bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere
Authors: Fajardo-Cavazos Patricia , Morrison Michael D. , Miller Kathleen M. , Schuerger Andrew C. , Nicholson Wayne L. 
Published: October 2018

AbstractResults from previous experiments indicated that the Gram-negative α-proteobacteriumSerratia liquefaciensstrain ATCC 27592 was capable of growth under low temperature (0 °C), low pressure (0.7 kPa), and anoxic, CO2-dominated atmosphere–conditions intended to simulate the near-subsurface environment of Mars. To probe the response of its transcriptome to this extreme environment,S. liquefaciensATCC 27592 was cultivated under 4 different environmental simulations: 0 °C, 0.7 kPa, CO2atmosphere (Condition A); 0 °C, ~101.3 kPa, CO2atmosphere (Condition B); 0 °C, ~101.3 kPa, ambient N2/O2atmosphere (Condition C); and 30 °C, ~101.3 kPa, N2/O2atmosphere (Condition D; ambient laboratory conditions). RNA-seq was performed on ribosomal RNA-depleted total RNA isolated from triplicate cultures grown under Conditions A-D and the datasets generated were subjected to transcriptome analyses. The data from Conditions A, B, or C were compared to laboratory Condition D. Significantly differentially expressed transcripts were identified belonging to a number of KEGG pathway categories. Up-regulated genes under all Conditions A, B, and C included those encoding transporters (ABC and PTS transporters); genes involved in translation (ribosomes and their biogenesis, biosynthesis of both tRNAs and aminoacyl-tRNAs); DNA repair and recombination; and non-coding RNAs. Genes down-regulated under all Conditions A, B, and C included: transporters (mostly ABC transporters); flagellar and motility proteins; genes involved in phenylalanine metabolism; transcription factors; and two-component systems. The results are discussed in the context of Mars astrobiology and planetary protection.
Exosomes from normal and diabetic human corneolimbal keratocytes differentially regulate migration, proliferation and marker expression of limbal epithelial cells
Authors: Leszczynska Aleksandra , Kulkarni Mangesh , Ljubimov Alexander V. , Saghizadeh Mehrnoosh 
Published: October 2018

AbstractLimbal epithelial stem cells (LESC) maintenance requires communication between stem cells and neighboring stromal keratocytes. Extracellular vesicles (EVs) are important for intercellular communication in various stem cell niches. We explored the regulatory roles of limbal stromal cell (LSC)-derived exosomes (Exos), an EV sub-population, in limbal epithelial cells (LEC) in normal and diabetic limbal niche and determined differences in Exo cargos from normal and diabetic LSC. Wound healing and proliferation rates in primary normal LEC were significantly enhanced upon treatment by normal Exos (N-Exos), but not by diabetic Exos (DM-Exos). Western analysis showed increased Akt phosphorylation in wounded LECs and organ-cultured corneas treated with N-Exos, compared to untreated wounded cells and DM-Exos treated fellow corneas, respectively. N-Exos treated organ-cultured corneas showed upregulation of putative LESC markers, keratin 15 (K15) and Frizzled-7, compared to the DM-Exos treated fellow corneas. By next generation sequencing, we identified differentially expressed small RNAs including microRNAs in DM-Exos vs. N-Exos. Overall, N-Exos have greater effect on LEC proliferation and wound healing than DM-Exos, likely by activating Akt signaling. The small RNA differences in Exos from diabetic vs. normal LSC could contribute to the disease state. Our study suggests that exosomes may serve as novel therapeutic tools for diabetic cornea.
Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas
Authors: Guan Hong-Hsiang , Hsieh Yin-Cheng , Lin Pei-Ju , Huang Yen-Chieh , Yoshimura Masato , Chen Li-Ying , Chen Shao-Kang , Chuankhayan Phimonphan , Lin Chien-Chih , Chen Nai-Chi , Nakagawa Atsushi , Chan Sunney I. , Chen Chun-Jung 
Published: October 2018

AbstractThe membrane-embedded quinol:fumarate reductase (QFR) in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain. The electron/proton-transfer pathways in QFRs remain controversial. Here we report the crystal structure of QFR from the anaerobic sulphate-reducing bacterium Desulfovibrio gigas (D. gigas) at 3.6 Å resolution. The structure of the D. gigas QFR is a homo-dimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme bL in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes. The observed bound menaquinone might serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane. Armed with these structural insights, we propose electron/proton-transfer pathways in the quinol reduction of fumarate to succinate in the D. gigas QFR.
The Plasmodium falciparum male gametocyte protein P230p, a paralog of P230, is vital for ookinete formation and mosquito transmission
Authors: Marin-Mogollon Catherin , van de Vegte-Bolmer Marga , van Gemert Geert-Jan , van Pul Fiona J. A. , Ramesar Jai , Othman Ahmad Syibli , Kroeze Hans , Miao Jun , Cui Liwang , Williamson Kim C. , Sauerwein Robert W. , Janse Chris J. , Khan Shahid M. 
Published: October 2018

AbstractTwo members of 6-cysteine (6-cys) protein family, P48/45 and P230, are important for gamete fertility in rodent and human malaria parasites and are leading transmission blocking vaccine antigens. Rodent and human parasites encode a paralog of P230, called P230p. While P230 is expressed in male and female parasites, P230p is expressed only in male gametocytes and gametes. In rodent malaria parasites this protein is dispensable throughout the complete life-cycle; however, its function in P. falciparum is unknown. Using CRISPR/Cas9 methodology we disrupted the gene encoding Pfp230p resulting in P. falciparum mutants (PfΔp230p) lacking P230p expression. The PfΔp230p mutants produced normal numbers of male and female gametocytes, which retained expression of P48/45 and P230. Upon activation male PfΔp230p gametocytes undergo exflagellation and form male gametes. However, male gametes are unable to attach to red blood cells resulting in the absence of characteristic exflagellation centres in vitro. In the absence of P230p, zygote formation as well as oocyst and sporozoite development were strongly reduced (>98%) in mosquitoes. These observations demonstrate that P230p, like P230 and P48/45, has a vital role in P. falciparum male fertility and zygote formation and warrants further investigation as a potential transmission blocking vaccine candidate.
Porphyromonas gingivalis bypasses epithelial barrier and modulates fibroblastic inflammatory response in an in vitro 3D spheroid model
Authors: Bugueno Isaac Maximiliano , Batool Fareeha , Keller Laetitia , Kuchler-Bopp Sabine , Benkirane-Jessel Nadia , Huck Olivier 
Published: October 2018

AbstractPorphyromonas gingivalis-induced inflammatory effects are mostly investigated in monolayer cultured cells. The aim of this study was to develop a 3D spheroid model of gingiva to take into account epithelio-fibroblastic interactions. Human gingival epithelial cells (ECs) and human oral fibroblasts (FBs) were cultured by hanging drop method to generate 3D microtissue (MT) whose structure was analyzed on histological sections and the cell-to-cell interactions were observed by scanning and transmission electron microscopy (SEM and TEM). MTs were infected by P. gingivalis and the impact on cell death (Apaf-1, caspase-3), inflammatory markers (TNF-α, IL-6, IL-8) and extracellular matrix components (Col-IV, E-cadherin, integrin β1) was evaluated by immunohistochemistry and RT-qPCR. Results were compared to those observed in situ in experimental periodontitis and in human gingival biopsies. MTs exhibited a well-defined spatial organization where ECs were organized in an external cellular multilayer, while, FBs constituted the core. The infection of MT demonstrated the ability of P. gingivalis to bypass the epithelial barrier in order to reach the fibroblastic core and induce disorganization of the spheroid structure. An increased cell death was observed in fibroblastic core. The development of such 3D model may be useful to define the role of EC–FB interactions on periodontal host-immune response and to assess the efficacy of new therapeutics.
Computational B-cell epitope identification and production of neutralizing murine antibodies against Atroxlysin-I
Authors: Kozlova Edgar Ernesto Gonzalez , Cerf Loïc , Schneider Francisco Santos , Viart Benjamin Thomas , NGuyen Christophe , Steiner Bethina Trevisol , de Almeida Lima Sabrina , Molina Franck , Duarte Clara Guerra , Felicori Liza , Chávez-Olórtegui Carlos , Machado-de-Ávila Ricardo Andrez 
Published: October 2018

AbstractEpitope identification is essential for developing effective antibodies that can detect and neutralize bioactive proteins. Computational prediction is a valuable and time-saving alternative for experimental identification. Current computational methods for epitope prediction are underused and undervalued due to their high false positive rate. In this work, we targeted common properties of linear B-cell epitopes identified in an individual protein class (metalloendopeptidases) and introduced an alternative method to reduce the false positive rate and increase accuracy, proposing to restrict predictive models to a single specific protein class. For this purpose, curated epitope sequences from metalloendopeptidases were transformed into frame-shifted Kmers (3 to 15 amino acid residues long). These Kmers were decomposed into a matrix of biochemical attributes and used to train a decision tree classifier. The resulting prediction model showed a lower false positive rate and greater area under the curve when compared to state-of-the-art methods. Our predictions were used for synthesizing peptides mimicking the predicted epitopes for immunization of mice. A predicted linear epitope that was previously undetected by an experimental immunoassay was able to induce neutralizing-antibody production in mice. Therefore, we present an improved prediction alternative and show that computationally identified epitopes can go undetected during experimental mapping.
Multiple intrasyntenic rearrangements and rapid speciation in voles
Authors: Romanenko Svetlana A. , Serdyukova Natalya A. , Perelman Polina L. , Trifonov Vladimir A. , Golenishchev Feodor N. , Bulatova Nina Sh. , Stanyon Roscoe , Graphodatsky Alexander S. 
Published: October 2018

AbstractRemarkably stable genomic chromosome elements (evolutionary conserved segments or syntenies) are the basis of large-scale chromosome architecture in vertebrate species. However, these syntenic elements harbour evolutionary important changes through intrachromosomal rearrangements such as inversions and centromere repositioning. Here, using FISH with a set of 20 region-specific probes on a wide array of 28 species, we analyzed evolution of three conserved syntenic regions of the Arvicolinae ancestral karyotype. Inside these syntenies we uncovered multiple, previously cryptic intrachromosomal rearrangements. Although in each of the three conserved blocks we found inversions and centromere repositions, the blocks experienced different types of rearrangements. In two syntenies centromere repositioning predominated, while in the third region, paracentric inversions were more frequent, whereas pericentric inversions were not detected. We found that some of the intrachromosomal rearrangements, mainly paracentric inversions, were synapomorphic for whole arvicoline genera or tribes: genera Alexandromys and Microtus, tribes Ellobini and Myodini. We hypothesize that intrachromosomal rearrangements within conserved syntenic blocks are a major evolutionary force modulating genome architecture in species-rich and rapidly-evolving rodent taxa. Inversions and centromere repositioning may impact speciation and provide a potential link between genome evolution, speciation, and biogeography.
Melatonin inhibits attention-deficit/hyperactivity disorder caused by atopic dermatitis-induced psychological stress in an NC/Nga atopic-like mouse model
Authors: Park Gunhyuk , Jung Young-Suk , Park Moon-Ki , Yang Chae Ha , Kim Yong-ung 
Published: October 2018

AbstractAtopic dermatitis (AD) is a chronic inflammatory skin disease with the hallmark characteristics of pruritus, psychological stress, and sleep disturbance, all possibly associated with an increased risk of attention-deficit/hyperactivity disorder (ADHD). However, the etiology of the possible association between AD and ADHD is still not well understood. 2,4-dinitrochlorobenzene or corticosterone was used to evaluate the atopic symptom and its psychologic stress in the atopic mice model. Melatonin, corticotropin-releasing hormone, corticotropin-releasing hormone receptor, urocortin, proopiomelanocortin, adrenocorticotropic hormone, corticosterone, cAMP, cAMP response element-binding protein, dopamine and noradrenaline were analyzed spectrophotometrically, and the expression of dopamine beta-hydroxylase and tyrosine hydroxylase were measured by Western blotting or immunohistochemistry. AD-related psychological stress caused an increase in the levels of dopamine beta-hydroxylase and tyrosine hydroxylase, degradation of melatonin, hyper-activity of the hypothalamic-pituitary-adrenal axis, and dysregulation of dopamine and noradrenaline levels (ADHD phenomena) in the locus coeruleus, prefrontal cortex, and striatum of the AD mouse brain. Notably, melatonin administration inhibited the development of ADHD phenomena and their-related response in the mouse model. This study demonstrated that AD-related psychological stress increased catecholamine dysfunction and accelerated the development of psychiatric comorbidities, such as ADHD.
The influence of container geometry and thermal conductivity on evaporation of water at low pressures
Authors: Kazemi Mohammad Amin , Elliott Janet A. W. , Nobes David S. 
Published: October 2018

AbstractEvaporation is a ubiquitous phenomenon that occurs ceaselessly in nature to maintain life on earth. Given its importance in many scientific and industrial fields, extensive experimental and theoretical studies have explored evaporation phenomena. The physics of the bulk fluid is generally well understood. However, the near-interface region has many unknowns, including the presence and characteristics of the thin surface-tension-driven interface flow, and the role and relative importance of thermodynamics, fluid mechanics and heat transfer in evaporation at the surface. Herein, we report a theoretical study on water evaporation at reduced pressures from four different geometries using a validated numerical model. This study reveals the profound role of heat transfer, not previously recognized. It also provides new insight into when a thermocapillary flow develops during water evaporation, and how the themocapillary flow interacts with the buoyancy flow. This results in a clearer picture for researchers undertaking fundamental studies on evaporation and developing new applications.
Hyaluronic acid-CD44 interactions promote BMP4/7-dependent Id1/3 expression in melanoma cells
Authors: Wu Ruo-Lin , Sedlmeier Georg , Kyjacova Lenka , Schmaus Anja , Philipp Julia , Thiele Wilko , Garvalov Boyan K. , Sleeman Jonathan P. 
Published: October 2018

AbstractBMP4/7-dependent expression of inhibitor of differentiation/DNA binding (Id) proteins 1 and 3 has been implicated in tumor progression and poor prognosis of malignant melanoma patients. Hyaluronic acid (HA), a pericellular matrix component, supports BMP7 signalling in murine chondrocytes through its receptor CD44. However, its role in regulating BMP signalling in melanoma is not clear. In this study we found that depletion of endogenously-produced HA by hyaluronidase treatment or by inhibition of HA synthesis by 4-methylumbelliferone (4-MU) resulted in reduced BMP4/7-dependent Id1/3 protein expression in mouse melanoma B16-F10 and Ret cells. Conversely, exogenous HA treatment increased BMP4/7-dependent Id1/3 protein expression. Knockdown of CD44 reduced BMP4/7-dependent Id1/3 protein expression, and attenuated the ability of exogenous HA to stimulate Id1 and Id3 expression in response to BMP. Co-IP experiments demonstrated that CD44 can physically associate with the BMP type II receptor (BMPR) ACVR2B. Importantly, we found that coordinate expression of Id1 or Id3 with HA synthases HAS2, HAS3, and CD44 is associated with reduced overall survival of cutaneous melanoma patients. Our results suggest that HA-CD44 interactions with BMPR promote BMP4/7-dependent Id1/3 protein expression in melanoma, contributing to reduced survival in melanoma patients.
Evaluation of ENSO simulations in CMIP5 models: A new perspective based on percolation phase transition in complex networks
Authors: Lu Zhenghui , Fu Zuntao , Hua Lijuan , Yuan Naiming , Chen Lin 
Published: October 2018

AbstractIn this study, the performance of CMIP5 models in simulating the El Niño-Southern Oscillation (ENSO) is evaluated by using a new metric based on percolation theory. The surface air temperatures (SATs) over the tropical Pacific Ocean are constructed as a SAT network, and the nodes within the network are linked if they are highly connected (e.g., high correlations). It has been confirmed from reanalysis datasets that the SAT network undergoes an abrupt percolation phase transition when the influences of the sea surface temperature anomalies (SSTAs) below are strong enough. However, from simulations of the CMIP5 models, most models are found incapable of capturing the observed phase transition at a proper critical point Pc. For the 15 considered models, four even miss the phase transition, indicating that the simulated SAT network is too stable to be significantly changed by the SSTA below. Only four models can be considered cautiously with some skills in simulating the observed phase transition of the SAT network. By comparing the simulated SSTA patterns with the node vulnerabilities, which is the chance of each node being isolated during a ENSO event, we find that the improperly simulated sea-air interactions are responsible for the missing of the observed percolation phase transition. Accordingly, a careful study of the sea-air couplers, as well as the atmospheric components of the CMIP5 models is suggested. Since the percolation phase transition of the SAT network is a useful phenomenon to indicate whether the ENSO impacts can be transferred remotely, it deserves more attention for future model development.
Temperature affects the biology of Schmidtea mediterranea
Authors: Hammoudi Nassim , Torre Cédric , Ghigo Eric , Drancourt Michel 
Published: October 2018

AbstractStudies of tissue regeneration and host-pathogen interactions using the model planarian Schmidtea mediterranea have been performed at an experimental temperature of 19 °C. S. mediterranea planarians exposed to 19 °C–32 °C were observed for survival, mobility, feeding and regeneration for three months and elimination of the Staphylococcus aureus pathogen over six days. S. mediterranea planarians died at 30 °C–32 °C after 18 days of observation but tolerated temperatures of 19 °C up to 28 °C with non-significant differences in mobility and feeding behavior. Genetic malleability tested by RNAi feeding was still efficient at 26 °C and 28 °C. Concerning the immune capacity of planarians, we reported an exacerbation of the immune response in worms infected by S. aureus at 26 °C and 28 °C. These observations suggest a temperature modulation of planarian stem cells and illustrate the importance of modulating experimental temperature when using planarians as model organisms to study regeneration and immune response.
Adaptive effect of sericin on hepatic mitochondrial conformation through its regulation of apoptosis, autophagy and energy maintenance: a proteomics approach
Authors: Ampawong Sumate , Isarangkul Duangnate , Reamtong Onrapak , Aramwit Pornanong 
Published: October 2018

AbstractWe recently demonstrated that in addition to its protective effect on pancreatic and adrenal biosynthesis, antioxidant properties of sericin decrease blood cholesterol levels and improve the liver mitochondrial architecture. However, little is known about the detailed mechanisms underlying these effects. Using proteomics and electron microscopy, we identified mitochondrial proteins that play important roles in the preservation of the mitochondrial ultrastructure and cholesterol-lowering properties of sericin. Our results showed that sericin maintains the mitochondrial architecture during conditions of high blood cholesterol by regulating apoptotic (NADH-ubiquinone oxidoreductase 75 kDa subunit) and autophagic (mitochondrial elongation factor Tu and prohibitin-2) proteins as well as energy maintenance proteins [haloacid dehalogenase-like hydrolase domain-containing protein 3, succinate dehydrogenase (ubiquinone) flavoprotein subunit, ATP synthase-α subunit precursor, enoyl-CoA hydratase domain-containing protein 3 and electron transfer flavoprotein subunit-α]. Sericin also exerts anti-oxidative properties via aconitate hydratase and Chain A, crystal structure of rat carnitine palmitoyltrasferase 2 proteins. Together, these activities may reduce hepatocytic triglyceride deposition, thereby decreasing steatosis, as demonstrated by the modulatory effects on ornithine aminotransferase, mitochondrial aspartate aminotransferase, acyl-CoA synthase, hydroxyacyl-CoA dehydrogenase and D-beta-hydroxybutyrate dehydrogenase. Sericin activity further balanced nitrogenous waste detoxification, characterised by carbamoyl-phosphate synthase (ammonia), aldehyde dehydrogenase and uricase, or folate biosynthesis via sarcosine dehydrogenase and dimethyl glycine dehydrogenase. These results suggest that sericin maintains the hepatic mitochondrial architecture through apoptotic, autophagic, energy maintenance and anti-oxidative mitochondrial proteins for alleviating hepatic steatosis and promoting liver function under conditions of hypercholesterolaemia.
Sulphide Re-Os geochronology links orogenesis, salt and Cu-Co ores in the Central African Copperbelt
Authors: Saintilan N. J. , Selby D. , Creaser R. A. , Dewaele S. 
Published: October 2018

AbstractThe origin of giant, sedimentary rock-hosted copper-cobalt (Cu-Co) provinces remains contentious, in part due to the lack of precise and reliable ages for mineralisation. As such, no consensus has been reached on the genetic model for ore formation, and the relationships between tectonism, palaeo-fluid circulation and mineralisation. Here, we link the timing of Cu-Co mineralisation in the Central African Copperbelt to compressional tectonics during the Lufilian Orogeny by using new ca. 609–473 Ma ages given by rhenium-osmium (Re-Os) isotope data for individual Cu-Co sulphides (carrolite and bornite) from the Cu-Co Kamoto deposit. The initial Os isotope composition of carrolite is compatible with the leaching of Os and Cu(-Co) from Mesoproterozoic Cu sulphide deposits hosted in fertile basement. In contrast, the ca. 473 Ma Cu-Au mineralisation stage, which is coeval with late- to post-compressional deformation, may be a distal expression of fluid flow and heat transfer caused by magmatic intrusions in the core of the collisional orogen. The Re-Os ages support a model for mineralisation driven by evaporite dissolution and percolation of large volumes of dense brines in the Katangan Basin during the Lufilian Orogeny.