bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-Specific Marker Discovery in Tilapia
Authors: Syaifudin Mochamad , Bekaert Michaël , Taggart John B. , Bartie Kerry L. , Wehner Stefanie , Palaiokostas Christos , Khan M. G. Q. , Selly Sarah-Louise C. , Hulata Gideon , D’Cotta Helena , Baroiller Jean-Francois , McAndrew Brendan J. , Penman David J. 
Published: September 2019

AbstractTilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.
Functional analysis of new human Bardet-Biedl syndrome loci specific variants in the zebrafish model
Authors: Castro-Sánchez Sheila , Suarez-Bregua Paula , Novas Rossina , Álvarez-Satta María , Badano Jose L. , Rotllant Josep , Valverde Diana 
Published: September 2019

AbstractThe multiple genetic approaches available for molecular diagnosis of human diseases have made possible to identify an increasing number of pathogenic genetic changes, particularly with the advent of next generation sequencing (NGS) technologies. However, the main challenge lies in the interpretation of their functional impact, which has resulted in the widespread use of animal models. We describe here the functional modelling of seven BBS loci variants, most of them novel, in zebrafish embryos to validate their in silico prediction of pathogenicity. We show that target knockdown (KD) of known BBS (BBS1, BB5 or BBS6) loci leads to developmental defects commonly associated with ciliopathies, as previously described. These KD pleiotropic phenotypes were rescued by co-injecting human wild type (WT) loci sequence but not with the equivalent mutated mRNAs, providing evidence of the pathogenic effect of these BBS changes. Furthermore, direct assessment of cilia located in Kupffer’s vesicle (KV) showed a reduction of ciliary length associated with all the studied variants, thus confirming a deleterious effect. Taken together, our results seem to prove the pathogenicity of the already classified and unclassified new BBS variants, as well as highlight the usefulness of zebrafish as an animal model for in vivo assays in human ciliopathies.
Electron cryomicroscopy observation of acyl carrier protein translocation in type I fungal fatty acid synthase
Authors: Lou Jennifer W. , Iyer Kali R. , Hasan S. M. Naimul , Cowen Leah E. , Mazhab-Jafari Mohammad T. 
Published: September 2019

AbstractDuring fatty acid biosynthesis, acyl carrier proteins (ACPs) from type I fungal fatty acid synthase (FAS) shuttle substrates and intermediates within a reaction chamber that hosts multiple spatially-fixed catalytic centers. A major challenge in understanding the mechanism of ACP-mediated substrate shuttling is experimental observation of its transient interaction landscape within the reaction chamber. Here, we have shown that ACP spatial distribution is sensitive to the presence of substrates in a catalytically inhibited state, which enables high-resolution investigation of the ACP-dependent conformational transitions within the enoyl reductase (ER) reaction site. In two fungal FASs with distinct ACP localization, the shuttling domain is targeted to the ketoacyl-synthase (KS) domain and away from other catalytic centers, such as acetyl-transferase (AT) and ER domains by steric blockage of the KS active site followed by addition of substrates. These studies strongly suggest that acylation of phosphopantetheine arm of ACP may be an integral part of the substrate shuttling mechanism in type I fungal FAS.
Effects of early adversity and social discrimination on empathy for complex mental states: An fMRI investigation
Authors: Fourie Melike M. , Stein Dan J. , Solms Mark , Gobodo-Madikizela Pumla , Decety Jean 
Published: September 2019

AbstractThere is extensive evidence of an association between early adversity and enduring neural changes that impact socioemotional processing throughout life. Yet little is known about the effects of on-going social discrimination on socioemotional functioning. Here we examined how cumulative experiences of social discrimination impact brain response during empathic responding—a crucial issue in South Africa, given its historical apartheid context and continuing legacies. White and Black South Africans completed measures of social adversity (early adversity and social discrimination), and underwent fMRI while viewing video clips depicting victims and perpetrators of apartheid crimes. Increased neural response was detected in brain regions associated with cognitive rather than affective empathy, and greater social adversity was associated with reduced reported compassion across participants. Notably, social discrimination (due to income level, weight, gender) in White participants was associated with increased amygdala reactivity, whereas social discrimination (due to race) in Black participants mediated the negative associations of temporoparietal junction and inferior frontal gyrus activation with compassion during emotionally provocative conditions. These findings suggest that (i) social discrimination has comparable associations at the neural level as other psychosocial stressors, and that (ii) the mechanisms underlying empathic responding vary as a function of the type of social discrimination experienced.
Luminescence Studies and Judd–Ofelt Analysis on SiO2@LaPO4:Eu@SiO2 Submicro-spheres with Different Size of Intermediate Shells
Authors: Zhu Xiaowei , Yang Kuisuo , Wu Anping , Bai He , Bao Jinrong , Qiao Yan , Yang Yunjiang , Li Wenxian , Liu Ying 
Published: September 2019

AbstractThe novel submicro-spheres SiO2@LaPO4:Eu@SiO2 with core-shell-shell structures were prepared by connecting the SiO2 submicro-spheres and the rare earth ions through an organosilane HOOCC6H4N(CONH(CH2)3Si(OCH2CH3)3 (MABA-Si). The as-prepared products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and infrared spectroscopy (IR). It is found that the intermediate shell of the submicro-spheres was composed by LaPO4:Eu nanoparticles with the size of about 4, 5–7, or 15–34 nm. A possible formation mechanism for the SiO2@LaPO4:Eu@SiO2 submicro-spheres has been proposed. The dependence of the photoluminescence intensity on the size of the LaPO4:Eu nanoparticles has been investigated. The intensity ratios of electrical dipole transition 5D0 → 7F2 to magnetic dipole transition 5D0 → 7F1 of Eu3+ ions were increased with decreasing the size of LaPO4:Eu nanoparticles. According to the Judd-Ofelt (J-O) theory, when the size of LaPO4:Eu nanoparticles was about 4, 5–7 and 15–34 nm, the calculated J-O parameter Ω2 (optical transition intensity parameter) was 2.30 × 10−20, 1.80 × 10−20 and 1.20 × 10−20, respectively. The increase of Ω2 indicates that the symmetry of Eu3+ in the LaPO4 lattice was gradually reduced. The photoluminescence intensity of the SiO2@LaPO4:Eu@SiO2 submicro-spheres was unquenched in aqueous solution even after 15 days.
A new perspective on membrane-embedded Bax oligomers using DEER and bioresistant orthogonal spin labels
Authors: Teucher Markus , Zhang Hui , Bader Verian , Winklhofer Konstanze F. , García-Sáez Ana J. , Rajca Andrzej , Bleicken Stephanie , Bordignon Enrica 
Published: September 2019

AbstractBax is a Bcl-2 protein crucial for apoptosis initiation and execution, whose active conformation is only partially understood. Dipolar EPR spectroscopy has proven to be a valuable tool to determine coarse-grained models of membrane-embedded Bcl-2 proteins. Here we show how the combination of spectroscopically distinguishable nitroxide and gadolinium spin labels and Double Electron-Electron Resonance can help to gain new insights into the quaternary structure of active, membrane-embedded Bax oligomers. We show that attaching labels bulkier than the conventional MTSL may affect Bax fold and activity, depending on the protein/label combination. However, we identified a suitable pair of spectroscopically distinguishable labels, which allows to study complex distance networks in the oligomers that could not be disentangled before. Additionally, we compared the stability of the different spin-labeled protein variants in E. coli and HeLa cell extracts. We found that the gem-diethyl nitroxide-labeled Bax variants were reasonably stable in HeLa cell extracts. However, when transferred into human cells, Bax was found to be mislocalized, thus preventing its characterization in a physiological environment. The successful use of spectroscopically distinguishable labels on membrane-embedded Bax-oligomers opens an exciting new path towards structure determination of membrane-embedded homo- or hetero-oligomeric Bcl-2 proteins via EPR.
Rhythmic pattern facilitates speech production: An ERP study
Authors: Zhang Ning , Zhang Qingfang 
Published: September 2019

AbstractRhythm affects the speech perception of events unfolding over time. However, it is not clear to what extent the rhythm could affect the processes of sentence speech production. In this event-related potential (ERP) study, we examined whether a particular rhythmic pattern could affect the planning of speech production before articulation. We recorded electrophysiological (EEG) and behavioural (reaction time) data while participants read aloud a target speech in Chinese. Target speeches were sentences or phrases consisting four characters, with regular (e.g., the 2 + 2 pattern; numbers in the brackets represent the number of syllables) or irregular (e.g., 1 + 3) rhythmic patterns, which were preceded by congruent or incongruent musical rhythmic patterns formed by simple pure tones with different temporal intervals. Behavioural and ERP findings indicated a rhythmic priming effect in comparing congruent and incongruent conditions in the regular target speeches, but not in the irregular ones. An early component (N100) that was elicited in response to target speeches that were rhythmically mismatched to primes was linked to the detection of hierarchical linguistic units, which did not conform to expectations. A later negative component (N400) was thought to reflect the violation of expectation on rhythmic pattern in speech production. These findings suggest that rhythmic pattern constrains grammatical and prosodic encoding during speech production, and support the hypothesis that speakers form a grammatical or a prosodic abstract frame before articulation.
Quantitative mathematical modeling of clinical brain metastasis dynamics in non-small cell lung cancer
Authors: Bilous M. , Serdjebi C. , Boyer A. , Tomasini P. , Pouypoudat C. , Barbolosi D. , Barlesi F. , Chomy F. , Benzekry S. 
Published: September 2019

AbstractBrain metastases (BMs) are associated with poor prognosis in non-small cell lung cancer (NSCLC), but are only visible when large enough. Therapeutic decisions such as whole brain radiation therapy would benefit from patient-specific predictions of radiologically undetectable BMs. Here, we propose a mathematical modeling approach and use it to analyze clinical data of BM from NSCLC. Primary tumor growth was best described by a gompertzian model for the pre-diagnosis history, followed by a tumor growth inhibition model during treatment. Growth parameters were estimated only from the size at diagnosis and histology, but predicted plausible individual estimates of the tumor age (2.1–5.3 years). Multiple metastatic models were further assessed from fitting either literature data of BM probability (n = 183 patients) or longitudinal measurements of visible BMs in two patients. Among the tested models, the one featuring dormancy was best able to describe the data. It predicted latency phases of 4.4–5.7 months and onset of BMs 14–19 months before diagnosis. This quantitative model paves the way for a computational tool of potential help during therapeutic management.
Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors
Authors: Mercey Olivier , Al Jord Adel , Rostaing Philippe , Mahuzier Alexia , Fortoul Aurélien , Boudjema Amélie-Rose , Faucourt Marion , Spassky Nathalie , Meunier Alice 
Published: September 2019

AbstractReproductive and respiratory organs, along with brain ventricles, are lined by multiciliated epithelial cells (MCC) that generate cilia-powered fluid flows. MCC hijack the centrosome duplication pathway to form hundreds of centrioles and nucleate motile cilia. In these cells, the large majority of procentrioles are formed associated with partially characterized organelles called deuterosomes. We recently challenged the paradigm that deuterosomes and procentrioles are formed de novo by providing data, in brain MCC, suggesting that they are nucleated from the pre-existing centrosomal younger centriole. However, the origin of deuterosomes and procentrioles is still under debate. Here, we further question centrosome importance for deuterosome and centriole amplification. First, we provide additional data confirming that centriole amplification occurs sequentially from the centrosomal region, and that the first procentriole-loaded deuterosomes are associated with the daughter centriole or in the centrosomal centriole vicinity. Then, to further test the requirement of the centrosome in deuterosome and centriole formation, we depleted centrosomal centrioles using a Plk4 inhibitor. We reveal unexpected limited consequences in deuterosome/centriole number in absence of centrosomal centrioles. Notably, in absence of the daughter centriole only, deuterosomes are not seen associated with the mother centriole. In absence of both centrosomal centrioles, procentrioles are still amplified sequentially and with no apparent structural defects. They seem to arise from a focal region, characterized by microtubule convergence and pericentriolar material (PCM) assembly. The relevance of deuterosome association with the daughter centriole as well as the role of the PCM in the focal and sequential genesis of centrioles in absence of centrosomal centrioles are discussed.
The double inhibition of PDK1 and STAT3-Y705 prevents liver metastasis in colorectal cancer
Authors: Qin Wenjuan , Tian Yun , Zhang Jing , Liu Wenjian , Zhou Qiming , Hu Sheng , Yang Fei , Lu Li , Lu Haijie , Cui Shuzhong , Wen Lu , Wei Shaozhong 
Published: September 2019

AbstractAs a key glycolysis enzyme, the significance of pyruvate dehydrogenase kinase 1 (PDK1) in the development of colorectal cancer (CRC) remains unknown. This study revealed that the prognosis of CRC patients with high levels of PDK1 was poor, and PDK1 knockdown significantly reduced liver metastasis of CRC in both nude mice and immune competent BALB/C mice. When combined with cryptotanshinone (CPT), an inhibitor of STAT3-p-Y705, the liver metastasis was further inhibited. PDK1 knockdown obviously increased reactive oxygen species level in anoikis conditions and subsequently resulted in an elevated anoikis, but the combination of PDK1 knockdown and CPT showed a reduced effect on anoikis. Based on this discrepancy, the adherence ability of CRC cells to matrix protein fibronectin was further detected. It showed that PDK1 knockdown significantly decreased the adherence of CRC cells to fibronectin when combined with CPT. These results suggest that inhibition of PDK1 can decrease the surviving CRC cells in blood circulation via up-regulation of anoikis, and inhibition of STAT3-p-Y705 can prevent it to settle down on the liver premetastatic niche, which ultimately reduces liver metastasis.
Exchange bias in ferromagnetic bilayers with orthogonal anisotropies: the case of GaMnAsP/GaMnAs combination
Authors: Choi Suho , Bac Seul-Ki , Liu Xinyu , Lee Sanghoon , Dong Sining , Dobrowolska M. , Furdyna J. K. 
Published: September 2019

AbstractWe report the observation of exchange bias in a ferromagnetic Ga0.94Mn0.06As0.77P0.23/ Ga0.94Mn0.06As bilayer, in which the easy axis in one layer is oriented out-of-plane, and in the other in-plane. Magnetization reversal in this system is explored using planar Hall effect (PHE) measurements under various initial conditions and with various field-cooling orientations. Our results show that the two magnetic layers are ferromagnetically exchange-coupled, and that such coupling results in pronounced exchange-bias-like shifts of magnetic hysteresis loops during reversal of in-plane magnetization. The presence of exchange bias in this system can be understood on the basis of magnetic closure domains formed in the layer with the out-of-plane easy axis.
High Fluence Chromium and Tungsten Bowtie Nano-antennas
Authors: Morshed Monir , Li Ziyuan , Olbricht Benjamin C. , Fu Lan , Haque Ahasanul , Li Li , Rifat Ahmmed A. , Rahmani Mohsen , Miroshnichenko Andrey E. , Hattori Haroldo T. 
Published: September 2019

AbstractNano-antennas are replicas of antennas that operate at radio-frequencies, but with considerably smaller dimensions when compared with their radio frequency counterparts. Noble metals based nano-antennas have the ability to enhance photoinduced phenomena such as localized electric fields, therefore-they have been used in various applications ranging from optical sensing and imaging to performance improvement of solar cells. However, such nano-structures can be damaged in high power applications such as heat resisted magnetic recording, solar thermo-photovoltaics and nano-scale heat transfer systems. Having a small footprint, nano-antennas cannot handle high fluences (energy density per unit area) and are subject to being damaged at adequately high power (some antennas can handle just a few milliwatts). In addition, given that nano-antennas are passive devices driven by external light sources, the potential damage of the antennas limits their use with high power lasers: this liability can be overcome by employing materials with high melting points such as chromium (Cr) and tungsten (W). In this article, we fabricate chromium and tungsten nano-antennas and demonstrate that they can handle 110 and 300 times higher fluence than that of gold (Au) counterpart, while the electric field enhancement is not significantly reduced.
Recent decline in vegetative regeneration of bamboo (Yushania alpina), a key food plant for primates in Volcanoes National Park, Rwanda
Authors: van der Hoek Yntze , Emmanuel Faida , Eckardt Winnie , Kwizera Innocent , Derhé Mia , Caillaud Damien , Stoinski Tara S. , Tuyisingize Deogratias 
Published: September 2019

AbstractThe African montane bamboo Yushania alpina provides both habitat and food for many species in the Albertine Rift region. In Volcanoes National Park (VNP), Rwanda, it is especially important as a key food resource for the Endangered mountain gorilla Gorilla beringei beringei and Endangered golden guenon Cercopithecus mitis kandti. We examined temporal and spatial variation in bamboo shoots regeneration and consumption by primates, monitored between 2013 and 2018 in 82 16-m2 plots located along transects in VNP. Our analyses revealed a decline in vegetative regeneration of bamboo in recent years, which is mirrored by a decline in bamboo shoot consumption by primates; but an increase in proportional intake. Local declines in regeneration are potentially due to high intensities of herbivory, decreased amounts of rainfall during growing seasons, and natural processes that form part of the life cycle of bamboo. Moreover, spatial variation in bamboo regeneration can be explained by elevation, as well as by stand-level variation in soil acidity, vegetation density, and the density of dead bamboo culms. We discuss the potential mechanisms underlying observed temporal and spatial variations and outline possible effects of a decline in bamboo regeneration for primates and other aspects of biodiversity in VNP.
Transcriptome profiles of hypothalamus and adrenal gland linked to haplotype related to coping behavior in pigs
Authors: Gley Kevin , Murani Eduard , Trakooljul Nares , Zebunke Manuela , Puppe Birger , Wimmers Klaus , Ponsuksili Siriluck 
Published: September 2019

AbstractThe hypothalamic-pituitary-adrenal (HPA) axis is an important component of neuroendocrine stress regulation and coping behavior. Transcriptome profiles of the hypothalamus and adrenal gland were assessed to identify molecular pathways and candidate genes for coping behavior in pigs. Ten each of high- (HR) and low- (LR) reactive pigs (n = 20) were selected for expression profiling based haplotype information of a prominent QTL-region on SSC12 discovered in our previous genome-wide association study (GWAS) on coping behavior. Comparing the HR and LR pigs showed 692 differentially expressed genes (DEGs) in the adrenal gland and 853 DEGs in the hypothalamus, respectively. Interestingly, 47% (17 out of 36) of DEGs found in both tissues were located in GWAS regions identified on SSC12, indicating that there are significant functional positional candidate genes for coping behaviour. Pathway analysis assigned DEGs to glucocorticoid receptor signaling in the adrenal gland. Furthermore, oxidative phosphorylation, mitochondrial dysfunction, and NGF signaling as well as cholecystokinin/Gastrin-mediated were identified in the hypothalamus. We narrowed the list of candidate genes in GWAS regions by analyzing their DEGs in the HPA axis. The top identified transcripts, including ATP1B2, AURKB, MPDU1 and NDEL1 provide evidence for molecular correlates of coping behavior in GWAS regions.
Root water uptake and its pathways across the root: quantification at the cellular scale
Authors: Zarebanadkouki Mohsen , Trtik Pavel , Hayat Faisal , Carminati Andrea , Kaestner Anders 
Published: September 2019

AbstractThe pathways of water across root tissues and their relative contribution to plant water uptake remain debated. This is mainly due to technical challenges in measuring water flux non-invasively at the cellular scale under realistic conditions. We developed a new method to quantify water fluxes inside roots growing in soils. The method combines spatiotemporal quantification of deuterated water distribution imaged by rapid neutron tomography with an inverse simulation of water transport across root tissues. Using this non-invasive technique, we estimated for the first time the in-situ radial water fluxes [m s−1] in apoplastic and cell-to-cell pathways. The water flux in the apoplast of twelve days-old lupins (Lupinus albus L. cv. Feodora) was seventeen times faster than in the cell-to-cell pathway. Hence, the overall contribution of the apoplast in water flow [m3 s−1] across the cortex is, despite its small volume of 5%, as large as 57 ± 8% (Mean ± SD for n = 3) of the total water flow. This method is suitable to non-invasively measure the response of cellular scale root hydraulics and water fluxes to varying soil and climate conditions.