bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome analysis and genetic transformation of a water surface-floating microalga Chlorococcum sp. FFG039
Authors: Maeda Yoshiaki , Nojima Daisuke , Sakurai Miki , Nomaguchi Tatsuhiro , Ichikawa Momoko , Ishizuka Yuki , Tanaka Tsuyoshi 
Published: August 2019

AbstractMicroalgal harvesting and dewatering are the main bottlenecks that need to be overcome to tap the potential of microalgae for production of valuable compounds. Water surface-floating microalgae form robust biofilms, float on the water surface along with gas bubbles entrapped under the biofilms, and have great potential to overcome these bottlenecks. However, little is known about the molecular mechanisms involved in the water surface-floating phenotype. In the present study, we analysed the genome sequence of a water surface-floating microalga Chlorococcum sp. FFG039, with a next generation sequencing technique to elucidate the underlying mechanisms. Comparative genomics study with Chlorococcum sp. FFG039 and other non-floating green microalgae revealed some of the unique gene families belonging to this floating microalga, which may be involved in biofilm formation. Furthermore, genetic transformation of this microalga was achieved with an electroporation method. The genome information and transformation techniques presented in this study will be useful to obtain molecular insights into the water surface-floating phenotype of Chlorococcum sp. FFG039.
Push-pull driving of the Central America Forearc in the context of the Cocos-Caribbean-North America triple junction
Authors: Álvarez-Gómez José A. , Staller Vázquez Alejandra , Martínez-Díaz José J. , Canora Carolina , Alonso-Henar Jorge , Insua-Arévalo Juan M. , Béjar-Pizarro Marta 
Published: August 2019

AbstractDifferent kinematic models have been proposed for the triple junction between the North American, Cocos and Caribbean plates. The two most commonly accepted hypotheses on its driving mechanism are (a) the North American drag of the forearc and (b) the Cocos Ridge subduction push. We present an updated GPS velocity field which is analyzed together with earthquake focal mechanisms and regional relief. The two hypotheses have been used to make kinematic predictions that are tested against the available data. An obliquity analysis is also presented to discuss the potential role of slip partitioning as driving mechanism. The North American drag model presents a better fit to the observations, although the Cocos Ridge push model explains the data in Costa Rica and Southern Nicaragua. Both mechanisms must be active, being the driving of the Central American forearc towards the NW analogous to a push-pull train. The forearc sliver moves towards the west-northwest at a rate of 12–14 mm/yr, being pinned to the North American plate in Chiapas and western Guatemala, where the strike-slip motion on the volcanic arc must be very small.
Serum enterolactone concentrations are low in colon but not in rectal cancer patients
Authors: Tuomisto Anne , Nørskov Natalja P. , Sirniö Päivi , Väyrynen Juha P. , Mutt Shivaprakash J. , Klintrup Kai , Mäkelä Jyrki , Bach Knudsen Knud Erik , Mäkinen Markus J. , Herzig Karl-Heinz 
Published: August 2019

AbstractThe dietary lignan metabolite, enterolactone, has been suggested to have anti-cancer functions, and high serum enterolactone concentrations have been associated with decreased risk of breast and prostate cancers. We hypothesized that serum enterolactone concentrations as a marker of plant-based foods are associated with decreased risk in colorectal cancer (CRC). We measured serum enterolactone glucuronide and sulfate concentrations by liquid chromatography-tandem mass spectrometry in 115 CRC patients and 76 sex- and age-matched controls and analyzed the results with respect to tumor parameters, clinical parameters, and systemic inflammatory markers. Patients with colon cancer had significant lower serum enterolactone glucuronide and sulfate concentrations than controls (glucuronide: median 3.14 nM vs. 6.32 nM, P < 0.001; sulfate: median 0.13 nM vs. 0.17 nM, P = 0.002), whereas rectal cancer patients had similar enterolactone levels as controls (glucuronide: median 5.39 nM vs. 6.32 nM, P = 0.357; sulfate: median 0.19 nM vs. 0.17 nM, P = 0.452). High serum enterolactone concentrations were associated with low tumor grade, high serum creatinine levels, and concomitant diabetes. In summary, our results suggest that serum enterolactone concentrations are decreased in colon but not in rectal cancer. Further investigations are required to assess whether this reflects an altered lignan metabolism by the colon microbiome.
Association between mild anemia and physical fitness in a military male cohort: The CHIEF study
Authors: Tsai Kun-Zhe , Lai Shiue-Wei , Hsieh Chia-Jung , Lin Chin-Sheng , Lin Yen-Po , Tsai Sung-Chiao , Chung Pei-Shou , Lin Yu-Kai , Lin Tzu-Chiao , Ho Ching-Liang , Han Chih-Lu , Kwon Younghoon , Hsieh Chung-Bao , Lin Gen-Min 
Published: August 2019

AbstractAnemia defined as reduced hemoglobin levels of red blood cells may carry less oxygen to skeletal muscle and impair physical performance. Previous studies have shown that exercise intolerance was related to moderate or severe anemia, however, the relationship to mild anemia was unknown. We investigated the cross-sectional association of mild anemia defined as a hemoglobin level of 10.0–13.9 g/dL with physical fitness in 3,666 military young males in Taiwan in 2014. Aerobic fitness was evaluated by 3000-meter run test, and anaerobic fitness was evaluated by 2-minute sit-ups and 2-minute push-ups, respectively. Multiple logistic regressions for the best 10% and the worst 10% performers were used to determine the relationship. There were 343 mild anemic males in whom 47.8% were microcytic anemia and 3,323 non-anemic males for the analysis. The multiple logistic regression shows that as compared with non-anemic males, mild anemic males were more likely to be the worst 10% performers in the 3000-meter run test (odds ratios (OR) and 95% confidence intervals: 1.47, 1.01–2.14) after adjusting for age, service specialty, body mass index, waist size, mean blood pressure, unhealthy behaviors, lipid profiles, and exercise frequency. On the contrary, mild anemic males had higher possibility to be the best 10% performers in the 2-minute push-ups test (OR: 1.48, 1.08–2.04). However, there was no association between mild anemia and 2-minute sit-ups. Our findings suggest that unspecified mild anemia might be associated with lower cardiorespiratory fitness but not with anaerobic fitness in physically active military males.
Gene-edited murine cell lines for propagation of chronic wasting disease prions
Authors: Walia Rupali , Ho Cheng Ching , Lee Chi , Gilch Sabine , Schatzl Hermann M. 
Published: August 2019

AbstractPrions cause fatal infectious neurodegenerative diseases in humans and animals. Cell culture models are essential for studying the molecular biology of prion propagation. Defining such culture models is mostly a random process, includes extensive subcloning, and for many prion diseases few or no models exist. One example is chronic wasting disease (CWD), a highly contagious prion disease of cervids. To extend the range of cell models propagating CWD prions, we gene-edited mouse cell lines known to efficiently propagate murine prions. Endogenous prion protein (PrP) was ablated in CAD5 and MEF cells, using CRISPR-Cas9 editing. PrP knock-out cells were reconstituted with mouse, bank vole and cervid PrP genes by lentiviral transduction. Reconstituted cells expressing mouse PrP provided proof-of-concept for re-established prion infection. Bank voles are considered universal receptors for prions from a variety of species. Bank vole PrP reconstituted cells propagated mouse prions and cervid prions, even without subcloning for highly susceptible cells. Cells reconstituted with cervid PrP and infected with CWD prions tested positive in prion conversion assay, whereas non-reconstituted cells were negative. This novel cell culture platform which is easily adjustable and allows testing of polymorphic alleles will provide important new insights into the biology of CWD prions.
Grazing enhances species diversity in grassland communities
Authors: Pulungan Muhammad Almaududi , Suzuki Shota , Gavina Maica Krizna Areja , Tubay Jerrold M. , Ito Hiromu , Nii Momoka , Ichinose Genki , Okabe Takuya , Ishida Atsushi , Shiyomi Masae , Togashi Tatsuya , Yoshimura Jin , Morita Satoru 
Published: August 2019

AbstractIn grassland studies, an intermediate level of grazing often results in the highest species diversity. Although a few hypotheses have been proposed to explain this unimodal response of species diversity to grazing intensity, no convincing explanation has been provided. Here, we build a lattice model of a grassland community comprising multiple species with various levels of grazing. We analyze the relationship between grazing and plant diversity in grasslands under variable intensities of grazing pressure. The highest species diversity is observed at an intermediate grazing intensity. Grazers suppress domination by the most superior species in birth rate, resulting in the coexistence of inferior species. This unimodal grazing effect disappears with the introduction of a small amount of nongrazing natural mortality. Unimodal patterns of species diversity may be limited to the case where grazers are the principal source of natural mortality.
Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain
Authors: Knapik Kamila , Becerra Manuel , González-Siso María-Isabel 
Published: August 2019

AbstractHere, we describe the metagenome composition of a microbial community in a hot spring sediment as well as a sequence-based and function-based screening of the metagenome for identification of novel xylanases. The sediment was collected from the Lobios Hot Spring located in the province of Ourense (Spain). Environmental DNA was extracted and sequenced using Illumina technology, and a total of 3.6 Gbp of clean paired reads was produced. A taxonomic classification that was obtained by comparison to the NCBI protein nr database revealed a dominance of Bacteria (93%), followed by Archaea (6%). The most abundant bacterial phylum was Acidobacteria (25%), while Thaumarchaeota (5%) was the main archaeal phylum. Reads were assembled into contigs. Open reading frames (ORFs) predicted on these contigs were searched by BLAST against the CAZy database to retrieve xylanase encoding ORFs. A metagenomic fosmid library of approximately 150,000 clones was constructed to identify functional genes encoding thermostable xylanase enzymes. Function-based screening revealed a novel xylanase-encoding gene (XynA3), which was successfully expressed in E. coli BL21. The resulting protein (41 kDa), a member of glycoside hydrolase family 11 was purified and biochemically characterized. The highest activity was measured at 80 °C and pH 6.5. The protein was extremely thermostable and showed 94% remaining activity after incubation at 60 °C for 24 h and over 70% remaining activity after incubation at 70 °C for 24 h. Xylanolytic activity of the XynA3 enzyme was stimulated in the presence of β-mercaptoethanol, dithiothreitol and Fe3+ ions. HPLC analysis showed that XynA3 hydrolyzes xylan forming xylobiose with lower proportion of xylotriose and xylose. Specific activity of the enzyme was 9080 U/mg for oat arabinoxylan and 5080 U/mg for beechwood xylan, respectively, without cellulase activity.
A new transgenic reporter line reveals Wnt-dependent Snai2 re-expression and cranial neural crest differentiation in Xenopus
Authors: Li Jiejing , Perfetto Mark , Materna Christopher , Li Rebecca , Thi Tran Hong , Vleminckx Kris , Duncan Melinda K. , Wei Shuo 
Published: August 2019

AbstractDuring vertebrate embryogenesis, the cranial neural crest (CNC) forms at the neural plate border and subsequently migrates and differentiates into many types of cells. The transcription factor Snai2, which is induced by canonical Wnt signaling to be expressed in the early CNC, is pivotal for CNC induction and migration in Xenopus. However, snai2 expression is silenced during CNC migration, and its roles at later developmental stages remain unclear. We generated a transgenic X. tropicalis line that expresses enhanced green fluorescent protein (eGFP) driven by the snai2 promoter/enhancer, and observed eGFP expression not only in the pre-migratory and migrating CNC, but also the differentiating CNC. This transgenic line can be used directly to detect deficiencies in CNC development at various stages, including subtle perturbation of CNC differentiation. In situ hybridization and immunohistochemistry confirm that Snai2 is re-expressed in the differentiating CNC. Using a separate transgenic Wnt reporter line, we show that canonical Wnt signaling is also active in the differentiating CNC. Blocking Wnt signaling shortly after CNC migration causes reduced snai2 expression and impaired differentiation of CNC-derived head cartilage structures. These results suggest that Wnt signaling is required for snai2 re-expression and CNC differentiation.
Dual Quantum Zeno Superdense Coding
Authors: Zaman Fakhar , Jeong Youngmin , Shin Hyundong 
Published: August 2019

AbstractQuantum superdense coding enables a sender to encode a two-bit classical message in one qubit using the preshared entanglement. In this paper, we develop a superdense coding protocol using a dual quantum Zeno (DQZ) gate to take the full advantage of quantum superdense coding from the complete Bell-state analysis. We verify that the DQZ gate allows remote parties to achieve the distinguishability of orthonormal Bell states in a semi-counterfactual manner and the DQZ superdense coding achieves high throughput efficiency as a function of cycle numbers for the Bell-state analyzer.
Structural basis for the inhibitory effects of a novel reversible covalent ligand on PPARγ phosphorylation
Authors: Jang Jun Young , Kim Hyunsoo , Kim Hyun-Jung , Suh Se Won , Park Seung Bum , Han Byung Woo 
Published: August 2019

AbstractPeroxisome proliferator-activated receptor γ (PPARγ) is a major therapeutic target for the treatment of type 2 diabetes. However, the use of PPARγ-targeted drugs, such as rosiglitazone and pioglitazone, is limited owing to serious side effects caused by classical agonism. Using a rational drug discovery approach, we recently developed SB1495, a novel reversible covalent inhibitor of the cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation of PPARγ at Ser245, a key factor in the insulin-sensitizing effect of PPARγ-targeted drugs. In this study, we report the crystal structures of PPARγ in complex with SB1495 and its enantiomeric analogue SB1494, which rarely exhibits inhibitory activity, to visualize the mechanistic basis for their distinct activities. SB1495 occupies the Arm3 region near the Ω loop of the PPARγ ligand-binding domain, whereas its enantiomeric analogue SB1494 binds to the Arm2 region. In addition, the piperazine moiety of SB1495 directly pushes the helix H2′, resulting in the stabilization of the Ω loop just behind the helix H2′. Our results may contribute to the development of a new generation of antidiabetic drugs that selectively block PPARγ phosphorylation without classical agonism.
Regioisomer-independent quantification of fatty acid oxidation products by HPLC-ESI-MS/MS analysis of sodium adducts
Authors: Ahern Katelyn W. , Serbulea Vlad , Wingrove Catherine L. , Palas Zachary T. , Leitinger Norbert , Harris Thurl E. 
Published: August 2019

AbstractDespite growing acknowledgement of the role of oxidized fatty acids (oxFA) as cellular signaling molecules and in the pathogenesis of disease, developing methods to measure these species in biological samples has proven challenging. Here we describe a novel method utilizing HPLC-ESI-MS/MS to identify and quantify multiple full-length oxFA species in a regioisomer-independent manner without the need for time-consuming sample preparation or derivatization. Building on recent progress in the characterization of FA and their oxidation products by MS/MS, we employed positive-ion ionization by measuring sodium adducts in conjunction with Differential Energy Qualifier Ion Monitoring to unequivocally verify the presence of the hydroperoxide, hydroxide, and ketone oxidation products of linoleic and arachidonic acid. Our HPLC method achieved separation of these oxidized species from their unoxidized counterparts while maintaining regioisomer-independent elution, allowing quantification over a 5 log10 range with a lower limit of quantification of 0.1 picomoles. With a simple sample preparation and a runtime as low as 11 minutes, our method allows the rapid and facile detection and measurement of full-length oxFA in biological samples. We believe this approach will allow for new insight and further investigation into the role of oxFA in metabolic disease.
Experimental demonstration of single-shot quantum and classical signal transmission on single wavelength optical pulse
Authors: Kumar Rupesh , Wonfor Adrian , Penty Richard , Spiller Tim , White Ian 
Published: August 2019

AbstractAdvances in highly sensitive detection techniques for classical coherent communication systems have reduced the received signal power requirements to a few photons per bit. At this level one can take advantage of the quantum noise to create secure communication, using continuous variable quantum key distribution (CV-QKD). In this work therefore we embed CV-QKD signals within classical signals and transmit classical data and secure keys simultaneously over 25 km of optical fibre. This is achieved by using a novel coherent displacement state generator, which has the potential for being used in a wide range of quantum optical experiments. This approach removes the need for separate channels for quantum communication systems and allows reduced system bandwidth for a given communications specification. This demonstration therefore demonstrates a way of implementing direct quantum physical layer security within a conventional classical communications system, offering a major advance in term of practical and low cost implementation.
Effect of low sperm quality on progeny: a study on zebrafish as model species
Authors: Riesco Marta F. , Valcarce David G. , Martínez-Vázquez Juan Manuel , Robles Vanesa 
Published: August 2019

AbstractNowadays a decrease tendency in human sperm quality has been reported mainly in developed countries. Reproductive technologies have been very valuable in achieving successful pregnancies with low quality sperm samples. However, considering that spermatozoa molecular contribution is increasingly important in recent studies, it is crucial to study whether fertilization with low sperm quality could leave a molecular mark on progeny. This study explores the consequences that fertilization with low sperm quality may have on progeny, using zebrafish as a model. Good and bad breeders were established attending to sperm quality analyses and were individually tracked. Significant differences in fertilization and malformation rates were obtained in progenies between high and low quality sperm samples. Moreover an altered miR profile was found in the progenies of bad zebrafish breeders (upregulation of miR-141 and miR -122 in 24 hpf embryos) and as a consequence, some of their targets involved in male sex development such asdmrt1, suffered downregulation. Our results indicate that fertilizing with high sperm quality samples becomes relevant from a new perspective: to avoid molecular alterations in the progeny that could remain masked and therefore produce unexpected consequences in it.
Root hairs enhance Arabidopsis seedling survival upon soil disruption
Authors: Choi Hee-Seung , Cho Hyung-Taeg 
Published: August 2019

AbstractRoot hairs form a substantial portion of the root surface area. Compared with their nutritional function, the physical function of root hairs has been poorly characterised. This study investigates the physical role of root hairs of Arabidopsis thaliana seedlings in interaction of the root with water and soil and in plant survival upon soil disruption. Five transgenic lines with different root hair lengths were used to assess the physical function of root hairs. Upon soil disruption by water falling from a height (mimicking rainfall), long-haired lines showed much higher anchorage rates than short-haired lines. The root-pulling test revealed that a greater amount of soil adhered to long-haired roots than to short-haired roots. When seedlings were pulled out and laid on the soil surface for 15 d, survival rates of long-haired seedlings were higher than those of short-haired seedlings. Moreover, the water holding capacity of roots was much greater among long-haired seedlings than short-haired seedlings. These results suggest that root hairs play a significant role in plant survival upon soil disruption which could be fatal for young seedlings growing on thin soil surface with a short primary root and root hairs as the only soil anchoring system.
The millimeter-wave spectrum and astronomical search of succinonitrile and its vibrational excited states
Authors: Cabezas C. , Bermúdez C. , Gallego J. D. , Tercero B. , Hernández J. M. , Tanarro I. , Herrero V. J. , Doménech J. L. , Cernicharo J. 
Published: August 2019

Context. Dinitriles with a saturated hydrocarbon skeleton and a −C≡N group at each end can have large electric dipole moments. Their formation can be related to highly reactive radicals such as CH2CN, C2N, or CN. Thus, these saturated dinitriles are potential candidates to be observed in the interstellar medium (ISM).
Aims. Our goal is the investigation of the rotational spectrum of one of the simplest dinitriles N≡C−CH2−CH2−C≡N, succinonitrile, whose actual rotational parameters are not precise enough to allow its detection in the ISM. In addition, the rotational spectra for its vibrational excited states will be analysed.
Methods. The rotational spectra of succinonitrile was measured in the frequency range 72−116.5 GHz using a new broadband millimeter-wave spectrometer based on radio astronomy receivers with Fast Fourier Transform backends. The identification of the vibrational excited states of succinonitrile was supported by high-level ab initio calculations on the harmonic and anharmonic force fields.
Results. A total of 459 rotational transitions with maximum values of J and Ka quantum numbers 70 and 14, respectively, were measured for the ground vibrational state of succinonitrile. The analysis allowed us to accurately determine the rotational, quartic, and sextic centrifugal distortion constants. Up to eleven vibrational excited states, resulting from the four lowest frequency vibrational modes ν13, ν12, ν24, and ν23 were identified. In addition to the four fundamental modes, we observed overtones together with some combination states. The rotational parameters for the ground state were employed to unsuccessfully search for succinonitrile in the cold and warm molecular clouds Orion KL, Sgr B2(N), B1-b, and TMC-1, using the spectral surveys captured by IRAM 30 m at 3 mm and the Yebes 40 m at 1.3 cm and 7 mm.