bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving kangaroo phylogeny and overcoming retrotransposon ascertainment bias
Authors: Dodt William G. , Gallus Susanne , Phillips Matthew J. , Nilsson Maria A. 
Published: November 2017

AbstractReconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the generaMacropusandWallabia. An exhaustivein silicoscreening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses. We identified robust support for the enigmatic swamp wallaby (Wallabia bicolor) falling within a paraphyletic genus,Macropus. Our statistical approach provides a means to test for incomplete lineage sorting and introgression/hybridization in the presence of the ascertainment bias. Using retrotransposons as “molecular fossils”, we reveal one of the most complex patterns of hemiplasy yet identified, during the rapid diversification of kangaroos and wallabies. Ancestral state reconstruction incorporating the new retrotransposon phylogenetic information reveals multiple independent ecological shifts among kangaroos into more open habitats, coinciding with the Pliocene onset of increased aridification in Australia from ~3.6 million years ago.
Intracellular biomass flocculation as a key mechanism of rapid bacterial killing by cationic, amphipathic antimicrobial peptides and peptoids
Authors: Chongsiriwatana Nathaniel P. , Lin Jennifer S. , Kapoor Rinki , Wetzler Modi , Rea Jennifer A. C. , Didwania Maruti K. , Contag Christopher H. , Barron Annelise E. 
Published: November 2017

AbstractMany organisms rely on antimicrobial peptides (AMPs) as a first line of defense against pathogens. In general, most AMPs are thought to kill bacteria by binding to and disrupting cell membranes. However, certain AMPs instead appear to inhibit biomacromolecule synthesis, while causing less membrane damage. Despite an unclear understanding of mechanism(s), there is considerable interest in mimicking AMPs with stable, synthetic molecules. Antimicrobial N-substituted glycine (peptoid) oligomers (“ampetoids”) are structural, functional and mechanistic analogs of helical, cationic AMPs, which offer broad-spectrum antibacterial activity and better therapeutic potential than peptides. Here, we show through quantitative studies of membrane permeabilization, electron microscopy, and soft X-ray tomography that both AMPs and ampetoids trigger extensive and rapid non-specific aggregation of intracellular biomacromolecules that correlates with microbial death. We present data demonstrating that ampetoids are “fast killers”, which rapidly aggregate bacterial ribosomes in vitro and in vivo. We suggest intracellular biomass flocculation is a key mechanism of killing for cationic, amphipathic AMPs, which may explain why most AMPs require micromolar concentrations for activity, show significant selectivity for killing bacteria over mammalian cells, and finally, why development of resistance to AMPs is less prevalent than developed resistance to conventional antibiotics.
17β-Estradiol sensitizes ovarian surface epithelium to transformation by suppressing Disabled-2 expression
Authors: Vuong Nhung H. , Salah Salah Omar , Vanderhyden Barbara C. 
Published: November 2017

AbstractEstrogen replacement therapy increases the risk of human ovarian cancer and exogenous estradiol accelerates the onset of ovarian cancer in mouse models. This study uses primary cultures of mouse ovarian surface epithelium (OSE) to demonstrate that one possible mechanism by which estrogen accelerates the initiation of ovarian cancer is by up-regulation of microRNA-378 via the ESR1 pathway to result in the down-regulation of a tumour suppressor calledDisabled-2(Dab2). Estrogen suppression ofDab2was reproduciblein vivoand across many cell types including mouse oviductal epithelium and primary cultures of human ovarian cancer cells. Suppression ofDab2resulted in increased proliferation, loss of contact inhibition, morphological dysplasia, and resistance to oncogene-induced senescence – all factors that can sensitize OSE to transformation. Given thatDAB2is highly expressed in healthy human OSE and is absent in the majority of ovarian tumours, this study has taken the first steps to provide a mechanistic explanation for how estrogen therapy may play a role in the initiation of ovarian cancer.
Repair of the TGFBI gene in human corneal keratocytes derived from a granular corneal dystrophy patient via CRISPR/Cas9-induced homology-directed repair
Authors: Taketani Yukako , Kitamoto Kohdai , Sakisaka Toshihiro , Kimakura Mikiko , Toyono Tetsuya , Yamagami Satoru , Amano Shiro , Kuroda Masahiko , Moore Tara , Usui Tomohiko , Ouchi Yasuo 
Published: November 2017

AbstractGranular corneal dystrophy (GCD) is an autosomal dominant hereditary disease in which multiple discrete and irregularly shaped granular opacities are deposited in the corneal stroma. GCD is caused by a point mutation in the transforming growth factor-β-induced (TGFBI) gene, located on chromosome 5q31. Here, we report the first successful application of CRISPR-Cas9-mediated genome editing for the correction of a TGFBI mutation in GCD patient-derived primary corneal keratocytes via homology-directed repair (HDR). To correct genetic defects in GCD patient cells, we designed a disease-specific guide RNA (gRNA) targeting the R124H mutation of TGFBI, which causes GCD type 2 (GCD2). An R124H mutation in primary human corneal keratocytes derived from a GCD2 patient was corrected by delivering a CRISPR plasmid expressing Cas9/gRNA and a single-stranded oligodeoxynucleotide HDR donor template in vitro. The gene correction efficiency was 20.6% in heterozygous cells and 41.3% in homozygous cells. No off-target effects were detected. These results reveal a new therapeutic strategy for GCD2; this method may also be applicable to other heredity corneal diseases.
Effects of neuroactive agents on axonal growth and pathfinding of retinal ganglion cells generated from human stem cells
Authors: Yokoi Tadashi , Tanaka Taku , Matsuzaka Emiko , Tamalu Fuminobu , Watanabe Shu-Ichi , Nishina Sachiko , Azuma Noriyuki 
Published: November 2017

AbstractWe recently established a novel method for generating functional human retinal ganglion cells (RGCs) from human induced pluripotent cells (hiPSCs). Here, we confirmed that RGCs can also be generated from human embryonic stem cells (hESCs). We investigated the usefulness of human RGCs with long axons for assessing the effects of chemical agents, such as the neurotrophic factor, nerve growth factor (NGF), and the chemorepellent factors, semaphorin 3 A (SEMA3A) and SLIT1. The effects of direct and local administration of each agent on axonal projection were evaluated by immunohistochemistry, real-time polymerase chain reaction (PCR), and real-time imaging, in which the filopodia of the growth cone served as an excellent marker. A locally sustained agent system showed that the axons elongate towards NGF, but were repelled by SEMA3A and SLIT1. Focally transplanted beads that released SLIT1 bent the pathfinding of axons, imitating normal retinal development. Our innovative system for assessing the effects of chemical compounds using human RGCs may facilitate development of novel drugs for the examination, prophylaxis, and treatment of diseases. It may also be useful for observing the physiology of the optic nerve in vitro, which might lead to significant progress in the science of human RGCs.
Rational design and dynamics of self-propelled colloidal bead chains: from rotators to flagella
Authors: Vutukuri Hanumantha Rao , Bet Bram , van Roij René , Dijkstra Marjolein , Huck Wilhelm T. S. 
Published: November 2017

AbstractThe quest for designing new self-propelled colloids is fuelled by the demand for simple experimental models to study the collective behaviour of their more complex natural counterparts. Most synthetic self-propelled particles move by converting the input energy into translational motion. In this work we address the question if simple self-propelled spheres can assemble into more complex structures that exhibit rotational motion, possibly coupled with translational motion as in flagella. We exploit a combination of induced dipolar interactions and a bonding step to create permanent linear bead chains, composed of self-propelled Janus spheres, with a well-controlled internal structure. Next, we study how flexibility between individual swimmers in a chain can affect its swimming behaviour. Permanent rigid chains showed only active rotational or spinning motion, whereas longer semi-flexible chains showed both translational and rotational motion resembling flagella like-motion, in the presence of the fuel. Moreover, we are able to reproduce our experimental results using numerical calculations with a minimal model, which includes full hydrodynamic interactions with the fluid. Our method is general and opens a new way to design novel self-propelled colloids with complex swimming behaviours, using different complex starting building blocks in combination with the flexibility between them.
Human CRMP4 mutation and disrupted Crmp4 expression in mice are associated with ASD characteristics and sexual dimorphism
Authors: Tsutiya Atsuhiro , Nakano Yui , Hansen-Kiss Emily , Kelly Benjamin , Nishihara Masugi , Goshima Yoshio , Corsmeier Don , White Peter , Herman Gail E. , Ohtani-Kaneko Ritsuko 
Published: November 2017

AbstractAutism spectrum disorders (ASD) are more common among boys than girls. The mechanisms responsible for ASD symptoms and their sex differences remain mostly unclear. We previously identified collapsin response mediator protein 4 (CRMP4) as a protein exhibiting sex-different expression during sexual differentiation of the hypothalamic sexually dimorphic nucleus. This study investigated the relationship between the sex-different development of autistic features and CRMP4 deficiency. Whole-exome sequencing detected a de novo variant (S541Y) of CRMP4 in a male ASD patient. The expression of mutated mouse CRMP4S540Y, which is homologous to human CRMP4S541Y, in cultured hippocampal neurons derived from Crmp4-knockout (KO) mice had increased dendritic branching, compared to those transfected with wild-type (WT) Crmp4, indicating that this mutation results in altered CRMP4 function in neurons. Crmp4-KO mice showed decreased social interaction and several alterations of sensory responses. Most of these changes were more severe in male Crmp4-KO mice than in females. The mRNA expression levels of some genes related to neurotransmission and cell adhesion were altered in the brain of Crmp4-KO mice, mostly in a gender-dependent manner. These results indicate a functional link between a case-specific, rare variant of one gene, Crmp4, and several characteristics of ASD, including sexual differences.
Greenhouse gas emissions and carbon sequestration by agroforestry systems in southeastern Brazil
Authors: Torres Carlos Moreira Miquelino Eleto , Jacovine Laércio Antônio Gonçalves , Nolasco de Olivera Neto Sílvio , Fraisse Clyde William , Soares Carlos Pedro Boechat , de Castro Neto Fernando , Ferreira Lino Roberto , Zanuncio José Cola , Lemes Pedro Guilherme 
Published: November 2017

AbstractAgrosilvopastoral and silvopastoral systems can increase carbon sequestration, offset greenhouse gas (GHG) emissions and reduce the carbon footprint generated by animal production. The objective of this study was to estimate GHG emissions, the tree and grass aboveground biomass production and carbon storage in different agrosilvopastoral and silvopastoral systems in southeastern Brazil. The number of trees required to offset these emissions were also estimated. The GHG emissions were calculated based on pre-farm (e.g. agrochemical production, storage, and transportation), and on-farm activities (e.g. fertilization and machinery operation). Aboveground tree grass biomass and carbon storage in all systems was estimated with allometric equations. GHG emissions from the agroforestry systems ranged from 2.81 to 7.98 t CO2e ha−1. Carbon storage in the aboveground trees and grass biomass were 54.6, 11.4, 25.7 and 5.9 t C ha−1, and 3.3, 3.6, 3.8 and 3.3 t C ha−1 for systems 1, 2, 3 and 4, respectively. The number of trees necessary to offset the emissions ranged from 17 to 44 trees ha−1, which was lower than the total planted in the systems. Agroforestry systems sequester CO2 from the atmosphere and can help the GHG emission-reduction policy of the Brazilian government.
The origin of human handedness and its role in pre-birth motor control
Authors: Parma Valentina , Brasselet Romain , Zoia Stefania , Bulgheroni Maria , Castiello Umberto 
Published: November 2017

AbstractThe vast majority of humans are right-handed, but how and when this bias emerges during human ontogenesis is still unclear. We propose an approach that explains postnatal handedness starting from 18 gestational weeks using a kinematic analysis of different fetal arm movements recorded during ultrasonography. Based on the hand dominance reported postnatally at age 9, the fetuses were classified as right-handed (86%) or left-handed, in line with population data. We revealed that both right-handed and left-handed fetuses were faster to reach to targets requiring greater precision (i.e., eye and mouth), with their dominant (vs. non-dominant) hand. By using either movement times or deceleration estimates, handedness can be inferred with a classification accuracy ranging from 89 to 100% from gestational week 18. The reliability of this inference hints to the yet unexplored potential of standard ultrasonography to advance our understanding of prenatal life.
Repurposing a photosynthetic antenna protein as a super-resolution microscopy label
Authors: Barnett Samuel F. H. , Hitchcock Andrew , Mandal Amit K. , Vasilev Cvetelin , Yuen Jonathan M. , Morby James , Brindley Amanda A. , Niedzwiedzki Dariusz M. , Bryant Donald A. , Cadby Ashley J. , Holten Dewey , Hunter C. Neil 
Published: November 2017

AbstractTechniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd1 ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy.
Abstract spatial, but not body-related, visual information guides bimanual coordination
Authors: Brandes Janina , Rezvani Farhad , Heed Tobias 
Published: November 2017

AbstractVisual spatial information is paramount in guiding bimanual coordination, but anatomical factors, too, modulate performance in bimanual tasks. Vision conveys not only abstract spatial information, but also informs about body-related aspects such as posture. Here, we asked whether, accordingly, visual information induces body-related, or merely abstract, perceptual-spatial constraints in bimanual movement guidance. Human participants made rhythmic, symmetrical and parallel, bimanual index finger movements with the hands held in the same or different orientations. Performance was more accurate for symmetrical than parallel movements in all postures, but additionally when homologous muscles were concurrently active, such as when parallel movements were performed with differently rather than identically oriented hands. Thus, both perceptual and anatomical constraints were evident. We manipulated visual feedback with a mirror between the hands, replacing the image of the right with that of the left hand and creating the visual impression of bimanual symmetry independent of the right hand’s true movement. Symmetrical mirror feedback impaired parallel, but improved symmetrical bimanual performance compared with regular hand view. Critically, these modulations were independent of hand posture and muscle homology. Thus, visual feedback appears to contribute exclusively to spatial, but not to body-related, anatomical movement coding in the guidance of bimanual coordination.
Conservation of folding and association within a family of spidroin N-terminal domains
Authors: Heiby Julia C. , Rajab Suhaila , Rat Charlotte , Johnson Christopher M. , Neuweiler Hannes 
Published: November 2017

AbstractWeb spiders synthesize silk fibres, nature’s toughest biomaterial, through the controlled assembly of fibroin proteins, so-called spidroins. The highly conserved spidroin N-terminal domain (NTD) is a pH-driven self-assembly device that connects spidroins to super-molecules in fibres. The degree to which forces of self-assembly is conserved across spider glands and species is currently unknown because quantitative measures are missing. Here, we report the comparative investigation of spidroin NTDs originating from the major ampullate glands of the spider species Euprosthenops australis, Nephila clavipes, Latrodectus hesperus, and Latrodectus geometricus. We characterized equilibrium thermodynamics and kinetics of folding and self-association using dynamic light scattering, stopped-flow fluorescence and circular dichroism spectroscopy in combination with thermal and chemical denaturation experiments. We found cooperative two-state folding on a sub-millisecond time scale through a late transition state of all four domains. Stability was compromised by repulsive electrostatic forces originating from clustering of point charges on the NTD surface required for function. pH-driven dimerization proceeded with characteristic fast kinetics yielding high affinities. Results showed that energetics and kinetics of NTD self-assembly are highly conserved across spider species despite the different silk mechanical properties and web geometries they produce.
Molecular Identification of ten species of stored-product psocids through microarray method based on ITS2 rDNA
Authors: Liu Li-Jun , Pang Ao-Han , Feng Shi-Qian , Cui Bing-Yi , Zhao Zi-Hua , Kučerová Zuzana , Stejskal Václav , Opit George , Aulicky Radek , Cao Yang , Li Fu-Jun , Wu Yi , Zhang Tao , Li Zhi-Hong 
Published: November 2017

AbstractStored-product psocids (Psocoptera: Liposcelididae) are cosmopolitan storage pests that can damage stored products and cause serious economic loss. However, because of the body size (~1 mm) of eggs, nymphs, and adults, morphological identification of most stored-product psocids is difficult and hampers effective identification. In this study, 10 economically important stored-productLiposcelisspp. psocids (Liposcelis brunnea, L. entomophila, L. decolor, L. pearmani,L. rufa, L.mendax,L. bostrychophila,L. corrodens,L. paeta, and L. tricolor) were collected from 25 geographic locations in 3 countries (China, Czech Republic, and the United States). Ten species-specific probes for identifying these 10 psocid species were designed based on ITS2 sequences. The microarray method and reaction system were optimized. Specificity of each of the ten probes was tested, and all probes were found suitable for use in identification of the respective10Liposcelis spp. psocids at 66 °C. This method was also used to identify an unknown psocid species collected in Taian, China. This work has contributed to the development of a molecular identification method for stored-product psocids, and can provide technical support not only to facilitate identification of intercepted samples in relation to plant quarantine, but also for use in insect pest monitoring.
On the effect of low oxygen concentrations on bacterial degradation of sinking particles
Authors: Le Moigne Frédéric A. C. , Cisternas-Novoa Carolina , Piontek Judith , Maßmig Marie , Engel Anja 
Published: November 2017

AbstractIn marine oxygen (O2) minimum zones (OMZs), the transfer of particulate organic carbon (POC) to depth via the biological carbon pump might be enhanced as a result of slower remineralisation under lower dissolved O2 concentrations (DO). In parallel, nitrogen (N) loss to the atmosphere through microbial processes, such as denitrification and anammox, is directly linked to particulate nitrogen (PN) export. However it is unclear (1) whether DO is the only factor that potentially enhances POC transfer in OMZs, and (2) if particle fluxes are sufficient to support observed N loss rates. We performed a degradation experiment on sinking particles collected from the Baltic Sea, where anoxic zones are observed. Sinking material was harvested using surface-tethered sediment traps and subsequently incubated in darkness at different DO levels, including severe suboxia (<0.5 mg l−1 DO). Our results show that DO plays a role in regulating POC and PN degradation rates. POC(PN) degradation was reduced by approximately 100% from the high to low DO to the lowest DO. The amount of NH4+ produced from the pool of remineralising organic N matched estimations of NH4+ anammox requirements during our experiment. This anammox was likely fueled by DON degradation rather than PON degradation.
Validation of SinoSCORE for isolated CABG operation in East China
Authors: Ma Xiue , Wang Yunqian , Shan Lingtong , Cang Zhengqiang , Gu Chang , Qu Nianyi , Li Qifan , Li Jun , Wang Zhenhua , Zhang Yangyang 
Published: November 2017

AbstractFrom January 2010 to December 2016, 1616 consecutive patients who underwent isolated coronary artery bypass grafting (CABG) were evaluated for their predicted mortality according to the online Sino System for Coronary Operative Risk Evaluation (SinoSCORE), European System for Cardiac Operative Risk Evaluation II (EuroSCORE II) and Society of Thoracic Surgeons (STS) risk evaluation system. The calibration and discrimination in the total and in the subsets were assessed by the Hosmer-Lemeshow (H-L) statistics and by the C statistics respectively, to evaluate the efficiency of the three risk evaluation systems. The realized mortality was 1.92% (31/1616). The predictive mortality of SinoSCORE, EuroSCORE II and STS risk evaluation system were 1.35%, 1.74% and 1.05%, respectively. SinoSCORE achieved best discrimination. When grouping by risk, SinoSCORE also achieved the best discrimination in high-risk group, followed by STS risk evaluation system and EuroSCORE II while SinoSCORE and EuroSCORE II had excellent performance in low-risk group. In terms of calibration, SinoSCORE, EuroSCORE II and STS risk evaluation system all achieved positive calibrations (H-L: P > 0.05) in the overall population and grouped subsets. SinoSCORE achieved good predictive efficiency in East China patients undergoing isolated CABG and showed no compromise when compared with EuroSCORE II and STS risk evaluation system.