an initial recommended set of 8 ligands, 2 of which exhibited micromolar activity against REL1. A subsequent hierarchical similarity search with the most active compound over the full National Cancer Institute database and RCS rescoring resulted in an additional set of 6 ligands, 2 of which were confirmed as REL1 inhibitors with IC
50
values of ≈1 μM. Tests of the 3 most promising compounds against the most closely related bacteriophage T4 RNA ligase 2, as well as against human DNA ligase IIIβ, indicated a considerable degree of selectivity for RNA ligases. These compounds are promising scaffolds for future drug design and discovery efforts against these important pathogens.
NFκB activation is associated with its
O
-GlcNAcylation state under hyperglycemic conditions
Authors: Yang Won Ho , Park Sang Yoon , Nam Hyung Wook , Kim Do Hyun , Kang Jeong Gu , Kang Eun Seok , Kim Yu Sam , Lee Hyun Chul , Kim Kwan Soo , Cho Jin Won
Published: November 2008

The transcription factor NFκB is activated by phosphorylation and acetylation and plays important roles in inflammatory and immune responses in the cell. Additionally, posttranslational modification of the NFκB p65 subunit by
O
-linked
N
-acetylglucosamine (
O
-GlcNAc) has been reported, but the modification site of
O
-GlcNAc on NFκB p65 and its exact function have not been elucidated. In this work, we show that
O
-GlcNAcylation of NFκB p65 decreases binding to IκBα and increases transcriptional activity under hyperglycemic conditions. Also, we demonstrate that both Thr-322 and Thr-352 of NFκB p65 can be modified with
O
-GlcNAc, but modification on Thr-352, not Thr-322, is important for transcriptional activation. Our findings suggest that site-specific
O
-GlcNAcylation may be a reason why NFκB activity increases continuously under hyperglycemic conditions.
Evaluating the links between climate, disease spread, and amphibian declines
Authors: Rohr Jason R. , Raffel Thomas R. , Romansic John M. , McCallum Hamish , Hudson Peter J.
Published: November 2008

Human alteration of the environment has arguably propelled the Earth into its sixth mass extinction event and amphibians, the most threatened of all vertebrate taxa, are at the forefront. Many of the worldwide amphibian declines have been caused by the chytrid fungus,
Batrachochytrium dendrobatidis
(Bd), and two contrasting hypotheses have been proposed to explain these declines. Positive correlations between global warming and Bd-related declines sparked the chytrid-thermal-optimum hypothesis, which proposes that global warming increased cloud cover in warm years that drove the convergence of daytime and nighttime temperatures toward the thermal optimum for Bd growth. In contrast, the spatiotemporal-spread hypothesis states that Bd-related declines are caused by the introduction and spread of Bd, independent of climate change. We provide a rigorous test of these hypotheses by evaluating (
i
) whether cloud cover, temperature convergence, and predicted temperature-dependent Bd growth are significant positive predictors of amphibian extinctions in the genus
Atelopus
and (
ii
) whether spatial structure in the timing of these extinctions can be detected without making assumptions about the location, timing, or number of Bd emergences. We show that there is spatial structure to the timing of
Atelopus spp.
extinctions but that the cause of this structure remains equivocal, emphasizing the need for further molecular characterization of Bd. We also show that the reported positive multi-decade correlation between
Atelopus spp.
extinctions and mean tropical air temperature in the previous year is indeed robust, but the evidence that it is causal is weak because numerous other variables, including regional banana and beer production, were better predictors of these extinctions. Finally, almost all of our findings were opposite to the predictions of the chytrid-thermal-optimum hypothesis. Although climate change is likely to play an important role in worldwide amphibian declines, more convincing evidence is needed of a causal link.
Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary
Authors: Banik Jacob J. , Brady Sean F.
Published: November 2008

Glycopeptide antibiotics have long served as drugs of last resort for the treatment of antibiotic-resistant Gram-positive bacterial infections. Resistance to the clinically relevant glycopeptides, vancomycin and teicoplanin, threatens to undermine the usefulness of this important class of antibiotics. DNA extracted from a geographically diverse collection of soil samples was screened by PCR for the presence of sequences related to OxyC, an oxidative coupling enzyme found in glycopeptide biosynthetic gene clusters. Every soil sample examined contained at least 1 unique OxyC gene sequence. In an attempt to access the biosynthetic gene clusters associated with these OxyC sequences, a 10,000,000-membered environmental DNA (eDNA) megalibrary was created from a single soil sample. Two unique glycopeptide gene clusters were recovered from this eDNA megalibrary. Using the teicoplanin aglycone and the 3 sulfotransferases found in one of these gene clusters, mono-, di-, and trisulfated glycopeptide congeners were produced. The high frequency with which OxyC genes were found in environmental samples indicates that soil eDNA libraries are likely to be a rewarding source of glycopeptide gene clusters. Enzymes found in these gene clusters should be useful for generating new glycopeptides analogs. Environmental DNA megalibraries, like the one constructed for this study, can provide access to many of the natural product biosynthetic gene clusters that are predicted to be present in soil microbiomes.
Sustaining biodiversity in ancient tropical countryside
Authors: Ranganathan Jai , Daniels R. J. Ranjit , Chandran M. D. Subash , Ehrlich Paul R. , Daily Gretchen C.
Published: November 2008

With intensifying demands for food and biofuels, a critical threat to biodiversity is agricultural expansion into native tropical ecosystems. Tropical agriculture, particularly intensive agriculture, often supports few native organisms, and consequently has been largely overlooked in conservation planning; yet, recent work in the Neotropics demonstrates that tropical agriculture with certain features can support significant biodiversity, decades after conversion to farmland. It remains unknown whether this conservation value can be sustained for centuries to millennia. Here, we quantify the bird diversity affiliated with agricultural systems in southwest India, a region continuously cultivated for >2,000 years. We show that arecanut palm (Areca catechu) production systems retain 90% of the bird species associated with regional native forest. Two factors promote this high conservation value. First, the system involves intercropping with multiple, usually woody, understory species and, thus, has high vertical structural complexity that is positively correlated with bird species richness. Second, the system encompasses nearby forests, where large quantities of leaf litter are extracted for mulch. The preservation of these forests on productive land traces back to their value in supplying inputs to arecanut cultivation. The long-term biodiversity value of an agricultural ecosystem has not been documented in South and Southeast Asia. Our findings open a new conservation opportunity for this imperiled region that may well extend to other crops. Some of these working lands may be able to sustain native species over long-time scales, indicating that conservation investments in agriculture today could pay off for people and for nature.
Signatures of combinatorial regulation in intrinsic biological noise
Authors: Warmflash Aryeh , Dinner Aaron R.
Published: November 2008

Gene expression is controlled by the action of transcription factors that bind to DNA and influence the rate at which a gene is transcribed. The quantitative mapping between the regulator concentrations and the output of the gene is known as the
cis
-regulatory input function (CRIF). Here, we show how the CRIF shapes the form of the joint probability distribution of molecular copy numbers of the regulators and the product of a gene. Namely, we derive a class of fluctuation-based relations that relate the moments of the distribution to the derivatives of the CRIF. These relations are useful because they enable statistics of naturally arising cell-to-cell variations in molecular copy numbers to substitute for traditional manipulations for probing regulatory mechanisms. We demonstrate that these relations can distinguish super- and subadditive gene regulatory scenarios (molecular analogs of AND and OR logic operations) in simulations that faithfully represent bacterial gene expression. Applications and extensions to other regulatory scenarios are discussed.
Toll-like receptor 4 restricts retinal progenitor cell proliferation
Authors: Shechter Ravid , Ronen Ayal , Rolls Asya , London Anat , Bakalash Sharon , Young Michael J. , Schwartz Michal
Published: November 2008

Retinal neurogenesis ceases by the early postnatal period, although retinal progenitor cells (RPCs) persist throughout life. In this study, we show that in the mammalian eye, the function of Toll-like receptor 4 (TLR4) extends beyond regulation of the innate immune response; it restricts RPC proliferation. In TLR4-deficient mice, enhanced proliferation of cells reminiscent of RPCs is evident during the early postnatal period. In vitro experiments demonstrate that TLR4 acts as an intrinsic regulator of RPC fate decision. Increased TLR4 expression in the eye correlates with the postnatal cessation of cell proliferation. However, deficient TLR4 expression is not sufficient to extend the proliferative period but rather contributes to resumption of proliferation in combination with growth factors. Proliferation in vivo is inhibited by both MyD88-dependent and -independent pathways, similar to the mechanisms activated by TLR4 in immune cells. Thus, our study attributes a novel role to TLR4 as a negative regulator of RPC proliferation.
Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7
Authors: Rojas Raul , van Vlijmen Thijs , Mardones Gonzalo A. , Prabhu Yogikala , Rojas Adriana L. , Mohammed Shabaz , Heck Albert J.R. , Raposo Graça , van der Sluijs Peter , Bonifacino Juan S.
Published: November 2008

The retromer complex mediates retrograde transport of transmembrane cargo from endosomes to the trans-Golgi network (TGN). Mammalian retromer is composed of a sorting nexin (SNX) dimer that binds to phosphatidylinositol 3-phosphate–enriched endosomal membranes and a vacuolar protein sorting (Vps) 26/29/35 trimer that participates in cargo recognition. The mammalian SNX dimer is necessary but not sufficient for recruitment of the Vps26/29/35 trimer to membranes. In this study, we demonstrate that the guanosine triphosphatase Rab7 contributes to this recruitment. The Vps26/29/35 trimer specifically binds to Rab7–guanosine triphosphate (GTP) and localizes to Rab7-containing endosomal domains. Interference with Rab7 function causes dissociation of the Vps26/29/35 trimer but not the SNX dimer from membranes. This blocks retrieval of mannose 6-phosphate receptors to the TGN and impairs cathepsin D sorting. Rab5-GTP does not bind to the Vps26/29/35 trimer, but perturbation of Rab5 function causes dissociation of both the SNX and Vps26/29/35 components from membranes through inhibition of a pathway involving phosphatidylinositol 3-kinase. These findings demonstrate that Rab5 and Rab7 act in concert to regulate retromer recruitment to endosomes.
Coordinated regulation of AP2 uncoating from clathrin-coated vesicles by rab5 and hRME-6
Authors: Semerdjieva Sophia , Shortt Barry , Maxwell Emma , Singh Sukhdeep , Fonarev Paul , Hansen Jonathan , Schiavo Giampietro , Grant Barth D. , Smythe Elizabeth
Published: November 2008

Here we investigate the role of rab5 and its cognate exchange factors rabex-5 and hRME-6 in the regulation of AP2 uncoating from endocytic clathrin-coated vesicles (CCVs). In vitro, we show that the rate of AP2 uncoating from CCVs is dependent on the level of functional rab5. In vivo, overexpression of dominant-negative rab5S34N, or small interfering RNA (siRNA)–mediated depletion of hRME-6, but not rabex-5, resulted in increased steady-state levels of AP2 associated with endocytic vesicles, which is consistent with reduced uncoating efficiency. hRME-6 guanine nucleotide exchange factor activity requires hRME-6 binding to α-adaptin ear, which displaces the ear-associated μ2 kinase AAK1. siRNA-mediated depletion of hRME-6 increases phospho-μ2 levels, and expression of a phosphomimetic μ2 mutant increases levels of endocytic vesicle-associated AP2. Depletion of hRME-6 or rab5S35N expression also increases the levels of phosphoinositide 4,5-bisphosphate (PtdIns(4,5)P2) associated with endocytic vesicles. These data are consistent with a model in which hRME-6 and rab5 regulate AP2 uncoating in vivo by coordinately regulating μ2 dephosphorylation and PtdIns(4,5)P2 levels in CCVs.
Deletion of IFT20 in the mouse kidney causes misorientation of the mitotic spindle and cystic kidney disease
Authors: Jonassen Julie A. , San Agustin Jovenal , Follit John A. , Pazour Gregory J.
Published: November 2008

Primary cilia project from the surface of most vertebrate cells and are thought to be sensory organelles. Defects in primary cilia lead to cystic kidney disease, although the ciliary mechanisms that promote and maintain normal renal function remain incompletely understood. In this work, we generated a floxed allele of the ciliary assembly gene Ift20. Deleting this gene specifically in kidney collecting duct cells prevents cilia formation and promotes rapid postnatal cystic expansion of the kidney. Dividing collecting duct cells in early stages of cyst formation fail to properly orient their mitotic spindles along the tubule, whereas nondividing cells improperly position their centrosomes. At later stages, cells lacking cilia have increased canonical Wnt signaling and increased rates of proliferation. Thus, IFT20 functions to couple extracellular events to cell proliferation and differentiation.
ICOS-dependent extrafollicular helper T cells elicit IgG production via IL-21 in systemic autoimmunity
Authors: Odegard Jared M. , Marks Benjamin R. , DiPlacido Leah D. , Poholek Amanda C. , Kono Dwight H. , Dong Chen , Flavell Richard A. , Craft Joe
Published: November 2008

The role of specialized follicular helper T (TFH) cells in the germinal center has become well recognized, but it is less clear how effector T cells govern the extrafollicular response, the dominant pathway of high-affinity, isotype-switched autoantibody production in the MRL/MpJ-Faslpr (MRLlpr) mouse model of lupus. MRLlpr mice lacking the Icos gene have impaired extrafollicular differentiation of immunoglobulin (Ig) G+ plasma cells accompanied by defects in CXC chemokine receptor (CXCR) 4 expression, interleukin (IL) 21 secretion, and B cell helper function in CD4 T cells. These phenotypes reflect the selective loss of a population of T cells marked by down-regulation of P-selectin glycoprotein ligand 1 (PSGL-1; also known as CD162). PSGL-1lo T cells from MRLlpr mice express CXCR4, localize to extrafollicular sites, and uniquely mediate IgG production through IL-21 and CD40L. In other autoimmune strains, PSGL-1lo T cells are also abundant but may exhibit either a follicular or extrafollicular phenotype. Our findings define an anatomically distinct extrafollicular population of cells that regulates plasma cell differentiation in chronic autoimmunity, indicating that specialized humoral effector T cells akin to TFH cells can occur outside the follicle.
Unrecognized Burden of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus Carriage in the Pediatric Intensive Care Unit
Authors: Milstone Aaron M. , Song Xiaoyan , Beers Claire , Berkowitz Ivor , Carroll Karen C. , Perl Trish M.
Published: November 2008

Routinely, children's hospitals use data from clinical cultures to estimate the burden of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) carriage. In our pediatric intensive care unit, a program of weekly surveillance cultures uncovered an unrecognized reservoir of MRSA and VRE carriers. This weekly surveillance enabled more accurate estimates of the incidence rates of MRSA and VRE carriage and led to an increased number of isolation-days for patients.
EnteropathogenicEscherichia coliSubverts Phosphatidylinositol 4,5-Bisphosphate and Phosphatidylinositol 3,4,5-Trisphosphate upon Epithelial Cell Infection
Authors: Sason Hagit , Milgrom Michal , Weiss Aryeh M. , Melamed-Book Naomi , Balla Tamas , Grinstein Sergio , Backert Steffen , Rosenshine Ilan , Aroeti Benjamin
Published: November 2008

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] are phosphoinositides (PIs) present in small amounts in the inner leaflet of the plasma membrane (PM) lipid bilayer of host target cells. They are thought to modulate the activity of proteins involved in enteropathogenic Escherichia coli (EPEC) infection. However, the role of PI(4,5)P2and PI(3,4,5)P3in EPEC pathogenesis remains obscure. Here we show that EPEC induces a transient PI(4,5)P2accumulation at bacterial infection sites. Simultaneous actin accumulation, likely involved in the construction of the actin-rich pedestal, is also observed at these sites. Acute PI(4,5)P2depletion partially diminishes EPEC adherence to the cell surface and actin pedestal formation. These findings are consistent with a bimodal role, whereby PI(4,5)P2contributes to EPEC association with the cell surface and to the maximal induction of actin pedestals. Finally, we show that EPEC induces PI(3,4,5)P3clustering at bacterial infection sites, in a translocated intimin receptor (Tir)-dependent manner. Tir phosphorylated on tyrosine 454, but not on tyrosine 474, forms complexes with an active phosphatidylinositol 3-kinase (PI3K), suggesting that PI3K recruited by Tir prompts the production of PI(3,4,5)P3beneath EPEC attachment sites. The functional significance of this event may be related to the ability of EPEC to modulate cell death and innate immunity.
Effects of light intensity on activity and pelagic dispersion of fish: studies with a seabed-mounted echosounder
Authors: Didrikas Tomas , Hansson Sture
Published: November 2008

Didrikas, T., and Hansson, S. 2009. Effects of light intensity on activity and pelagic dispersion of fish: studies with a seabed-mounted echosounder. – ICES Journal of Marine Science, 66: 388–395. A seabed-mounted, upwards-pinging echosounder was used to study fish activity and pelagic dispersion in relation to fish size, light, and temperature. Four phases (day, dusk, night, dawn) in fish dispersion were distinguished over the diel cycle, and the swimming speed of fish varied among these phases. Notably, average swimming speed by day was twice as high as by night. For all phases combined, fish size, light intensity, and temperature explained 52% of the variability in swimming speed. When different phases were analysed separately, fish size was the most important variable by day, whereas light had the strongest effects on swimming speed in the evening. During the mornings, variability in swimming speed was best correlated with temperature, but by night all factors (fish size, light intensity, temperature) had similar effects on activity. These results have implications for fish bioenergetics models. Such models should account for seasonal, light-driven cycles in activity-induced respiration estimates, in particular when modelling populations at high latitudes.
Tobacco mosaic virus 126-kDa Protein Increases the Susceptibility of Nicotiana tabacum to Other Viruses and Its Dosage Affects Virus-Induced Gene Silencing
Authors: Harries Phillip A. , Palanichelvam Karuppaiah , Bhat Sumana , Nelson Richard S.
Published: November 2008

The Tobacco mosaic virus (TMV) 126-kDa protein is a suppressor of RNA silencing previously shown to delay the silencing of transgenes in Nicotiana tabacum and N. benthamiana. Here, we demonstrate that expression of a 126-kDa protein–green fluorescent protein (GFP) fusion (126-GFP) in N. tabacum increases susceptibility to a broad assortment of viruses, including Alfalfa mosaic virus, Brome mosaic virus, Tobacco rattle virus (TRV), and Potato virus X. Given its ability to enhance TRV infection in tobacco, we tested the effect of 126-GFP expression on TRV-mediated virus-induced gene silencing (VIGS) and demonstrate that this protein can enhance silencing phenotypes. To explain these results, we examined the poorly understood effect of suppressor dosage on the VIGS response and demonstrated that enhanced VIGS corresponds to the presence of low levels of suppressor protein. A mutant version of the 126-kDa protein, inhibited in its ability to suppress silencing, had a minimal effect on VIGS, suggesting that the suppressor activity of the 126-kDa protein is indeed responsible for the observed dosage effects. These findings illustrate the sensitivity of host plants to relatively small changes in suppressor dosage and have implications for those interested in enhancing silencing phenotypes in tobacco and other species through VIGS.
Analysis of Flagellin Perception Mediated by flg22 Receptor OsFLS2 in Rice
Authors: Takai Ryota , Isogai Akira , Takayama Seiji , Che Fang-Sik
Published: November 2008

Plants have sensitive perception systems that recognize various pathogen-derived molecules. We previously reported that rice detects flagellin from a rice-incompatible strain of gram-negative phytopathogenic bacterium, Acidovorax avenae, which induces subsequent immune responses involving cell death. The mechanism of flagellin perception in rice, however, has remained obscure. In this study, we found that flg22, a peptide derived from the flagellin N-terminus, induced weak immune responses without cell death in cultured rice cells. To elucidate the mechanism by which flg22 induced signaling in rice, we characterized OsFLS2, the rice ortholog of AtFLS2, which mediates flg22 perception. Heterologous expression of OsFLS2 functions in Arabidopsis, showing the conservation of the flg22 signaling pathway across divergent plant taxa. OsFLS2-overexpressing rice cultured cells generated stronger immune responses with the induction of cell death following stimulation with flg22 and flagellin. However, examination of the growth rate of the compatible strain in inoculated OsFLS2-overexpressing rice could not confirm bacterial growth suppression compared with wild-type rice. These results suggest that rice possesses a conserved flagellin perception system utilizing the FLS2 receptor which, when upregulated, hardly affects resistance against compatible A. avenae.
Selection on sperm morphology under relaxed sperm competition in a wild passerine bird
Authors: Calhim Sara , Lampe Helene M , Slagsvold Tore , Birkhead Tim R
Published: November 2008

Theories regarding the role of sexual selection on the evolution of sperm traits are based on an association between pre-copulatory (e.g. female preference) and post-copulatory (e.g. ejaculate quality) male reproductive traits. In tests of these hypotheses, sperm morphology has rarely been used, despite its high heritability and intra-individual consistency. We found evidence of selection for longer sperm through positive phenotypic associations between sperm size and the two major female preference traits in the pied flycatcher,
Ficedula hypoleuca
. Our results support the sexually selected sperm hypothesis in a species under low sperm competition and demonstrate that natural and pre-copulatory sexual selection forces should not be overlooked in studies of intraspecific sperm morphology evolution.