bluuebunny/crossref_metadata_2025 huggingface dataset:
A precise packing sequence for self-assembled convex structures
Authors: Chen Ting , Zhang Zhenli , Glotzer Sharon C.
Published: January 2007

Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self-assemble into clusters and that clusters comprised of particular numbers of cones (e.g., 4–17, 20, 27, 32, and 42) have a unique and precisely packed structure that is robust over a range of cone angles. These precise clusters form a sequence of structures at specific cluster sizes (a “precise packing sequence”) that for small sizes is identical to that observed in evaporation-driven assembly of colloidal spheres. We further show that this sequence is reproduced and extended in simulations of two simple models of spheres self-assembling from random initial conditions subject to convexity constraints, including an initial spherical convexity constraint for moderate- and large-sized clusters. This sequence contains six of the most common virus capsid structures obtained
in vivo
, including large chiral clusters and a cluster that may correspond to several nonicosahedral, spherical virus capsids obtained
in vivo
. Our findings suggest that this precise packing sequence results from free energy minimization subject to convexity constraints and is applicable to a broad range of assembly processes.
Soil nutrients influence spatial distributions of tropical tree species
Authors: John Robert , Dalling James W. , Harms Kyle E. , Yavitt Joseph B. , Stallard Robert F. , Mirabello Matthew , Hubbell Stephen P. , Valencia Renato , Navarrete Hugo , Vallejo Martha , Foster Robin B.
Published: January 2007

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005)
Ecology
86:1757–1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<10
4
km
2
) and regional scales. At local scales (<1 km
2
), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three diverse neotropical forest plots in Colombia (La Planada), Ecuador (Yasuni), and Panama (Barro Colorado Island). Using spatial distribution maps of >0.5 million individual trees of 1,400 species and 10 essential plant nutrients, we used Monte Carlo simulations of species distributions to test plant–soil associations against null expectations based on dispersal assembly. We found that the spatial distributions of 36–51% of tree species at these sites show strong associations to soil nutrient distributions. Neutral dispersal assembly cannot account for these plant–soil associations or the observed niche breadths of these species. These results indicate that belowground resource availability plays an important role in the assembly of tropical tree communities at local scales and provide the basis for future investigations on the mechanisms of resource competition among tropical tree species.
Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water
Authors: Athawale Manoj V. , Goel Gaurav , Ghosh Tuhin , Truskett Thomas M. , Garde Shekhar
Published: January 2007

We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer–water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, Δ
G
= γ(
T
)Δ
A
, where the surface tension, γ, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000)
Proc Natl Acad Sci USA
97:
8324–8327
] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer–water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor–liquid interface.
Differential distribution of NCX1 contributes to spine–dendrite compartmentalization in CA1 pyramidal cells
Authors: Lőrincz Andrea , Rózsa Balázs , Katona Gergely , Vizi E. Sylvester , Tamás Gábor
Published: January 2007

Compartmentalization of Ca
2+
between dendritic spines and shafts is governed by diffusion barriers and a range of Ca
2+
extrusion mechanisms. The distinct contribution of different Ca
2+
clearance systems to Ca
2+
compartmentalization in dendritic spines versus shafts remains elusive. We applied a combination of ultrastructural and functional imaging methods to assess the subcellular distribution and role of NCX1 in rat CA1 pyramidal cells. Quantitative electron microscopic analysis of preembedding immunogold reactions revealed uniform densities of NCX1 along the shafts of apical and basal dendrites, but densities in dendritic shafts were approximately seven times higher than in dendritic spines. In line with these results, two-photon imaging of synaptically activated Ca
2+
transients during NCX blockade showed preferential action localized to the dendritic shafts for NCXs in regulating spine–dendrite coupling.
A consensus view of protein dynamics
Authors: Rueda Manuel , Ferrer-Costa Carles , Meyer Tim , Pérez Alberto , Camps Jordi , Hospital Adam , Gelpí Josep Lluis , Orozco Modesto
Published: January 2007

The dynamics of proteins in aqueous solution has been investigated through a massive approach based on “state of the art” molecular dynamics simulations performed for all protein metafolds using the four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis of the massive database of trajectories (>1.5 terabytes of data obtained using ≈50 years of CPU) allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution.
Structure of the light-harvesting bacteriochlorophyll
c
assembly in chlorosomes from
Chlorobium limicola
determined by solid-state NMR
Authors: Egawa Ayako , Fujiwara Toshimichi , Mizoguchi Tadashi , Kakitani Yoshinori , Koyama Yasushi , Akutsu Hideo
Published: January 2007

We have determined the atomic structure of the bacteriochlorophyll
c
(BChl
c
) assembly in a huge light-harvesting organelle, the chlorosome of green photosynthetic bacteria, by solid-state NMR. Previous electron microscopic and spectroscopic studies indicated that chlorosomes have a cylindrical architecture with a diameter of ≈10 nm consisting of layered BChl molecules. Assembly structures in huge noncrystalline chlorosomes have been proposed based mainly on structure-dependent chemical shifts and a few distances acquired by solid-state NMR, but those studies did not provide a definite structure. Our approach is based on
13
C dipolar spin-diffusion solid-state NMR of uniformly
13
C-labeled chlorosomes under magic-angle spinning. Approximately 90 intermolecular C

C distances were obtained by simultaneous assignment of distance correlations and structure optimization preceded by polarization-transfer matrix analysis. It was determined from the ≈90 intermolecular distances that BChl
c
molecules form piggyback-dimer-based parallel layers. This finding rules out the well known monomer-based structures. A molecular model of the cylinder in the chlorosome was built by using this structure. It provided insights into the mechanisms of efficient light harvesting and excitation transfer to the reaction centers. This work constitutes an important advance in the structure determination of huge intact systems that cannot be crystallized.
A comprehensive transposon mutant library of
Francisella novicida
, a bioweapon surrogate
Authors: Gallagher Larry A. , Ramage Elizabeth , Jacobs Michael A. , Kaul Rajinder , Brittnacher Mitchell , Manoil Colin
Published: January 2007

Francisella tularensis
, the causative agent of tularemia, is one of the most infectious bacterial pathogens known and is a category A select agent. We created a sequence-defined, near-saturation transposon mutant library of
F. tularensis novicida
, a subspecies that causes a tularemia-like disease in rodents. The library consists of 16,508 unique insertions, an average of >9 insertions per gene, which is a coverage nearly twice that of the greatest previously achieved for any bacterial species. Insertions were recovered in 84% (1,490) of the predicted genes. To achieve high coverage, it was necessary to construct transposons carrying an endogenous
Francisella
promoter to drive expression of antibiotic resistance. An analysis of genes lacking (or with few) insertions identified nearly 400 candidate essential genes, most of which are likely to be required for growth on rich medium and which represent potential therapeutic targets. To facilitate genome-scale screening using the mutant collection, we assembled a sublibrary made up of two purified mutants per gene. The library provides a resource for virtually complete identification of genes involved in virulence and other nonessential processes.
A G protein/cAMP signal cascade is required for axonal convergence into olfactory glomeruli
Authors: Chesler Alexander T. , Zou Dong-Jing , Le Pichon Claire E. , Peterlin Zita A. , Matthews Glennis A. , Pei Xin , Miller Michael C. , Firestein Stuart
Published: January 2007

The mammalian odorant receptors (ORs) comprise a large family of G protein-coupled receptors that are critical determinants of both the odorant response profile and the axonal identity of the olfactory sensory neurons in which they are expressed. Although the pathway by which ORs activate odor transduction is well established, the mechanism by which they direct axons into proper glomerular relationships remains unknown. We have developed a gain-of-function approach by using injection of retroviral vectors into the embryonic olfactory epithelium to study the ORs′ contribution to axon guidance. By ectopically expressing ORs, we demonstrate that functional OR proteins induce axonal coalescence. Furthermore, ectopic expression of Gα mutants reveals that activation of the signal transduction cascade is sufficient to cause axonal convergence into glomeruli. Analysis of Gα subunit expression indicates that development and odorant transduction use separate transduction pathways. Last, we establish that the generation of cAMP through adenylyl cyclase 3 is necessary to establish proper axonal identity. Our data point to a model in which axonal sorting is accomplished by OR stimulation of cAMP production by coupling to Gαs.
A compensation election for binary social choice
Authors: Oprea Ryan D. , Smith Vernon L. , Winn Abel M.
Published: January 2007

We report experimental results examining the properties of a bidding mechanism, the “Compensation Election,” which is designed to implement a simple binary choice between two options. We may think of the group decision problem as a choice between a new rule and the status quo. The rule and the status quo are each common outcomes that apply across all individuals, but the value or cost that they induce on each individual differs according to each individual's circumstances: some gain, some lose, and others are unaffected by a change to the new from the old. Rather than casting votes, each subject submits a bid reflecting his willingness to pay to induce the group to select one option and the amount he wishes to be paid if the alternative option is selected. The Compensation Election chooses the option that receives the highest sum of bids. We find that, although the Compensation Election allows subjects to strategically bid above their value (or even for the option they do not prefer), such behavior is not the norm. We also find that subjects' bids more truthfully reveal their values when there are more bidders in the election.
A functional SNP of interferon-γ gene is important for interferon-α-induced and spontaneous recovery from hepatitis C virus infection
Authors: Huang Ying , Yang Huiying , Borg Brian B. , Su Xiaowen , Rhodes Shannon L. , Yang Kai , Tong Xiaomei , Tang George , Howell Charles D. , Rosen Hugo R. , Thio Chloe L. , Thomas David L. , Alter Harvey J. , Sapp Ronda K. , Liang T. Jake
Published: January 2007

Cytokine polymorphisms are associated with disease outcome and interferon (IFN) treatment response in hepatitis C virus (HCV) infection. We genotyped eight SNPs spanning the entire IFN-γ gene in two cohorts and assessed the association between those polymorphisms and treatment response or spontaneous viral clearance. The first cohort was composed of 284 chronically HCV-infected patients who had received IFN-α-based therapy and the second was 251 i.v. drug users who had either spontaneously cleared HCV or become chronically infected. A SNP variant located in the proximal IFN-γ promoter region next to the binding motif of heat shock transcription factor (HSF), −764G, was significantly associated with sustained virological response [
P
= 0.04, odds ratio (OR) = 3.51 (confidence interval 1.0–12.5)]. The association was independently significant in multiple logistic regression (
P
= 0.04) along with race, viral titer, and genotype. This variant was also significantly associated with spontaneous recovery [
P
= 0.04, OR = 3.51 (1.0–12.5)] in the second cohort. Functional analyses show that the G allele confers a two- to three-fold higher promoter activity and stronger binding affinity to HSF1 than the C allele. Our study suggests that the IFN-γ promoter SNP −764G/C is functionally important in determining viral clearance and treatment response in HCV-infected patients and may be used as a genetic marker to predict sustained virological response in HCV-infected patients.
DNA folding and melting observed in real time redefine the energy landscape
Authors: Ma Hairong , Wan Chaozhi , Wu Aiguo , Zewail Ahmed H.
Published: January 2007

We report real-time observations of the folding and melting of DNA by probing two active sites of a hairpin structure, the bases and the stem end, and using an ultrafast
T
-jump. Studies at different initial temperatures (before, during, and after melting) provide the time scale of water heating (<20 ps), single-strand destacking (700 ps to 2 ns), and hairpin destacking (microseconds and longer) in solutions of various ionic strengths and pH values. The behavior of transient changes gives direct evidence to the existence of intermediate collapsed structures, labile in destacking but compact in nature, and indicates that melting is not a two-state process. We propose a landscape that is defined by these nucleation structures and destacking for efficient folding and melting.
Pituitary autoantibodies in autoimmune polyendocrine syndrome type 1
Authors: Bensing Sophie , Fetissov Sergueï O. , Mulder Jan , Perheentupa Jaakko , Gustafsson Jan , Husebye Eystein S. , Oscarson Mikael , Ekwall Olov , Crock Patricia A. , Hökfelt Tomas , Hulting Anna-Lena , Kämpe Olle
Published: January 2007

Autoimmune polyendocrine syndrome type 1 (APS1) is a rare autosomal recessive disorder caused by mutations in the autoimmune regulator (
AIRE
) gene. High titer autoantibodies (Aabs) toward intracellular enzymes are a hallmark for APS1 and serve as diagnostic markers and predictors for disease manifestations. In this study, we aimed to identify pituitary autoantigens in patients with APS1. A pituitary cDNA expression library was screened with APS1 sera and a tudor domain containing protein 6 (TDRD6) cDNA clone was isolated. Positive immunoreactivity against
in vitro
translated TDRD6 fragments was shown in 42/86 (49%) APS1 patients but not in patients with other autoimmune diseases or in healthy controls. By using immunohistochemistry, sera from 3/6 APS1 patients with growth hormone (GH) deficiency showed immunostaining of a small number of guinea pig anterior pituitary cells, and 40–50% of these cells were GH-positive. No such immunostaining was seen with sera from healthy controls. The APS1 Aab-positive, GH-negative cells may represent a novel subpopulation of anterior pituitary cells. In addition, 4/6 patient sera showed staining of a fiber-plexus in the pituitary intermediate lobe recognizing enzymes of monoamine and GABA synthesis. Thus, we have identified TDRD6 as a major autoantigen in APS1 patients and shown that several sera from GH-deficient patients stain specific cell populations and nerves in the pituitary gland.
A quantitative, theoretical framework for understanding mammalian sleep
Authors: Savage Van M. , West Geoffrey B.
Published: January 2007

Sleep is one of the most noticeable and widespread phenomena occurring in multicellular animals. Nevertheless, no consensus for a theory of its origins has emerged. In particular, no explicit, quantitative theory exists that elucidates or distinguishes between the myriad hypotheses proposed for sleep. Here, we develop a general, quantitative theory for mammalian sleep that relates many of its fundamental parameters to metabolic rate and body size. Several mechanisms suggested for the function of sleep can be placed in this framework, e.g., cellular repair of damage caused by metabolic processes as well as cortical reorganization to process sensory input. Our theory leads to predictions for sleep time, sleep cycle time, and rapid eye movement time as functions of body and brain mass, and it explains, for example, why mice sleep ≈14 hours per day relative to the 3.5 hours per day that elephants sleep. Data for 96 species of mammals, spanning six orders of magnitude in body size, are consistent with these predictions and provide strong evidence that time scales for sleep are set by the brain's, not the whole-body, metabolic rate.
Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase
Authors: Zhang Xiaodong , Reddy Swarnalatha Y. , Bruice Thomas C.
Published: January 2007

At neutral pH, oxidation of CH
3
OH → CH
2
O by an
o
-quinone requires general-base catalysis and the reaction is endothermic. The active-site –CO
2
−
groups of Glu-171 and Asp-297 (Glu-171–CO
2
−
and Asp-297–CO
2
−
) have been considered as the required general base catalysts in the bacterial
o
-quinoprotein methanol dehydrogenase (MDH) reaction. Based on quantum mechanics/molecular mechanics (QM/MM) calculations, the free energy for MeOH reduction of
o
-PQQ when MeOH is hydrogen bonded to Glu-171–CO
2
−
and the crystal water (Wat1) is hydrogen bonded to Asp-297–CO
2
−
is Δ
G
‡
= 11.7 kcal/mol, which is comparable with the experimental value of 8.5 kcal/mol. The calculated Δ
G
‡
when MeOH is hydrogen bonded to Asp-297–CO
2
−
is >50 kcal/mol. The Asp-297–CO
2
−
···Wat1 complex is very stable. Molecular dynamics (MD) simulations on MDH·PQQ·Wat1 complex in TIP3P water for 5 ns does not result in interchange of Asp-297–CO
2
−
bound Wat1 for a solvent water. Starting with Wat1 removed and MeOH hydrogen bonded to Asp-297–CO
2
−
, we find that MeOH returns to be hydrogen bonded to Glu-171–CO
2
−
and Asp-297–CO
2
−
coordinates to Ca
2+
during 3 ns simulation. The Asp-297–CO
2
−
···Wat1 of reactant complex does play a crucial role in catalysis. By QM/MM calculation Δ
G
‡
= 1.1 kcal/mol for Asp-297–CO
2
−
general-base catalysis of Wat1 hydration of the immediate CH
2

O product → CH
2
(OH)
2
. By this means, the endothermic oxidation-reduction reaction is pulled such that the overall conversion of MeOH to CH
2
(OH)
2
is exothermic.
Mild mitochondrial uncoupling impacts cellular aging in human muscles
in vivo
Authors: Amara Catherine E. , Shankland Eric G. , Jubrias Sharon A. , Marcinek David J. , Kushmerick Martin J. , Conley Kevin E.
Published: January 2007

Faster aging is predicted in more active tissues and animals because of greater reactive oxygen species generation. Yet age-related cell loss is greater in less active cell types, such as type II muscle fibers. Mitochondrial uncoupling has been proposed as a mechanism that reduces reactive oxygen species production and could account for this paradox between longevity and activity. We distinguished these hypotheses by using innovative optical and magnetic resonance spectroscopic methods applied to noninvasively measured ATP synthesis and O
2
uptake
in vivo
in human muscle. Here we show that mitochondrial function is unchanged with age in mildly uncoupled tibialis anterior muscle (75% type I) despite a high respiratory rate in adults. In contrast, substantial uncoupling and loss of cellular [ATP] indicative of mitochondrial dysfunction with age was found in the lower respiring and well coupled first dorsal interosseus (43–50% type II) of the same subjects. These results reject respiration rate as the sole factor impacting the tempo of cellular aging. Instead, they support mild uncoupling as a mechanism protecting mitochondrial function and contributing to the paradoxical longevity of the most active muscle fibers.
Intramolecular interaction in the tail of
Acanthamoeba
myosin IC between the SH3 domain and a putative pleckstrin homology domain
Authors: Hwang Kae-Jung , Mahmoodian Fatemeh , Ferretti James A. , Korn Edward D. , Gruschus James M.
Published: January 2007

The 466-aa tail of the heavy chain of
Acanthamoeba
myosin IC (AMIC) comprises an N-terminal 220-residue basic region (BR) followed by a 56-residue Gly/Pro/Ala-rich region (GPA1), a 55-residue Src homology 3 (SH3) domain, and a C-terminal 135-residue Gly/Pro/Ala-rich region (GPA2). Cryo-electron microscopy of AMIC had shown previously that the AMIC tail is folded back on itself, suggesting the possibility of interactions between its N- and C-terminal regions. We now show specific differences between the NMR spectrum of bacterially expressed full-length tail and the sum of the spectra of individually expressed BR and GPA1-SH3-GPA2 (GSG) regions. These results are indicative of interactions between the two subdomains in the full-length tail. From the NMR data, we could assign many of the residues in BR and GSG that are involved in these interactions. By combining homology modeling with the NMR data, we identify a putative pleckstrin homology (PH) domain within BR, and show that the PH domain interacts with the SH3 domain.
Polycomb
-like genes are necessary for specification of dopaminergic and serotonergic neurons in
Caenorhabditis elegans
Authors: Yang Yong , Sun Yinyan , Luo Xin , Zhang Yuxia , Chen Yaoyao , Tian E. , Lints Robyn , Zhang Hong
Published: January 2007

The molecular mechanisms underlying the formation of neurons with defined neurotransmitters are not well understood. In this study, we demonstrate that the
PcG
-like genes in
Caenorhabditis elegans, sop-2
and
sor-3
, regulate the formation of dopaminergic and serotonergic neurons and several other neuronal properties.
sor-3
encodes a novel protein containing an MBT repeat, a domain that contains histone-binding activity and is present in PcG proteins SCM and Sfmbt in other organisms. We further show that mutations in
sor-3
lead to ectopic expression of Hox genes and cause homeotic transformations. Specification of certain neuronal identities by these
PcG
-like genes appears to involve regulation of non-Hox gene targets. Our studies revealed that the
PcG
-like genes are crucial for coordinately regulating the expression of discrete aspects of neuronal identities in
C. elegans
.
Mitochondrial dysfunction in the pathogenesis of Ullrich congenital muscular dystrophy and prospective therapy with cyclosporins
Authors: Angelin Alessia , Tiepolo Tania , Sabatelli Patrizia , Grumati Paolo , Bergamin Natascha , Golfieri Cristina , Mattioli Elisabetta , Gualandi Francesca , Ferlini Alessandra , Merlini Luciano , Maraldi Nadir M. , Bonaldo Paolo , Bernardi Paolo
Published: January 2007

Ullrich congenital muscular dystrophy is a severe genetically and clinically heterogeneous muscle disorder linked to collagen VI deficiency. The pathogenesis of the disease is unknown. To assess the potential role of mitochondrial dysfunction in the onset of muscle fiber death in this form of dystrophy, we studied biopsies and myoblast cultures obtained from patients with different genetic defects of collagen VI and variable clinical presentations of the disease. We identified a latent mitochondrial dysfunction in myoblasts from patients with Ullrich congenital muscular dystrophy that matched an increased occurrence of spontaneous apoptosis. Unlike those in myoblasts from healthy donors, mitochondria in cells from patients depolarized upon addition of oligomycin and displayed ultrastructural alterations that were worsened by treatment with oligomycin. The increased apoptosis, the ultrastructural defects, and the anomalous response to oligomycin could be normalized by Ca
2+
chelators, by plating cells on collagen VI, and by treatment with cyclosporin A or with the specific cyclophilin inhibitor methylAla
3
ethylVal
4
-cyclosporin, which does not affect calcineurin activity. Here we demonstrate that mitochondrial dysfunction plays an important role in muscle cell wasting in Ullrich congenital muscular dystrophy. This study represents an essential step toward a pharmacological therapy of Ullrich congenital muscular dystrophy with cyclosporin A and methylAla
3
ethylVal
4
cyclosporin.
Improved evolutionary optimization from genetically adaptive multimethod search
Authors: Vrugt Jasper A. , Robinson Bruce A.
Published: January 2007

In the last few decades, evolutionary algorithms have emerged as a revolutionary approach for solving search and optimization problems involving multiple conflicting objectives. Beyond their ability to search intractably large spaces for multiple solutions, these algorithms are able to maintain a diverse population of solutions and exploit similarities of solutions by recombination. However, existing theory and numerical experiments have demonstrated that it is impossible to develop a single algorithm for population evolution that is always efficient for a diverse set of optimization problems. Here we show that significant improvements in the efficiency of evolutionary search can be achieved by running multiple optimization algorithms simultaneously using new concepts of global information sharing and genetically adaptive offspring creation. We call this approach a multialgorithm, genetically adaptive multiobjective, or AMALGAM, method, to evoke the image of a procedure that merges the strengths of different optimization algorithms. Benchmark results using a set of well known multiobjective test problems show that AMALGAM approaches a factor of 10 improvement over current optimization algorithms for the more complex, higher dimensional problems. The AMALGAM method provides new opportunities for solving previously intractable optimization problems.
Endoplasmic Reticulum and Golgi Localization Sequences for Mammalian Target of Rapamycin
Authors: Liu Xiangyu , Zheng X. F. Steven
Published: January 2007

Mammalian target of rapamycin (mTOR) forms two complexes, mTORC1 and mTORC2, that play central roles in cell growth and functions. Only mTORC1 is directly inhibited by the immunosuppressive drug rapamycin. Despite recent progress in identifying new components and functions of the mTOR pathway, relatively little is known about the spatial arrangement of mTOR signaling and the underlying mechanisms. In a previous study, we showed that a large proportion of mTOR is localized to the endoplasmic reticulum (ER) and Golgi in many common cell lines. Here, we report the identification of an internal mTOR sequence that contains two HEAT (HT) repeats, HT18 and HT19, and two intervening interunit spacers (IUSs), IUS17 and IUS18, which is sufficient to target enhanced green fluorescent protein to the Golgi. Surprisingly, deletion of IUS17 from this Golgi localization sequence (GLS) converts it to an ER localization sequence (ELS). Deletion of HT19, a common element of both GLS and ELS from the full-length mTOR, causes delocalization of mTOR and inhibits the ability of mTOR to promote S6 phosphorylation. Moreover, overexpression of GLS and ELS inhibits both mTOR complexes. Together, our results reveal unusual ER- and Golgi-targeting sequences and suggest that anchoring to these organelles is important for the functions of mTOR complexes.
PP2B-mediated Dephosphorylation of c-Jun C Terminus Regulates Phorbol Ester-induced c-Jun/Sp1 Interaction in A431 Cells
Authors: Chen Ben-Kuen , Huang Chi-Chen , Chang Wei-Chiao , Chen Yun-Ju , Kikkawa Ushio , Nakahama Ken-ichi , Morita Ikuo , Chang Wen-Chang
Published: January 2007

The c-Jun/Sp1 interaction is essential for growth factor- and phorbol 12-myristate 13-acetate (PMA)-induced genes expression, including human 12(S)-lipoxygenase, keratin 16, cytosolic phospholipase A2, p21WAF1/CIP1, and neuronal nicotinic acetylcholine receptor β4. Here, we examined the mechanism underlying the PMA-induced regulation on the interaction between c-Jun and Sp1. We found that treatment of cells with PMA induced a dephosphorylation at the C terminus of c-Jun at Ser-243 and a concomitant inhibition of PP2B by using PP2B small interfering RNA, resulting in reduction of PMA-induced gene expression as well as the c-Jun/Sp1 interaction. The c-Jun mutant TAM-67-3A, which contains three substitute alanines at Thr-231, Ser-243, and Ser-249 compared with TAM-67, binds more efficaciously with Sp1 and is about twice as efficacious as TAM-67 in inhibiting the PMA-induced activation of the 12(S)-lipoxygenase promoter. Importantly, PP2B not only dephosphorylates the c-Jun at Ser-243 but also interacts with c-Jun in PMA-treated cells. PMA stimulates the association of the PP2B/c-Jun/Sp1 complex with the promoter. These findings indicate the dephosphorylation of c-Jun C terminus is required for the c-Jun/Sp1 interaction and reveal that PP2B plays an important role in regulating c-Jun/Sp1 interaction in PMA-induced gene expression.
VAMP8/Endobrevin as a General Vesicular SNARE for Regulated Exocytosis of the Exocrine System
Authors: Wang Cheng-Chun , Shi Hong , Guo Ke , Ng Chee Peng , Li Jie , Qi Gan Bin , Chien Liew Hwee , Leinonen Jukka , Rajaniemi Hannu , Hong Zhou Zhi , Zeng Qi , Hong Wanjin
Published: January 2007

The molecular mechanism governing the regulated secretion of most exocrine tissues remains elusive, although VAMP8/endobrevin has recently been shown to be the major vesicular SNARE (v-SNARE) of zymogen granules of pancreatic exocrine acinar cells. In this article, we have characterized the role of VAMP8 in the entire exocrine system. Immunohistochemical studies showed that VAMP8 is expressed in all examined exocrine tissues such as salivary glands, lacrimal (tear) glands, sweat glands, sebaceous glands, mammary glands, and the prostate. Severe anomalies were observed in the salivary and lacrimal glands of VAMP8-null mice. Mutant salivary glands accumulated amylase and carbonic anhydrase VI. Electron microscopy revealed an accumulation of secretory granules in the acinar cells of mutant parotid and lacrimal glands. Pilocarpine-stimulated secretion of saliva proteins was compromised in the absence of VAMP8. Protein aggregates were observed in mutant lacrimal glands. VAMP8 may interact with syntaxin 4 and SNAP-23. These results suggest that VAMP8 may act as a v-SNARE for regulated secretion of the entire exocrine system.
Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation
Authors: Luís C. , Juras R. , Oom M. M. , Cothran E. G.
Published: January 2007

There are three native Portuguese horse breeds: Lusitano, Sorraia and Garrano. This study compares diversity patterns of 17 protein and 12 microsatellite markers in these three as well as 30 other breeds to infer relationships among the breeds and to compare levels of polymorphism of these breeds for use in conservation efforts. The Garrano and the Lusitano showed a high level of genetic diversity, similar to that observed for most of the other analysed breeds, while the Sorraia and Friesian breeds showed low levels of variation for both genetic marker types. The combined protein and microsatellite data produced a tree that fit historical records well and with greater confidence levels than those for either data set alone. The combined genetic diversity and relationship information provides important baseline data for future breed conservation efforts, especially for a critically endangered breed such as the Sorraia.
A QTL for osteoporosis detected in an F2 population derived from White Leghorn chicken lines divergently selected for bone index
Authors: Dunn I. C. , Fleming R. H. , McCormack H. A. , Morrice D. , Burt D. W. , Preisinger R. , Whitehead C. C.
Published: January 2007

Osteoporosis, resulting from progressive loss of structural bone during the period of egg‐laying in hens, is associated with an increased susceptibility to bone breakage. To study the genetic basis of bone strength, an F2 cross was produced from lines of hens that had been divergently selected for bone index from a commercial pedigreed White Leghorn population. Quantitative trait loci (QTL) affecting the bone index and component traits of the index (tibiotarsal and humeral strength and keel radiographic density) were mapped using phenotypic data from 372 F2 individuals in 32 F1 families. Genotypes for 136 microsatellite markers in 27 linkage groups covering ∼80% of the genome were analysed for association with phenotypes using within‐family regression analyses. There was one significant QTL on chromosome 1 for bone index and the component traits of tibiotarsal and humeral breaking strength. Additive effects for tibiotarsal breaking strength represented 34% of the trait standard deviation and 7.6% of the phenotypic variance of the trait. These QTL for bone quality in poultry are directly relevant to commercial populations.
Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breeds
Authors: Brenneman R. A. , Chase C. C. , Olson T. A. , Riley D. G. , Coleman S. W.
Published: January 2007

The objective of this study was to quantify the genetic diversity among breeds under evaluation for tropical adaptability traits that affect the performance of beef cattle at the USDA/ARS SubTropical Agricultural Research Station (STARS) near Brooksville, FL, USA. Twenty‐six microsatellite loci were used to estimate parameters of genetic diversity among the breeds American Brahman, Angus, Senepol and Romosinuano; the latter was comprised of two distinct bloodlines (Costa Rican and Venezuelan). Genotypes of 47 animals from each of these STARS herds were analysed for genetic diversity and genetic distance. Using two methods, the greatest genetic distance was detected between the Costa Rican line of Romosinuano and the Senepol. Gene diversity ranged between 0.64 (Costa Rican line of Romosinuano) and 0.75 (American Brahman). The breed relationship inferences, which are based on genetic distance, provide additional tools for consideration in future crossbreeding studies and for testing the relationship between quantified breed diversity and observed heterosis.
Variation in ephippial buoyancy in Daphnia pulicaria
Authors: CÁCERES CARLA E. , CHRISTOFF ANNA N. , BOEING WIEBKE J.
Published: January 2007

1. Freshwater zooplankton often produce diapausing eggs to survive environmental stress. The diapausing eggs of Daphnia (Crustacea, Cladocera) are encased in an ephippium that either floats at the surface or sinks to the sediment. These two types of ephippia may represent different strategies between spatial (floaters) and temporal (sinkers) dispersal of offspring.

2. We observed floating and sinking characteristics of ephippia obtained from eight lakes. We then conducted an experiment with 26 Daphnia pulicaria clones obtained from six of these lakes and observed the production of buoyant and non‐buoyant ephippia under high and low food conditions.

3. Ephippia were more often non‐buoyant than buoyant both from females caught in nature and those reared in the laboratory. The experiment revealed that each clone was able to produce both types of ephippia, but that there was considerable among‐clone variation in the percentage of non‐buoyant ephippia produced.

4. We conclude that production of non‐buoyant versus buoyant ephippia may be driven by both genetic and environmental factors.
Maintenance of antigen‐specific immunological memory through variable regions of heavy and light chains of anti‐idiotypic antibody
Authors: Vani J. , Nayak R. , Shaila M. S.
Published: January 2007

Immunological memory is characterized by a quick and enhanced immune response after re‐exposure to the same antigen. To explain the mechanism involved in generation and maintenance of immunological memory, we had earlier proposed a hypothesis involving the relay of memory by idiotypic and anti‐idiotypic B cells. The peptidomimic present in the hypervariable region of anti‐idiotypic antibody was hypothesized to carry forward immunological memory. In the present work, we provide evidence supporting a role for the anti‐idiotypic antibody in eliciting antigen‐specific B‐cell and T‐cell responses. Employing the idiotypic monoclonal antibody (Ab1) specific for haemagglutinin (H) protein of rinderpest virus, Ab2β was generated, which possesses an internal image of the H protein in the region between amino acids 527 and 556. We demonstrate that antigen‐specific memory is perpetuated by immunization with Ab2, as shown by maintenance of antigen‐specific T‐cell responses upon restimulation in vitro of Ab2 immune splenocytes by antigen‐presenting cells expressing H protein or pulsed with H‐protein‐derived peptides. We have also shown that boosting with antigen‐specific anti‐idiotypic B cells generates a memory response in antigen‐primed mice. Evidence has been provided for the existence of an antigen‐specific B‐cell idiotypic network in the body that supports the perpetuation of immunological memory as proposed in the relay hypothesis.
Kinetic Models for Thermal Inactivation of Multiple Pectinesterases in Citrus Juices
Authors: CHEN C.S. , WU M.C.
Published: January 2007

First‐order kinetic model of a two‐component system was applied to investigate heat inactivation of multiple pectinesterases in citrus juices. The conventional log‐linear model was applied to determine D‐ and z‐values of thermolabile and thermostable pectinesterases in citrus juices, respectively, for use in the two‐component model. A parameter for concentration of enzyme populations in the juice was included in the model. The two‐component model predicted results were in better agreement with the observed heat pasteurization curves than those predicted by the log‐linear kinetic model. The two‐component model is especially useful for optimizing temperature‐time conditions for pasteurizing citrus juices.
Effective Partition Constant of Solute between Ice and Liquid Phases in Progressive Freeze‐Concentration
Authors: MIYAWAKI OSATO , LIU LING , NAKAMURA KOZO
Published: January 2007

Progressive freeze‐concentration was effectively applied to concentrate glucose in a model solution. Effective partition constants of the solute between the liquid and solid phases were determined experimentally. The constant was strongly dependent on the stirring rate at the ice front and the advance rate of the ice front. Increasing stirring rate and reduced rate of advance lowered the effective partition constant: an improvement in freeze concentration performance. A concentration polarization model was useful to describe the effects of the operating conditions on the effective partition constant.
Rapid CO2 Evolution Method for Determining Shelf Life of Refrigerated Catfish
Authors: CHEW S‐Y. , HSIEH Y‐H. P.
Published: January 2007

The feasibility of a CO2 evolution method using an IR analyzer to evaluate the shelf life of refrigerated (4deg;C) catfish was investigated. Aerobic plate count (APC), and isoelectric focusing (IEF) of samples were compared with the CO2 evolution rate (CER) determinations. The increase in CER (25.78 to 195.63 Lg−1h−1) for farm raised catfish stored from 0 to 10 days correlated highly with APCs (4.32 to 10.24 log CFU g−1). The IEF data also confirmed the APC and CER results. Catfish spoilage was evident after 6 days at 4°C. Direct measurement of CER is a rapid and effective method to determine the microbial quality of catfish.
Cooked Color in High pH Beef Patties as Related to Fat Content and Cooking from the Frozen or Thawed State
Authors: BERRY B. W.
Published: January 2007

Beef patties were processed from high pH (>6.0) beef to contain 5, 10, 15, 20 or 25% fat. Patties were cooked to 71°C from the frozen or thawed state before evaluating color. Neither fat content nor state of patties when cooked exerted any major influence on color, but linear effects (p<0.01) in association with increased fat content included higher L* values and hue angles and lower a* values (15.2% reduction). Higher values for L*, b* (but not for 5% fat patties), and hue angles were observed for patties cooked thawed rather than frozen. The use of high pH beef lessened the effects of increased fat and cooking from the thawed state on increased brown color in cooked patties.
Functional, Textural and Microstructural Properties of Low‐fat Bologna (Model System) with a Konjac Blend
Authors: CHIN K.B. , KEETON J.T. , LONGNECKER M.T. , LAMKEY J.W.
Published: January 2007

The form (dry vs prehydrated) and level (0, 0.5, 1.0 and 1.5%) of a konjac blend (KB) were evaluated to determine their effects on the characteristics of a low‐fat bologna model system (LFBMS). The system had a pH range of 6.01 to 6.12, moisture 74 to 76%, fat < 2.0% and protein 17 to 18%. Prehydrated KB had higher (p<0.05) texture profile analysis (TPA) hardness values than dry addition, whereas lower TPA values (p<0.05) were observed as the level of KB increased. In microstructural observation, the addition of prehydrated KB gels caused the protein matrix to appear more swollen in structure as compared to that after inclusion of a dry powder.
Low‐fat Bologna In A Model System With Varying Types And Levels Of Konjac Blends
Authors: CHIN K.B. , KEETON J.T. , LONGNECKER M.T. , LAMKEY J.W.
Published: January 2007

A low‐fat bologna model system (LFBMS) with a konjac blend (KB) level of 0.5% had higher moisture content and shear stress values (p<0.05) than a 1.0% KB. Increasing moisture:protein (M:P) ratios from 5.0 to 6.0 had the greatest effect on chemical and physical parameters. Three konjac types (KSS, KHC and KNC) had varying effects on these parameters. Allo‐Kramer shear, texture profile analysis (TPA) and torsion tests indicated that LFBMS with a 0.5% konjac level and a M:P ratio of 6.0 or a 1.0% konjac level and M:P ratios of 5.5 or 6.0 yielded similar products to the control (30% fat).
Porosity of Whey Protein‐Based Microcapsules Containing Anhydrous Milkfat Measured by Gas Displacement Pycnometry
Authors: MOREAU D.L. , ROSENBERG M.
Published: January 2007

Porosity characteristics of spray‐dried microcapsules consisting of whey proteins and anhydrous milkfat were investigated by gas displacement technique, using helium and nitrogen as displacing gases. Microcapsules exhibited molecular‐sieve type porosity. True and apparent densities as well as porosity characteristics were affected by wall solids concentration and by core load. Results indicated that about 10% of capsule volume was not accessible to helium. Pore volume inaccessible to nitrogen penetration was affected by core load and solid concentration. Results suggested that porosity, and hence gas‐permeation into microcapsules, could be tailored by adjusting microcapsules composition.
Whey Protein Edible Film Structures Determined by Atomic Force Microscope
Authors: LENT L. E. , VANASUPA L. S. , TONG P. S.
Published: January 2007

Atomic force microscopy was used to study edible films produced from whey proteins. The films were imaged under ambient conditions with no special sample preparation. Low resolution imaging of areas from 10 μm to 150 μm on a side was performed in the contact mode. Higher resolution scans of 350 nm to 2,700 nm required use of the noncontact imaging mode. Features about the same size as the primary protein in whey, beta‐lactoglobulin (7 nm), were identified in the film samples. Molecular aggregates in the range of 1 μm, reported in other studies using transmission electron microscopy of whey protein gels, were combined in results from atomic force microscopy.
Factors Affecting Pink Discoloration in Annatto‐colored Pasteurized Process Cheese
Authors: SHUMAKER E. K. , WENDORFF W. L.
Published: January 2007

The effects of cooking temperatures, cooling rates, pH, types of emulsifying salts, age of cheese, and sources of colorant were evaluated. Annatto emulsions showed less stability during continuous heating than annatto solutions or suspensions. Increased cooking temperatures resulted in slight decreases in Hunter a and b values, and overall decreases in hue angles. Emulsifying salt blends with increased amounts of sodium citrate resulted in decreased hue angles. Process cheeses made with more than 25% colored cheese showed lower hue angles than those samples made with uncolored cheese only. Whey powder as a source of added solids in process cheese food promoted discoloration, with acid whey resulting in the most pinking.
Extrusion of Apple Pomace Facilitates Pectin Extraction
Authors: HWANG JAE‐KWAN , KIM CHUL‐JIN , KIM CHONG‐TAI
Published: January 2007

Twin‐screw extruder was employed to disintegrate apple pomace (AP) to facilitate production of apple pectins by hot water extraction. AP was extruded under different conditions of screw speed, 250‐350 rpm; feed rate, 30‐40 kg/h; moisture, 20‐30%. The yield of water soluble polysaccharides (WSP) increased with increasing specific mechanical energy (SME), but intrinsic viscosity decreased with increasing SME. Considering both the WSP yield (g/dL) and intrinsic viscosity (dL/g), a dimensionless term, product yield ∞ intrinsic viscosity (Y[]), was an objective function for optimizing conditions for the solubilization of AP polysaccharides. Y[] of pectins in extruded WSP ranged 0.59‐1.34, while acid extracted WSP had Y[] of 1.12. Extruded WSP with Y[] comparable to acid extraction was obtained in the SME ranges of 110‐170 kWh/h.
Microfiltration and Ultrafiltration Ceramic Membranes for Apple Juice Clarification
Authors: FUKUMOTO L.R. , DELAQUIS P. , GIRARD B.
Published: January 2007

Depectinized control (CTJ) and ascorbic acid treated (AAJ) apple juices were filtered through microfiltration (MF, 0.2 m) and ultrafiltration (UF, 0.02 m) ceramic tubular membranes. Under optimal conditions (8 m/s, 414 kPa and 50°C), the UF membrane resulted in higher steady state flux and less fouling than the MF membrane for both juices. AAJ produced by addition of AA at milling had lower flux for both MF and UF. The chemical, physical and sensory properties of apple juices from MF and UF membranes were similar and changes during storage were comparable.
Quality and Shelf‐life of Fresh Cut Carrot Slices as Affected by Slicing Method
Authors: BARRY‐RYAN CATHERINE , O'BEIRNE DAVID
Published: January 2007

The effects of slicing method on the quality and storage‐life of modified atmosphere packaged carrot slices were determined using microscopy, sensory evaluation, microbial counts and a range of physical and chemical tests. Slicing caused physical damage, physiological stress and enhanced microbial growth. The severity of these effects were in the order of blunt machine blade > sharp machine blade > razor blade. These findings provide insights into the magnitude and basis of slicing effects and also confirm the importance of gentle processing and the use of a sharp blade.