bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Growth Enhances the Mean Fixation Time of Neutral Mutations and the Persistence of Neutral Variation
Authors: Waxman D 
Published: March 2012

AbstractA fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of ∼4Ne generations, where Ne is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4Ne,0 generations, where Ne,0 is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.
Allopolyploidization Lays the Foundation for Evolution of Distinct Populations: Evidence From Analysis of SyntheticArabidopsisAllohexaploids
Authors: Matsushita Starr C , Tyagi Anand P , Thornton Gerad M , Pires J Chris , Madlung Andreas 
Published: March 2012

AbstractPolyploidization is an important mechanism for introducing diversity into a population and promoting evolutionary change. It is believed that most, if not all, angiosperms have undergone whole genome duplication events in their evolutionary history, which has led to changes in genome structure, gene regulation, and chromosome maintenance. Previous studies have shown that polyploidy can coincide with meiotic abnormalities and somatic cytogenetic mosaics in Arabidopsis allotetraploids, but it is unclear whether this phenomenon can contribute to novel diversity or act as a mechanism for speciation. In this study we tested the hypothesis that mosaic aneuploidy contributes to the formation of incipient diversity in neoallopolyploids. We generated a population of synthesized Arabidopsis allohexaploids and monitored karyotypic and phenotypic variation in this population over the first seven generations. We found evidence of sibling line-specific chromosome number variations and rapidly diverging phenotypes between lines, including flowering time, leaf shape, and pollen viability. Karyotypes varied between sibling lines and between cells within the same tissues. Cytotypic variation correlates with phenotypic novelty, and, unlike in allotetraploids, remains a major genomic destabilizing factor for at least the first seven generations. While it is still unclear whether new stable aneuploid lines will arise from these populations, our data are consistent with the notion that somatic aneuploidy, especially in higher level allopolyploids, can act as an evolutionary relevant mechanism to induce rapid variation not only during the initial allopolyploidization process but also for several subsequent generations. This process may lay the genetic foundation for multiple, rather than just a single, new species.
A Non-Mendelian MAPK-Generated Hereditary Unit Controlled by a Second MAPK Pathway inPodospora anserina
Authors: Lalucque Hervé , Malagnac Fabienne , Brun Sylvain , Kicka Sébastien , Silar Philippe 
Published: March 2012

AbstractThe Podospora anserina PaMpk1 MAP kinase (MAPK) signaling pathway can generate a cytoplasmic and infectious element resembling prions. When present in the cells, this C element causes the crippled growth (CG) cell degeneration. CG results from the inappropriate autocatalytic activation of the PaMpk1 MAPK pathway during growth, whereas this cascade normally signals stationary phase. Little is known about the control of such prion-like hereditary units involved in regulatory inheritance. Here, we show that another MAPK pathway, PaMpk2, is crucial at every stage of the fungus life cycle, in particular those controlled by PaMpk1 during stationary phase, which includes the generation of C. Inactivation of the third P. anserina MAPK pathway, PaMpk3, has no effect on the development of the fungus. Mutants of MAPK, MAPK kinase, and MAPK kinase kinase of the PaMpk2 pathway are unable to present CG. This inability likely relies upon an incorrect activation of PaMpk1, although this MAPK is normally phosphorylated in the mutants. In PaMpk2 null mutants, hyphae are abnormal and PaMpk1 is mislocalized. Correspondingly, stationary phase differentiations controlled by PaMpk1 are defective in the mutants of the PaMpk2 cascade. Constitutive activation of the PaMpk2 pathway mimics in many ways its inactivation, including an effect on PaMpk1 localization. Analysis of double and triple mutants inactivated for two or all three MAPK genes undercover new growth and differentiation phenotypes, suggesting overlapping roles. Our data underscore the complex regulation of a prion-like element in a model organism.
V-ATPase V1 Sector Is Required for Corpse Clearance and Neurotransmission in Caenorhabditis elegans
Authors: Ernstrom Glen G , Weimer Robby , Pawar Divya R L , Watanabe Shigeki , Hobson Robert J , Greenstein David , Jorgensen Erik M 
Published: March 2012

Abstract
The vacuolar-type ATPase (V-ATPase) is a proton pump composed of two sectors, the cytoplasmic V1 sector that catalyzes ATP hydrolysis and the transmembrane Vo sector responsible for proton translocation. The transmembrane Vo complex directs the complex to different membranes, but also has been proposed to have roles independent of the V1 sector. However, the roles of the V1 sector have not been well characterized. In the nematode Caenorhabditis elegans there are two V1 B-subunit genes; one of them, vha-12, is on the X chromosome, whereas spe-5 is on an autosome. vha-12 is broadly expressed in adults, and homozygotes for a weak allele in vha-12 are viable but are uncoordinated due to decreased neurotransmission. Analysis of a null mutation demonstrates that vha-12 is not required for oogenesis or spermatogenesis in the adult germ line, but it is required maternally for early embryonic development. Zygotic expression begins during embryonic morphogenesis, and homozygous null mutants arrest at the twofold stage. These mutant embryos exhibit a defect in the clearance of apoptotic cell corpses in vha-12 null mutants. These observations indicate that the V1 sector, in addition to the Vo sector, is required in exocytic and endocytic pathways.
Emotions as a dynamical system: the interplay between the meta-control and communication function of emotions
Authors: Hasson C. , Gaussier P. , Boucenna S. 
Published: March 2012

AbstractClassical models of emotions consider either the communicational aspect of emotions (for instance the emotions conveyed by the facial expressions) or the second order control necessary for survival purpose when the autonomy of the system is an issue. Here, we show the interdependence of communication and meta-control aspects of emotion. We propose the idea that emotions must be understood as a dynamical system linking two controllers: one devoted to social interactions (i.e. communication aspects) and another one devoted to the interactions within the physical world (i.e metacontrol of a more classical controller). Illustrations will be provided from applications involving navigation among different goal places according to different internal drives or object grasping and avoidance.
MARCKS as a Negative Regulator of Lipopolysaccharide Signaling
Authors: Manček-Keber Mateja , Benčina Mojca , Japelj Boštjan , Panter Gabriela , Andrä Jörg , Brandenburg Klaus , Triantafilou Martha , Triantafilou Kathy , Jerala Roman 
Published: March 2012

Abstract
Myristoylated alanine-rich C kinase substrate (MARCKS) is an intrinsically unfolded protein with a conserved cationic effector domain, which mediates the cross-talk between several signal transduction pathways. Transcription of MARCKS is increased by stimulation with bacterial LPS. We determined that MARCKS and MARCKS-related protein specifically bind to LPS and that the addition of the MARCKS effector peptide inhibited LPS-induced production of TNF-α in mononuclear cells. The LPS binding site within the effector domain of MARCKS was narrowed down to a heptapeptide that binds to LPS in an extended conformation as determined by nuclear magnetic resonance spectroscopy. After LPS stimulation, MARCKS moved from the plasma membrane to FYVE-positive endosomes, where it colocalized with LPS. MARCKS-deficient mouse embryonic fibroblasts (MEFs) responded to LPS with increased IL-6 production compared with the matched wild-type MEFs. Similarly, small interfering RNA knockdown of MARCKS also increased LPS signaling, whereas overexpression of MARCKS inhibited LPS signaling. TLR4 signaling was enhanced by the ablation of MARCKS, which had no effect on stimulation by TLR2, TLR3, and TLR5 agonists. These findings demonstrate that MARCKS contributes to the negative regulation of the cellular response to LPS.
Selective Expansion of Allogeneic Regulatory T Cells by Hepatic Stellate Cells: Role of Endotoxin and Implications for Allograft Tolerance
Authors: Dangi Anil , Sumpter Tina L. , Kimura Shoko , Stolz Donna B. , Murase Noriko , Raimondi Giorgio , Vodovotz Yoram , Huang Chao , Thomson Angus W. , Gandhi Chandrashekhar R. 
Published: March 2012

Abstract
Hepatic stellate cells (HSCs) may play an important role in hepatic immune regulation by producing numerous cytokines/chemokines and expressing Ag-presenting and T cell coregulatory molecules. Due to disruption of the endothelial barrier during cold-ischemic storage and reperfusion of liver grafts, HSCs can interact directly with cells of the immune system. Endotoxin (LPS), levels of which increase in liver diseases and transplantation, stimulates the synthesis of many mediators by HSCs. We hypothesized that LPS-stimulated HSCs might promote hepatic tolerogenicity by influencing naturally occurring immunosuppressive CD4+CD25+Foxp3+ regulatory T cells (Tregs). Following their portal venous infusion, allogeneic CD4+ T cells, including Tregs, were found closely associated with HSCs, and this association increased in LPS-treated livers. In vitro, both unstimulated and LPS-stimulated HSCs upregulated Fas (CD95) expression on conventional CD4+ T cells and induced their apoptosis in a Fas/Fas ligand-dependent manner. By contrast, HSCs induced Treg proliferation, which required cell–cell contact and was MHC class II-dependent. This effect was augmented when HSCs were pretreated with LPS. LPS increased the expression of MHC class II, CD80, and CD86 and stimulated the production of IL-1α, IL-1β, IL-6, IL-10 and TNF-α by HSCs. Interestingly, production of IL-1α, IL-1β, IL-6, and TNF-α was strongly inhibited, but that of IL-10 enhanced in LPS-pretreated HSC/Treg cocultures. Adoptively transferred allogeneic HSCs migrated to the secondary lymphoid tissues and induced Treg expansion in lymph nodes. These data implicate endotoxin-stimulated HSCs as important immune regulators in liver transplantation by inducing selective expansion of tolerance-promoting Tregs and reducing inflammation and alloimmunity.
Heat Shock Protein 90-Mediated Peptide-Selective Presentation of Cytosolic Tumor Antigen for Direct Recognition of Tumors by CD4+ T Cells
Authors: Tsuji Takemasa , Matsuzaki Junko , Caballero Otavia L. , Jungbluth Achim A. , Ritter Gerd , Odunsi Kunle , Old Lloyd J. , Gnjatic Sacha 
Published: March 2012

AbstractTumor Ag-specific CD4+ T cells play important functions in tumor immunosurveillance, and in certain cases they can directly recognize HLA class II-expressing tumor cells. However, the underlying mechanism of intracellular Ag presentation to CD4+ T cells by tumor cells has not yet been well characterized. We analyzed two naturally occurring human CD4+ T cell lines specific for different peptides from cytosolic tumor Ag NY-ESO-1. Whereas both lines had the same HLA restriction and a similar ability to recognize exogenous NY-ESO-1 protein, only one CD4+ T cell line recognized NY-ESO-1+ HLA class II-expressing melanoma cells. Modulation of Ag processing in melanoma cells using specific molecular inhibitors and small interfering RNA revealed a previously undescribed peptide-selective Ag-presentation pathway by HLA class II+ melanoma cells. The presentation required both proteasome and endosomal protease-dependent processing mechanisms, as well as cytosolic heat shock protein 90-mediated chaperoning. Such tumor-specific pathway of endogenous HLA class II Ag presentation is expected to play an important role in immunosurveillance or immunosuppression mediated by various subsets of CD4+ T cells at the tumor local site. Furthermore, targeted activation of tumor-recognizing CD4+ T cells by vaccination or adoptive transfer could be a suitable strategy for enhancing the efficacy of tumor immunotherapy.
Recovery of duckweed from time-varying exposure to atrazine
Authors: Brain Richard A. , Hosmer Alan J. , Desjardins Debbie , Kendall Timothy Z. , Krueger Henry O. , Wall Steven B. 
Published: March 2012

Abstract
The purpose of the present study was to evaluate the recovery of duckweed (Lemna gibba L. G3) after being removed from multiple duration exposures to the herbicide atrazine. Consequently, L. gibba were exposed under various scenarios to atrazine at nominal concentrations ranging from 5 to 160 µg/L and durations of 1, 3, 5, 7, 9, and 14 d under static-renewal test conditions. Exposures were followed by a recovery phase in untreated media for either 7 or 14 d. The 3-, 5-, 7-, 9-, and 14-d median effective concentration (EC50) values were &gt;137, &gt;137, 124, &gt;77, and &gt;75 µg/L, respectively, based on mean growth rate. No clear effect trends were apparent between exposure duration and the magnitude of effective concentrations (EC50s or EC10s). No phytocidal effects of chlorosis or necrosis were identified for any treatment scenario. Nearly all L. gibba plants transferred from treatment groups of different exposure scenarios to media without atrazine during the recovery phase had growth rates that demonstrated immediate recovery, indicating effects were phytostatic in nature and reversible. Only the 1- and 5-d exposure scenarios had growth rates indicating marginally prolonged recovery at the higher concentrations (160 µg/L; additionally, at 40 µg/L for the 5-d exposure). Time to recovery, therefore, was found to be largely independent of exposure duration except at the highest concentrations assessed. Based on growth rate by interval, all treatments demonstrated recovery by the final assessment interval (days 5–7), indicating complete recovery in all exposure scenarios by 7 d, consistent with the mode of action of atrazine. Environ. Toxicol. Chem. 2012; 31: 1121–1128. © 2012 SETAC
Persistent organic pollutants in coastal sediment off South China in relation to the importance of anthropogenic inputs
Authors: Liu Liang-Ying , Wang Ji-Zhong , Qiu Jian-Wen , Liang Yan , Zeng Eddy Y. 
Published: March 2012

Abstract
Surface sediments collected from the coastal region off South China were analyzed for persistent organic pollutants (POPs), including polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), and organochlorine pesticides (OCPs). The concentrations of BDE-209, Σ12PBDE, Σ15PAH, Σ7PAH, and Σ11OCP were 0.22 to 26.3, 0.01 to 0.77, 13.9 to 271, 6 to 133, and 0.9 to 104 ng/g, respectively. The spatial distribution patterns of PBDEs and PAHs suggested that the eastern coastal region was slightly more contaminated than the western coast. In addition, the concentrations of dichlorodiphenyltrichloroethane (DDT) and its metabolites (DDXs) were highly variable, with the highest level found at a site in Zhanjiang Bay, which might have been reflective of the impact of antifouling paints mainly used in boat maintenance in harbor areas. The predominance of BDE-209 in the study region was consistent with the usage pattern of penta-, octa-, and deca-BDEs in China, whereas sediment PAHs appeared to have been derived largely from coal or wood and petroleum combustion. Preliminary assessments indicated that terrestrial inputs, such as atmospheric transport and riverine runoff, may have been the major input pathways for PBDEs and PAHs, respectively, to accumulate in coastal sediment off South China. Conversely, residues of DDT-containing antifouling paints associated with shipping activities and boat maintenance accounted for most of the accumulated sediment DDTs. Environ. Toxicol. Chem. 2012;31:1194–1201. © 2012 SETAC
Analysis of dammar resin with MALDI‐FT‐ICR‐MS and APCI‐FT‐ICR‐MS
Authors: Vahur Signe , Teearu Anu , Haljasorg Tõiv , Burk Piia , Leito Ivo , Kaljurand Ivari 
Published: March 2012

Comprehensive analysis of high‐resolution mass spectra of aged natural dammar resin obtained with Fourier transform ion cyclotron resonance mass spectrometer (FT‐ICR‐MS) using matrix‐assisted laser desorption/ionization (MALDI) and atmospheric pressure chemical ionization (APCI) is presented. Dammar resin is one of the most important components of painting varnishes. Dammar resin is a terpenoid resin (dominated by triterpenoids) with intrinsically very complex composition. This complexity further increases with aging.Ten different solvents and two‐component solvent mixtures were tested for sample preparation. The most suitable solvent mixtures for the MALDI‐FT‐ICR‐MS analysis were dichloromethane‐acetone and dichloromethane‐ethanol. The obtained MALDI‐FTMS mass spectrum contains nine clusters of peaks in the m/z range of 420–2200, and the obtained APCI‐FTMS mass spectrum contains three clusters of peaks in the m/z range of 380–910. The peaks in the clusters correspond to the oxygenated derivatives of terpenoids differing by the number of C15H24units. The clusters, in turn, are composed of subclusters differing by the number of oxygen atoms in the molecules.Thorough analysis and identification of the components (or groups of components) by their accurate m/z ratios was carried out, and molecular formulas (elemental compositions) of all major peaks in the MALDI‐FTMS and APCI‐FTMS spectra were identified (and groups of possible isomeric compounds were proposed). In the MALDI‐FTMS and APCI‐FTMS mass spectrum, besides the oxidized C30, triterpenoids also peaks corresponding to C29and C31derivatives of triterpenoids (demethylated and methylated, correspondingly) were detected.MALDI and APCI are complementary ionization sources for the analysis of natural dammar resin. In the MALDI source, preferably polar (extensively oxidized) components of the resin are ionized (mostly as Na+adducts), whereas in the APCI source, preferably nonpolar (hydrocarbon and slightly oxidized) compounds are ionized (by protonation). Either of the two ionization methods, when used alone, gives an incomplete picture of the dammar resin composition. Copyright © 2012 John Wiley & Sons, Ltd.
A symmetric method for weakly imposing Dirichlet boundary conditions in embedded finite element meshes
Authors: Baiges Joan , Codina Ramon , Henke Florian , Shahmiri Shadan , Wall Wolfgang A. 
Published: March 2012

SUMMARYIn this paper, we propose a way to weakly prescribe Dirichlet boundary conditions in embedded finite element meshes. The key feature of the method is that the algorithmic parameter of the formulation which allows to ensure stability is independent of the numerical approximation, relatively small, and can be fixeda priori. Moreover, the formulation is symmetric for symmetric problems. An additional element‐discontinuous stress field is used to enforce the boundary conditions in the Poisson problem. Additional terms are required in order to guarantee stability in the convection–diffusion equation and the Stokes problem. The proposed method is then easily extended to the transient Navier–Stokes equations. Copyright © 2012 John Wiley & Sons, Ltd.
RELATIONSHIPS BETWEEN RIVER DISCHARGE AND ABUNDANCE OF AGE 0 REDHORSES (MOXOSTOMA SPP.) IN THE OCONEE RIVER, GEORGIA, USA, WITH IMPLICATIONS FOR ROBUST REDHORSE
Authors: Peterson Rebecca Cull , Jennings Cecil A. , Peterson James T. 
Published: March 2012

ABSTRACTRobust redhorse (Moxostoma robustum) and notchlip redhorse (M. collapsum) are two species of redhorses that reside in the lower Oconee River, Georgia. Robust redhorse is listed as a state endangered species in Georgia and North Carolina, and attempts to investigate factors affecting its reproductive success have met with limited success. Therefore, catch of robust redhorse young were combined with catch of notchlip redhorse to increase sample size. These congeners with similar spawning repertoire were assumed to respond similarly to environmental conditions. River discharge during spawning and rearing seasons may affect abundance of both redhorses in the lower Oconee River. An information‐theoretic approach was used to evaluate the relative support of models relating abundance of age 0 redhorses to monthly discharge statistics that represented magnitude, timing, duration, variability and frequency of river discharge events for April through June 1995–2006. The best‐approximating model indicated a negative relationship between the abundance of redhorses and mean maximum river discharge and the number of high pulses during June as well as a positive relationship with intermediate duration of low flows during April–June. This model is 9.6 times more plausible than the next best‐fitting model, which revealed a negative relationship between the abundance of redhorses and mean maximum river discharge during May and the number of high pulses during June as well as a positive relationship between abundance and intermediate duration of low flows during April–June. Management implications from the results indicate low‐stable flows for at least a 2‐week period during spawning and rearing may increase reproductive success of robust and notchlip redhorses. Copyright © 2012 John Wiley & Sons, Ltd.