bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins
Authors: Torrens-Spence Michael P. , Chiang Ying-Chih , Smith Tyler , Vicent Maria A. , Wang Yi , Weng Jing-Ke 
Published: August 2018

AbstractRadiation of the plant pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.SignificancePlants biosynthesize their own proteinogenic aromatic L-amino acids, namely L-phenylalanine, L-tyrosine and L-tryptophan, not only for building proteins but also for the production of a plethora of aromatic-amino-acid-derived natural products. Pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family enzymes play important roles in channeling various aromatic L-amino acids into diverse downstream specialized metabolic pathways. Through comparative structural analysis of four functionally divergent plant AAAD proteins together with biochemical characterization and molecular dynamics simulations, we reveal the structural and mechanistic basis for the rich divergent and convergent evolutionary development within the plant AAAD family. Knowledge learned from this study aids our ability to engineer high-value aromatic-L-amino-acid-derived natural product biosynthesis in heterologous chassis organisms.
Genome-scale Capture C promoter interaction analysis implicates novel effector genes at GWAS loci for bone mineral density
Authors: Chesi Alessandra , Wagley Yadav , Johnson Matthew E. , Manduchi Elisabetta , Su Chun , Lu Sumei , Leonard Michelle E. , Hodge Kenyaita M. , Pippin James A. , Hankenson Kurt D. , Wells Andrew D. , Grant Struan F.A. 
Published: August 2018

ASBTRACTOsteoporosis is a devastating disease with an essential genetic component. Genome wide association studies (GWAS) have discovered genetic variants robustly associated with bone mineral density (BMD), however they only report genomic signals and not necessarily the precise localization of culprit effector genes. Therefore, we sought to carry out physical and direct ‘variant to gene mapping’ in a relevant primary human cell type. We developed ‘SPATIaL-seq’ (genome-Scale, Promoter-focused Analysis of chromaTIn Looping), a massively parallel, high resolution Capture-C based method to simultaneously characterize the genome-wide interactions of all human promoters. By intersecting our SPATIaL-seq and ATAC-seq data from human mesenchymal progenitor cell -derived osteoblasts, we observed consistent contacts between candidate causal variants and putative target gene promoters in open chromatin for ~30% of the 110 BMD loci investigated. Knockdown of two novel implicated genes,ING3at ‘CPED1-WNT16’ andEPDR1at ‘STARD3NL’, had pronounced inhibitory effects on osteoblastogenesis. Our approach therefore aids target discovery in osteoporosis and can be applied to other common genetic diseases.
Cerebral Cavernous Malformations Develop through Clonal Expansion of Mutant Endothelial Cells
Authors: Detter Matthew R. , Snellings Daniel A. , Marchuk Douglas A. 
Published: August 2018

AbstractRationaleVascular malformations arise in vessels throughout the entire body. Causative genetic mutations have been identified for many of these diseases; however, little is known about the mutant cell lineage within these malformations.ObjectiveWe utilize an inducible mouse model of cerebral cavernous malformations (CCMs) coupled with a multi-color fluorescent reporter to visualize the contribution of mutant endothelial cells (ECs) to the malformation.Methods and ResultsWe combined a Ccm3 mouse model with the confetti fluorescent reporter to simultaneously delete Ccm3 and label the mutant EC with one of four possible colors. We acquired Z-series confocal images from serial brain sections and created 3D reconstructions of entire CCMs to visualize mutant ECs during CCM development. We observed a pronounced pattern of CCMs lined with mutant ECs labeled with a single confetti color (n=42). The close 3D distribution, as determined by the nearest neighbor analysis, of the clonally dominant ECs within the CCM was statistically different than the background confetti labeling of ECs in non-CCM control brain slices as well as a computer simulation (p<0.001). Many of the small (<100μm diameter) CCMs consisted, almost exclusively, of the clonally dominant mutant ECs labeled with the same confetti color whereas the large (>100μm diameter) CCMs contained both the clonally dominant mutant cells and wildtype ECs. We propose of model of CCM development in which an EC acquires a second somatic mutation, undergoes clonal expansion to initiate CCM formation, and then incorporates neighboring wildtype ECs to increase the size of the malformation.ConclusionsThis is the first study to visualize, with single-cell resolution, the clonal expansion of mutant ECs within CCMs. The incorporation of wildtype ECs into the growing malformation presents another series of cellular events whose elucidation would enhance our understanding of CCMs and may provide novel therapeutic opportunities.
Hydroxymethylated-P16 Allele Is Transcription-Inactive
Authors: Gan Ying , Li Paiyun , Han Xiao , Qin Sisi , Cui Chenghua , Liu Zhaojun , Zhou Jing , Gu Liankun , Lu Zhe-ming , Zhang Baozhen , Deng Dajun 
Published: August 2018

ABSTRACTBackground5-Methylcytosine can be oxidized into 5-hydroxymethylcytosine (5hmC) in the genome. Methylated-P16 (P16M) can be oxidized into completely hydroxymethylated-P16 (P16H) in human cancer and precancer cells. The aim of this study is to investigate the biological function of P16H.MethodsTrue P16M and P16H were analyzed using bisulfite/TAB-based assays. A ZFP-based P16-specific dioxygenase (P16-TET) was constructed and used to induce P16H. Cell proliferation and migration were determined with a series of biological analyses.Results(A) The 5hmCs were enriched in the antisense-strand of the P16 exon-1 in HCT116 and AGS cells containing methylated-P16 alleles (P16M). (B) P16-TET induced both P16H and P16 demethylation in H1299 and AGS cells and reactivated P16 expression. Notably, P16H was only detectable in the sorted P16-TET H1299 and AGS cells that did not show P16 expression. (C) P16-TET significantly inhibited the xenograft growth derived from H1299 cells in NOD-SCID mice, but did not inhibit the growth of P16-deleted A549 control cells. P16-siRNA knockdown could rescue P16-TET-inhibited cell migration.ConclusionHydroxymethylated P16 alleles are transcriptionally inactive.AUTHOR SUMMARYIt is well known that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidations, a certain proportion of 5hmCs remain in the genome. Although it is supposed that occurrence of 5hmCs may contribute to the flexibility of chromatin and the protection of the bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In the present study, we engineered a zinc-finger protein-based P16-specific DNA dioxygenase and used it to induce P16 hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that the hydroxymethylated P16 alleles retain transcriptionally inactive. This is supported by our recent findings that mRNAs are always transcribed only from the unmethylated P16 strands, but not from the hydroxymethylated/methylated strands in HCT116 cells, and that the risks for malignant transformation are similar for patients with the P16 methylation-positive oral epithelial dysplasia with and without P16 hydroxymethylation in a prospective study.
Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability
Authors: Emden Thomas van , Forn Marta , Forné Ignasi , Sarkadi Zsuzsa , Capella Matías , Caballero Lucía Martín , Fischer-Burkart Sabine , Brönner Cornelia , Simonetta Marco , Toczyski David , Halic Mario , Imhof Axel , Braun Sigurd 
Published: August 2018

AbstractTelomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here we show that, in Schizosaccharomyces pombe, the telo-mere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelter-in, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA se-quences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by con-trolling nucleosome occupancy and genome stability.
Quantifying Molecular Forces with Serially Connected Force Sensors
Authors: Murad Y. , Li I. T.S. 
Published: August 2018

AbstractTo understand the mechanical forces involved in cell adhesion, molecular force sensors have been developed to study tension through adhesion proteins. Recently, a class of molecular force sensors called tension gauge tether (TGT) have been developed that rely on irreversible force-dependent dissociation of DNA duplex to study cell adhesion forces. While the TGT offer high signal-to-noise ratio and is ideal for studying fast / single molecular adhesion processes, quantitative interpretation of experimental results has been challenging. Here we used computational approach to investigate how TGT fluorescence readout can be quantitatively interpreted. In particular we studied force sensors made of a single TGT, multiplexed single TGTs, and two TGTs connected in series. Our results showed that fluorescence readout using a single TGT can result from drastically different combinations of force history and adhesion event density that span orders of magnitude. In addition, the apparent behaviour of the TGT is influenced by the tethered receptor-ligand, making it necessary to calibrate the TGT with every new receptor-ligand. To solve this problem, we proposed a system of two serially connected TGTs. Our result shows that not only is the ratiometric readout of serial TGT independent of the choice of receptor-ligand, it is able to reconstruct force history with sub-pN force resolution. This is also not possible by simply multiplexing different types of TGTs together. Lastly, we systematically investigated how sequence composition of the two serially connected TGTs can be tuned to achieve different dynamic range. This computational study demonstrated how serially connected irreversible molecular dissociation processes can accurately quantify molecular force, and laid the foundation for subsequent experimental studies.
Impending Regeneration Failure of the Iucn Vulnerable Borneo Ironwood (Eusideroxylon Zwageri)
Authors: Qie Lan , Elsy Alexander D. , Stumvoll Ashley , Kwasnicka Magdalena , Peel Anna L. , Sullivan Joseph A. , Ettinger Maisie S. , Robertson Alasdair J. , Brisbane Jeanelle K. , Sawyer Amber L. , Lui Yan N. , Ow Siew Ngim , Sebastianelli Matteo , Majcher Bartosz , Duan Muying , Vigus Hannah , Pounsin Grace , Nilus Reuben , Ewers Robert 
Published: August 2018

AbstractThe regeneration of many climax species in tropical forest critically depends on adequate seed dispersal and seedling establishment. Here we report the decreased abundance and increased spatial aggregation of younger trees of the Borneo ironwood (Eusideroxylon zwageri) in a protected forest in Sabah Malaysia. We observed a high level of seedling herbivory with strong density dependence, likely exacerbated by local aggregation and contributing to the progressively shrinking size-distribution. We also note the largely undocumented selective herbivory by sambar deer on E.zwageriseedlings. This study highlights the combined impact of altered megafauna community on a tree population through interlinked ecological processes and the need for targeted conservation intervention for this iconic tropical tree species.
Sensory neurons control heritable adaptation to stress through germline reprogramming
Authors: Zuco Giusy , Kache Vikas , Robles Pedro , Chaudhuri Jyotiska , Hill Beth , Bateson Christine , Pires-daSilva Andre 
Published: August 2018

AbstractMaternal neuronal signaling has been reported to program adaptive changes in offspring physiology in diverse organisms [1, 2]. However, the mechanisms for the inheritance of adaptive maternal effects through the germline are largely unknown. In the nematode Auanema freiburgensis, stress-resistance and sex of the offspring depend on environmental cues experienced by the mother. Maternal sensing of high population densities results in the production of stress-resistant larvae (dauers) that develop into hermaphrodites. Ablation of the maternal ASH chemosensory neurons results only in non-dauer offspring that develop into males or females. High population densities correlate with changes in the methylation status of H3K4 and H3K9 in the maternal germline. Inhibition of JMJD histone demethylases prevents mothers from producing dauers and hermaphrodite offspring in high-density conditions. Our results demonstrate a case of soma-to-germline transmission of environmental information that influences the phenotype of the following generation through changes in histone modifications of the maternal germline.HighlightsHigh population density leads to the production of hermaphrodite offspring.The ASH neuron in the hermaphrodite mother senses population density.Histone modifications in the maternal germline correlate with the sex of offspring.Inhibition of histone demethylases results in female offspring in all conditions.
Divergence in the face of gene flow in twoCharadriusplovers along the Chinese coast
Authors: Wang Xuejing , Que Pinjia , Heckel Gerald , Hu Junhua , Zhang Xuecong , Chiang Chung-Yu , Huang Qin , Liu Simin , Martinez Jonathan , Zhang Nan , Pagani-Núñez Emilio , Dingle Caroline , Yan Leung Yu , Székely Tamás , Zhang Zhengwang , Liu Yang 
Published: August 2018

AbstractSpeciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient species, the Kentish (Charadrius alexandrinus) and the white-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. These analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamical isolation and secondary contact due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. These findings imply that the ecology can indeed counter gene flow through divergent selection and thus contribute to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and underlying mechanisms of speciation.
Genome-wide Expression Profiling and Pathway Analysis in Cyclic Stretched Human Trabecular Meshwork Cells
Authors: Drewry Michelle D. , Cai Jingwen , Helwa Inas , Hu Eric , Liu Sabrina , Mu Hongmei , Hu Yanzhong , Johnson William M. , Gonzalez Pedro , Stamer W. Daniel , Liu Yutao 
Published: August 2018

AbstractPurposeRegulation of intraocular pressure is dependent upon homeostatic responses of trabecular meshwork (TM) cells to mechanical stretch. Despite the important roles of miRNAs in regulating TM function and aqueous outflow, it remains unclear how miRNA and their target genes interact in response to physiological cyclic mechanical stretch. We aimed to identify differentially expressed miRNAs and their potential targets in human TM cells in response to cyclic mechanical stress.MethodsMonolayers of TM cells from non-glaucomatous donors (n=3-6) were cultured in the presence or absence of 15% mechanical stretch, 1 cycle/s, for 6 or 24-hours using computer-controlled Flexcell Unit. We profiled the expression of 800 miRNAs using NanoString Human miRNA assays and identified differentially expressed miRNAs using the Bioconductor Limma package. We identified differentially expressed genes using Operon Human Oligo Arrays with GeneSpring software. Pathway analysis with WebGestalt identified stretch-related pathways. We used Integrative miRNA Target Finder from Ingenuity Pathway Analysis to identify potential miRNA-mRNA regulations.ResultsWe identified 540 unique genes and 74 miRNAs with differential expression in TM cells upon cyclic mechanical stretch. Pathway analysis indicated the significant enrichment of genes involved in Wnt-signaling, receptor protein serine/threonine kinase signaling, TGF-β pathway, and response to unfolded protein. We also identified several miRNA master regulators, including miR-19b-3p and miR-93-5p, which may act as switches to control several mechano-responsive genes.ConclusionsThis study suggests that cyclic mechanical stress of TM cells triggers alterations in the expression of both mRNAs and miRNAs implicated in glaucoma-associated pathways.
A conceptual model for e-textbook creation based on proposed characteristics
Authors: Pešut Darija 
Published: August 2018

PurposeThis paper is part of an extensive research conducted as part of a doctoral thesis. The purpose of this paper is to collect and present the comprehensive list of e-textbook characteristics acquired from research in the English as a foreign language (EFL) subject area in Croatian higher education and present a useful checklist in the form of a conceptual model for e-textbook creation.Design/methodology/approachLiterature was reviewed with the aim of collecting published e-textbook characteristics which were then combined with the characteristics obtained from research data. The data were collected through four distinct online questionnaires on the Survey Monkey platform.FindingsTeaching EFL requires the use of different materials, authentic and specifically published for this purpose. The research results are used to discuss the possibility of blending all materials into one electronically published unit by considering the proposed e-textbook characteristics. The presented conceptual model for e-textbook creation can be used as a foundation for e-textbook design and evaluation in all subject fields.Originality/valueThe paper presents a list of e-textbook characteristics as an extensive list which can be applied in e-textbook design and evaluation in any subject field.
Real‐world use of apremilast for patients with psoriasis in Japan
Authors: Kishimoto Megumi , Komine Mayumi , Hioki Tomoyuki , Kamiya Koji , Sugai Junichi , Ohtsuki Mamitaro 
Published: August 2018

AbstractApremilast is a novel oral phosphodiesterase 4 inhibitor effective for psoriasis. It regulates the production of pro‐inflammatory mediators. Apremilast was approved in December 2016 in Japan; however, its efficacy and safety in a real‐world setting among Japanese patients have not been reported. We report on 44 patients treated with apremilast between March and October 2017. The median treatment duration was 25 weeks (range, 2–33). Thirty‐five patients (79.5%) continued the drug for at least 23 weeks, and five (11.4%) achieved a Psoriasis Area and Severity Index 100 response within 12 weeks. Nine patients discontinued the drug within 24 weeks mainly due to insufficient efficacy (n = 3) and adverse events (n = 4). Seven patients continued their previous systemic therapies such as cyclosporin (n = 1), methotrexate (n = 1), etretinate + methotrexate (n = 1) and biologics (n = 4) combined with apremilast. Of these patients, 55.9% had at least one adverse event although no severe adverse events. The most common adverse event was diarrhea (31.8%), followed by nausea (25.0%), headache (13.6%), abdominal discomfort (6.8%) and vomiting (6.8%). The proportion of diarrhea in our patients was higher than those of previous clinical trials. Among 10 patients with psoriatic arthritis, apremilast did not improve joint pain in nine (90%). To investigate the relationship between treatment efficacy and plaque size, we defined a small plaque as an individual rash diameter of 1 inch or less. The efficacy of apremilast was greater in patients with small plaques than in patients with large plaques.