bluuebunny/crossref_metadata_2025 huggingface dataset:
piggyBac
transposition into primordial germ cells is an efficient tool for transgenesis in chickens
Authors: Park Tae Sub , Han Jae Yong
Published: May 2012

Transgenic birds embody one of the most potent and exciting research tools in biotechnology for agriculture, medicine, and model animals. To date, retrovirus- or lentivirus-mediated transgenesis has been established in chickens and quail. However, despite having a valid technique for viral transduction to achieve transgenic birds, many obstacles exist for practical applications because of relatively low and variable rates of germ-line transmission and transgenic offspring showing transgene silencing, as well as safety issues related to viral vector use. Thus, the generation of transgenic poultry by nonviral integration is a prerequisite for the introduction of biotechnology to practical applications. Herein, we show that a germ-line–competent chicken primordial germ-cell (PGC) line was established with high efficiency of transmission to offspring and that
piggyBac
transposition into PGCs improved the efficiency of transgenic chicken production and led to high-level transgene expression. GFP transgene-expressing donor PGC-transferred recipient chickens produced donor-derived progenies, and the germ-line transmission efficiency of donor PGCs was 95.2% on average. Subsequently, half of the donor-derived offspring (52.2%) were transgenic chicks because GFP-expressing donor PGCs, in which a transgene was inserted into one chromosome 20, were heterozygous. In all of the transgenic chickens, GFP expression was constant and strong, regardless of age. Our results demonstrate that
piggyBa
c transposition into the chicken PGC line could be the surest way to generate transgenic chickens safely for practical applications.
Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria
Authors: Cui Longzhu , Neoh Hui-min , Iwamoto Akira , Hiramatsu Keiichi
Published: May 2012

Genome inversions are ubiquitous in organisms ranging from prokaryotes to eukaryotes. Typical examples can be identified by comparing the genomes of two or more closely related organisms, where genome inversion footprints are clearly visible. Although the evolutionary implications of this phenomenon are huge, little is known about the function and biological meaning of this process. Here, we report our findings on a bacterium that generates a reversible, large-scale inversion of its chromosome (about half of its total genome) at high frequencies of up to once every four generations. This inversion switches on or off bacterial phenotypes, including colony morphology, antibiotic susceptibility, hemolytic activity, and expression of dozens of genes. Quantitative measurements and mathematical analyses indicate that this reversible switching is stochastic but self-organized so as to maintain two forms of stable cell populations (i.e., small colony variant, normal colony variant) as a bet-hedging strategy. Thus, this heritable and reversible genome fluctuation seems to govern the bacterial life cycle; it has a profound impact on the course and outcomes of bacterial infections.
Pacific bluefin tuna transport Fukushima-derived radionuclides from Japan to California
Authors: Madigan Daniel J. , Baumann Zofia , Fisher Nicholas S.
Published: May 2012

The Fukushima Dai-ichi release of radionuclides into ocean waters caused significant local and global concern regarding the spread of radioactive material. We report unequivocal evidence that Pacific bluefin tuna,
Thunnus orientalis
, transported Fukushima-derived radionuclides across the entire North Pacific Ocean. We measured γ-emitting radionuclides in California-caught tunas and found
134
Cs (4.0 ± 1.4 Bq kg
−1
) and elevated
137
Cs (6.3 ± 1.5 Bq kg
−1
) in 15 Pacific bluefin tuna sampled in August 2011. We found no
134
Cs and background concentrations (∼1 Bq kg
−1
) of
137
Cs in pre-Fukushima bluefin and post-Fukushima yellowfin tunas, ruling out elevated radiocesium uptake before 2011 or in California waters post-Fukushima. These findings indicate that Pacific bluefin tuna can rapidly transport radionuclides from a point source in Japan to distant ecoregions and demonstrate the importance of migratory animals as transport vectors of radionuclides. Other large, highly migratory marine animals make extensive use of waters around Japan, and these animals may also be transport vectors of Fukushima-derived radionuclides to distant regions of the North and South Pacific Oceans. These results reveal tools to trace migration origin (using the presence of
134
Cs) and potentially migration timing (using
134
Cs:
137
Cs ratios) in highly migratory marine species in the Pacific Ocean.
Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment withEscherichia coli
Authors: Le Gac Mickaël , Plucain Jessica , Hindré Thomas , Lenski Richard E. , Schneider Dominique
Published: May 2012

Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine twoEscherichia colilineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.
Identification of the platelet-derived chemokine CXCL4/PF-4 as a broad-spectrum HIV-1 inhibitor
Authors: Auerbach David J. , Lin Yin , Miao Huiyi , Cimbro Raffaello , DiFiore Michelle J. , Gianolini Monica E. , Furci Lucinda , Biswas Priscilla , Fauci Anthony S. , Lusso Paolo
Published: May 2012

The natural history of HIV-1 infection is highly variable in different individuals, spanning from a rapidly progressive course to a long-term asymptomatic infection. A major determinant of the pace of disease progression is the in vivo level of HIV-1 replication, which is regulated by a complex network of cytokines and chemokines expressed by immune and inflammatory cells. The chemokine system is critically involved in the control of HIV-1 replication by virtue of the role played by specific chemokine receptors, most notably CCR5 and CXCR4, as cell-surface coreceptors for HIV-1 entry; hence, the chemokines that naturally bind such coreceptors act as endogenous inhibitors of HIV-1. Here, we show that the CXC chemokine CXCL4 (PF-4), the most abundant protein contained within the α-granules of platelets, is a broad-spectrum inhibitor of HIV-1 infection. Unlike other known HIV-suppressive chemokines, CXCL4 inhibits infection by the majority of primary HIV-1 isolates regardless of their coreceptor-usage phenotype or genetic subtype. Consistent with the lack of viral phenotype specificity, blockade of HIV-1 infection occurs at the level of virus attachment and entry via a unique mechanism that involves direct interaction of CXCL4 with the major viral envelope glycoprotein, gp120. The binding site for CXCL4 was mapped to a region of the gp120 outer domain proximal to the CD4-binding site. The identification of a platelet-derived chemokine as an endogenous antiviral factor may have relevance for the pathogenesis and treatment of HIV-1 infection.
BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection
Authors: Lee Song Hee , Kalejta Robert F. , Kerry Julie , Semmes Oliver John , O’Connor Christine M. , Khan Zia , Garcia Benjamin A. , Shenk Thomas , Murphy Eain
Published: May 2012

Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.
Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire
Authors: Ostrov David A. , Grant Barry J. , Pompeu Yuri A. , Sidney John , Harndahl Mikkel , Southwood Scott , Oseroff Carla , Lu Shun , Jakoncic Jean , de Oliveira Cesar Augusto F. , Yang Lun , Mei Hu , Shi Leming , Shabanowitz Jeffrey , English A. Michelle , Wriston Amanda , Lucas Andrew , Phillips Elizabeth , Mallal Simon , Grey Howard M. , Sette Alessandro , Hunt Donald F. , Buus Soren , Peters Bjoern
Published: May 2012

Idiosyncratic adverse drug reactions are unpredictable, dose-independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkages between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8+T cells that required HLA-B*57:01 molecules for their function; however, the mechanism by which abacavir induces this pathologic T-cell response remains unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T cells, thus causing the equivalent of an alloreactive T-cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir and that were recognized by T cells of hypersensitive patients. The assays that we have established can be applied to test additional compounds with suspected HLA-linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA-linked hypersensitivities, and guide the development of safer drugs.
Regions of kinetic geodesic acoustic modes and streamers in JIPPT-IIU tokamak plasmas
Authors: Hamada Y. , Watari T. , Nishizawa A. , Yamagishi O. , Narihara K. , Kawasumi Y. , Ido T. , Kojima M. , Toi K.
Published: May 2012

The radial extent of kinetic geodesic acoustic modes (KGAMs) and streamers is measured using a heavy ion beam probe. Intense KGAM oscillations are observed in the core region of a low-density ohmic (OH) plasma where T
e ≫ T
i and outside this region, streamers characterized by steepening fronts are observed. The radial profile of plasma density stays flat in the region of the streamers, showing a rise in the plasma density in two regions, one at the scrape-off layer and the other in the core region during the radial scan of sample volumes. Intense (up to eΦ/kT
e ∼ 0.1) and broad GAM oscillations (δf/f ∼ 0.5) are observed in the r < a
p/2 region of tokamak plasmas. GAM oscillations and streamers are strongly reduced in the heated phase. In addition, the radial profile of the spectra of GAM in the heated phase is very different from that of a low-density OH plasma. The streamers and the two-step rise in the density radial profile disappear in the heated phase.
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
Authors: Noor Elad , Bar-Even Arren , Flamholz Avi , Lubling Yaniv , Davidi Dan , Milo Ron
Published: May 2012

Motivation: The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions.

Results: Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG○ of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K′ and pKa data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM–3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions.

Availability: Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux.

Contact:  ron.milo@weizmann.ac.il

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A common ancestry for BAP1 and Uch37 regulators
Authors: Sanchez-Pulido Luis , Kong Lesheng , Ponting Chris P.
Published: May 2012

Summary: To reveal how the polycomb repressive–deubiquitinase (PR–DUB) complex controls substrate selection specificity, we undertook a detailed computational sequence analysis of its components: additional sex combs like 1 (ASXL1) and BRCA1-associated protein 1 (BAP1) proteins. This led to the discovery of two previously unrecognized domains in ASXL1: a forkhead (winged-helix) DNA-binding domain and a deubiquitinase adaptor domain shared with two regulators of ubiquitin carboxyl-terminal hydrolase 37 (Uch37), namely adhesion regulating molecule 1 (ADRM1) and nuclear factor related to kappaB (NFRKB). Our analysis demonstrates a common ancestry for BAP1 and Uch37 regulators in PR–DUB, INO80 chromatin remodelling and proteosome complexes.

Contact:  luis.sanchezpulido@dpag.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Effects of Postharvest Onion Curing Parameters on the Development of Sour Skin and Slippery Skin in Storage
Authors: Schroeder B. K. , Humann J. L. , du Toit L. J.
Published: May 2012

The influence of postharvest curing temperature and duration on development of slippery skin (caused by Burkholderia gladioli pv. alliicola) and sour skin (caused by B. cepacia) in onion (Allium cepa) bulbs during storage was evaluated by inoculating bulbs of the storage cultivars ‘Redwing’ and ‘Vaquero’ with each of the pathogens after harvest, curing the bulbs at 25, 30, 35, or 40°C for 2 or 14 days, and storing the bulbs at 5°C for 1, 2, or 3 months. Noninoculated bulbs and bulbs injected with sterile water served as control treatments. The onion bulbs were from drip-irrigated, commercial onion crops grown in the semiarid Columbia Basin of central Washington in 2009 and 2010. Each bulb was cut through the point of inoculation from the neck to the basal plate to assess severity of bulb rot (percentage of cut bulb surface area with bacterial rot symptoms) after 1, 2, or 3 months of storage. Bulb rot severity in the 2009–10 and 2010–11 trials was negligible for noninoculated bulbs (mean of 4.0 and 4.5%, respectively) and bulbs injected with water (6.2 and 10.1%, respectively) compared with bulbs inoculated with B. cepacia (34.6 and 39.8%, respectively) and B. gladioli pv. alliicola (20.7 and 27.4%, respectively). Bulbs inoculated with B. cepacia developed significantly more severe rot than those inoculated with B. gladioli pv. alliicola, even though a 10-fold greater inoculum concentration was used for B. gladioli pv. alliicola, demonstrating the more aggressive nature of B. cepacia compared with B. gladioli pv. alliicola. Severity of bulb decay caused by B. cepacia or B. gladioli pv. alliicola was affected significantly (P < 0.05) by season (trial), cultivar, curing temperature, curing duration, and storage duration, with significant interactions among these factors. In both trials and for both pathogens, bulb rot was significantly more severe the greater the curing temperature and the severity of bulb rot was significantly greater when bulbs were cured for 14 versus 2 days prior to cold storage. Overall, the severity of bulb rot was greater with a longer duration of storage after curing. This increase in bulb rot severity, which resulted from an increase in curing temperature and duration, was significantly greater for Vaquero than Redwing and significantly greater for bulbs inoculated with B. cepacia than B. gladioli pv. alliicola. The results suggest that postharvest curing at temperatures <35°C for a limited duration can significantly reduce the severity of sour skin or slippery skin in storage.
First Report of Tomato yellow leaf curl virus Infecting Common Bean in China
Authors: Ji Y. H. , Cai Z. D. , Zhou X. W. , Liu Y. M. , Xiong R. Y. , Zhao T. M. , Yu W. G. , Tao X. R. , Zhou Y. J.
Published: May 2012

Common bean (Phaseolus vulgaris) is one of the most economically important vegetable crops in China. In November 2011, symptoms with thickening and crumpling of leaves and stunting were observed on common bean with incidence rate of 50 to 70% in the fields of Huaibei, northern Anhui Province, China. Diseased common bean plants were found to be infested with large population of whiteflies (Bemisia tabaci), which induced leaf crumple symptoms in healthy common beans, suggesting begomovirus etiology. To identify possible begomoviruses, 43 symptomatic leaf samples from nine fields were collected and total DNA of each sample was extracted. PCR was performed using degenerate primers PA and PB to amplify a specific region covering AV2 gene of DNA-A and part of the adjacent intergenic region (2). DNA fragments were successfully amplified from 37 out of 43 samples and PCR amplicons of 31 samples were used for sequencing. Sequence alignments among them showed that the nucleotide sequence identity ranged from 99 to 100%, which implied that only one type of begomovirus might be present. Based on the consensus sequences, a primer pair MB1AbF (ATGTGGGATCCACTTCTAAATGAATTTCC) and MB1AsR (GCGTCGACAGTGCAAGACAAACTACTTGGGGACC) was designed and used to amplify the circular viral DNA genome. The complete genome (Accession No. JQ326957) was 2,781 nucleotides long and had the highest sequence identity (over 99%) with Tomato yellow leaf curl virus (TYLCV; Accession Nos. GQ352537 and GU199587). These samples were also examined by dot immunobinding assay using monoclonal antibody against TYLCV and results confirmed that TYLCV was present in the samples. These results demonstrated that the virus from common bean is an isolate of TYLCV, a different virus from Tomato yellow leaf curl China virus (TYLCCNV). TYLCV is a devastating pathogen causing significant yield losses on tomato in China since 2006 (4). The virus has also been reported from cowpea in China (1) and in common bean in Spain (3). To our knowledge, this is the first report of TYLCV infecting common bean in China.

References: (1) F. M. Dai et al. Plant Dis. 95:362, 2011. (2) D. Deng et al. Ann. Appl. Biol. 125:327, 1994. (3) J. Navas-Castillo et al. Plant Dis. 83:29, 1999. (4) J. B. Wu et al. Plant Dis. 90:1359, 2006.
First Report of Nigrospora oryzae Causing Leaf Spot of Cotton in China
Authors: Zhang L. X. , Li S. S. , Tan G. J. , Shen J. T. , He T.
Published: May 2012

Cotton (Gossypium hirsutum L.) is widely cultivated for the important economic value of the fiber. In the summer of 2011, a leaf spot of cotton plants cv. Wanza40 was observed in 11 fields (total of about 4 ha) in Qianshan County in southwest Anhui Province, China. Approximately 30% of the plants in each field were symptomatic. Affected plants exhibited brown to reddish, irregular foliar lesions, each with a brown border near the vein of the leaves. A sign of fungal infection was a dark leaf mold observed on lesions on the abaxial surface of leaves. Sections of symptomatic leaf tissues were surface-sterilized (in 75% ethanol for 30 s, then 1% NaOCl for 1 min), rinsed three times in sterile distilled water, and plated onto potato dextrose agar (PDA). A fungus consistently recovered from symptomatic leaf samples produced colonies that were initially white and then became grayish brown with the onset of sporulation. Black, spherical to subspherical, single-celled conidia (10 to 12 × 14 to 16 μm) were borne on a hyaline vesicle at the tip of each conidiophore. Morphological characteristics of the fungus were similar to that of Nigrospora oryzae (2). The internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) from a representative strain of the fungus, AHC-1, was amplified using the primers ITS1/ITS4 (4) and sequenced (GenBank Accession No. JQ864579). The ITS sequence had 99% identity with >553 bp of the ITS sequence of an N. oryzae isolate (GenBank Accession No. EU918714.1). On the basis of morphological data and ITS rDNA sequence, the isolate was determined to be N. oryzae. A pathogenicity test was performed on detached, young leaves of 4-month-old healthy cotton plants of cv. Wanza40. Six leaves were inoculated by placing a colonized agar piece (5 mm in diameter) from 7-day-old cultures of the fungus on pushpin-wounded leaves. Another six leaves treated with sterile PDA plugs served as a negative control treatment. Leaves were incubated in petri dishes and maintained at 25°C in a growth chamber programmed for 12 hours of fluorescent white light/day. After 5 days, brown to black lesions were observed on all inoculated leaves, whereas no symptoms developed on control leaves. N. oryzae was consistently reisolated from symptomatic leaves but not from the control leaves. N. oryzae is a weak pathogen on a wide range of plants, and has been described as the causal agent of lint rot on cotton (1,3), but to our knowledge this is the first report of N. oryzae causing a leaf spot of cotton in China.

References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA, Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , April 8, 2012. (2) H. J. Hudson. Trans. Br. Mycol. Soc. 46:355, 1963. (3) A. J. Palmatter et al. Plant Dis. 87:873, 2003. (4) T. J. White et al. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.
Up-Regulation of Antioxidants in Tobacco by Low Concentrations of H2O2 Suppresses Necrotic Disease Symptoms
Authors: Hafez Yaser Mohamed , Bacsó Renáta , Király Zoltán , Künstler András , Király Lóránt
Published: May 2012

Pretreatment of tobacco leaves with low concentrations (5 to 10 mM) of H2O2 suppressed hypersensitive-type necrosis associated with resistance to Tobacco mosaic virus (TMV) or Pseudomonas syringae pv. phaseolicola. The same pretreatment resulted in suppression of normosensitive necrosis associated with susceptibility to Botrytis cinerea. This type of H2O2-mediated, induced disease symptom resistance correlated with enhanced host antioxidant capacity, i.e., elevated enzymatic activities of catalase (CAT), ascorbate peroxidase (APX), and guaiacol peroxidase (POX) after viral and bacterial infections. Induction of genes that encode the antioxidants superoxide dismutase (SOD), CAT, and APX was also enhanced early after TMV infection. Artificial application of SOD and CAT suppressed necroses caused by viral, bacterial, or fungal pathogens similarly as H2O2 pretreatment, implying that H2O2-mediated symptom resistance operates through enhancement of plant antioxidant capacity. Pathogen multiplication was not significantly affected in H2O2-pretreated plants. Salicylic acid (SA), a central component of plant defense, does not seem to function in this type of H2O2-mediated symptom resistance, indicated by unchanged levels of free and bound SA and a lack of early up-regulation of an SA glucosyltransferase gene in TMV-infected H2O2-pretreated tobacco. Taken together, H2O2-mediated, induced resistance to necrotic symptoms in tobacco seems to depend on enhanced antioxidant capacity.
Charles David Marsden. 15 April 1938 — 29 September 1998
Authors: Quinn Niall , Rothwell John , Jenner Peter
Published: May 2012

David Marsden was the most outstanding UK clinical neuroscientist of his generation, making key discoveries in the neurophysiology, neurochemistry and clinical aspects of diseases of the basal ganglia, and their normal function. His legacies are the establishment, with Stanley Fahn in the USA, of movement disorders as a subspecialty within neurology, of the international Movement Disorder Society, and of the journal
Movement Disorders
; his ex-students and fellows around the globe; and his research and teaching output embodied in his extraordinarily prolific publication record of more than 1360 papers, books and chapters, culminating in the posthumous completion and publication in December 2011 of
Marsden’s book of movement disorders
, a project he had started in 1984. All of these were achieved through the combination of his intellect and drive, his communication skills, and his forceful and charismatic personality.
Reflections concerning triply-periodic minimal surfaces
Authors: Schoen Alan H.
Published: May 2012

In recent decades, there has been an explosion in the number and variety of embedded triply-periodic minimal surfaces (TPMS) identified by mathematicians and materials scientists. Only the rare examples of low genus, however, are commonly invoked as shape templates in scientific applications. Exact analytic solutions are now known for many of the low genus examples. The more complex surfaces are readily defined with numerical tools such as SurfaceEvolversoftware or the Landau–Ginzburg model. Even though table-top versions of several TPMS have been placed within easy reach by rapid prototyping methods, the inherent complexity of many of these surfaces makes it challenging to grasp their structure. The problem of distinguishing TPMS, which is now acute because of the proliferation of examples, has been addressed by Lord & Mackay (Lord & Mackay 2003Curr. Sci.85, 346–362).
Fairness modulates non-conscious facial mimicry in women
Authors: Hofman Dennis , Bos Peter A. , Schutter Dennis J. L. G. , van Honk Jack
Published: May 2012

In societies with high cooperation demands, implicit consensus on social norms enables successful human coexistence. Mimicking other people's actions and emotions has been proposed as a means to synchronize behaviour, thereby enhancing affiliation. Mimicry has long been thought to be reflexive, but it has recently been suggested that mimicry might also be motivationally driven. Here, we show during an economic bargaining game that automatic happy mimicry of those making unfair offers disappears. After the bargaining game, when the proposers have acquired either a fair or unfair reputation, we observe increased angry mimicry of proposers with an unfair reputation and decreased angry mimicry of fair proposers. These findings provide direct empirical evidence that non-conscious mimicry is modulated by fairness. We interpret the present results as reflecting that facial mimicry in women functions conditionally, dependent on situational demands.
A tropical bird can use the equatorial change in sunrise and sunset times to synchronize its circannual clock
Authors: Goymann Wolfgang , Helm Barbara , Jensen Willi , Schwabl Ingrid , Moore Ignacio T.
Published: May 2012

At higher latitudes, most organisms use the periodic changes in day length to time their annual life cycle. At the equator, changes in day length are minimal, and it is unknown which cues organisms use to synchronize their underlying circannual rhythms to environmental conditions. Here, we demonstrate that the African stonechat (Saxicola torquatus axillaris)—an equatorial songbird—can use subtle solar cues for the annual timing of postnuptial moult, a reliable marker of the circannual cycle. We compared four groups that were kept over more than 3 years: (i) a control group maintained under constant equatorial day length, (ii) a 12-month solar time group maintained under equatorial day length, but including a simulation of the annual periodic change in sunrise and sunset times (solar time), (iii) a 14-month solar time group similar to the previous group but with an extended solar time cycle and (iv) a group maintained under a European temperate photoperiod. Within all 3 years, 12-month solar time birds were significantly more synchronized than controls and 14-month solar time birds. Furthermore, the moult of 12-month solar time birds occurred during the same time of the year as that of free-living Kenyan conspecifics. Thus, our data indicate that stonechats may use the subtle periodic pattern of sunrise and sunset at the equator to synchronize their circannual clock.
Am I seeing my hand? Visual appearance and knowledge of controllability both contribute to the visual capture of a person's own body
Authors: Hagura Nobuhiro , Hirose Satoshi , Matsumura Michikazu , Naito Eiichi
Published: May 2012

When confronted with complex visual scenes in daily life, how do we know which visual information represents our own hand? We investigated the cues used to assign visual information to one's own hand. Wrist tendon vibration elicits an illusory sensation of wrist movement. The intensity of this illusion attenuates when the actual motionless hand is visually presented. Testing what kind of visual stimuli attenuate this illusion will elucidate factors contributing to visual detection of one's own hand. The illusion was reduced when a stationary object was shown, but only when participants knew it was controllable with their hands. In contrast, the visual image of their own hand attenuated the illusion even when participants knew that it was
not
controllable. We suggest that long-term knowledge about the appearance of the body and short-term knowledge about controllability of a visual object are combined to robustly extract our own body from a visual scene.
A-to-I editing of microRNAs in the mammalian brain increases during development
Authors: Ekdahl Ylva , Farahani Hossein Shahrabi , Behm Mikaela , Lagergren Jens , Öhman Marie
Published: May 2012

Adenosine-to-inosine (A-to-I) RNA editing targets double-stranded RNA stem–loop structures in the mammalian brain. It has previously been shown that miRNAs are substrates for A-to-I editing. For the first time, we show that for several definitions of edited miRNA, the level of editing increases with development, thereby indicating a regulatory role for editing during brain maturation. We use high-throughput RNA sequencing to determine editing levels in mature miRNA, from the mouse transcriptome, and compare these with the levels of editing in pri-miRNA. We show that increased editing during development gradually changes the proportions of the two miR-376a isoforms, which previously have been shown to have different targets. Several other miRNAs that also are edited in the seed sequence show an increased level of editing through development. By comparing editing of pri-miRNA with editing and expression of the corresponding mature miRNA, we also show an editing-induced developmental regulation of miRNA expression. Taken together, our results imply that RNA editing influences the miRNA repertoire during brain maturation.
Bis{2-[bis(3,5-dimethyl-1H-pyrazol-1-yl-κN
2)methyl]pyridine-κN}cobalt(II) dinitrate
Authors: Xiao Chao-Hu , Song Xue-Yan , Sun Zan , Cao Ping , Pang Ting
Published: May 2012

The central CoII ion in the title complex, [Co(C16H19N5)2](NO3)2, is located on a twofold rotation axis and has a slightly distorted octahedral coordination sphere. It is bonded to six N atoms from two 2-[bis(3,5-dimethyl-1H-pyrazol-1-yl)methyl]pyridine ligands. In the crystal, molecules are linked by weak C—H...O interactions.
4-(1H-Pyrazol-3-yl)pyridine–terephthalic acid–water (2/1/2)
Authors: Tan Zheng-De , Tan Feng-Jiao , Tan Bo , Zhang Cheng-Ming
Published: May 2012

In the title compound, 2C8H7N3·C8H6O4·2H2O, the pyridine and pyrazole rings are approximately coplanar, the dihedral angle between them being 4.69 (9)°. The asymmetric unit consists of half of the terephthalic acid (an inversion centre generates the other half of the molecule), one 4-(1H-pyrazol-3-yl)pyridine (4pp) molecule and one water molecule. In the crystal, two 4pp and one terephthalic acid molecules form a linear three-molecule unit as a result of O—H...N hydrogen bonds. These units are further assembled into a three-dimensional network by two types of hydrogen bonds, viz. O—H...O and N—H...O.
Chlorido[1-diphenylphosphanyl-3-(phenylsulfanyl)propane-κ2
P,S](η5-pentamethylcyclopentadienyl)iridium(III) chloride monohydrate
Authors: Ludwig Gerd , Korb Marcus , Rüffer Tobias , Lang Heinrich , Steinborn Dirk
Published: May 2012

The crystal structure of the title compound, [Ir(C10H15)Cl(C21H21PS)]Cl·H2O, consists of discrete [Ir(η5-C5Me5)Cl{Ph2P(CH2)3SPh-κP,κS}]+ cations, chloride anions and water molecules. The IrIII atom is coordinated by an η5-C5Me5 ligand, a chloride and a Ph2P(CH2)3SPh-κP,κS ligand, leading to a three-legged piano-stool geometry. In the crystal, two water molecules and two chloride anions are linked by weak O—H...Cl hydrogen bonding into tetramers that are located on centers of inversion. The H atoms of one of the methyl groups are disordered and were refined using a split model.
3,8-Dimethyl-4-oxo-3,4-dihydroquinazoline-6-carbonitrile
Authors: Tian Hai-Yan , Bi Jian-Cong , Zhang Hong-Xia , Zhang Juan
Published: May 2012

In the title compound, C11H9N3O, the quinazoline unit is almost planar, with a mean deviation of 0.006 (1) Å from the least-squares plane defined by the ten constituent atoms. In the crystal, molecules are linked by weak C—H...N hydrogen bonds.
Bis(triethylammonium) tetrachloridocobaltate(II)
Authors: Azadbakht Reza , Hadadzadeh Hassan , Amiri Rudbari Hadi
Published: May 2012

The crystal structure of the title compound, (C6H16N)2[CoCl4], is comprised of a tetrahedral [CoCl4]2− anion and two independent triethylammonium cations. The latter are featureless while the [CoCl4]2− anion exhibits typical Co—Cl bond lengths [2.2428 (15)–2.2847 (16) Å] and a Cl—Co—Cl angular range of 107.58 (6)–112.73 (7)°. In the crystal, N—H...Cl hydrogen bonds between the two crystallographically independent cations and the [CoCl4]2− anion generate discrete ion triplets. The two Co—Cl bonds involved in these interactions are slightly longer than the remaining two.
Methyl 2-(but-3-enyl)-4-hydroxy-1,1-dioxo-2H-1λ6,2-benzothiazine-3-carboxylate
Authors: Arshad Muhammad Nadeem , Khan Islam Ullah , Zia-ur-Rehman Muhammad , Danish Muhammad , Holman K. Travis
Published: May 2012

In the title compound, C14H15NO5S, the thiazine ring adopts a sofa conformation and an intramolecular O—H...O hydrogen bond forms an S(6) ring. In the crystal, molecules are linked viaC—H...O interactions.
1-(3,3-Dichloroallyloxy)-4-methyl-2-nitrobenzene
Authors: Ren Dong-mei
Published: May 2012

In the title compound, C10H9Cl2NO3, the dihedral angle between the benzene ring and the plane of the nitro group is 39.1 (1)°, while that between the benzene ring and the plane through the three C and two Cl atoms of the dichloroallyloxy unit is 40.1 (1)°. In the crystal, C—H...O hydrogen bonds to the nitro groups form chains along the b axis. These chains are linked by inversion-related pairs of Cl...O interactions at a distance of 3.060 (3) Å, forming sheets approximately parallel to [-201] and generating R
2
2(18) rings. π–π contacts between benzene rings in adjacent sheets, with centroid–centroid distances of 3.671 (2) Å, stack molecules along c.
2-(3-Chloro-5,6-diphenyl-2,5-dihydro-1,2,4-triazin-5-yl)-2-methylpropanenitrile
Authors: Wolińska Ewa , Karczmarzyk Zbigniew , Rykowski Andrzej , Urbańczyk-Lipkowska Zofia , Kalicki Przemysław
Published: May 2012

The title compound, C19H17ClN4, was obtained from the reaction of 3-chloro-5,6-diphenyl-1,2,4-triazine with isobutyronitrile in the presence of lithium diisopropylamide as an unexpected product of covalent addition of isobutyronitrile carbanion to the C-5 atom of the 1,2,4-triazine ring. The 2,5-dihydro-1,2,4-triazine ring is essentially planar (r.m.s. deviation = 0.0059 Å) and the 5- and 6-phenyl substituents are inclined to its mean plane with dihedral angles of 89.97 (4) and 55.52 (5)°, respectively. Intramolecular C—H...N interactions occur. In the crystal, molecules related by a c-glide plane are linked into zigzag chains along [001] by N—H...N hydrogen bonds.
catena-Poly[[bis(nitrato-κO)cadmium]bis[μ-1,3-bis[(1H-1,2,4-triazol-1-yl)methyl]benzene-κ2
N
4:N
4′]]
Authors: Zhang Hong-Kun , Wang Xin , Wang Shuai , Wang Xiao-Dan
Published: May 2012

In the title compound, [Cd(NO3)2(C12H12N6)2]
n
, the CdII cation is located on an inversion center and is six-coordinated by four N atoms from four 1,3-bis[(1H-1,2,4-triazol-1-yl)methyl]benzene (L) ligands and two O atoms from two nitrate anions in a slightly distorted octahedral geometry. The ligands link different CdII ions into a ribbon-like structure along [001]. Two O atoms of the nitrate anion are disordered over two sets of sites with site occupancies of 0.575 (8) and 0.425 (8).
Tris(1H-benzimidazol-3-ium-2-ylmethyl)amine tris(2,4,6-trinitrophenolate) acetonitrile disolvate
Authors: Bai Ying , Yuan Jing-Kun , Wang Hua , Pan Guo-Long , Wu Hui-Lu
Published: May 2012

In the cation of the title salt, C24H24N7
3+·3C6H2N3O7
−·2C2H3N, the three benzimidazolium ring systems are oriented to each other at dihedral angles of 10.42 (7), 23.98 (7) and 22.17 (7)°. In the crystal, the cation links to the adjacent picrate anions via N—H...O hydrogen bonds; one of independent acetonitrile solvent molecules is also linked to the cation via an N—H...N hydrogen bond.
3,4,7,8-Tetramethyl-1,10-phenanthrolin-1-ium nitrate monohydrate
Authors: Zhang Ke-Jie , Zhang Yan-Fang
Published: May 2012

In the crystal of the title compound, C16H17N2
+·NO3
−·H2O, the tetramethyl-1,10-phenanthrolinium cations, nitrate anions and lattice water molecules are all located on a mirror plane with the methyl H atoms of the cation equally disordered over two sites about the mirror plane. The cation, anion and water molecule are linked by O—H...O and N—H...O hydrogen bonds into a sheet parallel to the bc plane. π–π stacking between phenanthroline ring systems is observed in the crystal structure, the centroid–centroid distance being 3.4745 (6) Å.
3-Methoxy-4-methyl-1H-1,2,4-triazol-5(4H)-one monohydrate
Authors: Gao Wei , Wang Xin-Ling , Yang Jing , Wu Xue-Fen
Published: May 2012

In the title hydrate, C4H7N3O2·H2O, all the non-H atoms lie on a crystallographic mirror plane. The H atoms of both methyl groups are disordered over two sets of sites. In the crystal, N—H...Ow and Ow—H...Ok (w = water and k = ketone) hydrogen bonds link the components into (010) sheets.
Bis(benzylaminium) 4,5-dichlorobenzene-1,2-dicarboxylate monohydrate
Authors: Smith Graham , Wermuth Urs D.
Published: May 2012

In the structure of the title salt, 2C7H10N+·C8H2Cl2O4
2−·H2O, the two benzylaminium anions have different conformations, one being essentially planar and the other having the side chain rotated out of the benzene plane [minimum ring to side-chain C—C—C—N torsion angles = −3.6 (6) and 50.1 (5)°, respectively]. In the 4,5-dichlorophthalate dianion, the carboxylate groups make dihedral angles of 23.0 (2) and 76.5 (2)° with the benzene ring. In the crystal, aminium N—H...O and water O—H...O hydrogen-bonding associations with carboxylate O-atom acceptors give a two-dimensional duplex sheet structure which extends along the (011) plane. Weak π–π interactions are also present between the benzene ring of the dianion and one of the cation rings [minimum ring centroid separation = 2.749 (3) Å].
Bis[(diphenylphosphanylmethyl)diphenylphosphane sulfide-κ2
P,S]copper(I) hexafluoridophosphate
Authors: Zhang Jing-Jing , Hu Feng , Duan Tai-Ke , Chen Qun , Zhang Qian-Feng
Published: May 2012

In the title compound, [Cu(C25H22P2S)2]PF6, the CuI atom, lying on a twofold rotation axis, adopts a distorted tetrahedral geometry. The (diphenylphosphanylmethyl)diphenylphosphane sulfide ligand coordinates to the CuI atom through one S and one P atom, forming a stable five-membered chelate ring. The P atom of the PF6
− anion also lies on a twofold rotation axis.
7-[(5,5-Dimethyl-2-oxido-1,3,2-dioxaphosphinan-2-yl)oxy]-4-methyl-2H-chromen-2-one
Authors: Zhao Yan-Ru , Hou Xu-Feng , Xu Zhi-Hong
Published: May 2012

The title compound, C15H17O6P, was obtained from a reaction of 4-methyl-7-hydroxycoumarin and 2-chloro-5,5-dimethyl-1,3,2-dioxaphosphinane 2-oxide. There are two molecules in the asymmetric unit in which the benzopyran ring system is almost planar [r.m.s. deviation for each molecule = 0.003 Å]. In the crystal, C—H...O hydrogen bonds and π–π stacking interactions [with centroid–centroid distances of 3.743 (3) and 3.727 (3) Å] link the two molecules. The dioxaphosphorinane ring adopts a chair conformation in both asymmetric molecules.
1-[(6-Chloropyridin-3-yl)methyl]imidazolidin-2-one
Authors: Kant Rajni , Gupta Vivek K. , Kapoor Kamini , Shripanavar Chetan S. , Banerjee Kaushik
Published: May 2012

In the title molecule, C9H10ClN3O, the dihedral angle between the pyridine ring and imidazoline ring mean plane [maximum deviation = 0.031–(3) Å] is 76.2 (1)°. In the crystal, N—H...O hydrogen bonds link pairs of molecules to form inversion dimers. In addition, weak C—H...N hydrogen bonds and π–π stacking interactions between pyridine rings [centroid–centroid distance = 3.977 (2) Å] are observed.
N-Cyclohexyl-2-oxo-2-phenylacetamide
Authors: Jia Ze-Jun , Wu Jin-Long
Published: May 2012

In the title compound, C14H17NO2, the two carbonyl groups are oriented with respect to each other with a torsion angle of −129.9 (3)°. The cyclohexane ring adopts a chair conformation. In the crystal, molecules are linked by N—H...O hydrogen bonds into a chain running along the a axis.
2-[(2,6-Diisopropylphenyl)iminomethyl]-4-iodophenol
Authors: Balamurugan P. , Raja K. Kanmani , Bilal I. Mohammed , Chakkaravarthi G. , Rajagopal G.
Published: May 2012

The asymmetric unit of title compound, C19H22INO, contains two independent molecules. Classical intramolecular O—H...N hydrogen bonds stabilize the molecular structures. The crystal structure is stabilized by weak intermolecular C—H...π and π–π [centroid–centroid = 3.8622 (18) Å] interactions. In both molecules, the aromatic rings are nearly perpendicular to each other [dihedral angles = 84.26 (17) and 86.69 (15)°].
2-Ethoxy-6-{[1-(3-ethoxy-2-hydroxybenzyl)-1H-benzimidazol-2-yl]methyl}phenol nitromethane monosolvate
Authors: Ha Kwang
Published: May 2012

In the title solvate, C24H24N2O4·CH3NO2, the benzene ring of the 2-ethoxy-6-methylphenol substituent is approximately perpendicular to the nearly planar benzimidazole ring [maximum deviation = 0.021 (2) Å], making a dihedral angle of 84.32 (7)°. The benzene ring of the 2-ethoxyphenol group is somewhat inclined to the benzimidazole ring plane by 28.03 (5)°. The dihedral angle between the benzene rings is 82.20 (9)°. The compound reveals strong intramolecular O—H...N and O—H...O hydrogen bonds, forming six- and five-membered rings, respectively. In the crystal, molecules are connected by bifurcated O—H...(O,O) hydrogen bonds, forming chains along the b axis.
2-(1H-Pyrrolo[2,3-b]pyridin-2-yl)pyridine
Authors: Huang Ping-Hsin , Wen Yuh-Sheng , Shen Jiun-Yi
Published: May 2012

In the title compound, C12H9N3, the dihedral angle between the pyridine and azaindole rings is 6.20 (2)°. In the crystal, pairs of N—H...N hydrogen bonds link molecules into inversion dimers.
4-(4-Nitrostyryl)-N,N-diphenylaniline
Authors: Zhang Zhi-Wen , Liu Yan-Qiu , Zhu Yu-Chao , Wu Jie-Ying
Published: May 2012

In the triarylamine group of the title compound, C26H20N2O2, the N atom adopts an approximately trigonal–planar geometry, lying 0.046 (5) Å from the plane P defined by its three neighbouring C atoms; the benzene and two terminal phenyl rings are twisted by 37.4 (1), 31.4 (1) and 47.8 (1)°, respectively from plane P. In the trans-stilbene fragment, the two benzene rings form a dihedral angle of 31.3 (1)°. In the crystal, weak intermolecular C—H...O interactions link the molecules into ribbons in [100].
Redetermination of Mg2B25 based on single-crystal X-ray data
Authors: Bindi Luca , Figini Albisetti Alessandro , Giunchi Giovanni , Malpezzi Luciana , Masciocchi Norberto
Published: May 2012

The crystal structure of Mg2B25, dimagnesium pentaeicosaboride, was reexamined from single-crystal X-ray diffraction data. The structural model previously reported on the basis of powder X-ray diffraction data [Giunchi et al. (2006). Solid State Sci.
8, 1202–1208] has been confirmed, although a much higher precision refinement was achieved, leading to much smaller standard uncertainties on bond lengths and refined occupancy factors. Moreover, all atoms were refined with anisotropic displacement parameters. Mg2B25 crystallizes in the β-boron structure type and is isostructural with other rhombohedral compounds of the boron-rich metal boride family. Magnesium atoms are found in interstitial sites on special positions (two with site symmetry .m, one with .2 and one with 3m), all with partial occupancies.
1-(4-Carboxybutan-2-ylidene)-4-phenylthiosemicarbazide
Authors: Mendoza-Meroño Rafael , Menéndez-Taboada Laura , García-Granda Santiago
Published: May 2012

The molecule of the title compound, C12H15N3O2S, which belongs to the family of thiosemicarbazones, containing an acid group, adopts a semi-closed conformation with an intramolecular N—H...N hydrogen bond. In the crystal, molecules are linked by strong N—H...O and O—H...S hydrogen bonds between the acid group and thiosemicarbazone unit, with one additional intermolecular hydrogen C—H...O interaction. These three interactions form R
2
2(8) and a R
2
1(7) rings and the molecules related by the c-glide plane are linked into a zigzag chain along [001].
catena-Poly[[tetrakis(hexamethylphosphoramide-κO)bis(nitrato-κ2
O,O′)terbium(III)] [silver(I)-di-μ-sulfido-tungstate(VI)-di-μ-sulfido]]
Authors: Zhang Jinfang
Published: May 2012

In the title compound, {[Tb(NO3)2(C6H18N3OP)4][AgWS4]}
n
, the polymeric anionic chain {[AgWS4]−}
n
extends along [001]. The TbIII atom in the cation is coordinated by eight O atoms from two nitrate and four hexamethylphosphate ligands in a distorted square-antiprismatic geometry. Together with the two nitrate ligands, the cation is univalent, which leads to the anionic chain having a [WS4Ag] repeat unit. The polymeric anionic chain has a distorted linear configuration with W—Ag—W and Ag—W—Ag angles of 161.49 (2) and 153.743 (13) °, respectively. The title complex is isotypic with the Y, Yb, Eu, Nd, La, Dy, Sm and Lu analogues.