bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris
Authors: He Qiang , He Zhili , Joyner Dominique C , Joachimiak Marcin , Price Morgan N , Yang Zamin K , Yen Huei-Che Bill , Hemme Christopher L , Chen Wenqiong , Fields Matthew M , Stahl David A , Keasling Jay D , Keller Martin , Arkin Adam P , Hazen Terry C , Wall Judy D , Zhou Jizhong
Published: May 2010

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mm NaNO3 but not by 70 mm NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.
High Rates of Obesity and Chronic Disease Among United Methodist Clergy
Authors: Proeschold‐Bell Rae Jean , LeGrand Sara H.
Published: May 2010

We used self‐reported data from United Methodist clergy to assess the prevalence of obesity and having ever been told certain chronic disease diagnoses. Of all actively serving United Methodist clergy in North Carolina (NC) 95% (n = 1726) completed self‐report height and weight items and diagnosis questions from the Behavioral Risk Factor Surveillance Survey (BRFSS). We calculated BMI categories and diagnosis prevalence rates for the clergy and compared them to the NC population using BRFSS data. The obesity rate among clergy aged 35–64 years was 39.7%, 10.3% (95% CI = 8.5%, 12.1%) higher than their NC counterparts. Clergy also reported significantly higher rates of having ever been given diagnoses of diabetes, arthritis, high blood pressure, angina, and asthma compared to their NC peers. Health interventions that address obesity and chronic disease among clergy are urgently needed.
Respiratory Quotient Predicts Fat Mass Gain in Premenopausal Women
Authors: Ellis Amy C. , Hyatt Tanya C. , Hunter Gary R. , Gower Barbara A.
Published: May 2010

High respiratory quotient (RQ) has been associated with fat mass (FM) gain in some, but not all studies. Variability among results may reflect differences in the RQ variable measured (fasting vs. 24‐h) or may be due to differences in control for factors that affect RQ, such as diet, energy balance, circulating insulin, and insulin sensitivity. The objective of this study was to determine whether different RQ values (fasting, sleeping, nonsleeping, and 24‐h) would predict change in FM over 2 years in obesity‐prone women, controlling for diet and adjusting for energy balance, circulating insulin, and insulin sensitivity. Participants were 33 previously overweight premenopausal women. Fasting, sleeping, nonsleeping, and 24‐h RQ values were measured during controlled‐diet conditions by respiratory chamber calorimetry. Intravenous glucose tolerance tests were also performed to adjust for fasting insulin, acute insulin response to glucose, and insulin sensitivity. Over the following 2 years, changes in FM were tracked annually by dual energy X‐ray absorptiometry. High nonsleeping RQ (NSRQ) predicted 2‐year change in FM independently of energy balance, circulating insulin, and insulin sensitivity. This observation suggests that low postprandial fat oxidation may uniquely predispose obesity‐prone individuals to accrual of adipose tissue.
Quantitative Magnetic Resonance Fat Measurements in Humans Correlate With Established Methods but Are Biased
Authors: Gallagher Dympna , Thornton John C. , He Qing , Wang Jack , Yu Wen , Bradstreet Thomas E. , Burke Joanne , Heymsfield Steven B. , Rivas Veronica M. , Kaufman Rhonda
Published: May 2010

Precision and accuracy of the quantitative magnetic resonance (QMR) system for measuring fat in phantoms and total body fat (TBF) in humans were investigated. Measurements were made using phantoms: oil, beef with water, beef with oil, and humans with oil and water. TBFQMR in humans was compared with TBF by a four‐compartment model (TBF4C). The coefficient of variation (CV) for replicate TBFQMR was 0.437%. QMR fat was lower at 23 °C vs. 37 °C. The fat increase in QMR phantom studies was consistent with the oil increase. When oil was added with humans, the increase in TBFQMR was >250 g for the initial 250 g of oil. With additional oil increments, the increase in TBFQMR was consistent with the amount of oil added. When water was added with humans, the TBFQMR increased independent of the amount of water added. TBFQMR was significantly less (mean ± s.e.) than TBF4C (females: −0.68 ± 0.27 kg, males: −4.66 ± 0.62 kg; P = 0.0001), TBFBV (females: −1.90 ± 0.40 kg; males: −5.68 ± 0.75 kg; P = 0.0001), and TBFD2O for males, but greater for females (1.19 ± 0.43 kg vs. −3.69 ± 0.81 kg for males; P = 0.0003). TBFQMR was lower than TBFiDXA with the difference greater in males (P = 0.001) and decreased with age (P = 0.011). The strong linear relationships between TBFQMR and TBF4C, TBFBV, and TBFD2O with slopes consistent with unity suggest that modifications are required to improve the accuracy. Should the latter be accomplished, QMR holds promise as a highly precise, rapid, and safe, noninvasive method for estimating the amount of and changes in TBF in overweight and severely obese persons.
Effects of Estrogen and Testosterone on Resting Energy Expenditure in Older Men
Authors: Santosa Sylvia , Khosla Sundeep , McCready Louise K. , Jensen Michael D.
Published: May 2010

The mechanisms by which sex hormones cause changes in body composition are unclear. Sex steroid deficiency might directly reduce energy expenditure/fat oxidation and thereby predispose to increased body fat. Alternatively, sex steroid deficiency could result in lean tissue loss and thus reduced energy expenditure. Our objective was to examine the independent and combined effects of acute testosterone and estrogen withdrawal on respiratory exchange ratio (RER) and resting energy expenditure (REE) in men. The objective of the study was to examine the independent and combined effects of acute estrogen and testosterone withdrawal on RER and REE in men. A total of 54 men aged 50–80 years, BMI range of 17–35 kg/m2 underwent a 3‐week eugonadal run‐in hormone‐treatment period involving suppression of endogenous sex steroids using letrozole and leuprolide acetate (Lupron) while sex steroid concentrations were maintained with transdermal testosterone (T) and estradiol (E). A second Lupron injection was then given and participants were randomized to one of the following four 3‐week treatment groups: group A (−T, −E), group B (−T, +E), group C (+T, −E), and group D (+T, +E). REE and RER were measured via indirect calorimetry before and after the 3‐week treatment period. Three‐week suppression and/or repletion of estrogen or testosterone did not produce changes in RER or REE within or between groups. We conclude that abrupt changes in sex steroids does not change resting substrate oxidation, indicating that changes that can be observed after more prolonged periods of deficiency are most likely due to direct effects of sex steroids on body composition.
Matrix semidiscrete Ablowitz–Ladik equation hierarchy and a matrix discrete second Painlevé equation
Authors: Gordoa Pilar R. , Pickering Andrew , Zhu Zuo-Nong
Published: May 2010

In this article, we first show that the semidiscrete Ablowitz–Ladik equation hierarchy can be extended to the matrix case by considering a matrix semidiscrete Ablowitz–Ladik isospectral linear problem. We then extend this linear problem to the nonisospectral case, and a new coupled matrix semidiscrete integrable equation is constructed. It is shown that the continuum limit of this new matrix semidiscrete integrable equation is the coupled matrix variable-coefficient modified Korteweg-de Vries equation and that a matrix discrete second Painlevé equation can be obtained as a stationary reduction in this new matrix semidiscrete equation.
Optical properties of integrated multiferroic BiFeO3 thin films for microwave applications
Authors: Allibe J. , Bougot-Robin K. , Jacquet E. , Infante I. C. , Fusil S. , Carrétéro C. , Reverchon J.-L. , Marcilhac B. , Creté D. , Mage J.-C. , Barthélémy A. , Bibes M.
Published: May 2010

BiFeO 3 is the prototypical multiferroic and one of the few with both (anti)ferroic ordering temperatures above 300 K. While its magnetic and ferroelectric properties and their coupling have been investigated intensely, offering opportunities in spintronics, little is known concerning its optical properties and their coupling to the ferroic orders. For applications in the microwave range, we report on the integration of BiFeO3 onto low permittivity substrates. Such integrated films show good ferroelectric and optical properties consistent with those of films grown on SrTiO3 substrates. Prospects for the use of BiFeO3 in optical applications are discussed.
Magnetic shielding constants calculated by the infinite-order Douglas–Kroll–Hess method with electron-electron relativistic corrections
Authors: Seino Junji , Hada Masahiko
Published: May 2010

We presented a two-component relativistic quantum-chemical theory for magnetic shielding constants, which is based on the infinite-order Douglas–Kroll (IODK) transformation. Two-electron relativistic corrections were also generated using the IODK transformation, although negligibly small terms were discarded. The use of small-component basis functions was completely excluded from the present theory. We examined the combination of the levels of relativistic one- and two-electron terms and magnetic interaction terms using the first-order Foldy–Wouthuysen (FW1), the second-order Douglas–Kroll (DK2), and the infinite-order Douglas–Kroll (IODK) transformations, as well as the lowest-order (c−2) Breit–Pauli approximation. We calculated the magnetic shielding constants of several closed-shell atoms using the FW1, DK2, IODK, and Breit–Pauli Hamiltonians. The IODK Hamiltonian reproduced well the results calculated by the four-component Dirac–Fock–Coulomb theory: The maximum deviation is only about 2.2%. We found that the accuracy of the magnetic shielding constants is strongly affected by the relativistic treatments of one-electron magnetic interaction, while the effect of the two-component two-electron relativistic corrections is relatively small. We also discussed the picture change effect on magnetic operators.
Terahertz electroluminescence of surface plasmons from nanostructured InN layers
Authors: Shubina T. V. , Andrianov A. V. , Zakhar’in A. O. , Jmerik V. N. , Soshnikov I. P. , Komissarova T. A. , Usikova A. A. , Kop’ev P. S. , Ivanov S. V. , Shalygin V. A. , Sofronov A. N. , Firsov D. A. , Vorob’ev L. E. , Gippius N. A. , Leymarie J. , Wang X. , Yoshikawa Akihiko
Published: May 2010

The terahertz (THz) emission with the maximum at the 3–5 THz is observed under electrical pumping from InN epilayers, where structural imperfections such as nanocolumns, pores, and In clusters are situated with a certain periodicity. This radiation is ascribed to the spontaneous emission of surface plasmon polariton like waves guided in thin surface/interior layers and coupled to electromagnetic field at these imperfections. These waves are generated thermally under applied electric field. The registered THz spectra and power dependences are well consistent with this plasmon-related radiation mechanism.
Mapping and comparing the distribution of soil carbon under cropping and grazing management practices in Narrabri, north-west New South Wales
Authors: Miklos Matthew , Short Michael G. , McBratney Alex B. , Minasny Budiman
Published: May 2010

The reliable assessment of soil carbon stock is of key importance for soil conservation and mitigation strategies related to reducing atmospheric carbon. Measuring and monitoring soil carbon is complex because carbon pools cycle and rates of carbon sequestration vary across the landscape due to climate, soil type, and management practices. A new methodology has been developed and applied to make an assessment of the distribution of total, organic, and inorganic carbon at a grains research and grazing property in northern New South Wales at a high spatial resolution. In this study, baseline soil carbon maps were created using fine resolution, geo-referenced, proximal sensor data. Coupled with a digital elevation model and secondary terrain attributes, all of the data layers were combined by k-means clustering to develop a stratified random soil sampling scheme for the survey area. Soil samples taken at 0.15-m increments to a depth of 1 m were scanned with a mid-infrared spectrometer, which was calibrated using a proportion of the samples that were analysed in a laboratory for total carbon and inorganic carbon content. This combination of new methodologies and technologies has the potential to provide large volumes of reliable, fine resolution and timely data required to make baseline assessments, mapping, monitoring, and verification possible. This method has the potential to make soil carbon management and trading at the farm-scale possible by quantifying the carbon stock to a depth of 1 m and at a high spatial resolution.
Modelling chemical and biological reactions during unsaturated flow through sandy soils
Authors: Ludwig B. , Herrmann S. , Michel K.
Published: May 2010

Predicting chemical and biological reactions during unsaturated flow through soils is complex, and the accuracy of model predictions is open to question. Objectives were to test how accurately the transport of nutrients (Ca2+, Mg2+, K+, NH4+, and NO3–) in soils can be predicted when differing amounts of nutrients or acid are added. Undisturbed columns of 2 sandy surface soils from arable sites in Darmstadt, Germany, and Sohar, Oman, were irrigated for 360 and 376 days with 3 mm/day at 10°C. Three treatments were carried out: the columns were irrigated with differing fertilising solutions (Fert-1 or Fert-2 treatments) or with HCl. The model PHREEQC2 was used to calculate 1-dimensional transport, inorganic complexation, dissolution or precipitation of CaCO3, multiple cation exchange, and nitrification. We compared 3 model variants: one with no adjustable parameters, a second with optimised nitrification rates and pCO2, and a third with an additional optimisation of the exchange coefficients. In model variant v2 and v3, the Fert-1 treatment was used for calibration. Model variant v1 was of little use in predicting cation transport in soils. The second was more appropriate for both soils, but an optimisation of the exchange coefficients (model variant v3) was required for a more accurate description (Fert-1) and prediction (Fert-2 and HCl) of ion transport. The included proton buffering reactions resulted in a moderately accurate prediction of pH and release of ions. Nitrification in the Fert-1 and Fert-2 experiments considered in the model variants accounted for a range of 0.03–0.04 µmol N/(day.g soil). Overall, our results indicate that calibration experiments are required for a reliable assessment of ion transport in soils during unsaturated flow. The parameter optimisation program PEST in combination with PHREEQC2 best simulated cation and anion transport in sandy soils under unsaturated conditions.
Importance of carbon dioxide physiological forcing to future climate change
Authors: Cao Long , Bala Govindasamy , Caldeira Ken , Nemani Ramakrishna , Ban-Weiss George
Published: May 2010

An increase in atmospheric carbon dioxide (CO
2
) concentration influences climate both directly through its radiative effect (i.e., trapping longwave radiation) and indirectly through its physiological effect (i.e., reducing transpiration of land plants). Here we compare the climate response to radiative and physiological effects of increased CO
2
using the National Center for Atmospheric Research (NCAR) coupled Community Land and Community Atmosphere Model. In response to a doubling of CO
2
, the radiative effect of CO
2
causes mean surface air temperature over land to increase by 2.86 ± 0.02 K (± 1 standard error), whereas the physiological effects of CO
2
on land plants alone causes air temperature over land to increase by 0.42 ± 0.02 K. Combined, these two effects cause a land surface warming of 3.33 ± 0.03 K. The radiative effect of doubling CO
2
increases global runoff by 5.2 ± 0.6%, primarily by increasing precipitation over the continents. The physiological effect increases runoff by 8.4 ± 0.6%, primarily by diminishing evapotranspiration from the continents. Combined, these two effects cause a 14.9 ± 0.7% increase in runoff. Relative humidity remains roughly constant in response to CO
2
-radiative forcing, whereas relative humidity over land decreases in response to CO
2
-physiological forcing as a result of reduced plant transpiration. Our study points to an emerging consensus that the physiological effects of increasing atmospheric CO
2
on land plants will increase global warming beyond that caused by the radiative effects of CO
2
.
Genome-wide patterns of population structure and admixture among Hispanic/Latino populations
Authors: Bryc Katarzyna , Velez Christopher , Karafet Tatiana , Moreno-Estrada Andres , Reynolds Andy , Auton Adam , Hammer Michael , Bustamante Carlos D. , Ostrer Harry
Published: May 2010

Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods
FRAPPE
and
STRUCTURE
to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method
LAMP
, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency
Authors: Hancock Angela M. , Witonsky David B. , Ehler Edvard , Alkorta-Aranburu Gorka , Beall Cynthia , Gebremedhin Amha , Sukernik Rem , Utermann Gerd , Pritchard Jonathan , Coop Graham , Di Rienzo Anna
Published: May 2010

Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of ecoregions and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. To understand the genetic basis of human adaptations, we combine population genetics data with ecological information to detect variants that increased in frequency in response to new selective pressures. Our approach detects SNPs that show concordant differences in allele frequencies across populations with respect to specific aspects of the environment. Genic and especially nonsynonymous SNPs are overrepresented among those most strongly correlated with environmental variables. This provides genome-wide evidence for selection due to changes in ecoregion, diet, and subsistence. We find particularly strong signals associated with polar ecoregions, with foraging, and with a diet rich in roots and tubers. Interestingly, several of the strongest signals overlap with those implicated in energy metabolism phenotypes from genome-wide association studies, including SNPs influencing glucose levels and susceptibility to type 2 diabetes. Furthermore, several pathways, including those of starch and sucrose metabolism, are enriched for strong signals of adaptations to a diet rich in roots and tubers, whereas signals associated with polar ecoregions are overrepresented in genes associated with energy metabolism pathways.
Phylogenomic evidence of adaptive evolution in the ancestry of humans
Authors: Goodman Morris , Sterner Kirstin N.
Published: May 2010

In Charles Darwin’s tree model for life’s evolution, natural selection adaptively modifies newly arisen species as they branch apart from their common ancestor. In accord with this Darwinian concept, the phylogenomic approach to elucidating adaptive evolution in genes and genomes in the ancestry of modern humans requires a well supported and well sampled phylogeny that accurately places humans and other primates and mammals with respect to one another. For more than a century, first from the comparative immunological work of Nuttall on blood sera and now from comparative genomic studies, molecular findings have demonstrated the close kinship of humans to chimpanzees. The close genetic correspondence of chimpanzees to humans and the relative shortness of our evolutionary separation suggest that most distinctive features of the modern human phenotype had already evolved during our ancestry with chimpanzees. Thus, a phylogenomic assessment of being human should examine earlier stages of human ancestry as well as later stages. In addition, with the availability of a number of mammalian genomes, similarities in phenotype between distantly related taxa should be explored for evidence of convergent or parallel adaptive evolution. As an example, recent phylogenomic evidence has shown that adaptive evolution of aerobic energy metabolism genes may have helped shape such distinctive modern human features as long life spans and enlarged brains in the ancestries of both humans and elephants.
The cognitive niche: Coevolution of intelligence, sociality, and language
Authors: Pinker Steven
Published: May 2010

Although Darwin insisted that human intelligence could be fully explained by the theory of evolution, the codiscoverer of natural selection, Alfred Russel Wallace, claimed that abstract intelligence was of no use to ancestral humans and could only be explained by intelligent design. Wallace's apparent paradox can be dissolved with two hypotheses about human cognition. One is that intelligence is an adaptation to a knowledge-using, socially interdependent lifestyle, the “cognitive niche.” This embraces the ability to overcome the evolutionary fixed defenses of plants and animals by applications of reasoning, including weapons, traps, coordinated driving of game, and detoxification of plants. Such reasoning exploits intuitive theories about different aspects of the world, such as objects, forces, paths, places, states, substances, and other people's beliefs and desires. The theory explains many zoologically unusual traits inHomo sapiens, including our complex toolkit, wide range of habitats and diets, extended childhoods and long lives, hypersociality, complex mating, division into cultures, and language (which multiplies the benefit of knowledge because know-how is useful not only for its practical benefits but as a trade good with others, enhancing the evolution of cooperation). The second hypothesis is that humans possess an ability ofmetaphorical abstraction, which allows them to coopt faculties that originally evolved for physical problem-solving and social coordination, apply them to abstract subject matter, and combine them productively. These abilities can help explain the emergence of abstract cognition without supernatural or exotic evolutionary forces and are in principle testable by analyses of statistical signs of selection in the human genome.
Gene-culture coevolution in the age of genomics
Authors: Richerson Peter J. , Boyd Robert , Henrich Joseph
Published: May 2010

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell andG6PDdeficiency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history.
Uniquely human evolution of sialic acid genetics and biology
Authors: Varki Ajit
Published: May 2010

Darwinian evolution of humans from our common ancestors with nonhuman primates involved many gene–environment interactions at the population level, and the resulting human-specific genetic changes must contribute to the “Human Condition.” Recent data indicate that the biology of sialic acids (which directly involves less than 60 genes) shows more than 10 uniquely human genetic changes in comparison with our closest evolutionary relatives. Known outcomes are tissue-specific changes in abundant cell-surface glycans, changes in specificity and/or expression of multiple proteins that recognize these glycans, and novel pathogen regimes. Specific events includeAlu-mediated inactivation of theCMAHgene, resulting in loss of synthesis of the SiaN-glycolylneuraminic acid (Neu5Gc) and increase in expression of the precursorN-acetylneuraminic acid (Neu5Ac); increased expression of α2–6-linked Sias (likely because of changed expression ofST6GALI); and multiple changes inSIGLECgenes encoding Sia-recognizing Ig-like lectins (Siglecs). The last includes binding specificity changes (in Siglecs -5, -7, -9, -11, and -12); expression pattern changes (in Siglecs -1, -5, -6, and -11); gene conversion (SIGLEC11); and deletion or pseudogenization (SIGLEC13,SIGLEC14,andSIGLEC16). A nongenetic outcome of theCMAHmutation is human metabolic incorporation of foreign dietary Neu5Gc, in the face of circulating anti-Neu5Gc antibodies, generating a novel “xeno-auto-antigen” situation. Taken together, these data suggest that both the genes associated with Sia biology and the related impacts of the environment comprise a relative “hot spot” of genetic and physiological changes in human evolution, with implications for uniquely human features both in health and disease.
Flow of energy in the outer retina in darkness and in light
Authors: Linton Jonathan D. , Holzhausen Lars C. , Babai Norbert , Song Hongman , Miyagishima Kiyoharu J. , Stearns George W. , Lindsay Ken , Wei Junhua , Chertov Andrei O. , Peters Theo A. , Caffe Romeo , Pluk Helma , Seeliger Mathias W. , Tanimoto Naoyuki , Fong Kimberly , Bolton Laura , Kuok Denise L. T. , Sweet Ian R. , Bartoletti Theodore M. , Radu Roxana A. , Travis Gabriel H. , Zagotta Willam N. , Townes-Anderson Ellen , Parker Ed , Van der Zee Catharina E. E. M. , Sampath Alapakkam P. , Sokolov Maxim , Thoreson Wallace B. , Hurley James B.
Published: May 2010

Structural features of neurons create challenges for effective production and distribution of essential metabolic energy. We investigated how metabolic energy is distributed between cellular compartments in photoreceptors. In avascular retinas, aerobic production of energy occurs only in mitochondria that are located centrally within the photoreceptor. Our findings indicate that metabolic energy flows from these central mitochondria as phosphocreatine toward the photoreceptor’s synaptic terminal in darkness. In light, it flows in the opposite direction as ATP toward the outer segment. Consistent with this model, inhibition of creatine kinase in avascular retinas blocks synaptic transmission without influencing outer segment activity. Our findings also reveal how vascularization of neuronal tissue can influence the strategies neurons use for energy management. In vascularized retinas, mitochondria in the synaptic terminals of photoreceptors make neurotransmission less dependent on creatine kinase. Thus, vasculature of the tissue and the intracellular distribution of mitochondria can play key roles in setting the strategy for energy distribution in neurons.
Working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history
Authors: Scheinfeldt Laura B. , Soi Sameer , Tishkoff Sarah A.
Published: May 2010

Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories.
pH-dependent modulation of voltage gating in connexin45 homotypic and connexin45/connexin43 heterotypic gap junctions
Authors: Palacios-Prado Nicolas , Briggs Stephen W. , Skeberdis Vytenis A. , Pranevicius Mindaugas , Bennett Michael V. L. , Bukauskas Feliksas F.
Published: May 2010

Intracellular pH (pHi) can change during physiological and pathological conditions causing significant changes of electrical and metabolic cell–cell communication through gap junction (GJ) channels. In HeLa cells expressing wild-type connexin45 (Cx45) as well as Cx45 and Cx43 tagged with EGFP, we examined how pHiaffects junctional conductance (gj) and gjdependence on transjunctional voltage (Vj). To characterize Vjgating, we fit the gj–Vjrelation using a stochastic four-state model containing one Vj-sensitive gate in each apposed hemichannel (aHC); aHC open probability was a Boltzmann function of the fraction of Vjacross it. Using the model, we estimated gating parameters characterizing sensitivity to Vjand number of functional channels. In homotypic Cx45 and heterotypic Cx45/Cx43-EGFP GJs, pHichanges from 7.2 to ~8.0 shifted gj–Vjdependence of Cx45 aHCs along the Vjaxis resulting in increased probability of GJ channels being in the fully open state without change in the slope of gjdependence on Vj. In contrast, acidification shifted gj–Vjdependence in the opposite direction, reducing open probability; acidification also reduced the number of functional channels. Correlation between the number of channels in Cx45-EGFP GJs and maximal gjachieved under alkaline conditions showed that only ~4% of channels were functional. The acid dissociation constant (pKa) of gj–pHidependence of Cx45/Cx45 GJs was ~7. The pKaof heterotypic Cx45/Cx43-EGFP GJs was lower, ~6.7, between the pKas of Cx45 and Cx43-EGFP (~6.5) homotypic GJs. In summary, pHisignificantly modulates junctional conductance of Cx45 by affecting both Vjgating and number of functional channels.
Cyclotomic 𝑞-Schur algebras associated to the Ariki-Koike algebra
Authors: Shoji Toshiaki , Wada Kentaro
Published: May 2010

Let

H

n
,
r

\mathcal {H}_{n,r}

be the Ariki-Koike algebra associated to the complex reflection group

S

n

⋉
(

Z

/

r

Z

)
n

\mathfrak {S}_n\ltimes (\mathbb {Z}/r\mathbb {Z})^n

, and let

S

(
Λ
)

\mathcal {S}(\varLambda )

be the cyclotomic

q
q

-Schur algebra associated to

H

n
,
r

\mathcal {H}_{n,r}

, introduced by Dipper, James and Mathas. For each

p

=
(

r
1

,
…
,

r
g

)
∈

Z

>
0

g

\mathbf {p} = (r_1, \dots , r_g) \in \mathbb {Z}_{>0}^g

such that

r
1

+
⋯
+

r
g

=
r

r_1 +\cdots + r_g = r

, we define a subalgebra

S

p

\mathcal {S}^{\mathbf {p}}

of

S

(
Λ
)

\mathcal {S}(\varLambda )

and its quotient algebra

S

¯

p

\overline {\mathcal {S}}^{\mathbf {p}}

. It is shown that

S

p

\mathcal {S}^{\mathbf {p}}

is a standardly based algebra and

S

¯

p

\overline {\mathcal {S}}^{\mathbf {p}}

is a cellular algebra. By making use of these algebras, we prove a product formula for decomposition numbers of

S

(
Λ
)

\mathcal {S}(\varLambda )

, which asserts that certain decomposition numbers are expressed as a product of decomposition numbers for various cyclotomic

q
q

-Schur algebras associated to Ariki-Koike algebras

H

n
i

,

r
i

\mathcal {H}_{n_i,r_i}

of smaller rank. This is a generalization of the result of N. Sawada. We also define a modified Ariki-Koike algebra

H

¯

p

\overline {\mathcal {H}}^{\mathbf {p}}

of type

p

\mathbf {p}

, and prove the Schur-Weyl duality between

H

¯

p

\overline {\mathcal {H}}^{\mathbf {p}}

and

S

¯

p

\overline {\mathcal {S}}^{\mathbf {p}}

.
Regulation of Oxysterol-binding Protein Golgi Localization through Protein Kinase D–mediated Phosphorylation
Authors: Nhek Sokha , Ngo Mike , Yang Xuemei , Ng Michelle M. , Field Seth J. , Asara John M. , Ridgway Neale D. , Toker Alex
Published: May 2010

Protein kinase D (PKD) plays a critical role at the trans-Golgi network by regulating the fission of transport carriers destined for the plasma membrane. Two known Golgi-localized PKD substrates, PI4-kinase IIIβ and the ceramide transfer protein CERT, mediate PKD signaling to influence vesicle trafficking to the plasma membrane and sphingomyelin synthesis, respectively. PKD is recruited and activated at the Golgi through interaction with diacylglycerol, a pool of which is generated as a by-product of sphingomyelin synthesis from ceramide. Here we identify a novel substrate of PKD at the Golgi, the oxysterol-binding protein OSBP. Using a substrate-directed phospho-specific antibody that recognizes the optimal PKD consensus motif, we show that PKD phosphorylates OSBP at Ser240 in vitro and in cells. We further show that OSBP phosphorylation occurs at the Golgi. Phosphorylation of OSBP by PKD does not modulate dimerization, sterol binding, or affinity for PI(4)P. Instead, phosphorylation attenuates OSBP Golgi localization in response to 25-hydroxycholesterol and cholesterol depletion, impairs CERT Golgi localization, and promotes Golgi fragmentation.
Welfare Effects of Food Labels and Bans with Alternative Willingness to Pay Measures
Authors: Lusk Jayson L. , Marette Stéphan
Published: May 2010

This paper integrates several areas of the literature by more fully developing the linkage between demand estimates and the welfare effects of food labels and bans for three common survey/experimental approaches used to elicit consumer preferences. We present empirical applications related to beef cloning and methylmercury in fish where, for the same data sets, we compare each value elicitation approach in terms of the consumer surplus changes that result from two regulations. Welfare measures vary significantly across the three methodologies, but the sign of the welfare change is invariant across method.
Taxpayer Beliefs about Farm Income and Preferences for Farm Policy
Authors: Ellison Brenna D. , Lusk Jayson L. , Briggeman Brian C.
Published: May 2010

One voice that is commonly overlooked in debates about farm policy and payment limitations is that of the average tax payer. Surprisingly little research has been done on what taxpayers believe about farms and what they prefer regarding farm policy. Our sample of taxpayers believes that farmers are doing well financially, and most people actually overestimate farmers' incomes. In addition, we found strong preferences for subsidizing small family farms over very large family farms, even though most of the people in our sample believe small family farms earn a higher level of income than their own household. A large majority of our sample supports government subsidies for farmers, primarily because people believe it ensures a secure food supply.
The geometric phase and the spin-statistics relation
Authors: Bandyopadhyay P.
Published: May 2010

The exchange phase for two spins is studied here from the point of view of the quantization of a fermion in the framework of Nelson’s stochastic mechanics. This introduces a direction vector attached to a space–time point depicting the spin degrees of freedom. In this formalism, a fermion appears as a scalar particle attached with a magnetic-flux quantum, and a quantum spin can be described in terms of an SU(2) gauge bundle. This helps us to recast the Berry–Robbins formalism where the exchange phase appears as an unfamiliar geometric phase arising out of the ‘exchange rotation’ in a transported spin basis in terms of gauge currents. However, for polarized fermions, the exchange phase is found to be given by the Berry phase.
High-latitude ionospheric response to co-rotating interaction region- and coronal mass ejection-driven geomagnetic storms revealed by GPS tomography and ionosondes
Authors: Pokhotelov D. , Jayachandran P. T. , Mitchell C. N. , Denton M. H.
Published: May 2010

Positive ionospheric anomalies induced in the polar cap region by co-rotating interaction region (CIR)- and coronal mass ejection (CME)-driven geomagnetic storms are analysed using four-dimensional tomographic reconstructions of the ionospheric plasma density based on measurements of the total electron content along ray paths of GPS signals. The results of GPS tomography are compared with ground-based observations of F region plasma density by digital ionosondes located in the Canadian Arctic. It is demonstrated that CIR- and CME-driven storms can produce large-scale polar cap anomalies of similar morphology in the form of the tongue of ionization (TOI) that appears on the poleward edge of the mid-latitude dayside storm-enhanced densities in positive ionospheric storms. The CIR-driven event of 14–16 October 2002 was able to produce ionospheric anomalies (TOI) comparable to those produced by the CME-driven storms of greater Dst magnitude. From the comparison of tomographic reconstructions and ionosonde data with solar wind measurements, it appears that the formation of large-scale polar cap anomalies is controlled by the orientation of the interplanetary magnetic field (IMF) with the TOI forming during the periods of extended southward IMF under conditions of high solar wind velocity.
Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies
Authors: Mutanen Marko , Wahlberg Niklas , Kaila Lauri
Published: May 2010

Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to ‘microlepidopteran’ groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.
Condition, innate immunity and disease mortality of inbred crows
Authors: Townsend Andrea K. , Clark Anne B. , McGowan Kevin J. , Miller Andrew D. , Buckles Elizabeth L.
Published: May 2010

Cooperatively breeding American crows (
Corvus brachyrhynchos
) suffer a severe disease-mediated survival cost from inbreeding, but the proximate mechanisms linking inbreeding to disease are unknown. Here, we examine indices of nestling body condition and innate immunocompetence in relationship to inbreeding and disease mortality. Using an estimate of microsatellite heterozygosity that predicts inbreeding in this population, we show that inbred crows were in relatively poor condition as nestlings, and that body condition index measured in the first 2–33 days after hatching, in addition to inbreeding index, predicted disease probability in the first 34 months of life. Inbred nestlings also mounted a weaker response along one axis of innate immunity: the proportion of bacteria killed in a microbiocidal assay increased as heterozygosity index increased. Relatively poor body condition and low innate immunocompetence are two mechanisms that might predispose inbred crows to ultimate disease mortality. A better understanding of condition-mediated inbreeding depression can guide efforts to minimize disease costs of inbreeding in small populations.
The missing stink: sulphur compounds can mediate a shift between fly and wasp pollination systems
Authors: Shuttleworth Adam , Johnson Steven D.
Published: May 2010

The radiation of the angiosperms is often attributed to repeated evolutionary shifts between different pollinators, as this process drives diversification of floral forms and can lead to reproductive isolation. Floral scent is an important functional trait in many pollination systems but has seldom been implicated as a key mechanism in pollinator transitions. In this study, we suggest a role for sulphur compounds in mediating a shift between specialized carrion-fly and pompilid-wasp pollination systems inEucomis(Hyacinthaceae). Flowers of closely relatedEucomisspecies pollinated by carrion flies or pompilid wasps have very similar greenish-white flowers, but differ markedly in floral scent chemistry (determined by GC–MS analysis of headspace extracts). Comparison of the floral colours of the fourEucomisspecies in the visual systems of flies and wasps suggests that colour plays little role in pollinator discrimination. Nectar properties and morphology also do not differ strongly between fly- and wasp-pollinated flowers. By comparing floral scent bouquets and experimentally manipulating the scent of plants in the field, we demonstrate that shifts between wasp and fly pollination in these four congeners can depend on the production or suppression of sulphur compounds (dimethyl disulphide and dimethyl trisulphide) in the fragrance bouquet. This suggests that mutations affecting the production of particular scent compounds could precipitate shifts between pollinators, independently of floral morphology, colour or nectar properties.
Natural selection on cis and trans regulation in yeasts
Authors: Emerson J.J. , Hsieh Li-Ching , Sung Huang-Mo , Wang Tzi-Yuan , Huang Chih-Jen , Lu Henry Horng-Shing , Lu Mei-Yeh Jade , Wu Shu-Hsing , Li Wen-Hsiung
Published: May 2010

Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we measure genome-wide allele-specific expression by deep sequencing to investigate the patterns of cis and trans expression variation between two strains of Saccharomyces cerevisiae. We propose a statistical modeling framework based on the binomial distribution that simultaneously addresses normalization of read counts derived from different parents and estimating the cis and trans expression variation parameters. We find that expression polymorphism in yeast is common for both cis and trans, though trans variation is more common. Constraint in expression evolution is correlated with other hallmarks of constraint, including gene essentiality, number of protein interaction partners, and constraint in amino acid substitution, indicating that both cis and trans polymorphism are clearly under purifying selection, though trans variation appears to be more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests a significant departure from a neutral model of molecular evolution. A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence.
Humane killing of fishes for scientific research: a comparison of two methods
Authors: Blessing J. J. , Marshall J. C. , Balcombe S. R.
Published: May 2010

Two killing methods were compared on the clupeid, bony bream Nematolosa erebi and it was found that ice‐slurry immersion was more humane than benzocaine overdose. The use of ice‐slurry for killing N. erebi should be accepted as a standard humane method and considered similarly for other warm‐water species.
Prey capture of pike Esox lucius larvae in turbid water
Authors: Salonen M. , Engström‐Öst J.
Published: May 2010

Pike Esox lucius larvae captured fewer calanoid and cyclopoid copepods in turbid than in clear water, whereas no differences were detected in feeding rates on Daphnia longispina. Decreased capture of copepods may lead to lower growth and survival of E. lucius larvae in turbid areas, in particular, if cladocerans are scarce.