Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis)

Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.published_or_final_versio

Dissociate lattice oxygen redox reactions from capacity and voltage drops of battery electrodes.

The oxygen redox (OR) activity is conventionally considered detrimental to the stability and kinetics of batteries. However, OR reactions are often confused by irreversible oxygen oxidation. Here, based on high-efficiency mapping of resonant inelastic x-ray scattering of both the transition metal and oxygen, we distinguish the lattice OR in Na0.6[Li0.2Mn0.8]O2 and compare it with Na2/3[Mg1/3Mn2/3]O2. Both systems display strong lattice OR activities but with distinct electrochemical stability. The comparison shows that the substantial capacity drop in Na0.6[Li0.2Mn0.8]O2 stems from non-lattice oxygen oxidations, and its voltage decay from an increasing Mn redox contribution upon cycling, contrasting those in Na2/3[Mg1/3Mn2/3]O2. We conclude that lattice OR is not the ringleader of the stability issue. Instead, irreversible oxygen oxidation and the changing cationic reactions lead to the capacity and voltage fade. We argue that lattice OR and other oxygen activities should/could be studied and treated separately to achieve viable OR-based electrodes

Skyrmion fluctuations at a first-order phase transition boundary

Magnetic skyrmions are topologically protected spin textures with promising prospects for applications in data storage. They can form a lattice state due to competing magnetic interactions and are commonly found in a small region of the temperature - magnetic field phase diagram. Recent work has demonstrated that these magnetic quasi-particles fluctuate at the μeV energy scale. Here, we use a coherent x-ray correlation method at an x-ray free-electron laser to investigate these fluctuations in a magnetic phase coexistence region near a first-order transition boundary where fluctuations are not expected to play a major role. Surprisingly, we find that the relaxation of the intermediate scattering function at this transition differs significantly compared to that deep in the skyrmion lattice phase. The observation of a compressed exponential behavior suggests solid-like dynamics, often associated with jamming. We assign this behavior to disorder and the phase coexistence observed in a narrow field-window near the transition, which can cause fluctuations that lead to glassy behavior

A Special Homotopy Continuation Method For A Class of Polynomial Systems

A special homotopy continuation method, as a combination of the polyhedral homotopy and the linear product homotopy, is proposed for computing all the isolated solutions to a special class of polynomial systems. The root number bound of this method is between the total degree bound and the mixed volume bound and can be easily computed. The new algorithm has been implemented as a program called LPH using C++. Our experiments show its efficiency compared to the polyhedral or other homotopies on such systems. As an application, the algorithm can be used to find witness points on each connected component of a real variety

Composition of gut microbiota in infants in China and global comparison

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Access to recreational physical activities by car and bus : an assessment of socio-spatial inequalities in mainland Scotland

Obesity and other chronic conditions linked with low levels of physical activity (PA) are associated with deprivation. One reason for this could be that it is more difficult for low-income groups to access recreational PA facilities such as swimming pools and sports centres than high-income groups. In this paper, we explore the distribution of access to PA facilities by car and bus across mainland Scotland by income deprivation at datazone level. GIS car and bus networks were created to determine the number of PA facilities accessible within travel times of 10, 20 and 30 minutes. Multilevel negative binomial regression models were then used to investigate the distribution of the number of accessible facilities, adjusting for datazone population size and local authority. Access to PA facilities by car was significantly (p<0.01) higher for the most affluent quintile of area-based income deprivation than for most other quintiles in small towns and all other quintiles in rural areas. Accessibility by bus was significantly lower for the most affluent quintile than for other quintiles in urban areas and small towns, but not in rural areas. Overall, we found that the most disadvantaged groups were those without access to a car and living in the most affluent areas or in rural areas

Nitric oxide blocks the development of the human parasite Schistosoma japonicum

Human schistosomiasis, caused by Schistosoma species, is a major public health problem affecting more than 700 million people in 78 countries, with over 40 mammalian host reservoir species complicating the transmission ecosystem. The primary cause of morbidity is considered to be granulomas induced by fertilized eggs of schistosomes in the liver and intestines. Some host species, like rats (Rattus norvegicus), are naturally intolerant to Schistosoma japonicum infection, and do not produce granulomas or pose a threat to transmission, while others, like mice and hamsters, are highly susceptible. The reasons behind these differences are still a mystery. Using inducible nitric oxide synthase knockout (iNOS−/−) Sprague–Dawley rats, we found that inherent high expression levels of iNOS in wild-type (WT) rats play an important role in blocking growth, reproductive organ formation, and egg development in S. japonicum, resulting in production of nonfertilized eggs. Granuloma formation, induced by fertilized eggs in the liver, was considerably exacerbated in the iNOS−/− rats compared with the WT rats. This inhibition by nitric oxide acts by affecting mitochondrial respiration and energy production in the parasite. Our work not only elucidates the innate mechanism that blocks the development and production of fertilized eggs in S. japonicum but also offers insights into a better understanding of host–parasite interactions and drug development strategies against schistosomiasis

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis

Understanding improved capacity retention at 4.3 V in modified single crystal Ni-rich NMC//graphite pouch cells at elevated temperature

The capacity retention of commercially-sourced pouch cells with single crystal Al surface-doped Ni-rich cathodes (LiNi0.834Mn0.095Co0.071O2) is examined. The degradation-induced capacity fade becomes more pronounced as the upper-cut-off voltage (UCV) increases from 4.2 V to 4.3 V (vs. graphite) at a fixed cycling temperature (either 25 or 40 °C). However, cycles with 4.3 V UCV (slightly below the oxygen loss onset) show better capacity retention upon increasing the cycling temperature from 25 °C to 40 °C. Namely, after 500 cycles at 4.3 V UCV, cycling temperature at 40 °C retains 85.5% of the initial capacity while cycling at 25 °C shows 75.0% capacity retention. By employing a suite of electrochemical, X-ray spectroscopy and secondary ion mass spectrometry techniques, we attribute the temperature-induced improvement of the capacity retention at high UCV to the combined effects of Al surface-dopants, electrochemically resilient single crystal Ni-rich particles, and thermally-improved Li kinetics translating into better electrochemical performance. If cycling remains below the lattice oxygen loss onset, improved capacity retention in industrial cells should be achieved in single crystal Ni-rich cathodes with the appropriate choice of cycling parameter, particle quality, and particle surface dopants

Transgenic plants of Petunia hybrida harboring the CYP2E1 gene efficiently remove benzene and toluene pollutants and improve resistance to formaldehyde

The CYP2E1 protein belongs to the P450 enzymes family and plays an important role in the metabolism of small molecular and organic pollutants. In this study we generated CYP2E1 transgenic plants of Petunia using Agrobacterium rhizogenes K599. PCR analysis confirmed that the regenerated plants contained the CYP2E1 transgene and the rolB gene of the Ri plasmid. Southern blotting revealed the presence of multiple copies of CYP2E1 in the genome of transgenic plants. Fluorescent quantitative PCR revealed exogenous CYP2E1 gene expression in CYP2E1 transgenic plants at various levels, whereas no like expression was detected in either GUS transgenic plants or wild-types. The absorption of benzene and toluene by transgenic plants was analyzed through quantitative gas chromatography. Transgenic plants with high CYP2E1 expression showed a significant increase in absorption capacity of environmental benzene and toluene, compared to control GUS transgenic and wild type plants. Furthermore, these plants also presented obvious improved resistance to formaldehyde. This study, besides being the first to reveal that the CYP2E1 gene enhances plant resistance to formaldehyde, also furnishes a new method for reducing pollutants, such as benzene, toluene and formaldehyde, by using transgenic flowering horticultural plants