bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stable maintenance of a hidden switch as a way to increase the gene expression stability
Authors: Kuwahara Hiroyuki , Gao Xin 
Published: April 2019

AbstractIn response to severe stress, wild-type organisms can release alternative phenotypes that are hidden under normal conditions and are associated with underlying genetic variations. A number of such stress-induced phenotypic switchings have been reported to be based on reactivation of hidden thresholds; under the normal condition, a high barrier separating alternative phenotypes ensures the expression of single discrete phenotype, but a severe perturbation can lower the barrier to a level at which to expose cryptic alternatives. While the importance of such threshold-based switches as the mechanism to generate adaptive novelties under variable environments has been appreciated, it still remains elusive how naturally selected organisms can maintain the phenotypic switching capability when such switching has been disused for a long period of time. Here, through the use of computer simulation, we analyzed adaptive evolution of gene circuits under stabilizing selection. We found that different strategies evolved to acquire reduced levels of gene expression noise around the optimum expression level. To incrementally improve the gene expression stability from a founding population with bistable individuals, the evolution consistently took the direction to raise the height of the potential barrier of bistable systems. Our results demonstrate that hidden phenotypic switches can be stably maintained during environmental stasis, facilitating the release of potentially adaptive phenotypic alternatives in the event of substantial perturbations.
Identification of Host Biomarkers of EBV Latency IIb and Latency III
Authors: Messinger Joshua E. , Dai Joanne , Stanland Lyla J. , Price Alexander M. , Luftig Micah A. 
Published: April 2019

ABSTRACTDeciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral and host gene expression. Epstein-Barr Virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of the immune suppressed. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs) serving as a model of these lymphomas. In previous studies, our lab has described a temporal model for immortalization with an initial phase characterized by expression of the Epstein-Barr Nuclear Antigens (EBNAs), high c-Myc activity, and hyper-proliferation in the absence of the Latent Membrane Proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly the NFκB-activating LMP1, defining latency III. LCLs, however, express a broad distribution of LMP1 such that a subset of these cells expresses LMP1 at levels seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA-Seq on early EBV-infected latency IIb cells and latency III LCLs sorted by NFκB activity. We found that latency IIb transcriptomes clustered independently from latency III independent of NFκB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-FISH targeting EBV EBNA2, LMP1, and human CCR7. This study defines latency IIb as abona fidelatency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity.IMPORTANCEEBV is a ubiquitous pathogen with >95% of adults harboring a life-long latent infection in memory B cells. In immunocompromised individuals, latent EBV infection can result in lymphoma. The established expression profile of these lymphomas is latency III, which includes expression of all latency genes. However, single cell analysis of EBV latent gene expression in these lymphomas suggests heterogeneity where most cells express the transcription factor, EBNA2, and only a fraction express the membrane protein LMP1. Our work describes an early phase after infection where the EBNAs are expressed without LMP1, called latency IIb. However, LMP1 levels within latency III vary widely making these states hard to discriminate. This may have important implications for therapeutic responses. It is crucial to distinguish these states to understand the molecular pathogenesis of these lymphomas. Ultimately, better tools to understand the heterogeneity of these cancers will support more efficacious therapies in the future.
Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
Authors: Frey Katharina , Pucker Boas 
Published: April 2019

AbstractMost protein encoding genes in eukaryotes contain introns which are interwoven with exons. After transcription, introns need to be removed in order to generate the final mRNA which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5’ end and AG at the 3’ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations which have been known for years. During the last years, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here we expand systematic investigations of non-canonical splice site combinations in plants to all eukaryotes by analysing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences such as a substantially increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts could be one explanation for this observation. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemora affinis and Oikopleura dioica. A variant in one U1 snRNA isoform might allow the recognition of GA as 5’ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3’ splice site compared to the 5’ splice site across animals, fungi, and plants.
Invasive species-driven trophic cascades: Are cane toads indirectly contributing to small mammal collapses across tropical Australia?
Authors: Radford Ian James , Woolley Leigh-Ann , Dickman Chris R. , Corey Ben , Trembath Dane , Fairman Richard 
Published: April 2019

AbstractApex predators are fundamentally important in regulating many ecosystems, and perturbations of their populations are frequently implicated in ecosystem declines or collapses. In considering small mammal declines in northern Australia, most attention has focused on interactions between a mammalian apex predator—the dingoCanis dingo—and a meso-predator, the feral cat—Felis catus. Little consideration has been given to the possible implications of changed reptilian predator assemblages resulting from invasion by a toxic anuran invader, the cane toad (Rhinella marina), on small mammals. We used reptile removal records from licenced reptile catchers in three widely spaced towns in the savannas of northern Australia to explore potential impacts of toads on apex and meso-predatory snakes and large lizards. In addition, simultaneous fauna survey data from one town with reptile removal records, coinciding with toad invasion, were used to identify cascading impacts through the savanna ecosystem. Intervention analyses revealed empirical linkages between toad invasion, apex predator declines, meso-predator increases and declines of small mammals and other prey groups. Based on the timing and strength of intervention we postulate a novel conceptual model linking recent mammal declines with trophic cascades following toad invasion, where the loss of large, anurophagous (toad-eating) reptilian apex predators allowed increases in mammal-eating meso-predatory snakes. The conceptual model is discussed in relation to prevailing hypotheses regarding northern Australia’s dramatic small mammal declines. Future studies will need to quantify these putative interactions and test their comparative importance so that appropriate management can be implemented to stem the ongoing losses of mammal fauna.
Rapid and highly sensitive detection of pyocyanin biomarker in differentPseudomonas aeruginosainfections using gold nanoparticles modified sensor
Authors: Elkhawaga Amal A. , Khalifa Marwa M. , El-badawy Omnia H.B. , Hassan Mona A. , El-Said Waleed A. 
Published: April 2019

AbstractSuccessful antibiotic treatment of infections relies on accurate and rapid identification of the infectious agents.Pseudomonas aeruginosais implicated in a wide range of human infections that almost complicated and become life threating especially in immunocompromised and critically ill patients. Conventional microbiological methods take more than 3 days to obtain accurate results. Pyocyanin is a distinctive electroactive biomarker forPseudomonas aeruginosa. Here, we have developed a rapid diagnostic (polyaniline) PANI gold nanoparticles (Au NPs) modified indium tin oxide (ITO) electrode that showed 100% sensitivity for pyocyanin in culture ofPseudomonas aeruginosaclinical isolates and high selectivity for pyocyanin at low concentration when measured in the presence of other substances like ascorbic acid, uric acid, and glucose as interferences. The constructed electrode was characterized using scanning electron microscopy and cyclic voltammetry. The determined linear range for pyocyanin detection was from 238 µM to 1.9 µM with a detection limit of 500 nM. Compared to the screen-printed electrode used before, the constructed electrode showed a 4-fold enhanced performance.
Monitoring soil microorganisms with community-level physiological profiles using Biolog EcoPlates™ in Chaohu lakeside wetland, east China
Authors: Teng Zhen , Fan Wei , Wang Huiling , Cao Xiaoqing , Xu Xiaoniu 
Published: April 2019

AbstractUnder the circumstance of wetland degradation, we used Biolog EcoPlates™ method to investigate the impact of ecological restoration on the function of topsoil microbial communities by monitoring their metabolic diversity around Chaohu lakeside wetland. Four restoration patterns including reed shoaly land (RL), poplar plantation land (PL), abandoned shoaly grassland (GL) and cultivated flower land (FL) were selected. The result showed a rapid growth trend at the initial stage of incubation, following the fastest change rate at 72 h in both dormant and growing seasons, and the AWCD values of RL pattern was the highest at the detection points of each culture time, while the GL were the lowest. The calculation of diversity indicators also displayed significant lower McIntosh index in dormant season and Shannon-Wiener index in growing season in GL than in the others (P < 0.05). Carbohydrates and carboxylic acids were found to be the dominant substrates used in dormant season, whereas amino acids, polymers and phenolic acids were increasingly utilized by the microbial communities in growing season. We observed soil total potassium as the key factor that significantly affected the utilization efficiency of different carbon sources in both seasons (P < 0.05).
Economic and technical feasibility studies: technologies for second generation biofuels
Authors: Mungodla Sarah Gabashwediwe , Linganiso Linda Zikhona , Mlambo Sukoluhle , Motaung Tshwafo 
Published: April 2019

PurposeIn 2008, a number of Southern African countries cultivated about 900,000 ha of Jatropha, with a number of biodiesel plants ready for production; however, none of the projects succeeded. In 2014, KiOR advanced biofuel Energy Company in the USA announced bankruptcy due to incompetent technology. Studies disclose that the reasons for biofuel plants failure are not only due to lack of incentives and unclear policies but also due to lack of economic feasibility and low production yields. This paper aims to review the techno-economy assessment of second-generation biofuel technologies. The purpose of this paper is to summarize specific techno-economic indicators such as production cost, technology efficiency and process life cycle analysis for advanced biofuel technology and to narrate and illustrate a clear view of what requires assessment to deploy a feasible advanced biofuel technology. This study also reviews assessment of biomass supply chain, feedstock availability and site selection criteria. The review also elaborates on the use of different processes, forecasting and simulation-modeling tools used in different techno-economic analysis studies. The review provides guidance for conducting a technical and economic feasibility study for the advanced biofuels energy business.Design/methodology/approachThe aim of this review is, therefore, to evaluate the techno-economic feasibility studies for the establishment of viable industrial scale production of second-generation biofuels. It does so by grouping studies based on technology selection, feedstock availability and suitability, process simulation and economies as well as technology environmental impact assessment.FindingsIn conclusion, techno-economic analysis tools offer researchers insight in terms of where their research and development should focus, to attain the most significant enhancement for the economics of a technology. The study patterns within the scope of techno-economics of advanced biofuel reveal that there is no generic answer as to which technology would be feasible at a commercial scale. It is therefore important to keep in mind that models can only simplify and give a simulation of reality to a certain extent. Nevertheless, reviewed studies do not reach the same results, but some results are logically similar.Originality/valueThe originality of this article specifically illustrates important technical and economic indicators that should be considered when conducting feasibility studies for advance biofuels.
The differential effects of separated vs. unseparated services
Authors: Keh Hean Tat , Hartley Nicole , Wang Di 
Published: April 2019

PurposeThe purpose of this paper is to examine the effects of service separation on perceived value and intention to enroll in the higher education context, as mediated by perceived performance risk and moderated by an individual’s regulatory focus.Design/methodology/approachFour experimental studies were conducted, a pilot study and three main studies. Participants evaluated higher education courses offered in either the unseparated (on-campus) or separated (online) mode.FindingsResults show that: service separation influences perceived value; this effect is mediated by performance risk; and moderated by regulatory focus. Specifically, participants perceive higher education courses offered in the separated mode to have greater performance risk, which lowers their perceived value. This effect is enhanced for prevention-focused participants and mitigated for promotion-focused participants. Finally, service separation is found to influence intention to enroll in a course via performance risk and perceived value.Practical implicationsThe findings suggest that higher education providers need to better understand students’ regulatory focus. In particular, online education providers should target potential students who are promotion-focused and implement strategies to reduce performance risk, which would give students greater assurance that the online course will be delivered as promised.Originality/valueThe present research is the first to examine the effects of service separation in the context of higher education, which has received relatively little attention in the services marketing literature. In particular, the findings shed new insights on the mechanisms underlying consumer perceptions of separated vs unseparated service offerings, which contribute to research on services marketing and higher education.
Trade‐off or coordination? Correlations between ballochorous and myrmecochorous phases of diplochory
Authors: Chen Si‐Chong , Pahlevani Amir H. , Malíková Lenka , Riina Ricarda , Thomson Fiona J. , Giladi Itamar 
Published: April 2019

Abstract

The combination of two dispersal syndromes (diplochory) brings additional benefits to seeds, yet the relative costs and benefits of the two phases are poorly understood. Our goal is to provide the first quantification to test the long‐standing assumption that there are trade‐offs between the two phases in ballistic–ant diplochory.

Dispersal investment data were empirically measured for 91 Euphorbiaceae species across different regions of the world. Dispersal distance data of ballochory (seed dispersal by explosion), myrmecochory (seed dispersal by ants) and diplochory was collated from the literature for 210 records (148 species from 44 families). The data were analysed using Model II regression, Kolmogorov–Smirnov test and t test, complemented by phylogenetic comparative approaches.

Across diaspores of diplochorous species, the relative investment in myrmecochory increased more than that in ballochory. Fruit coat mass and elaiosome mass covaried in an allometric manner, regardless of seed mass. Diplochorous diaspores were significantly heavier than diaspores dispersed solely by ballochory. Dispersal distances of the two diplochorous phases were independent and comparable to that of sole ballochory or sole myrmecochory.

Our results do not support a trade‐off, but a coordinated dispersal strategy between the two diplochorous phases. Large diaspores may evolve diplochory to overcome dispersal difficulties in term of dispersal distance. As the most comprehensive study of ballistic–ant diplochory, our findings advance the understanding of the relative importance of the two phases in diplochory.

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Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon
Authors: Martijn Joran , Lind Anders E. , Schön Max E. , Spiertz Ian , Juzokaite Lina , Bunikis Ignas , Pettersson Olga V. , Ettema Thijs J. G. 
Published: April 2019

SummaryAmplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost‐effective protocol that amplifies a large part of the rRNA operon and sequences the amplicons with PacBio technology. We tested our method on a mock community and developed a read‐curation pipeline that reduces the overall read error rate to 0.18%. Applying our method on four environmental samples, we captured near full‐length rRNA operon amplicons from a large diversity of prokaryotes. The method operated at moderately high‐throughput (22286–37,850 raw ccs reads) and generated a large amount of putative novel archaeal 23S rRNA gene sequences compared to the archaeal SILVA database. These long amplicons allowed for higher resolution during taxonomic classification by means of long (∼1000 bp) 16S rRNA gene fragments and for substantially more confident phylogenies by means of combined near full‐length 16S and 23S rRNA gene sequences, compared to shorter traditional amplicons (250 bp of the 16S rRNA gene). We recommend our method to those who wish to cost‐effectively and confidently estimate the phylogenetic diversity of prokaryotes in environmental samples at high throughput.
Environmental potassium regulates bacterial flotation, antibiotic production and turgor pressure in Serratia through the TrkH transporter
Authors: Quintero‐Yanes Alex , Monson Rita E. , Salmond George P. C. 
Published: April 2019

Summary
Serratia sp. strain ATCC 39006 (S39006) can float in aqueous environments due to natural production of gas vesicles (GVs). Expression of genes for GV morphogenesis is stimulated in low oxygen conditions, thereby enabling migration to the air–liquid interface. Quorum sensing (via SmaI and SmaR) and transcriptional and post‐transcriptional regulators, including RbsR and RsmA, respectively, connect the control of cell buoyancy, motility and secondary metabolism. Here, we define a new pleiotropic regulator found in screens of GV mutants. A mutation in the gene trkH, encoding a potassium transporter, caused upregulation of GV formation, flotation, and the prodigiosin antibiotic, and downregulation of flagellar motility. Pressure nephelometry revealed that the mutation in trkH affected cell turgor pressure. Our results show that osmotic change is an important physiological parameter modulating cell buoyancy and antimicrobial production in S39006, in response to environmental potassium levels.
Comparison of Water‐Assisted Decontamination Systems of Pulsed Light and Ultraviolet for Salmonella Inactivation on Blueberry, Tomato, and Lettuce
Authors: Huang Runze , Chen Haiqiang 
Published: April 2019

AbstractFresh produce are vulnerable to pathogens during pre‐ and postharvest stages. Most fresh vegetable and fruits are consumed directly or merely washed with chlorine. We investigated two emerging decontamination technologies, pulse light (PL) and ultraviolet (UV), in combination with washing (referred as water‐assisted PL [WPL] and water‐assisted UV [WUV]). Blueberries, grape tomatoes, and iceberg lettuce shreds were tested in this study to represent fresh vegetables and fruits with smooth and rough surfaces. Salmonella spp. were used as a model microorganism due to its prevalence in outbreaks. Spot‐inoculation and dip‐inoculation were used to simulate potential contaminations during irrigation, harvest, transportation, and processing. Two intensity levels of PL (∼0.15 and 0.3 J/cm2 per pulse; 3 pulses/s) and UV (∼13 and 28 mW/cm2) were tested for 1 and 2 min. For all three types of fresh produce, blueberries, grape tomatoes, and iceberg lettuce shreds, WPL and WUV showed similar Salmonella inactivation effects on fresh produce. For spot‐inoculated fresh produce, WPL and WUV treatments reduced 4.5 to 5.7, 4.4 to 5.4, and 1.9 to 3.1 logs of Salmonella on blueberries, tomatoes, and lettuce shreds, respectively. For dip‐inoculated fresh produce, WPL and WUV treatments reduced 1.8 to 2.3, 1.9 to 2.5, and 1.9 to 2.6 logs of Salmonella on blueberries, tomatoes, and lettuce shreds, respectively. The majority of the WUV and WPL treatments could eliminate Salmonella in the wash water for blueberries and tomatoes, but not for lettuce.Practical ApplicationTwo light systems, pulsed light and UV, for decontamination of fresh produce were evaluated and compared. Results demonstrated that the two systems showed similar decontamination effect on fresh produce, demonstrating that the UV system could be used to replace the pulsed light system to reduce equipment cost.