bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance
Authors: Tsai Kevin J. , Lu Mei-Yeh Jade , Yang Kai-Jung , Li Mengyun , Teng Yuchuan , Chen Shihmay , Ku Maurice S. B. , Li Wen-Hsiung 
Published: October 2016

AbstractThe diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
The anticonvulsant retigabine suppresses neuronal KV2-mediated currents
Authors: Stas Jeroen I. , Bocksteins Elke , Jensen Camilla S. , Schmitt Nicole , Snyders Dirk J. 
Published: October 2016

AbstractEnhancement of neuronal M-currents, generated through KV7.2-KV7.5 channels, has gained much interest for its potential in developing treatments for hyperexcitability-related disorders such as epilepsy. Retigabine, a KV7 channel opener, has proven to be an effective anticonvulsant and has recently also gained attention due to its neuroprotective properties. In the present study, we found that the auxiliary KCNE2 subunit reduced the KV7.2-KV7.3 retigabine sensitivity approximately 5-fold. In addition, using both mammalian expression systems and cultured hippocampal neurons we determined that low μM retigabine concentrations had ‘off-target’ effects on KV2.1 channels which have recently been implicated in apoptosis. Clinical retigabine concentrations (0.3–3 μM) inhibited KV2.1 channel function upon prolonged exposure. The suppression of the KV2.1 conductance was only partially reversible. Our results identified KV2.1 as a new molecular target for retigabine, thus giving a potential explanation for retigabine’s neuroprotective properties.
Large Tunable Thermophase in Superconductor – Quantum Dot – Superconductor Josephson Junctions
Authors: Kleeorin Yaakov , Meir Yigal , Giazotto Francesco , Dubi Yonatan 
Published: October 2016

AbstractIn spite of extended efforts, detecting thermoelectric effects in superconductors has proven to be a challenging task, due to the inherent superconducting particle-hole symmetry. Here we present a theoretical study of an experimentally attainable Superconductor – Quantum Dot – Superconductor (SC-QD-SC) Josephson Junction. Using Keldysh Green’s functions we derive the exact thermo-phase and thermal response of the junction, and demonstrate that such a junction has highly tunable thermoelectric properties and a significant thermal response. The origin of these effects is the QD energy level placed between the SCs, which breaks particle-hole symmetry in a gradual manner, allowing, in the presence of a temperature gradient, for gate controlled appearance of a superconducting thermo-phase. This thermo-phase increases up to a maximal value of ±π/2 after which thermovoltage is expected to develop. Our calculations are performed in realistic parameter regimes, and we suggest an experimental setup which could be used to verify our predictions.
Development of a one-pot assay for screening and identification of Mur pathway inhibitors in Mycobacterium tuberculosis
Authors: Eniyan Kandasamy , Kumar Anuradha , Rayasam Geetha Vani , Perdih Andrej , Bajpai Urmi 
Published: October 2016

AbstractThe cell wall of Mycobacterium tuberculosis (Mtb) consists of peptidoglycan, arabinogalactan and mycolic acids. The cytoplasmic steps in the peptidoglycan biosynthetic pathway, catalyzed by the Mur (A-F) enzymes, involve the synthesis of UDP-n-acetylmuramyl pentapeptide, a key precursor molecule required for the formation of the peptidoglycan monomeric building blocks. Mur enzymes are indispensable for cell integrity and their lack of counterparts in eukaryotes suggests them to be promising Mtb drug targets. However, the caveat is that most of the current assays utilize a single Mur enzyme, thereby identifying inhibitors against only one of the enzymes. Here, we report development of a one-pot assay that reconstructs the entire Mtb Mur pathway in vitro and has the advantage of eliminating the requirement for nucleotide intermediates in the pathway as substrates. The MurA-MurF enzymes were purified and a one-pot assay was developed through optimization of successive coupled enzyme assays using UDP-n-acetylglucosamine as the initial sugar substrate. The assay is biochemically characterized and optimized for high-throughput screening of molecules that could disrupt multiple targets within the pathway. Furthermore, we have validated the assay by performing it to identify D-Cycloserine and furan-based benzene-derived compounds with known Mur ligase inhibition as inhibitors of Mtb MurE and MurF.
Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes
Authors: Bolotin Evgeni , Hershberg Ruth 
Published: October 2016

AbstractGene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment.
Thermal signatures of voluntary deception in ecological conditions
Authors: Panasiti Maria Serena , Cardone Daniela , Pavone Enea F. , Mancini Alessandra , Merla Arcangelo , Aglioti Salvatore M. 
Published: October 2016

AbstractDeception is a pervasive phenomenon that greatly influences dyadic, groupal and societal interactions. Behavioural, physiological and neural signatures of this phenomenon have imporant implications for theoretical and applied research, but, because it is difficult for a laboratory to replicate the natural context in which deception occurs, contemporary research is still struggling to find such signatures. In this study, we tracked the facial temperature of participants who decided whether or not to deceive another person, in situations where their reputation was at risk or not. We used a high-sensitivity infrared device to track temperature changes to check for unique patterns of autonomic reactivity. Using a region-of-interest based approach we found that prior to any response there was a minimal increase in periorbital temperature (which indexes sympathetic activation, together with reduced cheek temperature) for the self-gain lies in the reputation-risk condition. Crucially, we found a rise in nose temperature (which indexes parasympathetic activation) for self-gain lies in the reputation-risk condition, not only during response preparation but also after the choice was made. This finding suggests that the entire deception process may be tracked by the nose region. Furthermore, this nasal temperature modulation was negatively correlated with machiavellian traits, indicating that sympathetic/parasympathetic regulation is less important for manipulative individuals who may care less about the consequences of lie-related moral violations. Our results highlight a unique pattern of autonomic reactivity for spontaneous deception in ecological contexts.
Early neuroimaging markers of FOXP2 intragenic deletion
Authors: Liégeois Frédérique J. , Hildebrand Michael S. , Bonthrone Alexandra , Turner Samantha J. , Scheffer Ingrid E. , Bahlo Melanie , Connelly Alan , Morgan Angela T. 
Published: October 2016

AbstractFOXP2 is the major gene associated with severe, persistent, developmental speech and language disorders. While studies in the original family in which a FOXP2 mutation was found showed volume reduction and reduced activation in core language and speech networks, there have been no imaging studies of different FOXP2 mutations. We conducted a multimodal MRI study in an eight-year-old boy (A-II) with a de novo FOXP2 intragenic deletion. A-II showed marked bilateral volume reductions in the hippocampus, thalamus, globus pallidus, and caudate nucleus compared with 26 control males (effect sizes from −1 to −3). He showed no detectable functional MRI activity when repeating nonsense words. The hippocampus is implicated for the first time in FOXP2 diseases. We conclude that FOXP2 anomaly is either directly or indirectly associated with atypical development of widespread subcortical networks early in life.
The fecal microbiota as a biomarker for disease activity in Crohn’s disease
Authors: Tedjo Danyta. I. , Smolinska Agnieszka , Savelkoul Paul H. , Masclee Ad A. , van Schooten Frederik J. , Pierik Marieke J. , Penders John , Jonkers Daisy M. A. E. 
Published: October 2016

AbstractMonitoring mucosal inflammation is crucial to prevent complications and disease progression in Crohn’s disease (CD). Endoscopy is the current standard, but is invasive. Clinical activity scores and non-invasive biochemical markers do not correlate well with mucosal inflammation. Microbial perturbations have been associated with disease activity in CD. Therefore, we aimed to investigate its potential use to differentiate CD patients in remission from those with an exacerbation. From 71 CD patients repeated fecal samples were collected, resulting in 97 active disease and 97 remission samples based on a combination of biochemical and clinical parameters. The microbiota composition was assessed by pyrosequencing of the 16S rRNA V1-V3 region. Random Forest analysis was used to find the most discriminatory panel of operational taxonomic units (OTUs) between active and remission samples. An independent internal validation set was used to validate the model. A combination of 50 OTUs was able to correctly predict 73% of remission and 79% of active samples with an AUC of 0.82 (sensitivity: 0.79, specificity: 0.73). This study demonstrates that fecal microbial profiles can be used to differentiate between active and remission CD and underline the potential of the fecal microbiota as a non-invasive tool to monitor disease activity in CD.
Characterization of a Ran gene from Puccinia striiformis f. sp. tritici involved in fungal growth and anti-cell death
Authors: Cheng Yulin , Yao Juanni , Zhang Yanru , Li Shumin , Kang Zhensheng 
Published: October 2016

AbstractRan, an important family of small GTP-binding proteins, has been shown to regulate a variety of important cellular processes in many eukaryotes. However, little is known about Ran function in pathogenic fungi. In this study, we report the identification and functional analysis of a Ran gene (designated PsRan) from Puccinia striiformis f. sp. tritici (Pst), an important fungal pathogen affecting wheat production worldwide. The PsRan protein contains all conserved domains of Ran GTPases and shares more than 70% identity with Ran proteins from other organisms, indicating that Ran proteins are conserved in different organisms. PsRan shows a low level of intra-species polymorphism and is localized to the nucleus. qRT-PCR analysis showed that transcript level of PsRan was induced in planta during Pst infection. Silencing of PsRan did not alter Pst virulence phenotype but impeded fungal growth of Pst. In addition, heterologous overexpression of PsRan in plant failed to induce cell death but suppressed cell death triggered by a mouse BAX gene or a Pst Ras gene. Our results suggest that PsRan is involved in the regulation of fungal growth and anti-cell death, which provides significant insight into Ran function in pathogenic fungi.
Core-shell Au-Pd nanoparticles as cathode catalysts for microbial fuel cell applications
Authors: Yang Gaixiu , Chen Dong , Lv Pengmei , Kong Xiaoying , Sun Yongming , Wang Zhongming , Yuan Zhenhong , Liu Hui , Yang Jun 
Published: October 2016

AbstractBimetallic nanoparticles with core-shell structures usually display enhanced catalytic properties due to the lattice strain created between the core and shell regions. In this study, we demonstrate the application of bimetallic Au-Pd nanoparticles with an Au core and a thin Pd shell as cathode catalysts in microbial fuel cells, which represent a promising technology for wastewater treatment, while directly generating electrical energy. In specific, in comparison with the hollow structured Pt nanoparticles, a benchmark for the electrocatalysis, the bimetallic core-shell Au-Pd nanoparticles are found to have superior activity and stability for oxygen reduction reaction in a neutral condition due to the strong electronic interaction and lattice strain effect between the Au core and the Pd shell domains. The maximum power density generated in a membraneless single-chamber microbial fuel cell running on wastewater with core-shell Au-Pd as cathode catalysts is ca. 16.0 W m−3 and remains stable over 150 days, clearly illustrating the potential of core-shell nanostructures in the applications of microbial fuel cells.
Solution-Processed One-Dimensional ZnO@CdS Heterojunction toward Efficient Cu2ZnSnS4 Solar Cell with Inverted Structure
Authors: Chen Rongrong , Fan Jiandong , Liu Chong , Zhang Xing , Shen Yanjiao , Mai Yaohua 
Published: October 2016

AbstractKesterite Cu2ZnSnS4 (CZTS) semiconductor has been demonstrated to be a promising alternative absorber in thin film solar cell in virtue of its earth-abundant, non-toxic element, suitable optical and electrical properties. Herein, a low-cost and non-toxic method that based on the thermal decomposition and reaction of metal-thiourea-oxygen sol-gel complexes to synthesize CZTS thin film was developed. The low-dimensional ZnO@CdS heterojunction nano-arrays coupling with the as-prepared CZTS thin film were employed to fabricate a novel solar cell with inverted structure. The vertically aligned nanowires (NWs) allow facilitating the charge carrier collection/separation/transfer with large interface areas. By optimizing the parameters including the annealing temperature of CZTS absorber, the thickness of CdS buffer layer and the morphology of ZnO NWs, an open-circuit voltage (VOC) as high as 589 mV was obtained by such solar cell with inverted structure. The all-solution-processed technic allows the realization of CZTS solar cell with extremely low cost.
Combined Transcriptomics and Chemical-Genetics Reveal Molecular Mode of Action of Valproic acid, an Anticancer Molecule using Budding Yeast Model
Authors: Golla Upendarrao , Joseph Deepthi , Tomar Raghuvir Singh 
Published: October 2016

AbstractValproic acid (VA) is a pharmacologically important histone deacetylase inhibitor that recently garnered attention as an anticancer agent. Since the molecular mechanisms behind the multiple effects of VA are unclear, this study was aimed to unravel the comprehensive cellular processes affected by VA and its molecular targets in vivo using budding yeast as a model organism. Interestingly, genome-wide transcriptome analysis of cells treated with VA showed differential regulation of 30% of the genome. Functional enrichment analysis of VA transcriptome evidenced alteration of various cellular processes including cell cycle, cell wall biogenesis, DNA repair, ion homeostasis, metabolism, stress response, transport and ribosomal biogenesis, etc. Moreover, our genetic screening analysis revealed VA molecular targets belonging to oxidative and osmotic stress, DNA repair, cell wall integrity, and iron homeostasis. Further, our results demonstrated the activation of mitogen-activated protein kinases (MAPKs) Hog1 (p38) and Slt2 (p44/42) upon VA treatment. Our results also exhibited that VA acts through alteration of mitochondrial, ER architecture and functions. Especially, VA effects were neutralized in cells lacking lipid particles. Altogether, our results deciphered the novel molecular insights and mechanistic links to strengthen our knowledge on diverse cellular effects of VA along with its probable therapeutic targets and detoxification approaches.
Differential responses of soil nematode community to pig manure application levels in Ferric Acrisols
Authors: Yang Yi-Ru , Li Xiao-Gang , Zhou Zhi-Gao , Zhang Tao-Lin , Wang Xing-Xiang 
Published: October 2016

AbstractExcessive pig manure application probably degrades arable soil quality in some intensive pig farming areas. The responses of the nematode community to dosages of pig manure were investigated in Ferric Acrisols under 3-season peanut monoculture. Varying dosages of manure (1.75, 3.5, 7, 14 and 28 t·ha−1·yr−1) in combination with chemical fertilizer were applied to field plots, and chemical fertilizer alone was also applied as a control. With increasing manure application, the abundance of bacterivores and omnivores-predators increased, the abundance of plant parasites decreased, and fungivores abundance exhibited hump-shaped variation. Simpson diversity index and plant parasite index/maturity index of the nematode communities increased to a maximum level at a manure application rate of 3.5 t·ha−1·yr−1 and then sharply decreased. The changes in the soil nematode community were further determined to be correlated with chemical properties; available phosphorus had the strongest quadratic correlation with the two indices, implying that available phosphorus had a better indicative effect than other soil properties to nematode community. Available phosphorus in soil was deduced from 49 to 64 mg·kg−1 with the best nematode communities. Our results emphasized the importance of regular applications of manure in agriculture field to balance nematode diversity and build healthy agro-ecosystems.
Prioritizing cancer-related microRNAs by integrating microRNA and mRNA datasets
Authors: Jin Daeyong , Lee Hyunju 
Published: October 2016

AbstractMicroRNAs (miRNAs) are small non-coding RNAs regulating the expression of target genes, and they are involved in cancer initiation and progression. Even though many cancer-related miRNAs were identified, their functional impact may vary, depending on their effects on the regulation of other miRNAs and genes. In this study, we propose a novel method for the prioritization of candidate cancer-related miRNAs that may affect the expression of other miRNAs and genes across the entire biological network. For this, we propose three important features: the average expression of a miRNA in multiple cancer samples, the average of the absolute correlation values between the expression of a miRNA and expression of all genes, and the number of predicted miRNA target genes. These three features were integrated using order statistics. By applying the proposed approach to four cancer types, glioblastoma, ovarian cancer, prostate cancer, and breast cancer, we prioritized candidate cancer-related miRNAs and determined their functional roles in cancer-related pathways. The proposed approach can be used to identify miRNAs that play crucial roles in driving cancer development, and the elucidation of novel potential therapeutic targets for cancer treatment.
Microenvironment complexity and matrix stiffness regulate breast cancer cell activity in a 3D in vitro model
Authors: Cavo Marta , Fato Marco , Peñuela Leonardo , Beltrame Francesco , Raiteri Roberto , Scaglione Silvia 
Published: October 2016

AbstractThree-dimensional (3D) cell cultures represent fundamental tools for the comprehension of cellular phenomena both in normal and in pathological conditions. In particular, mechanical and chemical stimuli play a relevant role on cell fate, cancer onset and malignant evolution. Here, we use mechanically-tuned alginate hydrogels to study the role of substrate elasticity on breast adenocarcinoma cell activity. The hydrogel elastic modulus (E) was measured via atomic force microscopy (AFM) and a remarkable range (150–4000 kPa) was obtained. A breast cancer cell line, MCF-7, was seeded within the 3D gels, on standard Petri and alginate-coated dishes (2D controls). Cells showed dramatic morphological differences when cultured in 3D versus 2D, exhibiting a flat shape in both 2D conditions, while maintaining a circular, spheroid-organized (cluster) conformation within the gels, similar to those in vivo. Moreover, we observed a strict correlation between cell viability and substrate elasticity; in particular, the number of MCF-7 cells decreased constantly with increasing hydrogel elasticity. Remarkably, the highest cellular proliferation rate, associated with the formation of cell clusters, occurred at two weeks only in the softest hydrogels (E = 150–200 kPa), highlighting the need to adopt more realistic and a priori defined models for in vitro cancer studies.
Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa
Authors: Corton M. , Avila-Fernández A. , Campello L. , Sánchez M. , Benavides B. , López-Molina M. I. , Fernández-Sánchez L. , Sánchez-Alcudia R. , da Silva L. R. J. , Reyes N. , Martín-Garrido E. , Zurita O. , Fernández-San José P. , Pérez-Carro R. , García-García F. , Dopazo J. , García-Sandoval B. , Cuenca N. , Ayuso C. 
Published: October 2016

AbstractRetinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation inSAMD11in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicatesSAMD11as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.