bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Coding sequence of firefly luciferase reporter gene affects specific hyperexpressionArabidopsis thaliana cpl1mutant
Authors: Koiwa Hisashi , Fukudome Akihito 
Published: June 2017

AbstractForward genetic screening of mutants using firefly luciferase (LUC) reporter gene became a standard practice in plant research. Such screenings frequently identified alleles ofCPL1(Carboxyl-terminal Phosphatase-Like 1) regardless of promoters or pathways studied. Expression of the corresponding endogenous genes often shows the minimal difference between wild type andcpl1.Here we show that theLUCcoding sequence is responsible for the high expression incpl1,using a classicalRD29a-LUC. Deletion of theLUC3’-UTR did not change hyperactivation ofLUCincpl1.However, a codon-modifiedLUC(LUC2) produced similar expression levels both in wild type and incpl1. These results indicate that the coding region ofLUCis responsible for thecpl1-specificLUCoverexpression uncoupled with the expression of the endogenous counterpart.
The Nasal and Oropharyngeal Microbiomes of Healthy Livestock Workers
Authors: Kates Ashley E. , Dalman Mark , Torner James C. , Smith Tara C. 
Published: June 2017

ABSTRACTLittle information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n=38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n=17), through Iowa county fairs (n=3), and through snowball sampling (n=1). We collected two sets of swabs from the nares and oropharynx of each participant. The first set of swabs was used to assess the microbiome via 16s rRNA sequencing and the second was used to cultureS. aureus.We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 26 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen withStreptococcusandProteobacteria.In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes.
The plastid genome in Cladophorales green algae is encoded by hairpin plasmids
Authors: Cortona Andrea Del , Leliaert Frederik , Bogaert Kenny A. , Turmel Monique , Boedeker Christian , Janouškovec Jan , Lopez-Bautista Juan M. , Verbruggen Heroen , Vandepoele Klaas , De Clerck Olivier 
Published: June 2017

AbstractVirtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes ofBoodlea compositaare encoded on 1-7 kb DNA contigs with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. TheBoodleachloroplast genes are highly divergent from their corresponding orthologs. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.
Evidence for the temporal regulation of insect segmentation by a conserved set of developmental transcription factors
Authors: Clark Erik , Peel Andrew D. 
Published: June 2017

ABSTRACTLong-germ insects, such as the fruit flyDrosophila melanogaster, pattern their segments simultaneously, whereas short germ insects, such as the beetleTribolium castaneum, pattern their segments sequentially, from anterior to posterior. While the two modes of segmentation at first appear to be very different, many details of segmentation gene expression are surprisingly similar between long-germ and short-germ species. Collectively, these observations hint that insect segmentation may involve fairly conserved patterning mechanisms, which occur within an evolutionarily malleable spatiotemporal framework. Based on genetic and comparative evidence, we now propose that, in bothDrosophilaandTriboliumembryos, the temporal progression of the segmentation process is regulated by a temporal sequence of Caudal, Dichaete, and Odd-paired expression. These three transcription factors are broadly expressed in segmenting tissues, providing spatiotemporal information that intersects with the information provided by periodically-expressed segmentation genes such as the pair-rule factors. However, they are deployed differently in long-germ versus short-germ insects, acting as simple timers inDrosophila, but as smooth, retracting wavefronts inTribolium, compatible with either gap gene-based or oscillator-based generation of periodicity, respectively.
The genomic health of ancient hominins
Authors: Berens Ali J. , Cooper Taylor L. , Lachance Joseph 
Published: June 2017

AbstractThe genomes of ancient humans, Neandertals, and Denisovans contain many alleles that influence disease risks. Using genotypes at 3180 disease-associated loci, we estimated the disease burden of 147 ancient genomes. After correcting for missing data, genetic risk scores were generated for nine disease categories and the set of all combined diseases. These genetic risk scores were used to examine the effects of different types of subsistence, geography, and sample age on the number of risk alleles in each ancient genome. On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past. This calls into question the idea that modern lifestyles have caused genetic load to increase over time. Focusing on individual genomes, we find that the overall genomic health of the Altai Neandertal is worse than 97% of present day humans and that Ötzi the Tyrolean Iceman had a genetic predisposition to gastrointestinal and cardiovascular diseases. As demonstrated by this work, ancient genomes afford us new opportunities to diagnose past human health, which has previously been limited by the quality and completeness of remains.
Structural basis for the specific recognition of DSR by the YTH domain containing protein Mmi1
Authors: Wu Baixing , Xu Jinhao , Su Shichen , Liu Hehua , Gan Jianhua , Ma Jinbiao 
Published: June 2017

AbstractMeiosis is one of the most dramatic differentiation programs accompanied by a striking change in gene expression profiles, whereas a number of meiosis-specific transcripts are expressed untimely in mitotic cells. The entry of meiosis will be blocked as the accumulation of meiosis-specific mRNAs during the mitotic cell in fission yeastSchizosaccharomyces pombe. A YTH domain containing protein Mmi1 was identified as a pivotal effector in a post-transcriptional event termed selective elimination of meiosis-specific mRNAs, Mmi1 can recognize and bind a class of meiosis-specific transcripts expressed inappropriately in mitotic cells, which contain a conservative motif called DSR as a mark to remove them in cooperation with nuclear exosomes. Here we report the 1.6 Å resolution crystal structure of the YTH domain of Mmi1 binds to high-affinity RNA targets r(A1U2U3A4A5A6C7A8) containing DSR core motif. Our structure observations, supported by site-directed mutations of key residues illustrate the mechanism for specific recognition of DSR-RNA by Mmi1. Moreover, different from other YTH domain family proteins, Mmi1 YTH domain has a distinctive function although it has a similar fold as other ones.
Simulated climate change affects how biocrusts modulate infiltration and desiccation dynamics
Authors: Lafuente Angela , Berdugo Miguel , Ladrón de Guevara Mónica , Gozalo Beatriz , Maestre Fernando T. 
Published: June 2017

AbstractSoil surface communities dominated by mosses, lichens and cyanobacteria (biocrusts) cover most of the soil surface between vegetation patches in drylands worldwide, and are known to affect soil wetting and drying after rainfall events. While ongoing climate change is already warming and changing rainfall patterns of drylands in many regions, little is known on how these changes may affect the hydrological behaviour of biocrust-covered soils. We used eight years of continuous soil moisture and rainfall data from a climate change experiment in central Spain to explore how biocrusts modify soil water gains and losses after rainfall events under simulated changes in temperature (2.5ºC warming) and rainfall (33% reduction). Both rainfall amount and biocrust cover increased soil water gains after rainfall events, whereas experimental warming, rainfall intensity and initial soil moisture decreased them. Initial moisture, maximum temperature and biocrust cover, by means of enhancing potential evapotranspiration or soil darkening, increased the drying rates and enhanced the exponential behaviour of the drying events. Meanwhile, the warming treatment reduced the exponential behaviour of these events. The effects of climate change treatments on soil water gains and losses changed through time, with important differences between the first two years of the experiment and after five years since its setup. These effects were mainly driven by the important reductions in biocrust cover and diversity observed under warming. Our results highlight the importance of long term studies to understand soil moisture responses to ongoing climate change in drylands.
Senkyunolide A protects corticosterone-induced cell apoptosis via modulating protein phosphatase 2A and α-synuclein
Authors: Gong Shenglan , Zhang Jin , Guo Zhouke , Fu Wenjun 
Published: June 2017

AbstractDan-zhi-xiao-yao-sanis a Traditional Chinese Medicine (TCM) formula that is widely used to treat depression related neurological disorders, however, the active compound(s) and underlying mechanisms are unclear. In the present study, we found that senkyunolide A (SenA) has neuroprotective effects in corticosterone (Cort)-induced depression cell model in PC12 cells. Firstly, we found that SenA protects Cort-induced cell injury in PC12 cells. In addition, SenA attenuates Cort-induced the reduction of phosphatase 2A (PP2A) activities, and the increase of p-PP2A, α-syn and p-α-syn-Ser129 levels. Furthermore, PP2A inhibitor okadaic acid (OA) decreased, and PP2A activator D-erythro-Sphingosine (SPH) increased Cort-induced cell apoptosis. Importantly, we also found that the neuroprotective effects of SenA in Cort-induced cell injury via modulating α-syn levels. Collectively, our results suggest that the neuroprotective effects of SenA in Cort-induced depression cell model via modulating PP2A activities and α-syn levels, and bring a breakthrough to the anti-depression mechanisms for natural compound SenA.
Deciphering Molecular Cascades in a Novel Acclimatization Strategy for Rapid Ascent to High Altitude
Authors: Paul Subhojit , Gangwar Anamika , Bhargava Kalpana , Ahmad Yasmin 
Published: June 2017

ABSTRACTThe repercussions of hypobaric hypoxia are dependent upon two factors-time and intensity of exposure. The effects of intensity i.e. variation of altitude are yet unknown although it is a significant factor in terms of acclimatization protocols. In this study we present the effects of acute (24 h) exposure to high (10,000 ft), very high (15,000 ft) and extreme altitude (25,000 ft) zones on lung and plasma using semi-quantitative redox specific transcripts and quantitative proteo-bioinformatics workflow in conjunction with redox stress assays. Our findings indicate that very high altitude exposure elicits systemic redox homeostatic processes due to failure of lung redox homeostasis without causing mortality. We also document a rapid acclimatization protocol causing a shift from 0 to 100% survival at 25,000 ft in male SD rats upon rapid induction. Finally we posit the various processes involved and the plasma proteins that can be used to ascertain the acclimatization status of an individual.
Resolving Three-State Ligand-Binding Mechanisms by Isothermal Titration Calorimetry: A Simulation Study
Authors: Kovrigin Evgenii L. 
Published: June 2017

ABSTRACTIn this paper, I theoretically analyzed ITC profiles for three-state equilibria involving ligand binding coupled to isomerization or dimerization transitions. Simulations demonstrate that the mechanisms where the free or ligand-bound protein undergoes dimerization (such that the ligand cannot bind to or dissociate from the dimer) produce very distinctive titration profiles. In contrast, profiles of the pre-existing equilibrium or induced-fit models cannot be distinguished from a simple two-state process, requiring data from additional techniques to positively identify these mechanisms.
Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions
Authors: Moutinho Thomas J. , Panagides John C. , Biggs Matthew B. , Medlock Gregory L. , Kolling Glynis L. , Papin Jason A. 
Published: June 2017

AbstractInteractions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung,Pseudomonas aeruginosaandBurkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.
Characterization ofNvLWamide-likeneurons reveals stereotypy inNematostellanerve net development
Authors: Havrilak Jamie A , Faltine-Gonzalez Dylan , Wen Yiling , Fodera Daniella , Simpson Ayanna C. , Magie Craig R. , Layden Michael J 
Published: June 2017

AbstractCnidarian nervous systems are traditionally described as diffuse nerve nets lacking true organization. However, there are examples of stereotypical structure in the nerve nets of multiple cnidarian species that suggest nerve nets are organized. We previously demonstrated that theNvashAtarget geneNvLWamide-likeis expressed in a small subset of theNematostellanerve net and speculated that observing a few neurons within the developing nerve net would provide a better indication of potential stereotypy. Here we documentNvLWamide-likeexpression more systematically.NvLWamide-likeis initially expressed in the typical neurogenic salt and pepper pattern within the ectoderm at the gastrula stage, and expression expands to include endodermal salt and pepper expression at the planula larval stage. Expression persists in both ectoderm and endoderm in adults. We generated anNvLWamide-like::mCherrytransgenic reporter line to visualize the neural architecture.NvLWamide-likeis expressed in six neural subtypes identifiable by neural morphology and location. Upon completing development the numbers of neurons in each neural subtype are minimally variable between animals and the projection patterns of each subtype are consistent. Between the juvenile polyp and adult stages the number of neurons for each subtype increases. We conclude that cnidarian nerve nets are organized, develop in a stereotyped fashion, and that one aspect of generating the adult nervous system is to modify the juvenile nervous system by increasing neural number proportionally with size.
Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
Authors: Chen Yun-Ching , Gotea Valer , Margolin Gennady , Elnitski Laura 
Published: June 2017

AbstractRecent evidence shows that mutations in several driver genes can cause aberrant methylation patterns, a hallmark of cancer. In light of these findings, we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected. We measured this relationship using principal component analyses and methylation-mutation associations applied at the nucleotide level and with respect to genome-wide trends. We found a few mutated driver genes were associated with genome-wide patterns of aberrant hypomethylation or CpG island hypermethylation in specific cancer types. We identified associations between 737 mutated driver genes and site-specific methylation changes. Moreover, using these mutation-methylation associations, we were able to distinguish between two uterine and two thyroid cancer subtypes. The driver gene mutation-associated methylation differences between the thyroid cancer subtypes were linked to differential gene expression in JAK-STAT signaling, NADPH oxidation, and other cancer-related pathways. These results establish that driver-gene mutations are associated with methylation alterations capable of shaping regulatory network functions. In addition, the methodology presented here can be used to subdivide tumors into more homogeneous subsets corresponding to their underlying molecular characteristics, which could improve treatment efficacy.Author summaryMutations that alter the function of driver genes by changing DNA nucleotides have been recognized as a key player in cancer progression. Recent evidence showed that DNA methylation, a molecular signature that is used for controlling gene expression and that consists of cytosine residues with attached methyl groups in the context of CG dinucleotides, is also highly dysregulated in cancer and contributes to carcinogenesis. However, whether those methylation alterations correspond to mutated driver genes in cancer remains unclear. In this study, we analyzed 4,302 tumors from 18 cancer types and demonstrated that driver gene mutations are inherently connected with the aberrant DNA methylation landscape in cancer. We showed that those driver gene-associated methylation patterns can classify heterogeneous tumors in a cancer type into homogeneous subtypes and have the potential to influence the genes that contribute to tumor growth. This finding could help us to better understand the fundamental connection between driver gene mutations and DNA methylation alterations in cancer and to further improve the cancer treatment.
Sugar metabolism changes in response to the ultraviolet B irradiation of peach (Prunus persicaL.)
Authors: Wang Xuxu , Fu Xiling , Chen Min , Huan Lei , Liu Wenhai , Gao Yangang , Xiao Wei , Chen Xiude , Li Ling , Gao Dongsheng 
Published: June 2017

AbstractThe protected cultivation of peach (PrunuspersicaL.) trees is more economical and efficient than traditional cultivation, resulting in increased farmers’ incomes, but the peach sugar contents are lower than in open planting. In the greenhouse, a high-sugar variety of peach ‘Lumi 1’ was irradiated with 1.44 KJ·m−2.d−1intensity ultraviolet B radiation. The soluble sugar contents in fruit, peel and leaf were quantified using liquid chromatography. Overall, sucrose and sorbitol increased before the second fruit-expansion period. To further understand the mechanisms regulating sucrose and sorbitol accumulation in peach fruit, expression profiles of genes involved in sugar metabolism and transport were measured. The activity and translocation protein contents of these enzymes were measured by enzyme-linked immunosorbent assay. The increased sucrose synthase activity and sucrose transporter level in the pericarp promoted the synthesis of sucrose and intake of sucrose into fruit. Sorbitol transport into fruit was promoted by the increased sorbitol transporter protein levels in leaves. In summary, greenhouse the sucrose and sorbitol contents were increased when supplemented with 1.44 kJ·m−2·d−1ultraviolet B radiation before the second fruit-expansion period of peach.
A Cross-Sectional Study of Set Shifting Impairments and Falling in Individuals with and without Parkinson’s Disease
Authors: McKay J. Lucas , Lang Kimberly C. , Ting Lena H. , Hackney Madeleine E. 
Published: June 2017

AbstractINTRODUCTION. Individuals with Parkinson’s disease (PD) are at increased risk for falls, and exhibit deficits in executive function, including Set Shifting, which can be measured as the difference between parts B and A of the Trailmaking Test. METHODS. We conducted a cross-sectional study using baseline data of PD patients with and without freezing of gait (FOG) (n=69) and community-dwelling neurologically-normal older adults (NON-PD) (n=84) who had volunteered to participate in clinical rehabilitation research. Multivariate logistic regression analyses were performed to determine associations between Set Shifting, PD, and faller status, as determined by ≥1 self-reported falls in the previous 6 months, after adjusting for demographic and cognitive factors and clinical disease characteristics. RESULTS. Impaired Set Shifting was associated with previous falls after controlling for age, sex, overall cognitive function, PD, FOG, and PD disease duration (OR=1.29 [1.03-1.60]; P=0.02). In models controlling for age, sex, and overall cognitive function, PD was associated with increased fall prevalence among the study sample (OR=4.15 [95% CI 1.65-10.44], P<0.01) and FOG was associated with increased fall prevalence among the PD sample (OR=3.63 [1.22-10.80], P=0.02). Although the strongest associations between Set Shifting and falling were observed among PD without FOG (OR=2.11) compared to HOA (OR=1.14) and PD with FOG (OR=1.46) in a multivariate model that allowed for interaction between set shifting and PD status, there was insufficient evidence to reject the null hypothesis of no interaction. CONCLUSIONS. Set Shifting is associated with previous falls in non-demented older adults with and without PD.HighlightsIndividuals with PD are at increased risk for falls, although causes are unclear.Impaired Set Shifting was associated with falls in older adults with and without PD.Associations were strongest among those with PD but without freezing of gait.