bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer-assisted design for scaling up systems based on DNA reaction networks
Authors: Aubert Nathanaël , Mosca Clément , Fujii Teruo , Hagiya Masami , Rondelez Yannick
Published: January 2014

In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual
in vitro
implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne
et al.
's Oligator or Padirac
et al.
's bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the possibility to use CMA-ES, a state-of-the-art optimization algorithm that will automatically evolve parameters chosen by the user to try to match a specified behaviour. Finally, because all possible functionality cannot be captured by a single software, DACCAD includes the possibility to export a system in the synthetic biology markup language, a widely used language for describing biological reaction systems. DACCAD can be downloaded online at
http://www.yannick-rondelez.com/downloads/
.
A Silurian short-great-appendage arthropod
Authors: Siveter Derek J. , Briggs Derek E. G. , Siveter David J. , Sutton Mark D. , Legg David , Joomun Sarah
Published: January 2014

A new arthropod,Enalikter aphsongen. et sp. nov., is described from the Silurian (Wenlock Series) Herefordshire Lagerstätte of the UK. It belongs to the Megacheira (=short-great-appendage group), which is recognized here, for the first time, in strata younger than mid-Cambrian age. Discovery of this new Silurian taxon allows us to identify a Devonian megacheiran representative,Bundenbachiellus giganteusfrom the Hunsrück Slate of Germany. The phylogenetic position of megacheirans is controversial: they have been interpreted as stem chelicerates, or stem euarthropods, but whenEnalikterandBundenbachiellusare added to the most comprehensive morphological database available, a stem euarthropod position is supported.Enalikterrepresents the only fully three-dimensionally preserved stem-group euarthropod, it falls in the sister clade to the crown-group euarthropods, and it provides new insights surrounding the origin and early evolution of the euarthropods. Recognition ofEnalikterandBundenbachiellusas megacheirans indicates that this major arthropod group survived for nearly 100 Myr beyond the mid-Cambrian.
A syndrome of mutualism reinforces the lifestyle of a sloth
Authors: Pauli Jonathan N. , Mendoza Jorge E. , Steffan Shawn A. , Carey Cayelan C. , Weimer Paul J. , Peery M. Zachariah
Published: January 2014

Arboreal herbivory is rare among mammals. The few species with this lifestyle possess unique adaptions to overcome size-related constraints on nutritional energetics. Sloths are folivores that spend most of their time resting or eating in the forest canopy. A three-toed sloth will, however, descend its tree weekly to defecate, which is risky, energetically costly and, until now, inexplicable. We hypothesized that this behaviour sustains an ecosystem in the fur of sloths, which confers cryptic nutritional benefits to sloths. We found that the more specialized three-toed sloths harboured more phoretic moths, greater concentrations of inorganic nitrogen and higher algal biomass than the generalist two-toed sloths. Moth density was positively related to inorganic nitrogen concentration and algal biomass in the fur. We discovered that sloths consumed algae from their fur, which was highly digestible and lipid-rich. By descending a tree to defecate, sloths transport moths to their oviposition sites in sloth dung, which facilitates moth colonization of sloth fur. Moths are portals for nutrients, increasing nitrogen levels in sloth fur, which fuels algal growth. Sloths consume these algae-gardens, presumably to augment their limited diet. These linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle.
Ocean warming and acidification have complex interactive effects on the dynamics of a marine fungal disease
Authors: Williams Gareth J. , Price Nichole N. , Ushijima Blake , Aeby Greta S. , Callahan Sean , Davy Simon K. , Gove Jamison M. , Johnson Maggie D. , Knapp Ingrid S. , Shore-Maggio Amanda , Smith Jennifer E. , Videau Patrick , Work Thierry M.
Published: January 2014

Diseases threaten the structure and function of marine ecosystems and are contributing to the global decline of coral reefs. We currently lack an understanding of how climate change stressors, such as ocean acidification (OA) and warming, may simultaneously affect coral reef disease dynamics, particularly diseases threatening key reef-building organisms, for example crustose coralline algae (CCA). Here, we use coralline fungal disease (CFD), a previously described CCA disease from the Pacific, to examine these simultaneous effects using both field observations and experimental manipulations. We identify the associated fungus as belonging to the subphylumUstilaginomycetesand show linear lesion expansion rates on individual hosts can reach 6.5 mm per day. Further, we demonstrate for the first time, to our knowledge, that ocean-warming events could increase the frequency of CFD outbreaks on coral reefs, but that OA-induced lowering of pH may ameliorate outbreaks by slowing lesion expansion rates on individual hosts. Lowered pH may still reduce overall host survivorship, however, by reducing calcification and facilitating fungal bio-erosion. Such complex, interactive effects between simultaneous extrinsic environmental stressors on disease dynamics are important to consider if we are to accurately predict the response of coral reef communities to future climate change.
Oestradiol and prostaglandin F2α regulate sexual displays in females of a sex-role reversed fish
Authors: Gonçalves David , Costa Silvia Santos , Teles Magda C. , Silva Helena , Inglês Mafalda , Oliveira Rui F.
Published: January 2014

The mechanisms regulating sexual behaviours in female vertebrates are still poorly understood, mainly because in most species sexual displays in females are more subtle and less frequent than displays in males. In a sex-role reversed population of a teleost fish, the peacock blenny
Salaria pavo
, an external fertilizer, females are the courting sex and their sexual displays are conspicuous and unambiguous. We took advantage of this to investigate the role of ovarian-synthesized hormones in the induction of sexual displays in females. In particular, the effects of the sex steroids oestradiol (E2) and testosterone (T) and of the prostaglandin F2α (PGF2α) were tested. Females were ovariectomized and their sexual behaviour tested 7 days (sex steroids and PGF2α) and 14 days (sex steroids) after ovariectomy by presenting females to an established nesting male. Ovariectomy reduced the expression of sexual behaviours, although a significant proportion of females still courted the male 14 days after the ovary removal. Administration of PGF2α to ovariectomized females recovered the frequency of approaches to the male's nest and of courtship displays towards the nesting male. However, E2 also had a positive effect on sexual behaviour, particularly on the frequency of approaches to the male's nest. T administration failed to recover sexual behaviours in ovariectomized females. These results suggest that the increase in E2 levels postulated to occur during the breeding season facilitates female mate-searching and assessment behaviours, whereas PGF2α acts as a short-latency endogenous signal informing the brain that oocytes are mature and ready to be spawned. In the light of these results, the classical view for female fishes, that sex steroids maintain sexual behaviour in internal fertilizers and that prostaglandins activate spawning behaviours in external fertilizers, needs to be reviewed.
Spatial scale and sampling resolution affect measures of gap disturbance in a lowland tropical forest: implications for understanding forest regeneration and carbon storage
Authors: Lobo Elena , Dalling James W.
Published: January 2014

Treefall gaps play an important role in tropical forest dynamics and in determining above-ground biomass (AGB). However, our understanding of gap disturbance regimes is largely based either on surveys of forest plots that are small relative to spatial variation in gap disturbance, or on satellite imagery, which cannot accurately detect small gaps. We used high-resolution light detection and ranging data from a 1500 ha forest in Panama to: (i) determine how gap disturbance parameters are influenced by study area size, and the criteria used to define gaps; and (ii) to evaluate how accurately previous ground-based canopy height sampling can determine the size and location of gaps. We found that plot-scale disturbance parameters frequently differed significantly from those measured at the landscape-level, and that canopy height thresholds used to define gaps strongly influenced the gap-size distribution, an important metric influencing AGB. Furthermore, simulated ground surveys of canopy height frequently misrepresented the true location of gaps, which may affect conclusions about how relatively small canopy gaps affect successional processes and contribute to the maintenance of diversity. Across site comparisons need to consider how gap definition, scale and spatial resolution affect characterizations of gap disturbance, and its inferred importance for carbon storage and community composition.
Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir
Authors: Huy Hangsak , Jin Long , Lee Keun Chul , Kim Song-Gun , Lee Jung-Sook , Ahn Chi-Yong , Oh Hee-Mock
Published: January 2014

Strain CH15-11T, isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria, was found to be a Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain CH15-11T grew optimally at pH 7 and 28–30 °C. According to a phylogenetic tree based on 16S rRNA gene sequences, strain CH15-11T belonged to the genus

Sphingomonas

and clustered with

Sphingomonas sediminicola

Dae 20T, with which it shared the highest 16S rRNA gene sequence similarity (97.6 %). Chemotaxonomic analysis showed that strain CH15-11T had characteristics typical of members of the genus

Sphingomonas

, such as the presence of sphingoglycolipid, ubiquinone Q-10 and sym-homospermidine. Plus, strain CH15-11T included summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The genomic DNA G+C content was 65.6 mol%. Sequence data showed that strain CH15-11T was most closely related to

Sphingomonas sediminicola

Dae 20T (97.6 %),

Sphingomonas ginsengisoli

Gsoil 634T (97.2 %) and
Sphingomonas jaspi TDMA-16T (97.0 %). However, the DNA–DNA relatedness values between strain CH15-11T and the most closely related type strains were within a range of 35–59 %. Thus, based on the phylogenetic, phenotypic and genetic data, strain CH15-11T was classified as a member of the genus

Sphingomonas

as a representative of a novel species, for which the name Sphingomonas daechungensis sp. nov. is proposed. The type strain is CH15-11T ( = KCTC 23718T = JCM 17887T).
Sneathiella chungangensis sp. nov., isolated from a marine sand, and emended description of the genus Sneathiella
Authors: Siamphan Chatuphon , Kim Hyungjin , Lee Jung-Sook , Kim Wonyong
Published: January 2014

A Gram-stain-negative, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1294T, was isolated from a sand sample and its taxonomic position was investigated using a polyphasic approach. The strain grew optimally at pH 6.5 and 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1294T formed a lineage with member of the genus

Sneathiella

and exhibited similarity to

Sneathiella glossodoripedis

MKT133T (96.3 % similarity) and

Sneathiella chinensis

LMG 23452T (95.1 % similarity). Strain CAU 1294T contained Q-10 as the predominant respiratory quinone. C18 : 1ω7c, C16 : 0 and cyclo-C19 : 0ω8c were the major cellular fatty acids. The polar lipids were composed of phosphatidylethanolamine, phosphatidylmethylethanolamine and two unidentified phospholipids. The DNA G+C content was 56.6 mol%. On the basis of these results, strain CAU 1294T is considered to represent a novel species of the genus

Sneathiella

, for which the name Sneathiella chungangensis is proposed. The type strain is CAU 1294T ( = KCTC 32476T = CECT 8513T). An emended description of the genus

Sneathiella

is also proposed.
Complex behavioral manipulation drives mismatch between host and parasite diversity
Authors: Baccaro Fabricio B. , de Araújo João P. M. , Evans Harry C. , Souza Jorge L. P. , Magnusson William E. , Hughes David P.
Published: January 2014

Parasites and hosts are intimately associated such that changes in the diversity of one partner are thought to lead to changes in the other. We investigated this linked diversity hypothesis in a specialized ant-Ophiocordycepssystem in three forests across 750 km in Central Amazonia. All species belonging to the fungal genusOphiocordycepsassociated with ants have evolved some degree of behavioral control to increase their own transmission, but the leaf-biting behavior is the most complex form of host manipulation. Such a system requires control of the mandibular muscles and a distinct shift in behavior, from climbing vegetation to walking on leaves to rasping leaf veins in the seconds before death. The need to induce complex behavior may limit host availability and represent a constraint on parasite diversity. The consequence for community structure is that complex behavioral manipulation leads to a mismatch between ant hosts and the diversity of their fungal parasites.
Particle size distribution and optimal capture of aqueous macrobial eDNA
Authors: Turner Cameron R. , Barnes Matthew A. , Xu Charles C.Y. , Jones Stuart E. , Jerde Christopher L. , Lodge David M.
Published: January 2014

1. Detecting aquatic macroorganisms with environmental DNA (eDNA) is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified, and assayed - are poorly understood. 2. The size of aquatic particles provides clues about their origin, state, and fate. We used sequential filtration size fractionation to measure, for the first time, the particle size distribution (PSD) of macrobial eDNA, specifically Common Carp (hereafter referred to as Carp) eDNA. We compared it to the PSDs of total eDNA (from all organisms) and suspended particle matter (SPM). We quantified Carp mitochondrial eDNA using a custom qPCR assay, total eDNA with fluorometry, and SPM with gravimetric analysis. 3. In a lake and a pond, we found Carp eDNA in particles from >180 to <0.2 µm, but it was most abundant from 1-10 µm. Total eDNA was most abundant below 0.2 µm and SPM was most abundant above 100 µm. SPM was ≤0.1% total eDNA, and total eDNA was ≤0.0004% Carp eDNA. 0.2 µm filtration maximized Carp eDNA capture (85%±6%) while minimizing total (i.e., non-target) eDNA capture (48%±3%), but filter clogging limited this pore size to a volume <250 mL. To mitigate this limitation we estimated a continuous PSD model for Carp eDNA and derived an equation for calculating isoclines of pore size and water volume that yield equivalent amounts of Carp eDNA. 4. Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling plays an important role in its fate. For optimal eDNA capture, we recommend 0.2 µm filtration or a combination of larger pore size and water volume that exceeds the 0.2 µm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms. Our method for eDNA particle size analysis enables future research to compare the PSDs of eDNA from other organisms and environments, and to easily apply them for ecological monitoring.
Widespread suppression of intragenic transcription initiation by H-NS
Authors: Singh Shivani S. , Singh Navjot , Bonocora Richard P. , Fitzgerald Devon M. , Wade Joseph T. , Grainger David C.
Published: January 2014

Widespread intragenic transcription initiation has been observed in many species. Here we show that the Escherichia coli ehxCABD operon contains numerous intragenic promoters in both sense and antisense orientations. Transcription from these promoters is silenced by the histone-like nucleoid structuring (H-NS) protein. On a genome-wide scale, we show that 46% of H-NS-suppressed transcripts in E. coli are intragenic in origin. Furthermore, many intergenic promoters repressed by H-NS are for noncoding RNAs (ncRNAs). Thus, a major overlooked function of H-NS is to prevent transcription of spurious RNA. Our data provide a molecular description for the toxicity of horizontally acquired DNA and explain how this is counteracted by H-NS.
An E4 Ligase Facilitates Polyubiquitination of Plant Immune Receptor Resistance Proteins in Arabidopsis
Authors: Huang Yan , Minaker Sean , Roth Charlotte , Huang Shuai , Hieter Philip , Lipka Volker , Wiermer Marcel , Li Xin
Published: January 2014

Proteins with nucleotide binding and leucine-rich repeat domains (NLRs) serve as immune receptors in animals and plants that recognize pathogens and activate downstream defense responses. As high accumulation of NLRs can result in unwarranted autoimmune responses, their cellular concentrations must be tightly regulated. However, the molecular mechanisms of this process are poorly detailed. The F-box protein Constitutive expressor of PR genes 1 (CPR1) was previously identified as a component of a Skp1, Cullin1, F-box protein E3 complex that targets NLRs, including Suppressor of NPR1, Constitutive 1 (SNC1) and Resistance to Pseudomonas syringae 2 (RPS2), for ubiquitination and further protein degradation. From a forward genetic screen, we identified Mutant, snc1-enhancing 3 (MUSE3), an E4 ubiquitin ligase involved in polyubiquitination of its protein targets. Knocking out MUSE3 in Arabidopsis thaliana results in increased levels of NLRs, including SNC1 and RPS2, whereas overexpressing MUSE3 together with CPR1 enhances polyubiquitination and protein degradation of these immune receptors. This report on the functional role of an E4 ligase in plants provides insight into the scarcely understood NLR degradation pathway.
5-Propyl-6-(p-tolylsulfanyl)pyrimidine-2,4(1H,3H)-dione
Authors: Al-Omary Fatmah A. M. , Ghabbour Hazem A. , El-Emam Ali A. , Chidan Kumar C. S. , Fun Hoong-Kun
Published: January 2014

In the title pymiridine-2,4-dione derivative, C14H16N2O2S, the dihedral angle between the six-membered rings is 66.69 (10)°. The molecule is twisted about the Cp—S (p = pyrimidine) bond, with a C—S—C—N torsion angle of −19.57 (16)°. In the crystal, adjacent molecules form inversion dimers through pairs of strong N—H...O hydrogen bonds, generating anR22(8) ring motif. The dimers are connected into chains extending along thec-axis direction through additional N—H...O hydrogen bonds.
5-Iodo-7-methyl-2-(4-methylphenyl)-3-methylsulfinyl-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: January 2014

In the title compound, C17H15IO2S, the dihedral angle between the benzofuran group (r.m.s. deviation = 0.009 Å) and the 4-methylbenzene ring is 12.69 (5)°. In the crystal, molecules are linkedviapairs of I...O [I...O = 3.164 (1) Å, C—I...O = 166.63 (5)°] contacts into inversion-related dimers.
7-Diethylamino-3-{(E)-4-[(E)-2-(pyridin-4-yl)ethenyl]styryl}-2H-chromen-2-one
Authors: Zhou Li-Ping , Long Ling-Liang
Published: January 2014

In the title coumarin derivative, C28H26N2O2, the coumarin unit is approximately planar, with a maximum deviation of 0.048 (3) Å. The central benzene ring is oriented at dihedral angles of 30.15 (14) and 10.51 (11)°, respectively, to the pyridine ring and coumarin ring system. In the crystal, weak C—H...O and C—H...N hydrogen bonds and weak C—H...π interactions link the molecules into a three-dimensional supramolecular architecture.
N-(3-Chloro-1-methyl-1H-indazol-5-yl)-4-methylbenzenesulfonamide
Authors: Chicha Hakima , Rakib El Mostapha , Amiri Ouafa , Saadi Mohamed , El Ammari Lahcen
Published: January 2014

The asymmetric unit of the title compound, C15H14ClN3O2S, contains two independent molecules showing different conformations: in one molecule, the indazole ring system makes a dihedral angle of 51.5 (1)° with the benzene ring whereas in the other, the indazole unit is almost perpendicular to the benzene ring [dihedral angle 77.7 (1)°]. In the crystal, the molecules are linked by N—H...N and N—H...O hydrogen bonds, forming a set of four molecules linked in pairs about an inversion centre.
Chlorido[5-methoxy-1H-benzimidazole-2(3H)-thione-κS]bis(triphenylphosphane-κP)copper(I) methanol disolvate
Authors: Meng Qing-Xuan
Published: January 2014

In the title complex, [CuCl(C8H8N2OS)(C18H15P)2]·2CH3OH, the CuIion is coordinated by one chloride anion, one S atom from the 5-methoxy-1H-benzimidazole-2(3H)-thione ligand and two P atoms from two triphenylphosphine ligands in a distorted tetrahedral geometry. One of the N-bound H atoms is involved in an intramolecular N—H...Cl hydrogen bond, while another one interacts with the solvent methanol moleculeviaan N—H...O hydrogen bond. Intermolecular O—H...Cl and O—H...O hydrogen bonds link two further complex molecules and four solvent molecules into a centrosymmetric structural unit. The short distance of 3.624 (4) Å between the centroids of the five- and the six-membered rings of two benzimidazole fragments indicates the presence of π–π interactions.
(E)-3-(9-Ethyl-9H-carbazol-3-yl)-1-(2-methoxyphenyl)prop-2-en-1-one
Authors: Lai Hongshan , Gallucci Judith C. , Li Chenglong
Published: January 2014

In the title molecule, C24H21NO2, the dihedral angle between the carbazole ring system [with a maximum deviation of 0.052 (2) Å] and the benzene ring is 38.6 (1)°. In the crystal, weak bifurcated (C—H)2...O hydrogen bonds link the molecules into chains along [100].
Cytosinium hydrogen selenite
Authors: Takouachet Radhwane , Benali-Cherif Rim , Benali-Cherif Nourredine
Published: January 2014

In the crystal structure of the title salt, C4H6N3O+·HSeO3−, systematic name 6-amino-2-methylidene-2,3-dihydropyrimidin-1-ium hydrogen selenite, the hydrogenselenite anions and the cytosinium cations are linkedviaN—H...O, N—H...Se, O—H...O, O—H··Se and C—H...O hydrogen bonds, forming a three-dimensional framework.
3,4-Dimethylphenyl benzoate
Authors: Moreno-Fuquen Rodolfo , Rendón Mauricio , Kennedy Alan R.
Published: January 2014

In the title compound, C15H14O2, the terminal rings form a dihedral angle of 52.39 (4)°. The mean plane of the central ester group [r.m.s. deviation = 0.0488 Å] is twisted away from the benzene and phenyl rings by 60.10 (4) and 8.67 (9)°, respectively. In the crystal, molecules are linked by weak C—H...O hydrogen bonds, formingC(6) chains which run along [100].
N-(4-Methoxybenzoyl)-2-methylbenzenesulfonamide
Authors: Sreenivasa S. , Palakshamurthy B. S. , Madankumar S. , Lokanath N. K. , Suchetan P. A.
Published: January 2014

In the title compound, C15H15NO4S, the dihedral angle between the aromatic rings is 80.81 (1)° and the dihedral angle between the planes defined by the S—N—C=O fragment and the sulfonyl benzene ring is 86.34 (1)°. In the extended structure, dimers related by a crystallographic twofold axis are connected by pairs of both N—H...O hydrogen bonds and C—H...O interactions, which generateR22(8) andR22(14) loops, respectively. A weak aromatic π–π stacking interaction is also observed [centroid–centroid separation = 3.7305 (3) Å].
2-(1H-Benzimidazol-2-yl)phenol
Authors: Prakash S. M. , Thiruvalluvar A. , Rosepriya S. , Srinivasan N.
Published: January 2014

The title molecule, C13H10N2O, is essentially planar, the maximum deviation from the plane of the non-H atoms being 0.016 (2) Å. The imidazole ring makes a dihedral angle of 0.37 (13)° with the attached benzene ring. An intramolecular O—H...N hydrogen bond generates anS(6) ring motif. In the crystal, molecules are linked through N—H...O hydrogen bonds, forming chains propagating in [001]. The crystal packing also features four π–π stacking interactions involving the imidazole ring, fused benzene ring and attached benzene ring system [centroid–centroid distances = 3.6106 (17), 3.6108 (17), 3.6666 (17) and 3.6668 (17) Å].
7-Methoxy-2-phenylquinoline-3-carbaldehyde
Authors: Hayour Hasna , Bouraiou Abdelmalek , Bouacida Sofiane , Benzerka Saida , Belfaitah Ali
Published: January 2014

In the title molecule, C17H13NO2, the phenyl ring is inclined to the quinoline ring system by 43.53 (4)°. In the crystal, molecules are linkedviaC—H...O hydrogen bonds, forming double-stranded chains propagating along [011]. These chains are linkedviaπ–π interactions involving inversion-related quinoline rings; the shortest centroid–centroid distance is 3.6596 (17) Å.
Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase
Authors: Mauracher Stephan Gerhard , Molitor Christian , Al-Oweini Rami , Kortz Ulrich , Rompel Annette
Published: January 2014

Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit) and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na6[TeW6O24]·22H2O as a co-crystallization agent.
Social capital and accountability in grass‐roots NGOs
Authors: Awio Godwin , Northcott Deryl , Lawrence Stewart
Published: January 2014

Purpose

This paper aims to examine how small, grass‐roots non‐governmental organisations (NGOs) account for their actions and expenditures and how this accountability is discharged to, and benefits, the citizens they serve.

Design/methodology/approach

The paper draws on social capital theory to inform an interpretive analysis of documentary and interview evidence. The empirical material is derived from CHAI policy and project documents, coupled with interviews with 75 participants at the national, district and community levels of the CHAI programme. An illustrative case study is presented of an NGO that delivers welfare services to a Ugandan community affected by the HIV/AIDS pandemic.

Findings

The research finds that, by harnessing the attributes of social capital, grass‐roots NGOs can supplement formal accountability obligations to funders with effective “bottom‐up” accountability to an often overlooked NGO stakeholder group – the service beneficiaries, with positive outcomes for social services delivery.

Research limitations/implications

The research examines a single community‐led public welfare initiative (the Ugandan CHAI), with a particular focus on one illustrative grass‐roots NGO within that programme. Nevertheless, it offers insights into how accountability mechanisms can be reconceptualised to suit the context of developing countries where smaller NGOs increasingly operate.

Practical implications

The potential for less formal, “bottom‐up” accountability mechanisms is illustrated using the case of the Ugandan community‐led HIV/AIDS initiative (CHAI), a programme for delivering social services to communities ravaged by the effects of the HIV/AIDS pandemic.

Originality/value

This research addresses the lack of empirical studies of smaller, grass‐roots NGOs in the accounting literature. It also contributes to the under‐researched area of how NGOs can appropriately discharge their accountability obligations to beneficiaries. The use of social capital theory to inform the study is also a novel contribution of this paper.
Open innovation and SMEs
Authors: Vega Arturo , Brown David , Chiasson Mike
Published: January 2014

Purpose

The purpose of this paper is to explore, through the use of a multidisciplinary lens, the policy context and the scope for improvements in university‐based public programmes focused on improving innovation in small and medium enterprises (SMEs).

Design/methodology/approach

The authors use the street‐level bureaucracy (SLB), combined with the systems of innovation approach (SIA) and diagnostic analysis (DA) to understand the context components that impact on public programme services. The study is part of a research programme oriented to the diffusion of information systems in SMEs and which used original interview‐based programme support case studies, interviews with regional policy managers, and documentation relating to the policy system and different public programmes. Although the empirical work was UK and European Union centric the results of the research have wide applicability.

Findings

The paper establishes the importance of programme contexts for diagnosing and providing a basis for public programme improvements. It further demonstrates the robustness of the context analysis framework to provide insights into proposed policy changes. The responsibility of improving programme contexts relies on actors that operate outside programme organisations, for instance EU funding bodies, government departments in charge of SME policies, public‐private partnerships, and private evaluators. Given this complexity it is suggested that SME associations have a potentially important role in increasing participation by SMEs in the public programme for innovation and knowledge support policy. Despite possible policy changes the requirement for public programme support for innovation and hence the role of universities as programme providers is confirmed and expanded.

Research limitations/implications

The results demonstrate the value of a multidisciplinary framework to analyse programme interventions at both macro and micro levels and provide a basis for programme policy and policy implementation improvements.

Originality/value

This research is a novel attempt to use the SLB, SIA and DA to public programme university‐based interventions in SMEs and SME policies in general. It complements extant research on open innovation and knowledge exchange by extending the concept of public programme contexts. Beneficiaries of the findings include policy makers, programme organisations, universities, SME associations, and researchers.
Restoration of a megaherbivore: landscape‐level impacts of white rhinoceros in Kruger National Park, South Africa
Authors: Cromsigt Joris P. G. M. , te Beest Mariska
Published: January 2014

Megaherbivores have been lost from most ecosystems world‐wide, and current increases in poaching of rhino and elephant spp. threaten their status in the systems where they still occur. Although megaherbivores are said to be key drivers of ecosystem structure and functioning, empirical evidence is strongly biased to studies on African elephant. We urgently need a better understanding of the impact of other megaherbivore species to predict the consequences of megaherbivore loss.

We used a unique ‘recolonization experiment’ to test how a megagrazer, white rhinoceros, is affecting the structure of savanna grasslands in Kruger National Park (KNP).

With a 30‐year record of rhinoceros distribution, we quantified how they recolonized KNP following their re‐introduction. This allowed us to identify landscapes with high rhino densities and long time since recolonization versus landscapes with low rhino densities that were recolonized more recently but were otherwise biophysically similar. We recorded grassland heterogeneity on 40 transects covering a total of 30 km distributed across both landscapes. We used two proxies of grassland heterogeneity: % short grass cover and number of grazing lawn patches. Grazing lawns are patches with specific communities of prostrate‐growing stoloniferous short grass species.

Short grass cover was clearly higher in the high rhino impact (17.5%) than low rhino impact landscape (10.7%). Moreover, we encountered ~20 times more grazing lawns in the high rhino impact landscape. The effect of rhino on number of lawns and on short grass cover was similar to the two dominant geologies in KNP, basalt‐derived versus granite‐derived soils.

Synthesis. We provide empirical evidence that white rhinoceros may have started to change the structure and composition of KNP's savanna grasslands. It remains to be tested if these changes lead to other ecological cascading effects. However, our results highlight that the current rhino poaching crisis may not only affect the species, but also threaten the potential key role of this megaherbivore as a driver of savanna functioning.
Phylogenomic reconstruction of archaeal fatty acid metabolism
Authors: Dibrova Daria V. , Galperin Michael Y. , Mulkidjanian Armen Y.
Published: January 2014

While certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analysing the genomic distribution of the key lipid‐related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial‐type β‐oxidation of fatty acids [acyl‐coenzyme A (CoA) dehydrogenase, enoyl‐CoA hydratase and 3‐hydroxyacyl‐CoA dehydrogenase] with paralogs of the archaeal acetyl‐CoA C‐acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β‐oxidation enzymes working in the reverse direction could potentially catalyse biosynthesis of fatty acids, with paralogs of acetyl‐CoA C‐acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy‐transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications.
Association study of human leukocyte antigen‐DRB1 alleles with rheumatoid arthritis in Algerian patients
Authors: Djidjik Réda , Allam Ines , Douaoui Sanaa , Meddour Yanis , Cherguelaîne Khaled , Tahiat Azzedine , Raaf Nabil , Abdessemed Amina , Khaldoun Naouel , Bahaz Naima , Chaib Samia , Ladjouze‐Rezig Aicha , Ghaffor Mohamed
Published: January 2014

Introduction

Rheumatoid arthritis (RA) is a chronic, systemic, inflammatory and multifactorial disease. Genetic predisposition seems to play an important role. The aim of this study is to explore the relationship between human leukocyte antigen (HLA)‐DRB1 alleles and susceptibility, clinical and biological features ofRAin an Algerian patient population.

Methods

Using polymerase chain reaction – sequence specific primers (SSP), 134RApatients and 132 healthy controls were genotyped forHLA‐DRB1 andHLA‐DRB1*04 subtypes.

Results

HLA‐DRB1*04 was found to have increased frequency in theRAgroup compared to controls (P < 0.001,OR = 3.14), and was associated with anti‐citrullinated protein antibodies positivity (ACPA) (P = 0.01,OR = 2.35). In contrast,HLA‐DRB1*07 was found to have a decreased frequency in patients compared to controls (P = 0.003,OR = 0.44) and significant decrease was observed in patients with the rheumatoid factor (RF) positivity subgroup (P = 0.009,OR = 0.29).HLA‐DRB1*04:05 was associated withRA(P = 0.005,OR = 3.41), whereas,HLA‐DRB1*04:02 showed a protective effect againstRA(P = 0.003,OR = 0.20).

Conclusions

HLA‐DRB1*04 was associated with increased risk forRAandACPApositivity, whileHLA‐DRB1*07 was associated with reduced risk forRAandRFsynthesis in Algerian patients.
The fourth‐corner solution – using predictive models to understand how species traits interact with the environment
Authors: Brown Alexandra M. , Warton David I. , Andrew Nigel R. , Binns Matthew , Cassis Gerasimos , Gibb Heloise
Published: January 2014

An important problem encountered by ecologists in species distribution modelling (SDM) and in multivariate analysis is that of understanding why environmental responses differ across species, and how differences are mediated by functional traits.

We describe a simple, generic approach to this problem – the core idea being to fit a predictive model for species abundance (or presence/absence) as a function of environmental variables, species traits and their interaction.

We show that this method can be understood as a model‐based approach to the fourth‐corner problem – the problem of studying the environment–trait association using matrices of abundance or presence/absence data across species, environmental data across sites and trait data across species. The matrix of environment–trait interaction coefficients is the fourth corner.

We illustrate that compared with existing approaches to the fourth‐corner problem, the proposed model‐based approach has advantages in interpretability and its capacity to perform model selection and make predictions.

To illustrate the method we used a generalized linear model with a LASSO penalty, fitted to data sets from four different studies requiring different models, illustrating the flexibility of the proposed approach.

Predictive performance of the model is compared with that of fitting SDMs separately to each species, and in each case, it is shown that the trait model, despite being much simpler, had comparable predictive performance, even significantly outperforming separate SDMs in some cases.
Cultural effects in emotion and gender recognition
Authors: Gul Amara , Humphreys Glyn W.
Published: January 2014

There is evidence for cultural differences in how people respond to basic properties of faces. We examined task switching between two properties of faces, emotion and gender, for individuals drawn fromWestern (WhiteUKcitizens) andAsian (Pakistani) cultures. There were three main results of interest. First, there was a double dissociation between gender and emotion classification across the participant populations –Western participants were faster to make gender than emotion classifications whileAsian participants were faster to make emotion than gender classifications. It is argued that the different patterns of results reflect the greater attentional weight given to contrasting face dimensions in the different cultures, and the dependence on using different attributes to make gender discriminations in individuals from varying cultures. Second,Asian participants showed smaller switch costs overall than didWhiteBritish participants. This result may be attributed to effects of bilingualism in theAsian participants, which results in their having greater executive resources. Third, emotion decisions showed larger switch costs than gender decisions but essentially because emotion decisions benefited from priming on non‐switch trials. It is argued that emotion decisions benefit from the activation of a specific processing module across consecutive trials.
Face recognition as a predictor of social cognitive ability: Effects of emotion and race on face processing
Authors: Chen Jiaqing
Published: January 2014

The human face conveys important social signals when people interact in social contexts. The current study investigated the relationship between face recognition and emotional intelligence, and how societal factors of emotion and race influence people's face recognition. Participants’ recognition accuracy, reaction time, sensitivity, and response bias were measured to examine their face‐processing ability. Fifty Caucasian undergraduates (38 females, 12 males; average age = 21.76 years) participated in a face recognition task in which they discriminated previously presented target faces from novel distractor faces. A positive correlation between participants’ emotional intelligence scores and their performance on the face recognition task was observed, suggesting that face recognition ability was associated with emotional or social intelligence. Additionally, Caucasian participants recognized happy faces better than angry or neutral faces. It was also observed that people recognized Asian faces better than Caucasian ones, which appears to be contradictory to the classic other‐race effect. The present study suggests that some societal factors could influence face processing, and face recognition ability could in turn predict social intelligence.
Homoisoflavanone prevents mast cell activation and allergic responses by inhibition of Syk signaling pathway
Authors: Lee Y. S. , Hur S. , Kim T.‐Y.
Published: January 2014

Background

Mast cells play important roles in allergic inflammatory responses because they produce leukotrienes (LTs), prostaglandins (PGs), and a variety of inflammatory cytokines. Thus, pharmacological interventions for allergies have focused on inhibiting mast cell activation. Homoisoflavanone (HIF), isolated from Cremastra appendiculata Makino, has anti‐angiogenic activities; however, its effects on allergic reactions have not been determined. The aim of this study was to assess the inhibitory effects of HIF on mast cell activation, which is critical for anti‐allergic reaction and the underlying mechanisms.

Methods

Enzyme‐linked immunosorbent assays, quantitative real‐time PCR, western blot analyses, and degranulation assay were performed to measure pro‐inflammatory and allergic mediators in PMA/A23187‐ or IgE/antigen‐stimulated mouse bone marrow‐derived mast cells (BMMCs), HMC‐1, RBL‐1, or human PBMC‐derived mast cells treated with or without HIF. The anti‐allergic effects of HIF were determined in mouse models using dinitrophenol‐immunoglobulin E‐induced passive cutaneous anaphylaxis (PCA) and compound 48/80‐induced ear swelling.

Results

Homoisoflavanone down‐regulated PGD2, LTB4, and LTC4 production and inhibited the production of pro‐inflammatory cytokines, such as interleukin‐6 and tumor necrosis factor‐α in PMA/A23187‐ or IgE/antigen‐stimulated mast cells. The molecular mechanisms by which HIF caused these inhibitory effects were determined to be the inactivation of spleen tyrosine kinase (Syk) signaling and the concurrent suppression of cPLA2. HIF inhibited IgE‐mediated PCA and compound 48/80‐induced ear swelling in mouse.

Conclusions

Homoisoflavanone inhibited mast cell activation through the suppression of Syk pathway together with the inhibition of cPLA2. Thus, it might be a good candidate molecule for allergic diseases.
Beyond Raised Fields: Exploring Farming Practices and Processes of Agricultural Change in the Ancient Lake Titicaca Basin of the Andes
Authors: Bruno Maria C.
Published: January 2014

In the Lake Titicaca Basin of the Andes, narratives of agricultural change have focused exclusively on a single innovation: raised fields. In this article, I examine macrobotanical remains and other archaeological datasets to elucidate a wider range of past farming practices that contributed to processes of agricultural change on the Taraco Peninsula, Bolivia, during the Formative Period (1500 B.C.E.–C.E. 500). This analysis reveals strong continuities in crop selection through time, with farmers gradually diversifying a basic set of cultigens—quinoa and tubers—but never abandoning them. Patterns in wild plant species indicate continuity in agropastoral land use up to the Late Formative Period (second century C.E.) when the unintended consequences of long‐term tilling and camelid grazing transformed the botanical landscape into one that required a new set of practices to remove weeds and replenish nutrients to the soils. Examining how these practices and the farmers enacting them articulated with broader processes of demographic, environmental, and sociopolitical change reveals dynamic, multivariate courses of agricultural change even before the inclusion of raised fields.
Public Indigeneity, Language Revitalization, and Intercultural Planning in a Native Amazonian Beauty Pageant
Authors: Wroblewski Michael
Published: January 2014

According to its 2008 Constitution, Ecuador is a “plurinational” and “intercultural” state. In this article, I examine the creative expounding of constitutional plurinationality–interculturality by indigenous Kichwa activists in the city of Tena in the Amazonian province of Napo. Through a popular annual native beauty pageant, members of a rising, elite sector of professional indigenous intellectuals draw on the rhetoric of constitutional interculturality in order to establish a space for local Kichwa cultural and linguistic practices in the dominant sociocultural order. Meanwhile, these visionaries are working to inscribe new models of public Amazonian Indian identity and institute a controversial new code of cultural expression. Their intercultural code blends standardized Kichwa language and its inherent political ideologies with symbols of an essentialized gendered Amazonian Kichwa identity. This intercultural code is then presented to multiethnic audiences as the urban speaking mode of the new intercultural Indian. The popularizing of the intercultural code represents a profound reconfiguration of long‐held ethnolinguistic categories and identities, challenging old dichotomies of “public” versus “private,” “power” versus “purity,” “dominant” versus “indigenous,” and even “Spanish” versus “Kichwa” that have long characterized coding principles in popular ideologies.