bluuebunny/crossref_metadata_2025 huggingface dataset:
Resistant Starch Escaped from Ethanol Production: Evidence from Confocal Laser Scanning Microscopy of Distiller's Dried Grains with Solubles (DDGS)
Authors: Li Jihong , Vasanthan Thava , Gao Jun , Naguleswaran Sabaratnam , Zijlstra Ruurd T. , Bressler David C.
Published: January 2014

The origin of resistant starch (RS) in distiller's dried grains with solubles (DDGS) of triticale, wheat, barley, and corn from dry‐grind ethanol production was studied. A considerable portion of starch (up to 18% in DDGS) escaped from either granular starch hydrolysis or conventional jet‐cooking and fermentation processes. Confocal laser scanning microscopy revealed that some starch granules were still encapsulated in cells of grain kernel or embedded in protein matrix after milling and were thus physically inaccessible to amylases (type RS1). The crystalline structures of native starch granules were not completely degraded by amylases, retaining the skeletal structures in residual starch during granular starch hydrolysis or leaving residue granules and fragments with layered structures after jet‐cooking followed by the liquefaction and saccharification process, indicating the presence of RS2. Moreover, retrograded starch molecules (mainly amylose) as RS3, complexes of starch with other nonfermentable components as RS4, and starch–lipid complexes as RS5 were also present in DDGS. In general, the RS that escaped from the granular starch hydrolysis process was mainly RS1 and RS2, whereas that from the jet‐cooking process contained all types of RS (RS1 to RS5). Thus, the starch conversion efficiency and ethanol yield could be potentially affected by the presence of various RS in DDGS.
First Report of Burkholderia glumae Causing Bacterial Panicle Blight on Rice in Ecuador
Authors: Riera-Ruiz C. , Vargas J. , Cedeño C. , Quirola P. , Escobar M. , Cevallos-Cevallos J. M. , Ratti M. , Peralta E. L.
Published: January 2014

Rice (Oryza sativa L.) is one of the leading crops and the basis of most diets in Ecuador and other countries. Diseases such as bacterial panicle blight (BPB), also known as seedling rot or grain rot, have the potential to threaten rice production worldwide. Burkholderia glumae, a causal agent of BPB, has severely affected the rice industry in many countries of Africa, Asia, and the Americas (1,2,4), but no report of this bacteria in Ecuador can be found in the literature. Rice plantations showing BPB-like symptoms including upright panicles with stained and vain grains were spotted in Palestina city, one of Ecuador's most extensive rice areas, in July 2013, but similar symptoms have been observed in the region since early 2012. Six symptomatic plants from two different groves were collected. Samples were plated on the semi-selective medium S-PG (KH2PO4 1.3 g, Na2HPO4 1.2 g, (NH4)2SO4 5 g, MgSO4·7H2O 0.25 g, Na2MoO4·2H2O 24 mg, EDTA-Fe 10 mg, L-cystine 10 μg, D-sorbitol 10 g, pheneticillin potassium 50 mg, ampicillin sodium 10 mg, cetrimide 10 mg, methyl violet 1 mg, phenol red 20 mg, agar 15 g/liter distilled water) and axenic colonies were transferred to potato dextrose agar (PDA) to test for fluorescence (3). Colonies of the potential pathogen were 1 mm, circular, entire margin, with a smooth and shiny surface. When cultured in PDA, isolates showed a moist texture, dull yellow color, and displayed fluorescence with exposure to UV light. Cells were bacterial gram-negative rods of 1 to 2 × 0.5 μm. Twelve presumptive isolates were submitted to biochemical tests (API 20NE). The biochemical profile (APIWEB) showed that all the isolates belonged to the Burkholderia genus with a 99.9% similarity. To determine the bacterial species, colonies were submitted to ELISA tests using specific antibodies for B. glumae from Agdia, Inc. The two isolates that were positive for B. glumae were sequenced using a part of the 16s rDNA amplified by the primers 536F: 5′-GTGCCAGCMGCCGCGGTAATAC-3′ and 1492R: 5′-GGTTACCTTGTTACGACTT-3′. The obtained sequences (deposited into GenBank as KF601202) shared 100% similarity with several B. glumae strains after a BLAST query. Isolates were then diluted to 108 UFC/ml and used to inoculate healthy rice plants. Inoculated plants produced BPB-like symptoms including upright panicles with stained vain grains and the bacterium was re-isolated from symptomatic plants. To the best of our knowledge, this is the first report of B. glumae in Ecuador. Further research is ongoing to identify and determine the pathogenicity of the remaining Burkholderia strains that tested negative for B. glumae.

References: (1) J. Luo et al. Plant Dis. 91:1363, 2007. (2) R. Nandakumar et al. Plant Dis. 93:896, 2009. (3) T. Urakami et al. Int. J. Syst. Bacteriol. 44:235, 1994. (4) X.-G. Zhou. Plant Dis. 98:566, 2014.
Biological and Molecular Characterization of Four Botryosphaeria Species Isolated from Pear Plants Showing Stem Wart and Stem Canker in China
Authors: Zhai Lifeng , Zhang Meixin , Lv Gang , Chen Xiaoren , Jia Nana , Hong Ni , Wang Guoping
Published: January 2014

Pear stem wart and pear stem canker, which have been considered as two different fungal diseases caused by pathogens belonging to Botryosphaeria spp., commonly occur and cause serious damage in the main pear-producing areas in China. To identify the species of this genus infecting pear in China, 131 Botryosphaeria isolates were recovered from pear samples exhibiting symptoms collected from 20 different provinces and areas. Morphological characterization and phylogenetic analyses of the ribosomal DNA internal transcribed spacer region and the β-tubulin and EF1-α genes revealed that Botryosphaeria dothidea, B. rhodina, B. obtusa, and B. parva were associated with different pear stem wart and stem canker symptoms. Remarkably, all isolates of B. dothidea were obtained from the samples showing either stem wart or stem canker lesions; however, the isolates of the other three species were obtained only from the samples showing stem canker. Pathogenicity tests on the pear shoots showed that B. dothidea isolates could induce stem wart or stem canker lesions but all the isolates of the other three species could only induce stem cankers. However, the isolates of B. parva, B. rhodina, and B. obtusa exhibited higher virulence than that of the B. dothidea isolates on the pear fruit. Our results suggest that B. dothidea is the common causal agent for these two diseases (a pear stem wart and a pear-related stem canker), whereas B. parva, B. rhodina, and B. obtusa only cause pear stem canker diseases. To our knowledge, this study represents the first report for biological and molecular characterization of four Botryosphaeria spp. isolated from pear plants showing stem wart and stem canker in China.
Migration and stress during reproduction govern telomere dynamics in a seabird
Authors: Schultner Jannik , Moe Børge , Chastel Olivier , Bech Claus , Kitaysky Alexander S.
Published: January 2014

Changes in telomere length are believed to reflect changes in physiological state and life expectancy in animals. However, much remains unknown about the determinants of telomere dynamics in wild populations, and specifically the influence of conditions during highly mobile life-history stages, for example migration. We tested whether telomere dynamics were associated with migratory behaviour and/or with stress during reproduction in free-living seabirds. We induced short-term stress during reproduction in chick-rearing, black-legged kittiwakes (Rissa tridactyla), tracked winter migration with geolocators and measured telomere length before and after winter migration. We found that time spent at wintering grounds correlated with reduced telomere loss, while stress during reproduction accelerated telomere shortening. Our results suggest that different life-history stages interact to influence telomere length, and that migratory patterns may be important determinants of variation in an individual's telomere dynamics.
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals
Authors: dos Reis Mario , Donoghue Philip C. J. , Yang Ziheng
Published: January 2014

O'Leary
et al
. (O'Leary
et al.
2013
Science
339
, 662–667. (
doi:10.1126/science.1229237
)) performed a fossil-only dating analysis of mammals, concluding that the ancestor of placentals post-dated the Cretaceous–Palaeogene boundary, contradicting previous palaeontological and molecular studies that placed the ancestor in the Cretaceous. They incorrectly used fossil ages as species divergence times for crown groups, while in fact the former should merely form minimum-age bounds for the latter. Statistical analyses of the fossil record have shown that crown groups are significantly older than the oldest ingroup fossil, so that fossils do not directly reflect the true ages of clades. Here, we analyse a 20 million nucleotide genome-scale alignment in conjunction with a probabilistic interpretation of the fossil ages from O'Leary
et al.
Our combined analysis of fossils and molecules demonstrates that Placentalia originated in the Cretaceous.
How to best smash a snail: the effect of tooth shape on crushing load
Authors: Crofts S. B. , Summers A. P.
Published: January 2014

Organisms that are durophagous, hard prey consumers, have a diversity of tooth forms. To determine why we see this variation, we tested whether some tooth forms break shells better than others. We measured the force needed with three series of aluminium tooth models, which varied in concavity and the morphology of a stress concentrating cusp, to break a shell. We created functionally identical copies of two intertidal snail shells: the thicker shelledNucella ostrinaand the more ornamentedNucella lamellosausing a three-dimensional printer. In this way, we reduced variation in material properties between test shells, allowing us to test only the interaction of the experimental teeth with the two shell morphologies. We found that for all tooth shapes, thicker shells are harder to break than the thinner shells and that increased ornamentation has no discernible effect. Our results show that for both shell morphologies, domed and flat teeth break shells better than cupped teeth, and teeth with tall or skinny cusps break shells best. While our results indicate that there is an ideal tooth form for shell breaking, we do not see this shape in nature. This suggests a probable trade-off between tooth function and the structural integrity of the tooth.
A method for estimating the oxygen consumption rate in multicellular tumour spheroids
Authors: Grimes David Robert , Kelly Catherine , Bloch Katarzyna , Partridge Mike
Published: January 2014

Hypoxia occurs when oxygen levels within a tissue drop below normal physiological levels. In tumours, hypoxia is associated with poor prognosis, increased likelihood of metastasis and resistance to therapy. Imaging techniques, for example, positron emission tomography, are increasingly used in the monitoring of tumour hypoxia and have the potential to help in the planning of radiotherapy. For this application, improved understanding of the link between image contrast and quantitative underlying oxygen distribution would be very useful. Mathematical models of tissue hypoxia and image formation can help understand this. Hypoxia is caused by an imbalance between vascular supply and tissue demand. While much work has been dedicated to the quantitative description of tumour vascular networks, consideration of tumour oxygen consumption is largely neglected. Oxidative respiration in standard two-dimensional cell culture has been widely studied. However, two-dimensional culture fails to capture the complexities of growing three-dimensional tissue which could impact on the oxygen usage. In this study, we build on previous descriptions of oxygen consumption and diffusion in three-dimensional tumour spheroids and present a method for estimating rates of oxygen consumption from spheroids, validated using stained spheroid sections. Methods for estimating the local partial pressure of oxygen, the diffusion limit and the extents of the necrotic core, hypoxic region and proliferating rim are also derived. These are validated using experimental data from DLD1 spheroids at different stages of growth. A relatively constant experimentally derived diffusion limit of 232 ± 22 μm and an O
2
consumption rate of 7.29 ± 1.4 × 10
−7
m
3
kg
−1
s
−1
for the spheroids studied was measured, in agreement with laboratory measurements.
Interplay of symmetries, null forms, Darboux polynomials, integrating factors and Jacobi multipliers in integrable second-order differential equations
Authors: Mohanasubha R. , Chandrasekar V. K. , Senthilvelan M. , Lakshmanan M.
Published: January 2014

In this work, we establish a connection between the extended Prelle–Singer procedure with five other analytical methods which are widely used to identify integrable systems in the contemporary literature, especially for second-order nonlinear ordinary differential equations (ODEs). By synthesizing these methods, we bring out the interplay between Lie point symmetries,
λ
-symmetries, adjoint symmetries, null-forms, Darboux polynomials, integrating factors and Jacobi last multiplier in identifying the integrable systems described by second-order ODEs. We also give new perspectives to the extended Prelle–Singer procedure developed by us. We illustrate these subtle connections with the modified Emden equation as a suitable example.
Understanding the chain fountain
Authors: Biggins J. S. , Warner M.
Published: January 2014

If a chain is initially at rest in a beaker at a height
h
1
above the ground, and the end of the chain is pulled over the rim of the beaker and down towards the ground and then released, the chain will spontaneously ‘flow’ out of the beaker under gravity. Furthermore, the beads do not simply drag over the edge of the beaker but form a fountain reaching a height
h
2
above it. We show that the formation of a fountain requires that the beads come into motion not only by being pulled upwards by the part of the chain immediately above the pile, but also by being pushed upwards by an anomalous reaction force from the pile of stationary chain. We propose possible origins for this force, argue that its magnitude will be proportional to the square of the chain velocity and predict and verify experimentally that
h
2
∝
h
1
.
Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes
Authors: Tucker Caroline M. , Fukami Tadashi
Published: January 2014

The order of species arrival during community assembly can greatly affect species coexistence, but the strength of these effects, known as priority effects, appears highly variable across species and ecosystems. Furthermore, the causes of this variation remain unclear despite their fundamental importance in understanding species coexistence. Here, we show that one potential cause is environmental variability. In laboratory experiments using nectar-inhabiting microorganisms as a model system, we manipulated spatial and temporal variability of temperature, and examined consequences for priority effects. If species arrived sequentially, multiple species coexisted under variable temperature, but not under constant temperature. Temperature variability prevented extinction of late-arriving species that would have been excluded owing to priority effects if temperature had been constant. By contrast, if species arrived simultaneously, species coexisted under both variable and constant temperatures. We propose possible mechanisms underlying these results using a mathematical model that incorporates contrasting effects of microbial species on nectar pH and amino acids. Overall, our findings suggest that understanding consequences of priority effects for species coexistence requires explicit consideration of environmental variability.
Food sharing is linked to urinary oxytocin levels and bonding in related and unrelated wild chimpanzees
Authors: Wittig Roman M. , Crockford Catherine , Deschner Tobias , Langergraber Kevin E. , Ziegler Toni E. , Zuberbühler Klaus
Published: January 2014

Humans excel in cooperative exchanges between unrelated individuals. Although this trait is fundamental to the success of our species, its evolution and mechanisms are poorly understood. Other social mammals also build long-term cooperative relationships between non-kin, and recent evidence shows that oxytocin, a hormone involved in parent–offspring bonding, is likely to facilitate non-kin as well as kin bonds. In a population of wild chimpanzees, we measured urinary oxytocin levels following a rare cooperative event—food sharing. Subjects showed higher urinary oxytocin levels after single food-sharing events compared with other types of social feeding, irrespective of previous social bond levels. Also, urinary oxytocin levels following food sharing were higher than following grooming, another cooperative behaviour. Therefore, food sharing in chimpanzees may play a key role in social bonding under the influence of oxytocin. We propose that food-sharing events co-opt neurobiological mechanisms evolved to support mother–infant bonding during lactation bouts, and may act as facilitators of bonding and cooperation between unrelated individuals via the oxytocinergic system across social mammals.
The groEL2 gene, but not groEL1, is required for biosynthesis of the secondary metabolite myxovirescin in Myxococcus xanthus DK1622
Authors: Wang Yan , Li Xi , Zhang Wenyan , Zhou Xiuwen , Li Yue-zhong
Published: January 2014

Myxococcus xanthus DK1622 possesses two copies of the groEL gene: groEL1, which participates in development, and groEL2, which is involved in the predatory ability of cells. In this study, we determined that the groEL2 gene is required for the biosynthesis of the secondary metabolite myxovirescin (TA), which plays essential roles in predation. The groEL2-knockout mutant strain was defective in producing a zone of inhibition and displayed decreased killing ability against Escherichia coli, while the groEL1-knockout mutant strain exhibited little difference from the wild-type strain DK1622. HPLC revealed that deletion of the groEL2 gene blocked the production of TA, which was present in the groEL1-knockout mutant. The addition of exogenous TA rescued the inhibition and killing abilities of the groEL2-knockout mutant against E. coli. Analysis of GroEL domain-swapping mutants indicated that the C-terminal equatorial domain of GroEL2 was essential for TA production, while the N-terminal equatorial or apical domains of GroEL2 were not sufficient to rescue TA production of the groEL2 knockout.
Phylogenetic characterization of Escherichia coli O157 : H7 based on IS629 distribution and Shiga toxin genotype
Authors: Stanton Eliot , Park Dongjin , Döpfer Dörte , Ivanek Renata , Kaspar Charles W.
Published: January 2014

Shiga toxin (stx)-producing Escherichia coli O157 : H7 is a prominent food-borne pathogen. Symptoms in human infections range from asymptomatic to haemorrhagic colitis and haemolytic uraemic syndrome, and there is a need for methods that yield information that can be used to better predict clinical and epidemiological outcomes. IS629 is an insertion sequence notable for its prevalence and variable distribution in the chromosome of E. coli O157 : H7, which has been exploited for subtyping and strain characterization. In particular, IS629 distribution is closely aligned with the major phylogenetic lineages that are known to be distinctive in their genome structure and virulence potential. In the present study, a comprehensive subtyping method in which IS629-typing was combined with stx genotyping was developed using a conventional PCR approach. This method consisted of a set of 32 markers based on the unique distribution of IS629 in the three major phylogenetic lineages of E. coli O157 : H7 and six additional markers to determine the stx genotype, a key virulence signature associated with each lineage. The analysis of IS629 loci variation with the 32 markers allowed us to determine the IS629 distribution profile (IDP), phylogenetic lineage and genetic relatedness of the 31 E. coli O157 : H7 strains examined. An association between IDP typing and stx genotype was observed. The use of both IDP and the stx genotype for strain characterization provided confirmative and complementary data in support of lineage placement of closely related strains. In addition, IS629/stx profiles were in agreement with strain segregation based on LSPA-6 (lineage-specific polymorphism assay) and PFGE subtyping, demonstrating its potential as a subtyping and strain tracking method.
Expertly validated models suggest responses to climate change are related to species traits: a phylogenetically-controlled analysis of the Order Lagomorpha
Authors: Leach Katie , Kelly Ruth , Cameron Alison , Montgomery W. Ian , Reid Neil
Published: January 2014

Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species’ bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian Order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical and habitat variables for all 87 species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current distribution models and only those deemed ‘modellable’ through our framework were projected under future climate scenarios (58 species). We then used phylogenetically-controlled regressions to test whether species traits were correlated with predicted responses to climate change. Climate change will impact more than two-thirds of the Lagomorpha, with leporids (rabbits, hares and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov’s Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management.
A Nuclear Factor Y Interacting Protein of the GRAS Family Is Required for Nodule Organogenesis, Infection Thread Progression, and Lateral Root Growth
Authors: Battaglia Marina , Rípodas Carolina , Clúa Joaquín , Baudin Maël , Aguilar O. Mario , Niebel Andreas , Zanetti María Eugenia , Blanco Flavio Antonio
Published: January 2014

A C subunit of the heterotrimeric nuclear factor Y (NF-YC1) was shown to play a key role in nodule organogenesis and bacterial infection during the nitrogen fixing symbiosis established between common bean (Phaseolus vulgaris) and Rhizobium etli. To identify other proteins involved in this process, we used the yeast (Saccharomyces cerevisiae) two-hybrid system to screen for NF-YC1-interacting proteins. One of the positive clones encodes a member of the Phytochrome A Signal Transduction1 subfamily of GRAS (for Gibberellic Acid-Insensitive (GAI), Repressor of GAI, and Scarecrow) transcription factors. The protein, named Scarecrow-like13 Involved in Nodulation (SIN1), localizes both to the nucleus and the cytoplasm, but in transgenic Nicotiana benthamiana cells, bimolecular fluorescence complementation suggested that the interaction with NF-YC1 takes place predominantly in the nucleus. SIN1 is expressed in aerial and root tissues, with higher levels in roots and nodules. Posttranscriptional gene silencing of SIN1 using RNA interference (RNAi) showed that the product of this gene is involved in lateral root elongation. However, root cell organization, density of lateral roots, and the length of root hairs were not affected by SIN1  RNAi. In addition, the expression of the RNAi of SIN1 led to a marked reduction in the number and size of nodules formed upon inoculation with R. etli and affected the progression of infection threads toward the nodule primordia. Expression of NF-YA1 and the G2/M transition cell cycle genes CYCLIN B and Cell Division Cycle2 was reduced in SIN1  RNAi roots. These data suggest that SIN1 plays a role in lateral root elongation and the establishment of root symbiosis in common bean.
Arabidopsis WRKY57 Functions as a Node of Convergence for Jasmonic Acid– and Auxin-Mediated Signaling in Jasmonic Acid–Induced Leaf Senescence
Authors: Jiang Yanjuan , Liang Gang , Yang Shizhuo , Yu Diqiu
Published: January 2014

Leaf senescence is regulated by diverse developmental and environmental factors. Exogenous jasmonic acid (JA) can induce leaf senescence, whereas auxin suppresses this physiological process. Crosstalk between JA and auxin signaling has been well studied, but not during JA-induced leaf senescence. Here, we found that upon methyl jasmonate treatment, Arabidopsis thaliana wrky57 mutants produced typical leaf senescence symptoms, such as yellowing leaves, low chlorophyll content, and high cell death rates. Further investigation suggested that senescence-associated genes were upregulated in the wrky57 mutants. Chromatin immunoprecipitation experiments revealed that WRKY57 directly binds to the promoters of SENESCENCE4 and SENESCENCE-ASSOCIATED GENE12 and represses their transcription. In vivo and in vitro experiments suggested that WRKY57 interacts with JASMONATE ZIM-DOMAIN4/8 (JAZ4/8) and the AUX/IAA protein IAA29, repressors of the JA and auxin signaling pathways, respectively. Consistent with the opposing functions of JA and auxin in JA-induced leaf senescence, JAZ4/8 and IAA29 also displayed opposite functions in JA-induced leaf senescence and competitively interacted with WRKY57. Our results suggested that the JA-induced leaf senescence process can be antagonized by auxin via WRKY57. Moreover, WRKY57 protein levels were downregulated by JA but upregulated by auxin. Therefore, as a repressor in JA-induced leaf senescence, WRKY57 is a common component of the JA- and auxin-mediated signaling pathways.
AUXIN BINDING PROTEIN1 Links Cell Wall Remodeling, Auxin Signaling, and Cell Expansion in Arabidopsis
Authors: Paque Sébastien , Mouille Grégory , Grandont Laurie , Alabadí David , Gaertner Cyril , Goyallon Arnaud , Muller Philippe , Primard-Brisset Catherine , Sormani Rodnay , Blázquez Miguel A. , Perrot-Rechenmann Catherine
Published: January 2014

Cell expansion is an increase in cell size and thus plays an essential role in plant growth and development. Phytohormones and the primary plant cell wall play major roles in the complex process of cell expansion. In shoot tissues, cell expansion requires the auxin receptor AUXIN BINDING PROTEIN1 (ABP1), but the mechanism by which ABP1 affects expansion remains unknown. We analyzed the effect of functional inactivation of ABP1 on transcriptomic changes in dark-grown hypocotyls and investigated the consequences of gene expression on cell wall composition and cell expansion. Molecular and genetic evidence indicates that ABP1 affects the expression of a broad range of cell wall–related genes, especially cell wall remodeling genes, mainly via an SCFTIR/AFB-dependent pathway. ABP1 also functions in the modulation of hemicellulose xyloglucan structure. Furthermore, fucosidase-mediated defucosylation of xyloglucan, but not biosynthesis of nonfucosylated xyloglucan, rescued dark-grown hypocotyl lengthening of ABP1 knockdown seedlings. In muro remodeling of xyloglucan side chains via an ABP1-dependent pathway appears to be of critical importance for temporal and spatial control of cell expansion.
Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications
Authors: Galek Peter T. A. , Chisholm James A. , Pidcock Elna , Wood Peter A.
Published: January 2014

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.
Competition between hydrogen and halogen bonding in the structures of 5,10-dihydroxy-5,10-dihydroboranthrenes
Authors: Durka Krzysztof , Luliński Sergiusz , Jarzembska Katarzyna N. , Smętek Jaromir , Serwatowski Janusz , Woźniak Krzysztof
Published: January 2014

X-ray crystallographic and computational studies are reported for a series of boranthrenes, substituted with halogen atoms. The role of competitive hydrogen (O—H...O, O—H...F, C—H...O) and halogen (Cl...Cl, O...Br, F...F) bonding interactions on the molecular arrangement in the crystal structures is discussed. The structural analysis and calculations reveal that the O—H...O hydrogen bond in the unsubstituted derivative 5,10-dihydroxy-5,10-dihydroboranthrene, C12H10B2O2, is of moderate strength (ca−20 kJ mol−1), but weaker than that in the related thiophene derivative 4,8-dihydro-4,8-dihydroxy-p-diborino[2,3-b:5,6-b]dithiophene, C8H6B2O2S2(ca−40 kJ mol−1). This is due to shielding of the OH group by the H atoms in the β-position of the boranthrene unit. Structural diversity derived from the flexibility of the O—H...O hydrogen bond facilitates the occurrence of other competitive interactions. For instance, in the 1,6-difluoro derivative, C12H8B2F2O2, the crystal packing results from O—H...F and F...F interactions. In turn, the 1,6-dibromo derivative, C12H8B2Br2O2, is dominated by Br...O halogen-bond interactions. In the most interesting case, the 1,6-dichloro derivative, C12H8B2Cl2O2, molecular disorder leads to the formation of two different supramolecular arrangements co-existing in the crystal lattice, one based on the Cl...Cl and C—H...O bonds, and the other stabilized by O—H...O hydrogen bonds. Calculations performed with density-functional theory (DFT;CRYSTAL09) andPIXELmethodologies show that both lattices are characterized by similar energy values (ca−100 kJ mol−1). A mixed arrangement with random or short-range-ordered molecular orientations can also be expected.
Direct phasing in femtosecond nanocrystallography. II. Phase retrieval
Authors: Chen Joe P. J. , Spence John C. H. , Millane Rick P.
Published: January 2014

X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental diffraction data [Spenceet al.(2011).Opt. Express,19, 2866–2873]. The estimated continuous transform is highly noisy however [Chenet al.(2014).Acta Cryst.A70, 143–153]. This second of a series of two papers describes a data-selection strategy to ameliorate the effects of the high noise levels and the subsequent use of iterative phase-retrieval algorithms to reconstruct the electron density. Simulation results show that employing such a strategy increases the noise levels that can be tolerated.
Dividend Payouts and Information Shocks
Authors: HAIL LUZI , TAHOUN AHMED , WANG CLARE
Published: January 2014

We examine changes in firms’ dividend payouts following an exogenous shock to the information asymmetry problem between managers and investors. Agency theories predict a decrease in dividend payments to the extent that improved public information lowers managers’ need to convey their commitment to avoid overinvestment via costly dividend payouts. Conversely, dividends could increase if minority investors are in a better position to extract cash dividends. We test these predictions by analyzing the dividend payment behavior of a global sample of firms around the mandatory adoption of IFRS and the initial enforcement of new insider trading laws. Both events serve as proxies for a general improvement of the information environment and, hence, the corporate governance structure in the economy. We find that, following the two events, firms are less likely to pay (increase) dividends, but more likely to cut (stop) such payments. The changes occur around the time of the informational shock, and only in countries and for firms subject to the regulatory change. They are more pronounced when the inherent agency issues or the informational shocks are stronger. We further find that the information content of dividends decreases after the events. The results highlight the importance of the agency costs of free cash flows (and changes therein) for shaping firms’ payout policies.
Nuptial gifts and female fecundity in the neotropical katydid Conocephalus ictus (Orthoptera: Tettigonidae)
Authors: Ortíz‐Jiménez Isabel , Castillo Raúl Cueva del
Published: January 2014

In general, female fitness is greatly increased in gift‐giving insects. In katydids, this nuptial gift consists of a gelatinous mass produced by accessory glands: the spermatophylax, which is attached to the ampulla. During mating, males of the neotropical katydid Conocephalus ictus transfer a spermatophylax that is ingested by the females. Fecundity, egg‐laying rate and longevity were higher in females that consumed the spermatophylax than in those that did not. Also, female receptivity turned off after mating. Females actively rejected other males by hitting them with their forelegs and moving away. Their refractory period lasted as long as 17 d. Only a few females accepted a 2nd mating and died a few days later. In C. ictus, spermatophylax consumption can be beneficial for both males and females. On one hand, the compounds in the spermatophylax or the ejaculate could prevent or delay females from copulating with rivals, thus avoiding sperm competition. On the other hand, such compounds can improve the females’ opportunity to increase their lifespan and fecundity. Moreover, a rise in egg‐laying rate may lower the risk of female prereproductive death caused by rapid oviposition. In any case, the boost in female egg laying might also be beneficial for males because their number of offspring increases.
PopGenReport: simplifying basic population genetic analyses in R
Authors: Adamack Aaron T. , Gruber Bernd
Published: January 2014

Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve.

PopGenReport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating function. The function popgenreport allows users to perform up to 13 pre‐defined and 1 user‐defined analyses through the use of a single command line. Each analysis generates figures and tables that are incorporated into a pdf report and are also made available as individual files (figures are provided in multiple formats, table contents are provided as csv files).

The package includes new R functions that simplify the importation of data from a spreadsheet file, examine allele distributions across populations and loci and identify private alleles, determine pairwise individual genetic distances using the methods of Smouse and Peakall () and Kosman and Leonard (), respectively, detect the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall ().

The package has a modular structure that makes the process of adding new functionality straightforward. To facilitate the addition of user‐designed functions, the package includes a fully customizable module that can be automatically included in the pdf report.

To support users not experienced in R, the website (www.popgenreport.org) has a tutorial for the package and a downloadable, portable version of the package with LaTeX pre‐configured for the Windows operating system.
Understanding epigenetic changes in aging stem cells – a computational model approach
Authors: Przybilla Jens , Rohlf Thimo , Loeffler Markus , Galle Joerg
Published: January 2014

During aging, a decline in stem cell function is observed in many tissues. This decline is accompanied by complex changes of the chromatin structure among them changes in histone modifications and DNA methylation which both affect transcription of a tissue‐specific subset of genes. A mechanistic understanding of these age‐associated processes, their interrelations and environmental dependence is currently lacking. Here, we discuss related questions on the molecular, cellular, and population level. We combine an individual cell‐based model of stem cell populations with a model of epigenetic regulation of transcription. The novel model enables to simulate age‐related changes of trimethylation of lysine 4 at histone H3 and of DNA methylation. These changes entail expression changes of genes that induce age‐related phenotypes (ARPs) of cells. We compare age‐related changes of regulatory states in quiescent stem cells occupying a niche with those observed in proliferating cells. Moreover, we analyze the impact of the activity of the involved epigenetic modifiers on these changes. We find that epigenetic aging strongly affects stem cell heterogeneity and that homing at stem cell niches retards epigenetic aging. Our model provides a mechanistic explanation how increased stem cell proliferation can lead to progeroid phenotypes. Adapting our model to properties observed for aged hematopoietic stem cell (HSC) clones, we predict that the hematopoietic ARP activates young HSCs and thereby retards aging of the entire HSC population. In addition, our model suggests that the experimentally observed high interindividual variance in HSC numbers originates in a variance of histone methyltransferase activity.
Association of the CHRNA4 Neuronal Nicotinic Receptor Subunit Gene with Frequency of Binge Drinking in Young Adults
Authors: Coon Hilary , Piasecki Thomas M. , Cook Edwin H. , Dunn Diane , Mermelstein Robin J. , Weiss Robert B. , Cannon Dale S.
Published: January 2014

Background

Binge drinking is responsible for over half of all alcohol‐related deaths and results in significant health and economic costs to individuals and society. Knowledge of genetic aspects of this behavior, particularly as it emerges in young adulthood, could lead to improved treatment and prevention programs.

Methods

We have focused on the association of variation in neuronal nicotinic receptor subunit genes (CHRNs) in a cohort of 702 Hispanic and non‐Hispanic White young adults who are part of the Social and Emotional Contexts of Adolescent Smoking Patterns (SECASP) study. Fifty‐five single nucleotide polymorphisms (SNPs) covering the variation in 5 CHRNs (CHRNA4, CHRNB2, CHRNA2, CHRNB3A6, and CHRNA5A3B4) were studied.

Results

Frequency of binge drinking and other correlated alcohol consumption measures were significantly associated with SNPs in CHRNA4 (p‐values ranged from 0.0003 to 0.02), but not with SNPs in other CHRNs. This association was independent of smoking status in our cohort.

Conclusions

Variants in CHRNA4 may contribute to risk of binge drinking in young adults in this cohort. Results will need to be confirmed in independent samples.
Determinants of tax haven utilization: evidence from Australian firms
Authors: Taylor Grantley , Richardson Grant , Taplin Ross
Published: January 2014

This paper examines the major determinants of tax haven utilization based on a sample of 200 publicly listed Australian firms, over the 2006–2010 period (1,000 firm‐years). Our regression results show that variables relating to transfer pricing, intangible assets, an interaction term between transfer pricing and intangible assets, withholding taxes, performance‐based management remuneration and multinationality are positively associated with tax haven utilization. We also find that corporate governance structures are negatively associated with tax haven utilization. The magnitude and significance of the regression coefficients indicate that transfer pricing, withholding taxes, intangible assets, an interaction term between transfer pricing and intangible assets, corporate governance and multinationality are the most important drivers of tax haven utilization.
Women and the prospects for partnership in professional accountancy firms
Authors: Whiting Rosalind H. , Gammie Elizabeth , Herbohn Kathleen
Published: January 2014

This paper examines three possible reasons (stereotypical discrimination, structural obstacles and employee's preferences) for the lack of women partners in professional accountancy firms in Australia,UKand New Zealand. Data are collected from an experimental survey and interviews of current partners. Whilst women's perceived preferences and organisational structural barriers contributed strongly to the lack of women partners in all sizes of firms, traditional stereotypical discrimination against women at the partnership decision point was only displayed in metropolitan large non‐Big 4 firms, and it is suggested that this is related to intense competitive pressure and a constrained partnership resource.
Skin temperature: its role in thermoregulation
Authors: Romanovsky A. A.
Published: January 2014

This review analyses whether skin temperature represents ambient temperature and serves as a feedforward signal for the thermoregulation system, or whether it is one of the body's temperatures and provides feedback. The body is covered mostly by hairy (non‐glabrous) skin, which is typically insulated from the environment (with clothes in humans and with fur in non‐human mammals). Thermal signals from hairy skin represent a temperature of the insulated superficial layer of the body and provide feedback to the thermoregulation system. It is explained that this feedback is auxiliary, both negative and positive, and that it reduces the system's response time and load error. Non‐hairy (glabrous) skin covers specialized heat‐exchange organs (e.g. the hand), which are also used to explore the environment. In thermoregulation, these organs are primarily effectors. Their main thermosensory‐related role is to assess local temperatures of objects explored; these local temperatures are feedforward signals for various behaviours. Non‐hairy skin also contributes to the feedback for thermoregulation, but this contribution is limited. Autonomic (physiological) thermoregulation does not use feedforward signals. Thermoregulatory behaviours use both feedback and feedforward signals. Implications of these principles to thermopharmacology, a new approach to achieving biological effects by blocking temperature signals with drugs, are discussed.
Species distribution modelling for plant communities: stacked single species or multivariate modelling approaches?
Authors: Henderson Emilie B. , Ohmann Janet L. , Gregory Matthew J. , Roberts Heather M. , Zald Harold
Published: January 2014

Aim

Landscape management and conservation planning require maps of vegetation composition and structure over large regions. Species distribution models (SDMs) are often used for individual species, but projects mapping multiple species are rarer. We compare maps of plant community composition assembled by stacking results from many SDMs with multivariate maps constructed using nearest‐neighbor imputation.

Location

Western Cascades ecoregion, Oregon and California, USA.

Methods

We mapped distributions and abundances of 28 tree species over 4,007,110 ha at 30‐m resolution using three approaches: SDMs using machine learning (random forest) to yield: (1) binary (RF_Bin); (2) basal area (abundance; RF_Abund) predictions; and (3) multi‐species basal area predictions using a nearest‐neighbor imputation variant based on random forest (RF_NN). We evaluated accuracy of binary predictions for all models, compared area mapped with plot‐based areal estimates, assessed species abundance at two spatial scales and evaluated communities for species richness, problematic compositional errors and overall community composition.

Results

RF_Bin yielded the strongest binary predictions (median True Skill Statistics; RF_Bin: 0.57, RF_NN: 0.38, RF_Abund: 0.27). Plot‐scale predictions of abundance were poor for RF_Abund and RF_NN (median Agreement Coefficient (AC): −1.77 and −2.28), but strong when summarized over 50‐km radius tessellated hexagons (median AC for both: 0.79). RF_Abund's strength with abundance and weakness with binary predictions stems from predicting small values instead of zeros. The number of zero value predictions from RF_NN was closest to counts of zeros in the plot data. Correspondingly, RF_NN's map‐based species area estimates closely matched plot‐based area estimates. RF_NN also performed best for community‐level accuracy metrics.

Conclusions

RF_NN was the best technique for building a broad‐scale map of diversity and composition because the modelling framework maintained inter‐species relationships from the input plot data. Re‐assembling communities from single variable maps often yielded unrealistic communities. Although RF_NN rarely excelled at single species predictions of presence or abundance, it was often adequate to many (but not all) applications in both dimensions. We discuss our results in the context of map utility for applications in the fields of ecology, conservation and natural resource management planning. We highlight how RF_NN is well‐suited for mapping current but not future vegetation.
Scandinavian Society for Cell Toxicology – Thirty Years of Scientific Pioneering
Authors: Walum Erik
Published: January 2014

In 1983, cell toxicologists from the Nordic countries formed the Scandinavian Society for Cell Toxicology, the SSCT, on the initiative of the Swedish cell toxicologist Björn Ekwall, 1940–2000. The missions of the Society were established: to arrange annual meetings for toxicologists to discuss and promote the study of effects of chemicals in cellular models and to take on the responsibility for performing a large international study. The second mission was concretized in the form of the Multicentre Evaluation of In vitro Cytotoxicity, that is, the MEIC programme, directed by B. Ekwall, at an evaluation of the predictive value for human toxicity of in vitro cytotoxicity tests.