bluuebunny/crossref_metadata_2025 huggingface dataset:
The Raman fingerprint of cyclic conjugation: the case of the stabilization of cations and dications in cycloparaphenylenes
Authors: Alvarez Miriam Peña , Ruiz Delgado M. Carmen , Taravillo Mercedes , Baonza Valentín G. , López Navarrete Juan T. , Evans Paul , Jasti Ramesh , Yamago Shigeru , Kertesz Miklos , Casado Juan
Published: April 2016

Cyclic conjugation and Biradical formation in charged cycloparaphenylenes are described by Raman spectroscopy and DFT.
Hybrid tantalum oxide nanoparticles from the hydrolysis of imidazolium tantalate ionic liquids: efficient catalysts for hydrogen generation from ethanol/water solutions
Authors: Souza Virgínia S. , Scholten Jackson D. , Weibel Daniel E. , Eberhardt Dario , Baptista Daniel L. , Teixeira Sérgio R. , Dupont Jairton
Published: April 2016

The reaction of BMI·Cl or DMI·Cl with TaCl5affords imidazolium tantalate ionic liquids BMI·TaCl61and DMI·TaCl62, precursors for the synthesis of Ta2O5nanoparticles.
Controllably self-assembled graphene-supported Au@Pt bimetallic nanodendrites as superior electrocatalysts for methanol oxidation in direct methanol fuel cells
Authors: Yuan Weiyong , Fan Xiuling , Cui Zhi Ming , Chen Tao , Dong Zhili , Li Chang Ming
Published: April 2016

Graphene-supported Au@Pt bimetallic nanodendrites were synthesized by combining self-assembly with in situ seeded growth, showing remarkable electrocatalytic performance toward methanol oxidation.
Dual-crosslinked hydrogel microwell system for formation and culture of multicellular human adipose tissue-derived stem cell spheroids
Authors: Jeon Oju , Marks Robyn , Wolfson David , Alsberg Eben
Published: April 2016

A novel biodegradable, biocompatible alginate-PEG hydrogel microwell system was developed with tailorable microwell physical and biochemical properties to control the uniform formation and behavior of three-dimensional multicellular human adipose tissue-derived stem cell spheroids.
Non-volatile organic ferroelectric memory transistors fabricated using rigid polyimide islands on an elastomer substrate
Authors: Jung Soon-Won , Koo Jae Bon , Park Chan Woo , Na Bock Soon , Park Nae-Man , Oh Ji-Young , Moon Yu Gyeong , Lee Sang Seok , Koo Kyung-Wan
Published: April 2016

The authors fabricated stretchable organic ferroelectric memory transistors (OFMTs) on a polydimethylsiloxane substrate using rigid polyimide island structures.
Nucleocytoplasmic human O-GlcNAc transferase is sufficient for O-GlcNAcylation of mitochondrial proteins
Authors: Trapannone Riccardo , Mariappa Daniel , Ferenbach Andrew T. , van Aalten Daan M.F.
Published: April 2016

O-linked N-acetylglucosamine modification (O-GlcNAcylation) is a nutrient-dependent protein post-translational modification (PTM), dynamically and reversibly driven by two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) that catalyse the addition and the removal of the O-GlcNAc moieties to/from serine and threonine residues of target proteins respectively. Increasing evidence suggests involvement of O-GlcNAcylation in many biological processes, including transcription, signalling, neuronal development and mitochondrial function. The presence of a mitochondrial O-GlcNAc proteome and a mitochondrial OGT (mOGT) isoform has been reported. We explored the presence of mOGT in human cell lines and mouse tissues. Surprisingly, analysis of genomic sequences indicates that this isoform cannot be expressed in most of the species analysed, except some primates. In addition, we were not able to detect endogenous mOGT in a range of human cell lines. Knockdown experiments and Western blot analysis of all the predicted OGT isoforms suggested the expression of only a single OGT isoform. In agreement with this, we demonstrate that overexpression of the nucleocytoplasmic OGT (ncOGT) isoform leads to increased O-GlcNAcylation of mitochondrial proteins, suggesting that ncOGT is necessary and sufficient for the generation of the O-GlcNAc mitochondrial proteome.
ETS2 and Twist1 promote invasiveness of Helicobacter pylori-infected gastric cancer cells by inducing Siah2
Authors: Das Lopamudra , Kokate Shrikant Babanrao , Rath Suvasmita , Rout Niranjan , Singh Shivaram Prasad , Crowe Sheila Eileen , Mukhopadhyay Asish K. , Bhattacharyya Asima
Published: April 2016

Helicobacter pylori infection is one of the most potent factors leading to gastric carcinogenesis. The seven in absentia homologue (Siah2) is an E3 ubiquitin ligase which has been implicated in various cancers but its role in H. pylori-mediated gastric carcinogenesis has not been established. We investigated the involvement of Siah2 in gastric cancer metastasis which was assessed by invasiveness and migration of H. pylori-infected gastric epithelial cancer cells. Cultured gastric cancer cells (GCCs) MKN45, AGS and Kato III showed significantly induced expression of Siah2, increased invasiveness and migration after being challenged with the pathogen. Siah2-expressing stable cells showed increased invasiveness and migration after H. pylori infection. Siah2 was transcriptionally activated by E26 transformation-specific sequence 2 (ETS2)- and Twist-related protein 1 (Twist1) induced in H. pylori-infected gastric epithelial cells. These transcription factors dose-dependently enhanced the aggressiveness of infected GCCs. Our data suggested that H. pylori-infected GCCs gained cell motility and invasiveness through Siah2 induction. As gastric cancer biopsy samples also showed highly induced expression of ETS2, Twist1 and Siah2 compared with noncancerous gastric tissue, we surmise that ETS2- and Twist1-mediated Siah2 up-regulation has potential diagnostic and prognostic significance and could be targeted for therapeutic purpose.
Septin oligomerization regulates persistent expression of ErbB2/HER2 in gastric cancer cells
Authors: Marcus Elizabeth A. , Tokhtaeva Elmira , Turdikulova Shahlo , Capri Joseph , Whitelegge Julian P. , Scott David R. , Sachs George , Berditchevski Fedor , Vagin Olga
Published: April 2016

Septins are a family of cytoskeletal GTP-binding proteins that assemble into membrane-associated hetero-oligomers and organize scaffolds for recruitment of cytosolic proteins or stabilization of membrane proteins. Septins have been implicated in a diverse range of cancers, including gastric cancer, but the underlying mechanisms remain unclear. The hypothesis tested here is that septins contribute to cancer by stabilizing the receptor tyrosine kinase ErbB2, an important target for cancer treatment. Septins and ErbB2 were highly over-expressed in gastric cancer cells. Immunoprecipitation followed by MS analysis identified ErbB2 as a septin-interacting protein. Knockdown of septin-2 or cell exposure to forchlorfenuron (FCF), a well-established inhibitor of septin oligomerization, decreased surface and total levels of ErbB2. These treatments had no effect on epidermal growth factor receptor (EGFR), emphasizing the specificity and functionality of the septin–ErbB2 interaction. The level of ubiquitylated ErbB2 at the plasma membrane was elevated in cells treated with FCF, which was accompanied by a decrease in co-localization of ErbB2 with septins at the membrane. Cathepsin B inhibitor, but not bafilomycin or lactacystin, prevented FCF-induced decrease in total ErbB2 by increasing accumulation of ubiquitylated ErbB2 in lysosomes. Therefore, septins protect ErbB2 from ubiquitylation, endocytosis and lysosomal degradation. The FCF-induced degradation pathway is distinct from and additive with the degradation induced by inhibiting ErbB2 chaperone Hsp90. These results identify septins as novel regulators of ErbB2 expression that contribute to the remarkable stabilization of the receptor at the plasma membrane of cancer cells and may provide a basis for the development of new ErbB2-targeting anti-cancer therapies.
Up-regulation of KIF14 is a predictor of poor survival and a novel prognostic biomarker of chemoresistance to paclitaxel treatment in cervical cancer
Authors: Wang Wenjing , Shi Yanhua , Li Jing , Cui Wei , Yang Baozhi
Published: April 2016

Kinesin family member 14 (KIF14) is a member of kinesin family proteins which have been found to be dysregulated in various cancer types. However, the expression of KIF14 and its potential prognostic significance have not been investigated in cervical cancer. Real-time PCR was performed to assess the expression levels of KIF14 in 47 pairs of cervical cancer tissues and their matched normal tissues from patients who had not been exposed to chemotherapy as well as tissue samples from 57 cervical cancer patients who are sensitive to paclitaxel treatment and 53 patients who are resistant. The association between KIF14 expression levels in tissue and clinicopathological features or chemosensitivity was examined. Kaplan–Meier analysis and Cox proportional hazards model were applied to assess the correlation between KIF14 expression levels and overall survival (OS) of cervical cancer patients. KIF14 expression levels were significantly increased in cervical cancer tissues compared with matched non-cancerous tissues and it was higher in tissues of patients who are chemoresistant compared with those who are chemosensitive. KIF14 expression was positively associated with high tumour stage (P=0.0044), lymph node metastasis (P=0.0034) and chemoresistance (P<0.0001). Kaplan–Meier analysis showed that high KIF14 expression levels predicted poor survival in patients with (P=0.0024) or without (P=0.0028) paclitaxel treatment. Multivariate analysis revealed that KIF14 was an independent prognostic factor for OS. Our study suggests that KIF14 may serve as a predictor of poor survival and a novel prognostic biomarker of chemoresistance to paclitaxel treatment in cervical cancer.
Smooth muscle titin formsin vitroamyloid aggregates
Authors: Bobylev Alexandr G. , Galzitskaya Oxana V. , Fadeev Roman S. , Bobyleva Liya G. , Yurshenas Darya A. , Molochkov Nikolay V. , Dovidchenko Nikita V. , Selivanova Olga M. , Penkov Nikita V. , Podlubnaya Zoya A. , Vikhlyantsev Ivan M.
Published: April 2016

Amyloids are insoluble fibrous protein aggregates, and their accumulation is associated with amyloidosis and many neurodegenerative diseases, including Alzheimer's disease. In the present study, we report that smooth muscle titin (SMT; 500 kDa) from chicken gizzard forms amyloid aggregates in vitro. This conclusion is supported by EM data, fluorescence analysis using thioflavin T (ThT), Congo red (CR) spectroscopy and X-ray diffraction. Our dynamic light scattering (DLS) data show that titin forms in vitro amyloid aggregates with a hydrodynamic radius (Rh) of approximately 700–4500 nm. The initial titin aggregates with Rh approximately 700 nm were observed beyond first 20 min its aggregation that shows a high rate of amyloid formation by this protein. We also showed using confocal microscopy the cytotoxic effect of SMT amyloid aggregates on smooth muscle cells from bovine aorta. This effect involves the disorganization of the actin cytoskeleton and result is cell damage. Cumulatively, our results indicate that titin may be involved in generation of amyloidosis in smooth muscles.
An Item Response Theory–Based, Computerized Adaptive Testing Version of the MacArthur–Bates Communicative Development Inventory: Words & Sentences (CDI:WS)
Authors: Makransky Guido , Dale Philip S. , Havmose Philip , Bleses Dorthe
Published: April 2016

Purpose

This study investigated the feasibility and potential validity of an item response theory (IRT)–based computerized adaptive testing (CAT) version of the MacArthur–Bates Communicative Development Inventory: Words & Sentences (CDI:WS; Fenson et al., 2007) vocabulary checklist, with the objective of reducing length while maintaining measurement precision.

Method

Parent-reported vocabulary for the American CDI:WS norming sample consisting of 1,461 children between the ages of 16 and 30 months was used to investigate the fit of the items to the 2-parameter logistic IRT model and to simulate CDI-CAT versions with 400, 200, 100, 50, 25, 10, and 5 items.

Results

All but 14 items fit the 2-parameter logistic IRT model, and real data simulations of CDI-CATs with at least 50 items recovered full CDI scores with correlations over .95. Furthermore, the CDI-CATs with at least 50 items had similar correlations with age and socioeconomic status as the full CDI:WS.

Conclusion

These results provide strong evidence that a CAT version of the CDI:WS has the potential to reduce length while maintaining the accuracy and precision of the full instrument.
Exactly solvable problems in the momentum space with a minimum uncertainty in position
Authors: Samar M. I. , Tkachuk V. M.
Published: April 2016

A new approach in solution of simple quantum mechanical problems in deformed space with minimal length is presented. We propose the generalization of Schrödinger equation in momentum representation on the case of deformed Heisenberg algebra with minimal length. Assuming that the kernel of potential energy operator does not change in the case of deformation, we obtain exact solution of eigenproblem of a particle in delta potential as well as double delta potential. Particle in Coulomb like potential is revisited and the problem of inversibility and hermicity of inverse coordinate operator is solved.
Physisorption versus chemisorption of oxygen molecules on Ag(100)
Authors: Mehlhorn Michael , Morgenstern Karina
Published: April 2016

We compare the adsorption of oxygen molecules on Ag(100) at 60 K and at 100 K. At both temperatures, the molecules form islands. Differences between the species adsorbed at the two temperatures in both low-temperature scanning tunneling microscopy and inelastic electron tunneling spectroscopy are attributed to two different adsorption states, a chemisorbed state after 100 K adsorption and a physisorbed state after 60 K adsorption.
Effect of sputtered titanium interlayers on the properties of nanocrystalline diamond films
Authors: Li Cuiping , Dai Wei , Li Mingji , Li Hongji , Xu Sheng , Wu Xiaoguo , Yang Baohe
Published: April 2016

Ti interlayers with different thicknesses were sputtered on Si substrates and then ultrasonically seeded in a diamond powder suspension. Nanocrystalline diamond (NCD) films were deposited using a dc arc plasma jet chemical vapor deposition system on the seeded Ti/Si substrates. Atomic force microscopy and scanning electron microscopy tests showed that the roughness of the prepared Ti interlayer increased with increasing thickness. The effects of Ti interlayers with various thicknesses on the properties of NCD films were investigated. The results show nucleation, growth, and microstructure of the NCD films are strongly influenced by the Ti interlayers. The addition of a Ti interlayer between the Si substrate and the NCD films can significantly enhance the nucleation rate and reduce the surface roughness of the NCD. The NCD film on a 120 nm Ti interlayer possesses the fastest nucleation rate and the smoothest surface. Raman spectra of the NCD films show trans-polyacetylene relevant peaks reduce with increasing Ti interlayer thickness, which can owe to the improvement of crystalline at grain boundaries. Furthermore, nanoindentation measurement results show that the NCD film on a 120 nm Ti interlayer displays a higher hardness and elastic modulus. High resolution transmission electron microscopy images of a cross-section show that C atoms diffuse into the Ti layer and Si substrate and form TiC and SiC hard phases, which can explain the enhancement of mechanical properties of NCD.
Field emission from optimized structure of carbon nanotube field emitter array
Authors: Chouhan V. , Noguchi T. , Kato S.
Published: April 2016

The authors report a detail study on the emission properties of field emitter array (FEA) of micro-circular emitters of multiwall carbon nanotubes (CNTs). The FEAs were fabricated on patterned substrates prepared with an array of circular titanium (Ti) islands on titanium nitride coated tantalum substrates. CNTs were rooted into these Ti islands to prepare an array of circular emitters. The circular emitters were prepared in different diameters and pitches in order to optimize their structure for acquiring a high emission current. The pitch was varied from 0 to 600 μm, while a diameter of circular emitters was kept constant to be 50 μm in order to optimize a pitch. For diameter optimization, a diameter was changed from 50 to 200 μm while keeping a constant edge-to-edge distance of 150 μm between the circular emitters. The FEA with a diameter of 50 μm and a pitch of 120 μm was found to be the best to achieve an emission current of 47 mA corresponding to an effective current density of 30.5 A/cm2 at 7 V/μm. The excellent emission current was attributed to good quality of CNT rooting into the substrate and optimized FEA structure, which provided a high electric field on a whole circular emitter of 50 μm and the best combination of the strong edge effect and CNT coverage. The experimental results were confirmed with computer simulation.
Theoretical insights on the electro-thermal transport properties of monolayer MoS2 with line defects
Authors: Saha Dipankar , Mahapatra Santanu
Published: April 2016

Two dimensional (2D) materials demonstrate several novel electrical, mechanical, and thermal properties which are quite distinctive to those of their bulk form. Among many others, one important potential application of the 2D material is its use in the field of energy harvesting. Owing to that, here we present a detailed study on electrical as well as thermal transport of monolayer MoS2, in quasi ballistic regime. Besides the perfect monolayer in its pristine form, we also consider various line defects which have been experimentally observed in mechanically exfoliated MoS2 samples. For calculating various parameters related to the electrical transmission, we employ the non-equilibrium Green's function-density functional theory combination. However, to obtain the phonon transmission, we take help of the parametrized Stillinger-Weber potential which can accurately delineate the inter-atomic interactions for the monolayer MoS2. Due to the presence of line defects, we observed significant reductions in both the charge carrier and the phonon transmissions through a monolayer MoS2 flake. Moreover, we also report a comparative analysis showing the temperature dependency of the thermoelectric figure of merit values, as obtained for the perfect as well as the other defective 2D samples.
Phase-field simulation of domain structures and magnetostrictive response in Tb1−xDyxFe2 alloys near morphotropic phase boundary
Authors: Hu Cheng-Chao , Yang Tian-Nan , Huang Hou-Bing , Hu Jia-Mian , Wang Jian-Jun , Shi Yang-Guang , Shi Da-Ning , Chen Long-Qing
Published: April 2016

Phase-field method micromagnetic microelastic modeling is employed to simulate the thermal domain stability and enhanced magnetostrictive responses around the ferromagnetic morphotropic phase boundary (MPB) in giant magnetostrictive Tb1−xDyxFe2 (x≈0.27) single crystal. The simulation shows that the rhombohedral and tetragonal phases coexist in equilibrium in the vicinity of MPB region due to the balance of weak magnetocrystalline anisotropy and strong exchange, magnetostatic and ferroelastic interaction. Enhanced magnetostrictive response is found in the vicinity of MPB, which could be attributed to the low-energy rotating pathways of local magnetization vectors in the phase coexisting region.
Large exchange-dominated domain wall velocities in antiferromagnetically coupled nanowires
Authors: Kuteifan Majd , Lubarda M. V. , Fu S. , Chang R. , Escobar M. A. , Mangin S. , Fullerton E. E. , Lomakin V.
Published: April 2016

Magnetic nanowires supporting field- and current-driven domain wall motion are envisioned for methods of information storage and processing. A major obstacle for their practical use is the domain-wall velocity, which is traditionally limited for low fields and currents due to the Walker breakdown occurring when the driving component reaches a critical threshold value. We show through numerical and analytical modeling that the Walker breakdown limit can be extended or completely eliminated in antiferromagnetically coupled magnetic nanowires. These coupled nanowires allow for large domain-wall velocities driven by field and/or current as compared to conventional nanowires.
Prion protein 2 (dublet) gene (PRND): role in ovine semen capacitation, cryopreservation and fertility
Authors: Ferreira L. M. , Garcia-Herreros M. , Domingos A. , Marques C. C. , Mesquita P. , Barbas J. P. , Baptista M. C. , Pimenta J. , Horta A. E. M. , Prates J. A. M. , Pereira R. M. L. N.
Published: April 2016

The aim of the present study was to examine the role of Doppel protein in the capacitation process and fertilising ability of both fresh and frozen–thawed (FT) spermatozoa from rams carrying different prion protein 2 (dublet) (PRND) gene polymorphisms. The detection efficacy of new anti-Doppel monoclonal antibodies and PRND mRNA quantification were also explored in ovine spermatozoa. Three different genotypes (AA, GA, GG) were identified for codon 26 of ovine PRND-c.78G>A. Using flow cytometry, a higher fluorescence was detected in fresh compared with FT sperm samples incubated with anti-Doppel primary and fluorescein isothiocyanate-conjugated secondary antibodies (P < 0.05). Capacitation was affected by semen treatment (fresh and FT) and male PRND genotype (P < 0.05). After IVF, the use of fresh semen resulted in a higher cleavage rate than the use of FT spermatozoa (P = 0.004). IVF using spermatozoa from individuals classified as carriers of the AA or GA PRND genotypes resulted in higher cleavage rates than seen using spermatozoa from GG carriers (P ≤ 0.0006). Finally, using semen from rams with the AA PRND genotype resulted in the highest Day 6 and Day 8 embryo rates (P ≤ 0.04). In conclusion, the results of the present study confirm that the identification of different PRND genotypes is important for studying the sperm capacitation process and for improving sperm cryoresistance and embryo production. Furthermore, the detection of Doppel in ejaculated ovine spermatozoa, along with its low expression after cryopreservation, strongly suggests an important physiological function of this protein in male fertility.
Pregnancy as a Possible Trigger for Heritable Pulmonary Arterial Hypertension
Authors: Limoges Maude , Langleben David , Fox Benjamin D. , Shear Roberta , Wieczorek Paul , Rudski Lawrence G. , Hirsch Andrew M. , Schlesinger Robert D. , Lesenko Lyda
Published: April 2016

It is unclear whether pregnancy is a trigger or accelerant for idiopathic pulmonary arterial hypertension (PAH). Alternatively, its frequency close to the onset of symptoms and diagnosis in the idiopathic PAH population may represent a coincidence in a disease that predominates in young women. We describe a carrier of a BMPR2 gene mutation who had an uneventful first pregnancy but had aggressive PAH during her second pregnancy and now has ongoing heritable PAH. The possible role of pregnancy as a trigger in this vulnerable patient is discussed. Databases of patients with heritable PAH should be explored to see whether pregnancy is related to overt manifestation of the disease.
The role of neoantigens in response to immune checkpoint blockade
Authors: Riaz Nadeem , Morris Luc , Havel Jonathan J. , Makarov Vladimir , Desrichard Alexis , Chan Timothy A.
Published: April 2016

Immune checkpoint blockade has demonstrated substantial promise for the treatment of several advanced malignancies. These agents activate the immune system to attack tumor cells. For example, agents targeting CTLA4 and programmed cell death 1 (PD-1) have resulted in impressive response rates and, in some cases, durable remissions. Neoantigens are mutations that encode immunologically active proteins that can cause the immune system to recognize the affected cell as foreign. Recent data have made it clear that these mutations are, in large part, the functional targets of immune checkpoint blockade. This review summarizes the key discoveries leading up to this important conclusion and discusses possible applications of neoantigens in cancer therapy.
The new primary X-ray component confirmed in the Seyfert I galaxy IC 4329A
Authors: Miyake Katsuma , Noda Hirofumi , Yamada Shin'ya , Makishima Kazuo , Nakazawa Kazuhiro
Published: April 2016

The bright and highly variable Seyfert I active galactic nucleus IC 4329A was observed with Suzaku five times in 2007 August, with intervals of ∼5 days and a net exposure of 24–31 ks each. Another longer observation was carried out in 2012 August with a net exposure of 118 ks. In the six observations, a source was detected in 2–45 keV with an average 2–10 keV fluxes of (0.67–1.2) × 10−10 erg cm−2 s−1. Its intensity changed by a factor of 2 among the five observations in 2007, and 1.5 within the 2012 observation. A difference of spectrum among these observations revealed that the variability of IC 4329A was carried mainly by a power-law component with a photon index Γ ∼ 2.0. However, in addition to this primary component and its associated reflection, the broad-band Suzaku data required another, harder, and less-variable component with Γ ∼ 1.4. The presence of this new continuum was also confirmed by analyzing the same six data sets through the spectral decomposition technique developed by Noda et al. (2013a, ApJ, 771, 100). This Γ ∼ 1.4 continuum is considered to be a new primary component that has not been recognized in the spectra of IC 4329A so far, although it was recently identified in those of several other Seyfert I galaxies (Noda et al. 2013a, ApJ, 771, 100; Noda et al. 2014, ApJ, 794, 2).
Does Fumigation of Durum Wheat and Semolina with Sulfuryl Fluoride Affect Quality of the Grain, Semolina, and Derived Spaghetti and Bread?
Authors: Hwaidi Mudhir I. , Sissons Mike , Pleming Denise , Collins Patrick J.
Published: April 2016

There is no information on the effect of sulfuryl fluoride (SF) on durum wheat technological properties and products made from fumigated durum wheat. Durum wheat and semolina were exposed to a range of SF applications under conditions that might be typically encountered in bulk storage facilities used in many countries. SF greatly reduced the germination percentage of fumigated durum wheat, with increasing impact under higher SF concentration, grain moisture content, and fumigation temperature. SF greatly reduced seed germination percentage, impacting more the higher the SF concentration. SF had little to no effect on grain test weight, 1,000‐grain weight, hardness, protein content, semolina ash content, and mixograph properties. At the highest SF concentration (31.25 mg/L for 48 h) there was a tendency for pasta cooking loss to be increased but still acceptable, and other pasta properties were largely unaffected. Fumigation with SF did not have any impact on the baking properties of a wholemeal durum flour–commercial flour mix. Therefore, SF is not recommended if the grains are to be used as seeds for agricultural production, but for the production of semolina, pasta, and bread, SF used under typical fumigation conditions has little to no impact on technological properties of durum wheat.
Long-term consequences of high incubation temperature in a wild bird population
Authors: Nord Andreas , Nilsson Jan-Åke
Published: April 2016

Because incubation by birds is energetically costly, parents frequently trade off investment in incubation against self-maintenance. This can be manifested by a reduction in incubation temperature, which comes at high somatic costs for nestlings. The extent to which these costs constrain fitness is poorly understood. We incubated wild blue tit clutches at three biologically relevant temperatures and subsequently recorded winter survival and survival to the breeding season. Fledglings from the coldest treatment (35.0°C) survived less well than other fledglings, but the proportion of winter and breeding survivors did not differ significantly between treatments. However, survival probability in both seasons increased with body mass at fledging in birds from low and mid incubation temperatures, but decreased with fledging body mass in the high-temperature treatment. Mid-temperature nestlings were heavier as adults, weighing 7% more than low- and high-temperature survivors. Thus, high incubation temperature can be beneficial in the short term, but costs of accelerated embryonic development may equal those of protracted development in the long term. Such hidden consequences of faster development could maintain natural selection for average incubation temperature.
Bridging the gap: wound healing in insects restores mechanical strength by targeted cuticle deposition
Authors: Parle Eoin , Dirks Jan-Henning , Taylor David
Published: April 2016

If an insect is injured, can it repair its skeleton in a manner which is mechanically strong and viable? Previous work has described the biological processes that occur during repair of insect cuticle, but until now, there has been no biomechanical assessment of the repaired area. We analysed the biomechanics of the injury repair process in the desert locust (Schistocerca gregaria). We show that after an incision, a healing process occurred which almost doubled the mechanical strength of locust tibial cuticle, restoring it to 66% of the original, intact strength. This repair process occurred by targeted cuticle deposition, stimulated by the presence of the injury. The cut surfaces remained unrepaired, but a patch of endocuticle was deposited, reinforcing the area and thus increasing the effective fracture toughness. The deposition rate of endocuticle inside the tibia increased fourfold compared with uninjured controls, but only on the dorsal side, where the incision was placed. The limb is highly loaded during jumping, so this partial restoration of strength will have a profound effect on the fitness of the insect. A finite-element model provided insights into the mechanics of the repair, predicting that the patch material reaches its ultimate strength before the fracture toughness of the existing cuticle is exceeded.
Emergence of proto-organisms from bistable stochastic differentiation and adhesion
Authors: Duran-Nebreda Salva , Bonforti Adriano , Montañez Raúl , Valverde Sergi , Solé Ricard
Published: April 2016

The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but little is known about the potential origins of multicellular aggregates before genetic programmes took full control of developmental processes. Such aggregates should involve spatial organization of differentiated cells and the modification of flows and concentrations of metabolites within well-defined boundaries. Here, we show that, in an environment where limited nutrients and toxic metabolites are introduced, a population of cells capable of stochastic differentiation and differential adhesion can develop into multicellular aggregates with conflict mediation mechanisms and a complex internal structure. The morphospace of possible patterns is shown to be very rich, including proto-organisms that display a high degree of organizational complexity, far beyond simple heterogeneous populations of cells. Our findings reveal that there is a potentially enormous richness of organismal complexity between simple mixed cooperators and embodied living organisms.
SepG coordinates sporulation-specific cell division and nucleoid organization inStreptomyces coelicolor
Authors: Zhang Le , Willemse Joost , Claessen Dennis , van Wezel Gilles P.
Published: April 2016

Bacterial cell division is a highly complex process that requires tight coordination between septum formation and chromosome replication and segregation. In bacteria that divide by binary fission a single septum is formed at mid-cell, a process that is coordinated by the conserved cell division scaffold protein FtsZ. In contrast, during sporulation-specific cell division in streptomycetes, up to a hundred rings of FtsZ (Z rings) are produced almost simultaneously, dividing the multinucleoid aerial hyphae into long chains of unigenomic spores. This involves the active recruitment of FtsZ by the SsgB protein, and at the same time requires sophisticated systems to regulate chromosome dynamics. Here, we show that SepG is required for the onset of sporulation and acts by ensuring that SsgB is localized to future septum sites. Förster resonance energy transfer imaging suggests direct interaction between SepG and SsgB. The beta-lactamase reporter system showed that SepG is a transmembrane protein with its central domain oriented towards the cytoplasm. Without SepG, SsgB fails to localize properly, consistent with a crucial role for SepG in the membrane localization of the SsgB–FtsZ complex. While SsgB remains associated with FtsZ, SepG re-localizes to the (pre)spore periphery. Expanded doughnut-shaped nucleoids are formed insepGnull mutants, suggesting that SepG is required for nucleoid compaction. Taken together, our work shows that SepG, encoded by one of the last genes in the conserveddcwcluster of cell division and cell-wall-related genes in Gram-positive bacteria whose function was still largely unresolved,coordinates septum synthesis and chromosome organization inStreptomyces.
Loss of reproductive output caused by an invasive species
Authors: Tremblay Maude E. M. , Morris Todd J. , Ackerman Josef D.
Published: April 2016

We investigated whether
Neogobius melanostomus
, an invader of biodiversity ‘hot-spots’ in the Laurentian Great Lakes region, facilitates or inhibits unionid mussel recruitment by serving as a host or sink for their parasitic larvae (glochidia). Infestation and metamorphosis rates of four mussel species with at-risk (conservation) status (
Epioblasma torulosa rangiana
,
Epioblasma triquetra
,
Lampsilis fasciola
and
Villosa iris
) and one common species (
Actinonaias ligamentina
) on
N. melanostomus
were compared with rates on known primary and marginal hosts in the laboratory. All species successfully infested
N. melanostomus,
but only
E. triquetra, V. iris
and
A. ligamentina
successfully metamorphosed into juveniles, albeit at very low rates well below those seen on even the marginal hosts.
Neogobius melanostomus
collected from areas of unionid occurrence in the Grand and Sydenham rivers (Ontario, Canada) exhibited glochidial infection rates of 39.4% and 5.1%, respectively, with up to 30 glochidia representing as many as six unionid species per fish. A mathematical model suggests that
N. melanostomus
serve more as a sink for glochidia than as a host for unionids, thereby limiting recruitment success. This represents a novel method by which an invasive species affects a native species.
Are migratory behaviours of bats socially transmitted?
Authors: Baerwald E. F. , Barclay R. M. R.
Published: April 2016

To migrate, animals rely on endogenous, genetically inherited programmes, or socially transmitted information about routes and behaviours, or a combination of the two. In long-lived animals with extended parental care, as in bats, migration tends to be socially transmitted rather than endogenous. For a young bat to learn migration via social transmission, they would need to follow an experienced individual, most likely one roosting nearby. Therefore, we predicted that bats travelling together originate from the same place. It is also likely that young bats would follow their mothers or other kin, so we predicted that bats travelling together are more closely related to each other than bats not travelling together. To test our predictions, we used microsatellite genotypes and stable isotope values ofδ13C,δ15N andδ2H to analyse the relatedness and geographical origins of migrating hoary bats (Lasiurus cinereus/Aeorestes cinereus(Bairdet al.2015J. Mammal. 96, 1255–1274 (doi:10.1093/jmammal/gyv135));n = 133) and silver-haired bats (Lasionycteris noctivagans;n = 87) killed at wind turbines over two consecutive autumn migrations. Contrary to our predictions, there was no evidence that related dyads of hoary bats or silver-haired bats were killed on the same night more frequently than expected by chance, or that the number of days between the fatalities of dyad members was influenced by relatedness or latitude of origin. Our data suggest that these bats do not socially transmit migration routes and behaviours among close kin.
Open research practices: unintended consequences and suggestions for averting them. (Commentary on the Peer Reviewers' Openness Initiative)
Authors: Bishop D. V. M.
Published: April 2016

The Peer Reviewers' Openness Initiative (PROI) is a move to enlist reviewers in the promotion of data-sharing. In this commentary, I discuss objections that can be raised, first to the specific proposals in the PROI, and second to data-sharing in general. I argue that although many objections have strong counter-arguments, others merit more serious consideration. Regarding the PROI, I suggest that it could backfire if editors and authors feel coerced into data-sharing and so may not be the most pragmatic way of encouraging greater openness. More generally, while promoting data-sharing, we need to be sensitive to cases where sharing of data from human participants could create ethical problems. Furthermore, those interested in promoting reproducible science need to defend against an increased risk of data-dredging when large, multivariable datasets are shared. I end with some suggestions to avoid these unintended consequences.
Paternal but not maternal age influences early-life performance of offspring in a long-lived seabird
Authors: Fay Rémi , Barbraud Christophe , Delord Karine , Weimerskirch Henri
Published: April 2016

Variability in demographic traits between individuals within populations has profound implications for both evolutionary processes and population dynamics. Parental effects as a source of non-genetic inheritance are important processes to consider to understand the causes of individual variation. In iteroparous species, parental age is known to influence strongly reproductive success and offspring quality, but consequences on an offspring fitness component after independence are much less studied. Based on 37 years longitudinal monitoring of a long-lived seabird, the wandering albatross, we investigate delayed effects of parental age on offspring fitness components. We provide evidence that parental age influences offspring performance beyond the age of independence. By distinguishing maternal and paternal age effects, we demonstrate that paternal age, but not maternal age, impacts negatively post-fledging offspring performance.
Rare species contribute disproportionately to the functional structure of species assemblages
Authors: Leitão Rafael P. , Zuanon Jansen , Villéger Sébastien , Williams Stephen E. , Baraloto Christopher , Fortunel Claire , Mendonça Fernando P. , Mouillot David
Published: April 2016

There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions.
The contribution of pUL74 to growth of human cytomegalovirus is masked in the presence of RL13 and UL128 expression
Authors: Laib Sampaio Kerstin , Stegmann Cora , Brizic Ilija , Adler Barbara , Stanton Richard J. , Sinzger Christian
Published: April 2016

The glycoproteins gH and gL of human cytomegalovirus (HCMV) form a complex either with pUL74 (trimeric complex) or with proteins of the UL128 locus (pentameric complex). While the pentameric complex is dispensable for viral growth in fibroblasts, deletion of pUL74 causes a small plaque phenotype in HCMV lab strains, accompanied by greatly reduced cell-free infectivity. As HCMV isolates, shortly after cultivation from clinical specimens, do not release cell-free infectious viruses, we wondered whether deletion of pUL74 would also affect virus growth in this background. To address this question, we took advantage of the bacterial artificial chromosome (BAC)-cloned virus Merlin-RL13tetO, which grows cell associated due to the inducible expression of the viral RL13 gene, thereby resembling clinical isolates. Stop codons were introduced by seamless mutagenesis into UL74 and/or the UL128 locus to prevent expression of the trimeric or pentameric complex, respectively. Virus mutants were reconstituted by transfection of the respective genomes into cultured cells and analysed with respect to focal growth. When the UL128 locus was intact, deletion of pUL74 did not notably affect focal growth of Merlin, irrespective of RL13 expression. In the absence of UL128 expression, foci were increased compared with wild-type, and infectious cell-free virus was produced. Under these conditions, disruption of UL74 completely prevented virus spread from initially transfected cells to surrounding cells. In conclusion the contribution of pUL74 is masked when the UL128 locus is expressed at high levels, and its role in cell-free virus spread is only revealed when expression of the pentameric complex is inhibited.
Wide genome involvement in response to long-term selection for antibody response in an experimental population of White Leghorn chickens
Authors: Lillie Mette , Sheng Zheya , Honaker Christa , Dorshorst Ben , Siegel Paul , Carlborg Örjan
Published: April 2016

Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation. They allow researchers to uncover the targets of selection and how these contribute to the mode and tempo of adaptation. Here we report results from a pooled genome re-sequencing study to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. We observed wide genome involvement in response to this selection regime, with over 200 candidate sweep regions characterised by spans of high genetic differentiation (FST). These sweep signatures, encompassing almost 20% of the chicken genome (208.8 Mb), are primarily the result from bidirectional selection on haplotypes present in the base population. These extensive genomic changes highlight both the extent of standing genetic variation at immune loci available at the onset of selection, as well as how the long-term selection response results from selection on a highly polygenic genetic architecture. Furthermore, we present three examples of strong candidate genes that may have contributed to the profound phenotypic response to selection.

Data Availability

Pooled genome data generated for this study will become available via SRA upon acceptance of manuscript
Zfp423regulates Sonic hedgehog signaling via primary cilium function
Authors: Hong Chen-Jei , Hamilton Bruce A.
Published: April 2016

Zfp423encodes a 30-zinc finger transcription factor that intersects several canonical signaling pathways.Zfp423mutations result in ciliopathy-related phenotypes, including agenesis of the cerebellar vermis in mice and Joubert syndrome (JBTS19) and nephronophthisis (NPHP14) in humans. Unlike most ciliopathy genes,Zfp423encodes a nuclear protein and its developmental expression is complex, leading to alternative proposals for cellular mechanisms. Here we show thatZfp423is expressed by cerebellar granule cell precursors, that loss ofZfp423in these precursors leads to cell-intrinsic reduction in proliferation, loss of response to Shh, and primary cilia abnormalities that include diminished frequency of both Smoothened and IFT88 localization. Loss ofZfp423alters expression of several genes encoding key cilium components, including increased expression ofTulp3.Tulp3is a direct binding target ofZfp423and reducing the overexpression ofTulp3inZfp423-deficient cells suppresses Smoothened translocation defects. These results defineZfp423deficiency as a bona fide ciliopathy, acting upstream of Shh signaling, and indicate a mechanism intrinsic to granule cell precursors for the resulting cerebellar hypoplasia.

Author Summary

Ciliopathies are a broad group of individually rare genetic disorders that share overlapping phenotypes and mutations in genes that make components of the primary cilium. Mutations inZNF423are an exception. Patients and mouse models show characteristic hypoplasia of the cerebellar midline (Joubert syndrome), but the gene encodes a nuclear transcription factor. The mouse gene,Zfp423, is expressed in a dynamic developmental pattern, leaving the cellular mechanism for this brain malformation unresolved. One report suggested reduced Purkinje cell expression of Shh, a key mitogen for cerebellar granule cell precursors (GCPs) whose signal transduction occurs at the primary cilium, as the key event. We show thatZfp423mutants expressed normal Shh levels, but thatZfp423-depleted GCPs were unable to respond. Primary cilia onZfp423-mutant GCPs in situ typically had a wider base and longer extension. ZNF423-depletion in a human cell culture model resulted in defective translocation of Smoothened, a key event in Shh signaling, and of the intraflagellar transport protein IFT88. RNA-Seq and RT-qPCR experiments identified known ciliopathy genes as potential conserved targets ofZNF423andZfp423. One of these,TULP3, was both up-regulated inZNF423/Zfp423-deficient cells and directly bound by Zfp423 in granule cell precursors. Reversing the overexpression of TULP3 in ZNF423-depleted human cell culture model reversed the defect in Smoothened translocation.