bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity
Authors: Hansen Simon , Stüber Jakob C. , Ernst Patrick , Koch Alexander , Bojar Daniel , Batyuk Alexander , Plückthun Andreas 
Published: November 2017

AbstractGreen fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced inE. coliin very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.
Invasive plants as potential food resource for native pollinators: A case study with two invasive species and a generalist bumble bee
Authors: Drossart Maxime , Michez Denis , Vanderplanck Maryse 
Published: November 2017

AbstractIt is now well established that invasive plants may induce drifts in the quantity and/or quality of floral resources. They are then often pointed out as a potential driver of bee decline. However, their impact on bee population remains quite unclear and still controversial, as bee responses are highly variable among species. Here, we compared the amino acid composition of pollen from three native and two invasive plant species included in diets of common pollinators in NW Europe. Moreover, the nutritional intake (i.e., pollen and amino acid intakes) ofBombus terrestriscolonies and the pollen foraging behaviour of workers (i.e., visiting rate, number of foraging trips, weight of pollen loads) were considered. We found significant differences in pollen nutrients among the studied species according to the plant invasive behaviour. We also found significant differences in pollen foraging behaviour according to the plant species, from few to several foraging trips carrying small or large pollen loads. Such behavioural differences directly impacted the pollen intake but depended more likely on plant morphology rather than on plant invasive behaviour. These results suggest that common generalist bumble bees might not always suffer from plant invasions, depending on their behavioural plasticity and nutritional requirements.
Fungal endophytes inhabiting mountain-cultivated ginseng (Panax ginseng Meyer): Diversity and biocontrol activity against ginseng pathogens
Authors: Park Young-Hwan , Kim Yoosam , Mishra Ratnesh Chandra , Bae Hanhong 
Published: November 2017

AbstractFungal endophytes isolated from mountain-cultivated ginseng (MCG, Panax ginseng Meyer) were explored for their diversity and biocontrol activity against ginseng pathogens (Alternaria panax, Botrytis cinerea, Cylindrocarpon destructans, Pythium sp. and Rhizoctonia solani). A total of 1,300 isolates were isolated from three tissues (root, stem and leaf) from MCGs grown in 24 different geographic locations in Korea. In total, 129 different fungal isolates were authenticated by molecular identification based on internal transcribed spacer (ITS) sequences. The fungal endophytes belonged to Ascomycota (81.7%), Basidiomycota (7.08%), Zygomycota (10%) and Unknown (1.15%), with 59 genera. Analysis of diversity indices across sampling sites suggested species abundance as a function of geographical and environmental factors of the locations. Shannon diversity index and richness in the different tissues revealed that root tissues are colonized more than stem and leaf tissues, and also certain fungal endophytes are tissue specific. Assessment of the ethyl acetate extracts from 129 fungal isolates for their biocontrol activity against 5 ginseng pathogens revealed that Trichoderma polysporum produces the antimcriobial metabolite against all the pathogens. This result indicates the promise of its potential usage as a biocontrol agent.
Silica formation with nanofiber morphology via helical display of the silaffin R5 peptide on a filamentous bacteriophage
Authors: Song In-Wong , Park Hyojung , Park Jung Han , Kim Hyunook , Kim Seong Hun , Yi Sung , Jaworski Justyn , Sang Byoung-In 
Published: November 2017

AbstractBiological systems often generate unique and useful structures, which can have industrial relevance either as direct components or as an inspiration for biomimetic materials. For fabrication of nanoscale silica structures, we explored the use of the silaffin R5 peptide fromCylindrotheca fusiformisexpressed on the surface of the fd bacteriophage. By utilizing the biomineralizing peptide component displayed on the bacteriophage surface, we found that low concentrations (0.09 mg/mL of the R5 bacteriophage, below the concentration range used in other studies) could be used to create silica nanofibers. An additional benefit of this approach is the ability of our R5-displaying phage to form silica materials without the need for supplementary components, such as aminopropyl triethoxysilane, that are typically used in such processes. Because this method for silica formation can occur under mild conditions when implementing our R5 displaying phage system, we may provide a relatively simple, economical, and environmentally friendly process for creating silica nanomaterials.
Rama: a machine learning approach for ribosomal protein prediction in plants
Authors: Carvalho Thales Francisco Mota , Silva José Cleydson F. , Calil Iara Pinheiro , Fontes Elizabeth Pacheco Batista , Cerqueira Fabio Ribeiro 
Published: November 2017

AbstractRibosomal proteins (RPs) play a fundamental role within all type of cells, as they are major components of ribosomes, which are essential for translation of mRNAs. Furthermore, these proteins are involved in various physiological and pathological processes. The intrinsic biological relevance of RPs motivated advanced studies for the identification of unrevealed RPs. In this work, we propose a new computational method, termed Rama, for the prediction of RPs, based on machine learning techniques, with a particular interest in plants. To perform an effective classification, Rama uses a set of fundamental attributes of the amino acid side chains and applies a two-step procedure to classify proteins with unknown function as RPs. The evaluation of the resultant predictive models showed that Rama could achieve mean sensitivity, precision, and specificity of 0.91, 0.91, and 0.82, respectively. Furthermore, a list of proteins that have no annotation in Phytozome v.10, and are annotated as RPs in Phytozome v.12, were correctly classified by our models. Additional computational experiments have also shown that Rama presents high accuracy to differentiate ribosomal proteins from RNA-binding proteins. Finally, two novel proteins of Arabidopsis thaliana were validated in biological experiments. Rama is freely available at http://inctipp.bioagro.ufv.br:8080/Rama.
The association between visual function and retinal structure in chronic central serous chorioretinopathy
Authors: Sugiura Aya , Fujino Ryosuke , Takemiya Nobuko , Shimizu Kimiko , Matsuura Masato , Murata Hiroshi , Inoue Tatsuya , Obata Ryo , Asaoka Ryo 
Published: November 2017

AbstractThe purpose of the current study was to investigate the association between visual function and retinal structure in central serous chorioretinopathy (CSC). In 22 eyes of 22 chronic CSC patients with serous retinal detachment at the macula, retinal sensitivity was measured using MP3 microperimetry (NIDEK, Japan) and mean sensitivity within two degrees (MS2), four degrees (MS4) and six degrees (MS6), as well as foveal sensitivity (MS0), were calculated. Retinal structure was measured using optical coherence tomography (OCT, Spectralis, Heidelberg). The relationship between visual function (LogMAR best-corrected visual acuity [LogMAR VA] and MS0, MS2, MS4, MS6) and serous retinal detachment height at the fovea (SRDH), central retinal thickness (CRT), macular volume (MV) and central choroidal thickness (CCT) was investigated. There were significant negative correlations between LogMAR VA and MS0 (p = 0.016), MS2 (p = 0.049). No significant relationship was observed between LogMAR VA and SRDH (p = 0.97) although there was a significant negative correlation between SRDH and MS2 (p = 0.028), MS4 (p = 0.049), MS6 (p = 0.023). In conclusion, in CSC, serous retinal detachment was significantly correlated with retinal sensitivity measured with MP3, but not with LogMAR VA.
Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating
Authors: Mazurenko Stanislav , Kunka Antonin , Beerens Koen , Johnson Christopher M. , Damborsky Jiri , Prokop Zbynek 
Published: November 2017

AbstractStudies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments. To extract this information, we propose fitting both first and second scans simultaneously. Four most common single-peak transition models are considered: (i) fully reversible, (ii) fully irreversible, (iii) partially reversible transitions, and (iv) general three-state models. The method is validated using calorimetry data for chicken egg lysozyme, mutated Protein A, three wild-types of haloalkane dehalogenases, and a mutant stabilized by protein engineering. We show that modelling of reheating increases the precision of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differences. Moreover, this modelling indicates whether alternative refolding pathways might occur upon cooling. The Matlab-based data fitting software tool and its user guide are provided as a supplement.
Membrane insertion of the BAX core, but not latch domain, drives apoptotic pore formation
Authors: Flores-Romero Hector , Garcia-Porras Miguel , Basañez Gorka 
Published: November 2017

AbstractDespite intensive research effort, how the paradigmatic proapoptotic protein BAX forms lethal apoptotic pores at the mitochondrial outer membrane (MOM) remains incompletely understood. Here, we used biophysical tools and minimalist model systems to identify the specific regions in BAX driving apoptotic pore formation, and to gain more insight into underlying mechanisms. Fluorescence mapping revealed that fully active BAX adopts a BH3-in-groove dimeric conformation in MOM-like membranes, with BAX α4-α5 helices belonging to its core domain inserting deeper into the membrane lipid bilayer than BAX α6-α8 helices belonging to its latch domain. In our reconstituted systems, antiapoptotic BCLXL formed canonical heterodimeric BH3-in-groove complexes with BAX, and blocked membrane insertion of BAX core α4-α5 helices, but not BAX latch α6-α8 helices. Moreover, poly(ethylene glycol) (PEG) conjugation (PEGylation) at multiple individual sites along the BAX core, but not latch domain, potently inhibited BAX pore-forming activity. Additional combined computational and experimental evidence revealed that the BAX core α5 helix displays a bilayer-destabilizing membrane interaction mode that is absent in BAX latch α6-α8 helices. Based on this collective set of evidence, we propose that membrane insertion of the BAX core, but not latch domain, is critical for BAX apoptotic pore formation.
A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes
Authors: Mimura Yasuhiro , Takemoto Satoko , Tachibana Taro , Ogawa Yutaka , Nishimura Masaomi , Yokota Hideo , Imamoto Naoko 
Published: November 2017

AbstractNuclear pore complexes (NPCs) maintain cellular homeostasis by mediating nucleocytoplasmic transport. Although cyclin-dependent kinases (CDKs) regulate NPC assembly in interphase, the location of NPC assembly on the nuclear envelope is not clear. CDKs also regulate the disappearance of pore-free islands, which are nuclear envelope subdomains; this subdomain gradually disappears with increase in homogeneity of the NPC in response to CDK activity. However, a causal relationship between pore-free islands and NPC assembly remains unclear. Here, we elucidated mechanisms underlying NPC assembly from a new perspective by focusing on pore-free islands. We proposed a novel framework for image-based analysis to automatically determine the detailed ‘landscape’ of pore-free islands from a large quantity of images, leading to the identification of NPC intermediates that appear in pore-free islands with increased frequency in response to CDK activity. Comparison of the spatial distribution between simulated and the observed NPC intermediates within pore-free islands showed that their distribution was spatially biased. These results suggested that the disappearance of pore-free islands is highly related to de novo NPC assembly and indicated the existence of specific regulatory mechanisms for the spatial arrangement of NPC assembly on nuclear envelopes.
Changes in gene expression and apoptotic response in Spodoptera exigua larvae exposed to sublethal concentrations of Vip3 insecticidal proteins
Authors: Hernández-Martínez Patricia , Gomis-Cebolla Joaquín , Ferré Juan , Escriche Baltasar 
Published: November 2017

AbstractThe insecticidal Vip3 proteins fromBacillus thuringiensis(Bt), along with the classical Bt Cry proteins, are currently used in Bt-crops to control insect pests, since they do not share the same mode of action. Here we characterized the response ofSpodoptera exigualarvae after Vip3 challenge. The expression profile of 47 genes was analyzed in larvae challenged with three concentrations of Vip3Ca. Results showed that the up-regulated genes were mainly involved in immune response, whereas the down-regulated genes were mainly involved in the digestion process. Other mechanisms of cellular response to the damage such as apoptosis were analyzed. For this analysis, sections from the midguts were examined by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. The nuclei of the midgut epithelial cells were stained at the highest concentration of the Vip3Ca protein and at lower concentrations of Vip3Aa in agreement with the different potency of the two proteins. In addition, apoptosis was also examined by the analysis of the expression of fivecaspasegenes. The present study shows that exposure ofS. exigualarvae to sublethal concentrations of Vip3 proteins activates different insect response pathways which trigger the regulation of some genes, APN shedding, and apoptotic cell death.
Organoids model distinct Vitamin E effects at different stages of prostate cancer evolution
Authors: Njoroge Rose N. , Unno Kenji , Zhao Jonathan C. , Naseem Anum F. , Anker Jonathan F. , McGee Warren A. , Nonn Larisa , Abdulkadir Sarki A. 
Published: November 2017

AbstractVitamin E increased prostate cancer risk in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) through unknown mechanisms while Selenium showed no efficacy. We determined the effects of the SELECT supplements on benign (primary), premalignant ( RWPE-1) and malignant (LNCaP) prostate epithelial organoids. While the supplements decreased proliferation and induced cell death in cancer organoids, they had no effect on the benign organoids. In contrast, Vitamin E enhanced cell proliferation and survival in the premalignant organoids in a manner that recapitulated the SELECT results. Indeed, while Vitamin E induced a pro-proliferative gene expression signature, Selenium alone or combined with Vitamin E produced an anti-proliferative signature. The premalignant organoids also displayed significant downregulation of glucose transporter and glycolytic gene expression pointing to metabolic alterations. Detached RWPE-1 cells had low ATP levels due to diminished glucose uptake and glycolysis which was rescued by Vitamin E through the activation of fatty acid oxidation (FAO). FAO inhibition abrogated the ATP rescue, diminished survival of the inner matrix detached cells, restoring the normal hollow lumen morphology in Vitamin E treated organoids. Organoid models therefore clarify the paradoxical findings from SELECT and demonstrate that Vitamin E promotes tumorigenesis in the early stages of prostate cancer evolution.
The use of microfluidic spinning fiber as an ophthalmology suture showing the good anastomotic strength control
Authors: Park DoYeun , Yong In Sung , Cho Kyong Jin , Cheng Jie , Jung Youngmee , Kim Soo Hyun , Lee Sang-Hoon 
Published: November 2017

AbstractAdjusting the mechanical strength of a biomaterial to suit its intended application is very important for realizing beneficial outcomes. Microfluidic spinning fiber have been attracting attention recently due to their various advantages, but their mechanical strength has unfortunately not been a subject of concentrated research, and this lack of research has severely limited their applications. In the current work, we showed the mechanical properties of microfibers can be tuned easily and provided a mathematical explanation for how the microfluidic spinning method intrinsically controls the mechanical properties of a microfluidic spinning fiber. But we were also able to adjust the mechanical properties of such fibers in various other ways, including by using biomolecules to coat the fiber or mixing the biomolecules with the primary component of the fiber and by using a customized twisting machine to change the number of single microfiber strands forming the fiber. We used the bundle fiber as an ophthalmology suture that resulted in a porcine eye with a smoother post-operative surface than did a nylon suture. The results showed the possibility that the proposed method can solve current problems of the microfibers in practical applications, and can thus extend the range of applications of these microfibers.
An extended cluster expansion for ground states of heterofullerenes
Authors: Cheng Yun-Hua , Liao Ji-Hai , Zhao Yu-Jun , Yang Xiao-Bao 
Published: November 2017

AbstractIt is challenging to determine the ground states of heterofullerenes due to the numerous isomers. Taking the C60-n
B
n
heterofullerenes (1 ≤ n ≤ 4) as an example, our first-principles calculations with the isomer enumeration present the most stable structure of C57B3, which is energetically favored by 0.73 eV than the reported counterpart. It was difficult to conduct the enumeration for the isomers with n beyond 4 because of the expensive first-principle calculations. Here, we propose a nomenclature to enhance structural recognition and adopt an extended cluster expansion to describe the structural stabilities, in which the energies of the heterofullerenes with various concentrations are predicted by linear combination of the multi-body interactions. Unlike the conventional cluster expansion, the interaction parameters are derived from the enumeration of C60-n
B
n
(n = 1~4), where there are only 4 coefficients to be fitted as a function of composition for the consideration of local bonding. The cross-validation scores are 1~2 meV per atom for both C55B5 and C54B6, ensuring the ground states obtained from our model are in line with the first-principles results. With the help of the structural recognition, the extended cluster expansion could be further applied to other binary systems as an effective complement to the first-principle calculations.
The Retinol Binding Protein Receptor 2 (Rbpr2) is required for Photoreceptor Outer Segment Morphogenesis and Visual Function in Zebrafish
Authors: Shi Yi , Obert Elisabeth , Rahman Bushra , Rohrer Bärbel , Lobo Glenn P. 
Published: November 2017

AbstractVitamin A (all-trans retinol) plays critical roles in mammalian development and vision. Since vitamin A is food-derived, tissue-specific uptake and storage mechanism are needed. In the eye, uptake of RBP4-retinol is mediated by the receptor Stra6, whereas the receptor mediating RBP4 binding and retinol transport into the liver has just recently been discovered. Here we examined the role of zebrafish retinol binding protein receptor 2 (Rbpr2) for RBP4-retinol uptake in developing embryos, using eye development and vision as sensitive readouts. In cultured cells, Rbpr2 localized to membranes and promoted RBP4-retinol uptake. In larvae, Rbpr2 expression was detected in developing intestinal enterocytes and liver hepatocytes. Two rbpr2 mutant zebrafish lines, each resulting in Rbpr2 deficiency, exhibit a small eye defect, and systemic malformations including hydrocephaly and cardiac edema, phenotypes associated with vitamin A deficiency. In the retina, Rbpr2 loss resulted in shorter photoreceptor outer segments, mislocalization and decrease in visual pigments, decreased expression of retinoic acid-responsive genes and photoreceptor cell loss, overall leading to a reduction of visual function. Together, these results demonstrate that Rbpr2-mediated RBP4-retinol uptake in developing liver and intestine is necessary to provide sufficient substrate for ocular retinoid production required for photoreceptor cell maintenance and visual function.
Hydrogen mobility in the lightest reversible metal hydride, LiBeH3
Authors: Mamontov Eugene , Kolesnikov Alexander I. , Sampath Sujatha , Yarger Jeffery L. 
Published: November 2017

AbstractLithium-beryllium metal hydrides, which are structurally related to their parent compound, BeH2, offer the highest hydrogen storage capacity by weight among the metal hydrides (15.93 wt. % of hydrogen for LiBeH3). Challenging synthesis protocols have precluded conclusive determination of their crystallographic structure to date, but here we analyze directly the hydrogen hopping mechanisms in BeH2 and LiBeH3 using quasielastic neutron scattering, which is especially sensitive to single-particle dynamics of hydrogen. We find that, unlike its parent compound BeH2, lithium-beryllium hydride LiBeH3 exhibits a sharp increase in hydrogen mobility above 265 K, so dramatic that it can be viewed as melting of hydrogen sublattice. We perform comparative analysis of hydrogen jump mechanisms observed in BeH2 and LiBeH3 over a broad temperature range. As microscopic diffusivity of hydrogen is directly related to its macroscopic kinetics, a transition in LiBeH3 so close to ambient temperature may offer a straightforward and effective mechanism to influence hydrogen uptake and release in this very lightweight hydrogen storage compound.