A novel active transposon creates allelic variation through altered translation rate to influence protein abundance.

Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for 'B73 active transposable element hAT', creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.

Virioplankton assemblages from challenger deep, the deepest place in the oceans.

Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

Narrow-band tunable optical filters based on cascaded Fabry-Perot cavities.

Narrow-band tunable optical filters (TOF) based on three cascaded Fabry-Perot (FP) cavities are demonstrated. The FP cavities are fabricated with Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT), which is a transparent electro-optic ceramic. With a reflective design, the optical signal passes the three FP cavities twice. Thus we can design the FP cavities with a relatively low reflectivity, which enables it more tolerant to the loss in the cavities. Two types of TOF samples are fabricated. The specifications of the transmissive type TOF with dual-ports are tuning range >48nm, FWHM (full width half maximum) <0.06nm, insertion loss <3.87dB, crosstalk <-39dB, which meet the requirements by optical performance monitor (OPM) applications. The specifications of the reflective type TOF with single-port are tuning range >48nm, FWHM (full width half maximum) <0.1nm, insertion loss <2.82dB, crosstalk <-30dB, which can be employed in tunable fiber lasers for wavelength selection and tuning.

DNA demethylation affects imprinted gene expression in maize endosperm.

BACKGROUND: DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. RESULTS: We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. CONCLUSIONS: Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.

Research on a Seepage Monitoring Model of a High Core Rockfill Dam Based on Machine Learning.

The seepage of a rockfill dam with a high core wall is an important and difficult issue in the safety monitoring of a core rockfill dam, something about which managers are immensely concerned. Seepage of a high core rockfill dam is mainly affected by factors such as water level, rainfall, temperature, filling height, and aging. The traditional research method is to establish a multiple linear regression model to analyze the influence factors of seepage. However, the multicollinearity between these factors affects parameter estimation, and random errors in the data cause the regression model to fail to be established. This paper starts with data collected by an osmometer, uses the 3δ criterion to process the outliers in the sample data, uses the R language to perform principal component analysis on the processed data to eliminate the multicollinearity of the factors, and finally uses multiple linear regression to model and analyze the data. Taking the Nuozhadu high core rockfill dam as an example, the influencing factors of seepage in the construction period and the impoundment period were studied and the seepage was then forecasted. This method provides guidance for further studies of the same type of dam seepage monitoring model.

In-Situ Formation of Holmium Oxide in Pores of Mesoporous Carbon Nanoparticles as Substrates for Neutron-Activatable Radiotherapeutics.

Radionuclide therapy with nano-sized carriers is a very promising approach to treat various types of cancer. The preparation of radioactive nanocarriers can be achieved with minimum handling using a neutron-activation approach. However, the nanocarrier material must possess certain characteristics such as low density, heat-resistance, high metal adsorption, easy surface modification and low toxicity in order to be useful. Mesoporous Carbon Nanoparticles (MCNs) in which holmium oxide is formed in their pores by a wet-impregnation process are investigated as a suitable material for this application. Holmium (165Ho) has a natural abundance of 100% and possesses a large cross-section for capturing thermal neutrons. After irradiation of Ho-containing MCNs in a neutron flux, 166Ho, which emits therapeutic high energy beta particles as well as diagnostic low energy gamma photons that can be imaged externally, is produced. The wet impregnation process (16 w/w% Ho loading) is shown to completely prevent the leaching of radioactive holmium from the MCNs without compromising their structural integrity. In vitro studies showed that the MCNs containing non-radioactive holmium do not exhibit toxicity and the same formulation with radioactive holmium (166Ho) demonstrated a tumoricidal effect. Post-irradiation PEGylation of the MCN surfaces endows dispersibility and biocompatibility.

Crystalline, thermal and swelling properties of starches from single-segment substitution lines with different Wx alleles in rice (Oryza sativa L.).

BACKGROUND: In rice, five common Wx alleles, wx, Wxt , Wxg1 , Wxg2 and Wxg3 , have been identified according to their apparent amylose content (AAC) phenotypes. Previous studies revealed that this Wx allelic variation may also affect other starch properties. However, so far, to what extent the five Wx alleles influence the crystalline structure, thermal and swelling properties of rice starch is still unclear. For this purpose, a set of single-segment substitution lines (SSSLs) harboring five different Wx alleles, varying widely in AAC, was used for comparative studies. RESULTS: The crystalline structure, thermal properties and swelling behavior of starches from the SSSLs varied widely depending on Wx genotype. Effects of different Wx alleles on relative crystallinity followed the order wx > Wxt > Wxg1 = Wxg2 > Wxg3 . The glutinous and Wxt genotype starches showed higher gelatinization temperatures and enthalpy compared with other Wx genotypes. The order for swelling power was wx > Wxt > Wxg1 > Wxg2 > Wxg3 , while the order for degree of solubility was Wxg3 > Wxg1 > Wxg2 > Wxt = wx. Correlation analysis indicated that AAC was significantly and negatively correlated with relative crystallinity (r = -0.996, P < 0.01) and swelling power (r = -0.982, P < 0.01). CONCLUSION: The present results provide new knowledge about the influence of different Wx alleles on the structural and physicochemical properties of rice starch. © 2016 Society of Chemical Industry.

Dehydration of Ions in Voltage-Gated Carbon Nanopores Observed by in Situ NMR.

Ion transport through nanochannels is of fundamental importance in voltage-gated protein ion channels and energy storage devices. Direct microscopic observations are critical for understanding the intricacy of ionic processes in nanoconfinement. Here we report an in situ nuclear magnetic resonance study of ion hydration in voltage-gated carbon nanopores. Nucleus-independent chemical shift was employed to monitor the ionic processes of NaF aqueous electrolyte in nanopores of carbon supercapacitors. The state of ion hydration was revealed by the chemical shift, which is sensitive to the hydration number. A large energy barrier was observed for ions to enter nanopores smaller than the hydrated ion size. Increasing the gating voltage above 0.4 V overcomes this barrier and brings F(-) into the nanopores without dehydration. Partial dehydration of F(-) occurs only at gating voltage above 0.7 V. No dehydration was observed for Na(+) cations, in agreement with their strong ion hydration.

Robust determination of surface relaxivity from nuclear magnetic resonance DT(2) measurements.

Nuclear magnetic resonance (NMR) is a powerful tool to probe into geological materials such as hydrocarbon reservoir rocks and groundwater aquifers. It is unique in its ability to obtain in situ the fluid type and the pore size distributions (PSD). The T1 and T2 relaxation times are closely related to the pore geometry through the parameter called surface relaxivity. This parameter is critical for converting the relaxation time distribution into the PSD and so is key to accurately predicting permeability. The conventional way to determine the surface relaxivity ρ2 had required independent laboratory measurements of the pore size. Recently Zielinski et al. proposed a restricted diffusion model to extract the surface relaxivity from the NMR diffusion-T2 relaxation (DT2) measurement. Although this method significantly improved the ability to directly extract surface relaxivity from a pure NMR measurement, there are inconsistencies with their model and it relies on a number of preset parameters. Here we propose an improved signal model to incorporate a scalable LT and extend their method to extract the surface relaxivity based on analyzing multiple DT2 maps with varied diffusion observation time. With multiple diffusion observation times, the apparent diffusion coefficient correctly describes the restricted diffusion behavior in samples with wide PSDs, and the new method does not require predetermined parameters, such as the bulk diffusion coefficient and tortuosity. Laboratory experiments on glass beads packs with the beads diameter ranging from 50 µm to 500 µm are used to validate the new method. The extracted diffusion parameters are consistent with their known values and the determined surface relaxivity ρ2 agrees with the expected value within ±7%. This method is further successfully applied on a Berea sandstone core and yields surface relaxivity ρ2 consistent with the literature.

Manganese-Vanadate Hybrids: Impact of Organic Ligands on Their Structures, Thermal Stabilities, Optical Properties, and Photocatalytic Activities.

Manganese(II)-vanadate(V)/organic hybrids were prepared in high purity using four different N-donor organic ligands (2,6:2',2″-terpyridine = terpy, 2,2'-bipyrimidine = bpym, o-phenanthroline = o-phen, and 4,4'-bipyridine = 4,4'-bpy), and their crystalline structures, thermal stabilities, optical properties, photocatalytic activities and electronic structures were investigated as a function of the organic ligand. Hydrothermal reactions were employed that targeted a 1:2 molar ratio of Mn(II)/V(V), yielding four hybrid solids with the compositions of Mn(terpy)V2O6·H2O (I), Mn2(bpym)V4O12·0.6H2O (II), Mn(H2O)(o-phen)V2O6 (III), and Mn(4,4'-bpy)V2O6·1.16H2O (IV). The inorganic component within these hybrid compounds, that is, [MnV2O6], forms infinite chains in I and layers in II, III, and IV. In each case, the organic ligand preferentially coordinates to the Mn(II) cations within their respective structures, either as chelating and three-coordinate (mer isomer in I) or two-coordinate (cis isomers in II and III), or as bridging and two coordinate (trans isomer in IV). The terminating ligands in I (terpy) and III (o-phen) yield nonbridged "MnV2O6" chains and layers, respectively, while the bridging ligands in II (bpym) and IV (4,4'-bpy) result in three-dimensional, pillared hybrid networks. The coordination number of the ligand, that is, two- or three-coordinate, has the predominant effect on the dimensionality of the inorganic component, while the connectivity of the combined metal-oxide/organic network is determined by the chelating versus bridging ligand coordination modes. Each hybrid compound decomposes into crystalline MnV2O6 upon heating in air with specific surface areas from ∼7 m(2)/g for III to ∼41 m(2)/g for IV, depending on the extent of structural collapse as the lattice water is removed. All hybrid compounds exhibit visible-light bandgap sizes from ∼1.7 to ∼2.0 eV, decreasing with the increased dimensionality of the [MnV2O6] network in the order of I > II ≈ III > IV. These bandgap sizes are smaller by ∼0.1-0.4 eV in comparison to related vanadate hybrids, owing to the addition of the higher-energy 3d orbital contributions from the Mn(II) cations. Each compound also exhibits temperature-dependent photocatalytic activities for hydrogen production under visible-light irradiation in 20% methanol solutions, with threshold temperatures of ∼30 °C for III, ∼36 °C for I, and ∼40 °C for II, IV, and V4O10(o-phen)2. Hydrogen production rates are ∼142 µmol H2 g(-1)·h(-1), ∼673 µmol H2 g(-1)·h(-1), ∼91 µmol H2 g(-1)·h(-1), and ∼218 µmol H2 g(-1)·h(-1) at 40 °C, for I, II, III, and IV, respectively, increasing with the oxide/organic network connectivity. In contrast, the related V4O10(o-phen)2 exhibits a much lower photocatalytic rate of ∼36 H2 g(-1)·h(-1). Electronic structure calculations based on density-functional theory methods show that the valence band edges are primarily derived from the half-filled Mn 3d(5) orbitals in each, while the conduction band edges are primarily comprised of contributions from the empty V 3d(0) orbitals in I and II and from ligand π* orbitals in III. Thus, the coordinating organic ligands are shown to significantly affect the local and extended structural features, which has elucidated the underlying relationships to their photocatalytic activities, visible-light bandgap sizes, electronic structures, and thermal stabilities.

Electroneutrality breakdown and specific ion effects in nanoconfined aqueous electrolytes observed by NMR.

Ion distribution in aqueous electrolytes near the interface plays a critical role in electrochemical, biological and colloidal systems, and is expected to be particularly significant inside nanoconfined regions. Electroneutrality of the total charge inside nanoconfined regions is commonly assumed a priori in solving ion distribution of aqueous electrolytes nanoconfined by uncharged hydrophobic surfaces with no direct experimental validation. Here, we use a quantitative nuclear magnetic resonance approach to investigate the properties of aqueous electrolytes nanoconfined in graphitic-like nanoporous carbon. Substantial electroneutrality breakdown in nanoconfined regions and very asymmetric responses of cations and anions to the charging of nanoconfining surfaces are observed. The electroneutrality breakdown is shown to depend strongly on the propensity of anions towards the water-carbon interface and such ion-specific response follows, generally, the anion ranking of the Hofmeister series. The experimental observations are further supported by numerical evaluation using the generalized Poisson-Boltzmann equation.

A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.).

Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world population. A japonica mutant 'Jiangtangdao 1' (RS = 11.67%) was crossed with an indica cultivar 'Miyang 23' (RS = 0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD = 36) using 178 F(2) plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F(3:4) families, sbe3-rs was fine mapped to a 573.3 Kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site where Leu-599 of the wild was changed to Pro-599 of the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Co-segregation of the digestion pattern with RS content among 178 F(2) plants further supported sbe3-rs responsible for RS in rice. As a result, the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS which is otherwise difficult to accurately assess in crops. Transgenic technology should be employed for a definitive conclusion of the sbe3-rs.

Wafer-scale high-throughput ordered arrays of Si and coaxial Si/Si(1-x)Ge(x) wires: fabrication, characterization, and photovoltaic application.

We have developed a method combining lithography and catalytic etching to fabricate large-area (uniform coverage over an entire 5-in. wafer) arrays of vertically aligned single-crystal Si nanowires with high throughput. Coaxial n-Si/p-SiGe wire arrays are also fabricated by further coating single-crystal epitaxial SiGe layers on the Si wires using ultrahigh vacuum chemical vapor deposition (UHVCVD). This method allows precise control over the diameter, length, density, spacing, orientation, shape, pattern and location of the Si and Si/SiGe nanowire arrays, making it possible to fabricate an array of devices based on rationally designed nanowire arrays. A proposed fabrication mechanism of the etching process is presented. Inspired by the excellent antireflection properties of the Si/SiGe wire arrays, we built solar cells based on the arrays of these wires containing radial junctions, an example of which exhibits an open circuit voltage (V(oc)) of 650 mV, a short-circuit current density (J(sc)) of 8.38 mA/cm(2), a fill factor of 0.60, and an energy conversion efficiency (η) of 3.26%. Such a p-n radial structure will have a great potential application for cost-efficient photovoltaic (PV) solar energy conversion.

Statistical optimization of parametric accelerated failure time model for mapping survival trait loci.

Most existing statistical methods for mapping quantitative trait loci (QTL) are not suitable for analyzing survival traits with a skewed distribution and censoring mechanism. As a result, researchers incorporate parametric and semi-parametric models of survival analysis into the framework of the interval mapping for QTL controlling survival traits. In survival analysis, accelerated failure time (AFT) model is considered as a de facto standard and fundamental model for data analysis. Based on AFT model, we propose a parametric approach for mapping survival traits using the EM algorithm to obtain the maximum likelihood estimates of the parameters. Also, with Bayesian information criterion (BIC) as a model selection criterion, an optimal mapping model is constructed by choosing specific error distributions with maximum likelihood and parsimonious parameters. Two real datasets were analyzed by our proposed method for illustration. The results show that among the five commonly used survival distributions, Weibull distribution is the optimal survival function for mapping of heading time in rice, while Log-logistic distribution is the optimal one for hyperoxic acute lung injury.

Robust Bayesian mapping of quantitative trait loci using Student-t distribution for residual.

In most quantitative trait loci (QTL) mapping studies, phenotypes are assumed to follow normal distributions. Deviations from this assumption may affect the accuracy of QTL detection, leading to detection of false positive QTL. To improve the robustness of QTL mapping methods, we replace the normal distribution assumption for residuals in a multiple QTL model with a Student-t distribution that is able to accommodate residual outliers. A Robust Bayesian mapping strategy is proposed on the basis of the Bayesian shrinkage analysis for QTL effects. The simulations show that Robust Bayesian mapping approach can substantially increase the power of QTL detection when the normality assumption does not hold and applying it to data already normally distributed does not influence the result. The proposed QTL mapping method is applied to mapping QTL for the traits associated with physics-chemical characters and quality in rice. Similarly to the simulation study in the real data case the robust approach was able to detect additional QTLs when compared to the traditional approach. The program to implement the method is available on request from the first or the corresponding author.