bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytokine profile in human olfactory cleft mucus and associated changes in olfactory function
Authors: Wang Hong , Jaen Cristina , Yoshikawa Keiichi , Haneoka Mai , Saito Naoko , Nakamura Junji , Adappa Nithin D. , Cohen Noam A. , Dalton Pamela 
Published: May 2018

AbstractMultiple factors, including physical changes of the nasal mucosa and epithelium and exposure to air-borne environmental agents, appear to contribute to age-related olfactory loss. However, the molecular aspects of aging-associated olfactory loss in humans are not well understood. Although inflammation can be a significant underlying cause for olfactory impairment, whether aging increases the levels of inflammatory cytokines in the human olfactory mucosa and whether any inflammatory markers are associated with age-related olfactory loss remain unclear. Using a noninvasive method for collecting human olfactory mucus, we characterized and compared inflammatory cytokines, chemokines, and some growth factors, in the mucus collected from the olfactory cleft or the anterior nasal cavity from 12 healthy, young (18-40 years old) and 12 elderly (60-85 years old) individuals. We also hoped to identify candidate molecular biomarkers associated with age-associated olfactory loss in humans. Olfactory thresholds were obtained for two odorants and individual mucus samples were analyzed using multiplex assays for the levels of 30 cytokines. Results indicated elevated levels of certain inflammatory cytokines (IL-12, MCP-1) in olfactory mucus of the elderly, and high levels of some inflammatory factors (MCP-1, IL-8, IL-13 and VEGF) were associated with reduced olfactory sensitivity, suggesting that inflammation may play a role in olfactory decline associated with aging.
NAT/NCS2-hound: A Webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase–cation symporters of the NAT/NCS2 family
Authors: Chaliotis A , Vlastaridis P , Ntountoumi C , Botou M , Yalelis V , Lazou P , Tatsaki E , Mossialos D , Frillingos S , Amoutzias GD 
Published: May 2018

AbstractNucleobase transporters are important for supplying the cell with purines and/or pyrimidines, for controlling the intracellular pool of nucleotides and for obtaining exogenous nitrogen/carbon sources for the metabolism. Nucleobase transporters are also evaluated as potential targets for antimicrobial therapies, since several pathogenic microorganisms rely on purine/pyrimidine salvage from their hosts. The majority of known nucleobase transporters belong to the evolutionarily conserved and ubiquitous NAT/NCS2 protein family. Based on a large-scale phylogenetic analysis that we performed on thousands of prokaryotic proteomes, we have developed a webserver that can detect and distinguish this family of transporters from other homologous families that recognize different substrates. We can further categorize these transporters to certain evolutionary groups with distinct substrate preferences. The webserver scans whole proteomes and graphically displays which proteins are identified as NAT/NCS2, to which evolutionary groups and subgroups they belong to and which conserved motifs they have. For key subgroups and motifs, the server displays annotated information from published crystal-structures and mutational studies pointing to key functional amino acids that may help experts assess the transport capability of the target sequences. The server is 100% accurate in detecting NAT/NCS2 family members. We also used the server to analyze 9109 prokaryotic proteomes and identified Clostridia, Bacilli, β- and γ-Proteobacteria, Actinobacteria and Fusobacteria as the taxa with the largest number of NAT/NCS2 transporters per proteome. An analysis of 120 representative eukaryotic proteomes also demonstrates the server’s capability of correctly analyzing this major lineage, with plants emerging as the group with the highest number of NAT/NCS2 members per proteome.
The structure of the genetic code as an optimal graph clustering problem
Authors: Błażej Paweł , Kowalski Dariusz R. , Mackiewicz Dorota , Wnetrzak Małgorzata , Aloqalaa Daniyah A. , Mackiewicz Paweł 
Published: May 2018

AbstractThe standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids. The questions about the origin and the main factor responsible for the present structure of the code are still under a hot debate. Various methodologies have been used to study the features of the code and assess the level of its potential optimality. Here, we introduced a new general approach to evaluate the quality of the genetic code structure. This methodology comes from graph theory and allows us to describe new properties of the genetic code in terms of conductance. This parameter measures the robustness of codon groups against the potential changes in translation of the protein-coding sequences generated by single nucleotide substitutions. We described the genetic code as a partition of an undirected and unweighted graph, which makes the model general and universal. Using this approach, we showed that the structure of the genetic code is a solution to the graph clustering problem. We presented and discussed the structure of the codes that are optimal according to the conductance. Despite the fact that the standard genetic code is far from being optimal according to the conductance, its structure is characterised by many codon groups reaching the minimum conductance for their size. The SGC represents most likely a local minimum in terms of errors occurring in protein-coding sequences and their translation.
UDP-glucose:anthocyanidin 3-O-glucoside-2”-O-glucosyltransferase catalyzes further glycosylation of anthocyanins in purple Ipomoea batatas
Authors: Wang Hongxia , Wang Chengyuan , Fan Weijuan , Yang Jun , Appelhagen Ingo , Wu Yinliang , Zhang Peng 
Published: May 2018

AbstractGlycosylation contributes to the diversity and stability of anthocyanins in plants. The process is catalyzed by various glucosyltransferases using different anthocyanidin aglycones and glycosyl donors. An anthocyanidin 3-O-glucoside-2”-O-glucosyltransferase (3GGT) from purple sweetpotato (cv. Ayamurasaki) served for the catalytic conversion of anthocyanidin 3-O-glucoside into anthocyanidin 3-O-sophoroside, which is functionally different from the 3GGT ortholog of Arabidopsis. The phylogenetic analysis indicates regioselectivity of 3GGT using UDP-xylose or UDP-glucose as the glycosyl is divergent between Convolvulaceae and Arabidopsis. Homology-based protein modeling and site-directed mutagenesis of Ib3GGT and At3GGT suggested that the Thr-138 of Ib3GGT is a key amino acid residue for UDP-glucose recognition and plays a major role in sugar donor selectivity. The wild type and ugt79b1 mutants of Arabidopsis plants overexpressing Ib3GGT produced the new component cyanidin 3-O-sophoroside. Moreover, Ib3GGT expression was associated with anthocyanin accumulation in different tissues during Ayamurasaki plant development and was regulated by the transcription factor IbMYB1. The localization assay of Ib3GGT showed that further glycosylation occurs in the cytosol and not endoplasmic reticulum. The present study revealed the function of Ib3GGT in further glycosylation of anthocyanins and its Thr-138 is the key amino acid residue for UDP-glucose recognition.
ProfPPIdb: pairs of physical protein-protein interactions predicted for entire proteomes
Authors: Tran Linh , Hamp Tobias , Rost Burkhard 
Published: May 2018

AbstractMotivationProtein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods.ResultsWe extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any interaction, in particular for less well-studied organisms. Thus, our work complements existing resources and is particularly helpful for designing experiments because of its uniqueness. Experimental annotations and computational predictions are strongly influenced by the fact that some proteins have many partners and others few. To optimize machine learning, recent methods explicitly ignored such a network-structure and rely either on domain knowledge or sequence-only methods. Our approach is independent of domain-knowledge and leverages evolutionary information. The database interface representing our results is accessible from https://rostlab.org/services/ppipair/. The data can also be downloaded from https://figshare.com/collections/ProfPPI-DB/4141784.
R51Q SNX10 induces osteopetrosis by promoting uncontrolled fusion of monocytes to form giant, non-functional osteoclasts
Authors: Barnea Maayan , Stein Merle , Winograd-Katz Sabina , Shalev Moran , Arman Esther , Brenner Ori , Thalji Fadi , Kanaan Moien , Elinav Hila , Stepensky Polina , Geiger Benjamin , Tuckermann Jan , Elson Ari 
Published: May 2018

SummaryThe molecular mechanisms that regulate fusion of monocytes into functional osteoclasts are virtually unknown. We describe a knock-in mouse model for the R51Q mutation in sorting nexin 10 (SNX10) that exhibits osteopetrosis and related symptoms of patients of autosomal recessive osteopetrosis linked to this mutation. Osteopetrosis arises in homozygous R51Q SNX10 mice due to a unique combination of reduced numbers of osteoclasts that are non-functional. Fusion of mutant monocytes is deregulated and occurs rapidly and continuously to form giant, non-functional osteoclasts. Mutant osteoclasts mature quickly and survive poorlyin vitro, possibly accounting for their scarcityin vivo. These cells also exhibit impaired ruffled borders, which are required for bone resorption, providing an additional basis for the osteopetrotic phenotype. More broadly, we propose that the maximal size of osteoclasts is actively determined by a genetically-regulated, cell-autonomous mechanism that limits precursor cell fusion, and for which SNX10 is required.
Histological, transcriptomic andin vitroanalysis reveal an intrinsic activated state of myogenic precursors in hyperplasic muscle of trout
Authors: Jagot Sabrina , Sabin Nathalie , Le Cam Aurélie , Bugeon Jérôme , Rescan Pierre-Yves , Gabillard Jean-Charles 
Published: May 2018

AbstractBackgroundThe dramatic increase in myotomal muscle mass in post-hatching fish is related to their ability to lastingly produce new muscle fibres, a process termed hyperplasia. The molecular and cellular mechanisms underlying fish muscle hyperplasia largely remain unknown. In this study, we aimed to characterize intrinsic properties of myogenic cells originating from fish hyperplasic muscle. For this purpose, we comparedin situproliferation,in vitrocell behavior and transcriptomic profile of myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) and from non-hyperplasic muscle of fasted juvenile trout (FJT) and adult trout (AT).ResultsFor the first time, we showed that myogenic precursors proliferate in hyperplasic muscle from JT as shown byin vivoBrdU labeling. This proliferative rate was very low in AT and FJT muscle. Transcriptiomic analysis revealed that myogenic cells from FJT and AT displayed close expression profiles with only 64 differentially expressed genes (BH corrected p-val < 0.001). In contrast, 2623 differentially expressed genes were found between myogenic cells from JT and from both FJT and AT. Functional categories related to translation, mitochondrial activity, cell cycle, and myogenic differentiation were inferred from genes up regulated in JT compared to AT and FJT myogenic cells. Conversely, Notch signaling pathway, that signs cell quiescence, was inferred from genes down regulated in JT compared to FJT and AT. In line with our transcriptomic data,in vitroJT myogenic precursors displayed higher proliferation and differentiation capacities than FJT and AT myogenic precursors.ConclusionsThe transcriptomic analysis and examination of cell behavior converge to support the view that myogenic cells extracted from hyperplastic muscle of juvenile trout are intrinsically more potent to form myofibres than myogenic cells extracted from non-hyperplasic muscle. The generation of gene expression profiles in myogenic cell extracted from muscle of juvenile trout may yield insights into the molecular and cellular mechanisms controlling hyperplasia and provides a useful list of potential molecular markers of hyperplasia.
Limits for resolving tandem mass tag reporter ions with identical integer mass using phase constrained spectrum deconvolution
Authors: Kelstrup Christian D. , Aizikov Konstantin , Batth Tanveer S. , Kreutzman Arne , Grinfeld Dmitry , Lange Oliver , Mourad Daniel , Makarov Alexander , Olsen Jesper V. 
Published: May 2018

ABSTRACTA popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT) which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. This contrasts with faster peptide sequencing capabilities enabled by lowered mass resolution on Orbitrap instruments. It is therefore important to determine the mass resolution limits for highly multiplexed quantification when maximizing proteome depth. Here we defined the lower boundaries for resolving TMT reporter ions with 0.0063 Da mass differences using an ultra-high-field Orbitrap mass spectrometer. We found the optimal method depends on the relative ratio between closely spaced reporter ions and that 64 ms transient acquisition time provided sufficient resolving power for separating TMT reporter ions with absolute ratio changes up to 16-fold. Furthermore, a 32 ms transient processed with phase-constrained spectrum deconvolution provides >50% more identifications with >99% quantified, but with a slight loss in quantification precision and accuracy. These findings should guide decisions on what Orbitrap resolution settings to use in future proteomics experiments relying on TMT reporter ion quantification with identical integer masses.
Modeling meiotic chromosome pairing: increased fidelity from a tug of war between telomere forces and a pairing-based Brownian ratchet
Authors: Marshall Wallace F. , Fung Jennifer C. 
Published: May 2018

AbstractMeiotic homolog pairing involves associations between homologous DNA regions scattered along the length of a chromosome. When homologs associate, they tend to do so by a processive zippering processive, which apparently results from avidity effects. Using a computational model, we show that this avidity-driven processive zippering reduces the selectivity of pairing. When active random forces are applied to telomeres, this drop in selectivity is eliminated in a force-dependent manner. Further simulations suggest that active telomere forces are engaged in a tug-of-war against zippering, which can be interpreted as a Brownian ratchet with a stall force that depends on the dissociation constant of pairing. When perfectly homologous regions of high affinity compete with homeologous regions of lower affinity, the affinity difference can be amplified through this tug of war effect provided the telomere force acts in a range that is strong enough to oppose zippering of homeologs while still permitting zippering of correct homologs. The degree of unzippering depends on the radius of the nucleus, such that complete unzippering of homeologous regions can only take place if the nucleus is large enough to pull the two chromosomes completely apart. A picture of meiotic pairing thus emerges that is fundamentally mechanical in nature, possibly explaining the purpose of active telomere forces, increased nuclear diameter, and the presence of “Maverick” chromosomes in meiosis.
The Portal Project: a long-term study of a Chihuahuan desert ecosystem
Authors: Ernest S. K. Morgan , Yenni Glenda M. , Allington Ginger , Bledsoe Ellen K. , Christensen Erica M. , Diaz Renata M. , Geluso Keith , Goheen Jacob R. , Guo Qinfeng , Heske Edward , Kelt Douglas , Meiners Joan M. , Munger Jim , Restrepo Carla , Samson Douglas A. , Schutzenhofer Michele R. , Skupski Marian , Supp Sarah R. , Thibault Kate , Taylor Shawn , White Ethan , Ye Hao , Davidson Diane W. , Brown James H. , Valone Thomas J. 
Published: May 2018

AbstractThis is a data paper for the Portal Project, a long-term ecological study of rodents, plants, and ants located in southeastern Arizona, U.S.A. This paper contains an overview of methods and information about the structure of the data files and the relational structure among the files. This is a living data paper and will be updated with new information as major changes or additions are made to the data. All data - along with more detailed data collection protocols and site information - is archived at:https://doi.org/10.5281/zenodo.1215988.
ERVcaller: Identify polymorphic endogenous retrovirus (ERV) and other transposable element (TE) insertions using whole-genome sequencing data
Authors: Chen Xun , Li Dawei 
Published: May 2018

AbstractMotivationApproximately 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years, an increasing number of human diseases have been found to be associated with ERVs. However, it remains challenging to accurately detect the full spectrum of polymorphic (unfixed) ERVs using next-generation sequencing (NGS) data.ResultsWe designed a new tool, ERVcaller, to detect and genotype transposable element (TE) insertions, including ERVs, in the human genome. We evaluated ERVcaller using both simulated and real benchmark whole-genome sequencing (WGS) datasets. By comparing with existing tools, ERVcaller consistently obtained both the highest sensitivity and precision for detecting simulated ERV and other TE insertions derived from real polymorphic TE sequences. For the WGS data from the 1000 Genomes Project, ERVcaller detected the largest number of TE insertions per sample based on consensus TE loci. By analyzing the experimentally verified TE insertions, ERVcaller had 94.0% TE detection sensitivity and 96.6% genotyping accuracy. PCR and Sanger sequencing in a small sample set verified 86.7% of examined insertion statuses and 100% of examined genotypes. In conclusion, ERVcaller is capable of detecting and genotyping TE insertions using WGS data with both high sensitivity and precision. This tool can be applied broadly to other species.Availabilitywww.uvm.edu/genomics/software/ERVcaller.htmlContactdawei.li@uvm.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Culture‐independent characterization of a novel magnetotactic member affiliated to the Beta class of the Proteobacteria phylum from an acidic lagoon
Authors: Abreu Fernanda , Leão Pedro , Vargas Gabriele , Cypriano Jefferson , Figueiredo Viviane , Enrich‐Prast Alex , Bazylinski Dennis A. , Lins Ulysses 
Published: May 2018

SummaryMagnetotactic bacteria (MTB) comprise a group of motile microorganisms common in most mesothermal aquatic habitats with pH values around neutrality. However, during the last two decades, a number of MTB from extreme environments have been characterized including: cultured alkaliphilic strains belonging to the Deltaproteobacteria class of the Proteobacteria phylum; uncultured moderately thermophilic strains belonging to the Nitrospirae phylum; cultured and uncultured moderately halophilic or strongly halotolerant bacteria affiliated with the Deltaproteobacteria and Gammaproteobacteria classes and an uncultured psychrophilic species belonging to the Alphaproteobacteria class. Here, we used culture‐independent techniques to characterize MTB from an acidic freshwater lagoon in Brazil (pH ∼ 4.4). MTB morphotypes found in this acidic lagoon included cocci, rods, spirilla and vibrioid cells. Magnetite (Fe3O4) was the only mineral identified in magnetosomes of these MTB while magnetite magnetosome crystal morphologies within the different MTB cells included cuboctahedral (present in spirilla), elongated prismatic (present in cocci and vibrios) and bullet‐shaped (present in rod‐shaped cells). Intracellular pH measurements using fluorescent dyes showed that the cytoplasmic pH was close to neutral in most MTB cells and acidic in some intracellular granules. Based on 16S rRNA gene phylogenetic analyses, some of the retrieved gene sequences belonged to the genus Herbaspirillum within the Betaproteobacteria class of the Proteobacteria phylum. Fluorescent in situ hybridization using a Herbaspirillum‐specific probe hybridized with vibrioid MTB in magnetically‐enriched samples. Transmission electron microscopy of the Herbaspirillum‐like MTB revealed the presence of many intracellular granules and a single chain of elongated prismatic magnetite magnetosomes. Diverse populations of MTB have not seemed to have been described in detail in an acid environment. In addition, this is the first report of an MTB phylogenetically affiliated with Betaproteobacteria class.
Buchanania obovata: An Australian Indigenous food for diet diversification
Authors: Fyfe Selina A. , Netzel Michael E. , Tinggi Ujang , Biehl Eva M. , Sultanbawa Yasmina 
Published: May 2018

AimBuchanania obovata Engl., the Green Plum, is a small green fruit eaten by Australian Indigenous peoples of the Northern Territory and Western Australia that has had limited study and has potential as a source of food for diet diversification. The flesh and seed of the fruit are eaten and the plant is used as bush medicine.MethodsPhysical characteristics of the fruit were measured. The flesh and seed freeze dried powders were measured separately for proximates, mineral/trace elements and heavy metals, and folate analysis. Vitamin C was analysed in the flesh.ResultsThe flesh is high in protein (12.8 g/100 g dry weight (DW)) and both flesh and seed are high in dietary fibre (55.1 and 87.7 g/100 g DW, respectively). The flesh is high in potassium (2274.7 mg/100 g DW), and is a good source of magnesium (570.5 mg/100 g DW), calcium (426.0 mg/100 g DW) and phosphorous (216.8 mg/100 g DW), whereas the seed is high in iron (8.15 mg/100 g DW). The flesh contains folate at 752.4 μg/100 g DW and the seed contains 109.5 μg/100 g DW as pteroylmonoglutamic acid equivalents.ConclusionsThe flesh and seed have good nutritional properties and the results support the use of the Green Plum for diet diversification and nutrition in Indigenous and non‐Indigenous populations in Australia.