Enriched Regions Research Articles

Atomic‐Scale Insights into Surface Lattice Oxygen Activation at the Spinel/Perovskite interface of Co3O4/La0.3Sr0.7CoO3

AbstractSurface lattice oxygen in transition‐metal oxides plays a vital role in catalytic processes. Mastering activation of surface lattice oxygen and identifying the activation mechanism are crucial for the development and design of advanced catalysts. A strategy is now developed to create a spinel Co3O4 /perovskite La0.3Sr0.7CoO3 interface by in situ reconstruction of the surface Sr enrichment region in perovskite LSC to activate surface lattice oxygen. XAS and XPS confirm that the regulated chemical interface optimizes the hybridized orbital between Co 3d and O 2p and triggers more electrons in oxygen site of LSC transferred into lattice of Co3O4 , leading to more inactive O2− transformed into active O2−x. Furthermore, the activated Co3O4/LSC exhibits the best catalytic activities for CO oxidation, oxygen evolution, and oxygen reduction. This work would provide a fundamental understanding to explain the activation mechanism of surface oxygen sites.

Atomic-Scale Insights into Surface Lattice Oxygen Activation at the Spinel/Perovskite interface of Co3 O4 /La0.3 Sr0.7 CoO3.

Surface lattice oxygen in transition-metal oxides plays a vital role in catalytic processes. Mastering activation of surface lattice oxygen and identifying the activation mechanism are crucial for the development and design of advanced catalysts. A strategy is now developed to create a spinel Co3 O4 /perovskite La0.3 Sr0.7 CoO3 interface by in situ reconstruction of the surface Sr enrichment region in perovskite LSC to activate surface lattice oxygen. XAS and XPS confirm that the regulated chemical interface optimizes the hybridized orbital between Co 3d and O 2p and triggers more electrons in oxygen site of LSC transferred into lattice of Co3 O4 , leading to more inactive O2- transformed into active O2-x . Furthermore, the activated Co3 O4 /LSC exhibits the best catalytic activities for CO oxidation, oxygen evolution, and oxygen reduction. This work would provide a fundamental understanding to explain the activation mechanism of surface oxygen sites.

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

BackgroundCUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding.ResultsHere we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from “gold standard” CUT&RUN datasets and efficiently identifies enriched regions for several different protein targets. We also introduce a web server (http://seacr.fredhutch.org) for plug-and-play analysis with SEACR that facilitates maximum accessibility across users of all skill levels.ConclusionsSEACR is a highly selective peak caller that definitively validates the accuracy of CUT&RUN for datasets with known true negatives. Its ease of use and performance in comparison with existing peak calling strategies make it an ideal choice for analyzing CUT&RUN data.

Genome-wide identification of the CLAVATA3/EMBRYO SURROUNDING REGION (CLE) family in grape (Vitis vinifera L.)

BackgroundCLE genes play various biological roles in plant growth and development, as well as in responses to environmental stimuli.ResultsIn the present study, we identified nine CLE genes in the grape genome using an effective identification method. We analyzed the expression profiles of grape CLE genes in different tissues and under environmental different stimuli. VvCLE3 was expressed in shoot apical meristem (SAM) enriched regions, and VvCLE6 was expressed in shoot tissue without SAM. When grapes were infected with bois noir, VvCLE2 was up-regulated. Under ABA treatment, VvCLE3 was down-regulated. VvCLE6 was up-regulated under high temperature stress. We found that VvCLE6 and VvCLE1 were highly expressed in root tissue. In addition, we compared the characteristics of CLEs from grape and other plant species. The CLE family in Sphagnum fallax underwent positive selection, while the CLE family in grape underwent purifying selection. The frequency of optimal codons and codon adaptation index of rice and grape CLE family members were positively correlated with GC content at the third site of synonymous codons, indicating that the dominant evolutionary pressure acting on rice and grape CLE genes was mutation pressure. We also found that closely related species had higher levels of similarity in relative synonymous codon usage in CLE genes. The rice CLE family was biased toward C and G nucleotides at third codon positions. Gene duplication and loss events were also found in grape CLE genes.ConclusionThese results demonstrate an effective identification method for CLE motifs and increase the understanding of grape CLEs. Future research on CLE genes may have applications for grape breeding and cultivation to better understand root and nodulation development.

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

Chromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency Hi-C encounters within and between TADs into direct loci interactions using cross-links at a given base-pair resolution. We reconstruct three TADs of the mammalian X chromosome for three stages of differentiation. We compute the radius of gyration of TADs and the encounter probability between genomic segments. We found 1) a synchronous compaction and decompaction of TADs throughout differentiation and 2) high order organization into meta-TADs resulting from weak inter-TAD interactions. Finally, the present framework allows to infer transient properties of the chromatin from steady-state statistics embedded in the Hi-C/5C data.

Geochronology, geochemistry and petrogenesis of Late Triassic dolerites associated with the Nibao gold deposit, Youjiang Basin, southwestern China: Implications for post-collisional magmatism and its relationships with Carlin-like gold mineralization

The relationship between gold mineralization and magmatism within the Youjiang Basin of SW China remains poorly constrained as a result of the lack of outcropping igneous units in this region. This study presents new geological, geochronological, and geochemical data for recently discovered dolerite dykes associated with the Nibao gold deposit, which is located within the NW Youjiang Basin of SW China. Zircon laser ablation-inductively coupled plasma-mass spectrometry (LA–ICP–MS) U-Pb dating of these dykes yielded an age of 213.6 ± 2.5 Ma, indicating that these dykes were emplaced during the Late Triassic and providing new evidence for Late Triassic magmatism within the study area. The dykes also represent an opportunity to investigate the petrogenesis of mafic rocks and the tectonic setting of the Late Triassic magmatism in the Youjiang Basin. These Nibao dolerite dykes contain relatively low concentrations of SiO2 (46.03–47.66 wt%), have moderate total alkali contents (K2O + Na2O = 2.71–3.15 wt%) and high total Fe as Fe2O3 (TFe2O3) contents (13.49–14.96 wt%). Their trace element compositions are indicative of an OIB-like geochemical affinity barring depletion in the high field strength elements (HFSE) such as Nb, Ta and Th. The Nibao dolerites have homogeneous Lu-Hf and Sr-Nd isotopic compositions with (87Sr/86Sr)i and (143Nd/144Nd)i values of 0.70562–0.70677 and 0.51233–0.51239, respectively. These dykes have a narrow range in associated εNd(t) and εHf(t) values from –0.70 to +0.51 and from +0.04 to +3.24, respectively. These geochemical data indicate that the dolerites associated with the Nibao gold deposit were derived from an enriched region of the asthenopheric mantle (>90 km depth) and the magmas that formed these dykes were generated by 5–10% partial melting of ∼75% garnet peridotite and ∼25% spinel peridotite material. The ascending magmas underwent both crustal contamination and the fractional crystallization of olivine, clinopyroxene and Fe oxides (e.g., magnetite or ilmenite) prior to emplacement. The Nibao dolerites are geochemically distinct from mafic rocks related to the Emeishan large igneous province, suggesting that they are not linked to this mantle plume event. Instead, they formed in an extensional setting generated by the subduction of the Song Ma oceanic plate beneath South China Block and the subsequent collision between the Indochina and South China blocks. The breakoff of the Song Ma oceanic slab caused the partial melting of the mantle source region for the Nibao dolerite dykes. These relationships suggest that the post-collision extensional environment associated with this breakoff contributed to the deeply sourced, mantle-derived Late Triassic magmatism in this area and, perhaps as well, the gold mineralization in the Youjiang Basin. Most importantly, combining the new geochronological data presented in this study with the timing of extension in this region and the results of previous research suggest that the Carlin-like gold deposits in the Youjiang Basin formed at around 213 Ma (i.e., the Late Triassic).

Distribution of harmful elements in dissected 125 m3 blast furnace

ABSTRACTThis paper investigates the distribution of harmful elements in furnace burden and refractory of a water-quenched blast furnace X (BFX) through SEM images, EDS spectra and XRD results. The results show that zinc is mainly concentrated on the lumpy zone while the dominant enrichment region of alkali metal is the cohesive zone. The microstructure and XRD results of refractories in various locations indicate that the erosion caused by harmful elements begins on the hot outer surface of higher stack with the adhesion of zinc, while potassium then completely permeates into the first-layer refractory in the lower part of stack. The local expansion of volume caused by the introduction of harmful elements leads to the erosion of refractory, while the enhanced erosion from the throat to the bottom of the furnace can be explained by the rising temperature. Owing to the shifting location of the temperature isothermal, the harmful elements enrichment region transforms from hot outer surface of refractory at higher part of BFX to the cold inner surface at lower part of BFX.

Synchrotron X-ray fluorescence mapping of Ca, Sr and Zn at the neonatal line in human deciduous teeth reflects changing perinatal physiology

ObjectivesOur first objective was to review the evidence describing the appearance and microstructure of the neonatal line in human deciduous teeth and to link this with known changes in neonatal physiology occurring at and around birth. A second objective was to explore ways to improve identification of the neonatal line by mapping the pre- and postnatal distribution of Ca, Sr and Zn in deciduous cuspal enamel and superimposing these maps onto transmitted light micrographs that included a clear true section of the neonatal line. Materials and methodsWe used synchrotron X-ray fluorescence to map elemental distributions in pre- and postnatal enamel and dentine. Two deciduous canines and 5 deciduous molars were scanned with an X-ray beam monochromatised to 17.0 keV at either 10.0, 2.5 or 1.0 μm resolution and 10 ms integration time. ResultsCalcium maps distinguished enamel and dentine but did not clearly demarcate tissues formed pre- or postnatally. Strontium maps reflected presumed pre- and postnatal maternal serum levels and what are likely to be diet-dependent regions of Sr enrichment or depletion. Prenatal Zn maps, particularly for dentine, mirror elevated levels in the fetus and in colostrum during the first few days of life. ConclusionsThe neonatal line, enamel dentine junction and surface enamel were all Zn-rich. Within the neonatal line Zn may be associated with increased crystallinity but also with caries resistance, both of which have been reported previously. Elemental mapping may improve the identification of ambiguous NNLs and so be useful in forensic and archaeological studies.

The impact of the surface morphology on optical features of the green emitting InGaN/GaN multiple quantum wells

AFM study of surface morphology in green LED structures and multifractal analysis allowed us to reveal a relationship between step-meandering morphology quantitatively characterized by a multifractal parameter, the degree of disorder, and features of In incorporation in InGaN/GaN MQW structures. These features manifest themselves in a shape of the distribution of peak external quantum efficiency values with wavelengths (DPEW) in the current range of 0.1–1000 mA. High values of degree of disorder result in spinodal alloy decomposition and/or local In enriched regions in InGaN alloy and in a twofold decrease in EQE values in green LEDs.

Improved detection of epigenomic marks with mixed-effects hidden Markov models.

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a technique to detect genomic regions containing protein-DNA interaction, such as transcription factor binding sites or regions containing histone modifications. One goal of the analysis of ChIP-seq experiments is to identify genomic loci enriched for sequencing reads pertaining to DNA bound to the factor of interest. The accurate identification of such regions aids in the understanding of epigenomic marks and gene regulatory mechanisms. Given the reduction of massively parallel sequencing costs, methods to detect consensus regions of enrichment across multiple samples are of interest. Here, we present a statistical model to detect broad consensus regions of enrichment from ChIP-seq technical or biological replicates through a class of zero-inflated mixed-effects hidden Markov models. We show that the proposed model outperforms existing methods for consensus peak calling in common epigenomic marks by accounting for the excess zeros and sample-specific biases. We apply our method to data from the Encyclopedia of DNA Elements and Roadmap Epigenomics projects and also from an extensive simulation study.

Nano-indentation and in-situ investigations of double-sided laser beam welded 2060-T8/2099-T83 Al-Li alloys T-joints

2060 and 2099 are both newly developed high-strength aluminum-lithium (Al-Li) alloys for fuselage panels of jetliners. In this work, double-sided laser beam welding of 2-mm-thick 2060-T8 and 2099-T83 Al-Li alloys was performed using AA4047 filler wire under optimized parameters. Weld zone microstructure and T-joint mechanical properties were investigated by means of scanning electron microscopy (SEM), electron backscattered diffraction (EBSD), nano-indentation and in-situ tensile test. Experimental results indicated that the equiaxed grain zone (EQZ) featured by dense large-angle (θ＞10°) grain boundaries was observed in the weld zone along the fusion lines. Besides the softening problem found in the partially melted zone (PMZ), local softening phenomenon was detected in the local enrichment region of the EQZ. During in-situ tensile tests, the crack was initiated at the weld toe and then propagated alternately in the PMZ and EQZ's local enrichment regions. Micro-voids induced the localized softening problem and the crack's intergranular expansion in the EQZ. Localized absence of silicon was most likely to cause continuous micro-voids in the EQZ.

Effect of the thermal annealing and the nominal composition in the elemental distribution of InxAl1-xAsySb1-y for triple junction solar cells

In this work, the effect of thermal annealing under As overpressure in the composition distribution of In8Al42As34.5Sb15.5 layers, lattice matched to InP for triple junction solar cells, is analysed by APT. We have found that in the as-grown sample there is a statistically significant number of In-rich regions with size ∼10 Å. Upon annealing, the composition gradient from the centre of the In-rich regions towards the homogeneous region is reduced, and the size of the enriched regions increases up to ∼35 Å. This points to In out-diffusion as an initial step of the material homogenization, which would explain previous results of PL emission. Additionally, the comparison of the obtained results with previous analysis by the authors has shown that the increase in the In content of InAlAsSb epitaxial layers has a strong effect on the composition distribution of the material, stimulating deviations from the random alloy in both the group III and the group V sub-lattices.

Identification and mapping of SNPs associated with number of intermuscular bone in blunt snout bream

Most of the freshwater aquaculture fish species in the world, especially cyprinid fishes, contain intermuscular bones (IBs). Different number of IBs had been indicated among different species and strains or individuals of same species, which suggested that the trait of IBs counts has the possibility of genetic improvement through selective breeding program. In this study, two groups with extreme differences for IB number were constructed to identify IB number-associated SNPs and genes in blunt snout bream (Megalobrama amblycephala), which is one of the most important aquaculture species in China. Through whole genome resequencing and bulked segregant analysis (BSA) for two groups with extreme IBs number (IB-more group with IBs number ≥130; IB-less group with IBs number ≤100), a total of 6074 high quality SNPs with |Delta-Index|≥0.5 were screened out by chi-square test and index analysis. The sliding-window analysis subsequently obtained two SNP enrichment regions, which located on chromosome 06 (32 M–34 M) and chromosome 11 (12 M–16 M), respectively, containing 21 and 300 candidate SNPs. Besides, 181 candidate SNPs with |Delta-Index|≥0.8 were detected and annotated within the genome-wide range beyond above two regions. Finally, 52 SNPs were used for data reliability verification. Genotyping of SNPs in IB-less individuals and IB-more individuals and correlation analysis between candidate SNPs and IB number traits indicated that five SNPs were significantly associated with the trait of IB number. The sequences or flanking sequences where SNPs located were then annotated to different genes, which maybe closely related to IB number trait. This is the first study to explore SNPs/genes related to the number of IBs in fish by BSA. The identified dataset provides an extensive resource for understanding the molecular mechanisms underlying IB counts in teleosts and also lays the foundation for the marker assisted breeding of IB number traits in M. amblycephala.

Practice and understanding of sidetracking horizontal drilling in old wells in Sulige Gas Field, NW China

Abstract To seek effective ways of lowering development cost and tapping inter-well remaining reserves, sidetracking horizontal wells from old wells in Su10 and Su53 Block were conducted. The engineering and geological problems such as leakage, collapse and sticking in slim-hole sidetracking, and difficult evaluation of remaining gas were gradually overcome, and a set of drilling and completion technology, well deployment optimization technology and geo-steering technology suitable for sidetracking horizontal wells in tight sandstone gas reservoirs have been worked out. By making full use of the old well, sidetracking horizontal wells can greatly reduce development costs, enhance the producing degree of inter-well remaining reserves, and get production 3-5 times of that of adjacent vertical wells. Its production effect is influenced by encountered sandstone length, the position of the horizontal segment in the reservoir, produced effective reservoir thickness, gas saturation, controlled reserves and fracturing effect, etc. Up to now, in Block Su10 and Su53, 12 sidetracking horizontal wells have been drilled, which have an average drilling cycle of 49 days, average horizontal section length of 689 m, average effective drilling ratio of 61.5%, average well-head pressure of 16.2 MPa, and daily output of 4.7×104 m3 at the initial stage after production. By the end of 2017, the average yield increment was more than 1 000×104 m3 with good effect. With the increase of low yield old wells, wells in the enrichment regions tend to be saturated and the rest gas-bearing areas are lower in grade, therefore, sidetracking horizontal well can be used for optimization of well pattern, well deployment mode and exploitation of remaining oil areas.

Sr–Nd–Hf isotopic compositions of lamprophyres in western Shandong, China: Implications for the nature of the early cretaceous lithospheric mantle beneath the eastern North China Craton

This paper presents new zircon UPb ages and Hf isotope data, and whole-rock geochemical and SrNd isotopic data, for lamprophyres in the western Shandong area of China. These data provide new insights into the nature of the lithospheric mantle beneath the eastern North China Craton (NCC) during the Early Cretaceous. The lamprophyres are divided into low-Ti (TiO2 < 1.1 wt%; Ti/Y < 270) and high-Ti (TiO2 > 2 wt%; Ti/Y > 370) suites, where the Xiaya and Jingziyu minettes are defined as low-Ti lamprophyres and the Jingziyu pyroxene lamprophyres are defined as high-Ti lamprophyres. The igneous zircons yield weighted-mean ages of 126, 132, and 130 Ma for the low- and high-Ti lamprophyres, respectively, indicating these units formed during the Early Cretaceous. The inherited zircons within the Xiaya and Jingziyu minettes define six (2517, 1852, 725, 375, 276, and 236 Ma) and two (2523 and 462 Ma) main age populations, respectively. In comparison, the inherited zircons from the Jingziyu pyroxene lamprophyres yield two main age populations (2523 and 1848 Ma). The low-Ti lamprophyres are enriched in the light rare earth elements (LREE) and large-ion lithophile elements (LILE), depleted in the heavy REE (HREE) and high-field-strength elements (HFSE), and have small negative Eu anomalies. In comparison, the high-Ti lamprophyres are enriched in the LREE but are slightly depleted in the HFSE. The low-Ti lamprophyres also have high 87Sr/86Sr(t) ratios (0.7121–0.7123), low εNd(t) values (−18.81 to −18.62), and contain igneous zircons with relatively high εHf(t) values (generally between −9.94 and −3.36). In comparison, the high-Ti lamprophyres have 87Sr/86Sr(t) ratios of 0.7066–0.7068, εNd(t) values from −5.01 to −4.64, and contain igneous zircons with εHf(t) values from −11.77 to −8.50. These data indicate the low-Ti lamprophyres formed from primary magmas generated by the partial melting of an enriched region of the lithospheric mantle that was previously strongly modified jointly by subduction breakoff of the downgoing Yangtze Craton basement material and delamination of the lower continental crust within the NCC. In comparison, the magmas that formed the high-Ti lamprophyres were generated by the partial melting of an enriched region of the lithospheric mantle that was weakly modified by interaction with the lower continental crust of the NCC. Both the low- and high-Ti lamprophyres formed in an extensional tectonic environment during lithospheric thinning, and the presence of these two suites of lamprophyres indicates that lithospheric thinning of the eastern NCC peaked during the Early Cretaceous.

A smoothed enriched meshfree Galerkin method with two-level nesting triangular sub-domains for stress intensity factors at crack tips

A smoothed enriched meshfree Galerkin method with two-level nesting triangular sub-domains (NSEMM) is presented for linear elastic fracture mechanics. In the present method, displacement fields are constructed by using the linear MLS approximation in linear region away from the crack tip and the enriched MLS approximation in enriched region around the crack tip respectively. To overcome the discontinuous problem of the coupling approximations and accelerate meshfree computations, two-level nesting triangular sub-domains based on the triangular background integration cells are designed and used to construct the smoothing strain. Each two-level nesting sub-domains includes the triangular background cell itself and four equal-area triangular sub-cells. The discretized system equations are created by the Generalized smoothed Galerkin (GS-Garlerkin) weak form and Richardson extrapolation method. The values of SIFs are evaluated by using the domain form of interaction integral. Numerical examples have been simulated to demonstrate the effectiveness and robustness of the present method for crack problems with complicated configurations, and very satisfactory results have been obtained. The NSEMM takes advantages of both EFGM and generalized strain smoothing technique such as lower computational cost, high accurate and easy to implementation.

RECAP reveals the true statistical significance of ChIP-seq peak calls.

MotivationChromatin Immunopreciptation (ChIP)-seq is used extensively to identify sites of transcription factor binding or regions of epigenetic modifications to the genome. A key step in ChIP-seq analysis is peak calling, where genomic regions enriched for ChIP versus control reads are identified. Many programs have been designed to solve this task, but nearly all fall into the statistical trap of using the data twice—once to determine candidate enriched regions, and again to assess enrichment by classical statistical hypothesis testing. This double use of the data invalidates the statistical significance assigned to enriched regions, thus the true significance or reliability of peak calls remains unknown.ResultsUsing simulated and real ChIP-seq data, we show that three well-known peak callers, MACS, SICER and diffReps, output biased P-values and false discovery rate estimates that can be many orders of magnitude too optimistic. We propose a wrapper algorithm, RECAP, that uses resampling of ChIP-seq and control data to estimate a monotone transform correcting for biases built into peak calling algorithms. When applied to null hypothesis data, where there is no enrichment between ChIP-seq and control, P-values recalibrated by RECAP are approximately uniformly distributed. On data where there is genuine enrichment, RECAP P-values give a better estimate of the true statistical significance of candidate peaks and better false discovery rate estimates, which correlate better with empirical reproducibility. RECAP is a powerful new tool for assessing the true statistical significance of ChIP-seq peak calls.Availability and implementationThe RECAP software is available through www.perkinslab.ca or on github at https://github.com/theodorejperkins/RECAP.Supplementary information Supplementary data are available at Bioinformatics online.

QTL mapping analysis of maize plant type based on SNP molecular marker

In this study, the elite maize inbred line (Zheng683-1) was used as a recurrent parent and the four maize inbred lines (ZPH1388, ZPH5, Dong 237 and Chang 7-2) were used as donor parents. The four F1 hybrids were produced by crossing between them and were continued backcrossing to the recurrent parent to produce four BC3F1s. The BC3F1 were pollinated by selfing four generations to generate the recombinant inbred lines (BC3F5) that showed variation in plant height, ear height, leaf angle. There were 53 lines for Zheng683-1 x ZPH1388, 53 lines for Zheng683-1 x ZPH5, 48 lines for Zheng683-1 x Dong237 and 61 lines for Zheng683-1 x Chang 7-2. The four populations were genotyped by using SNP marker and identified the QTLs of targeted traits by using QTL IciMapping V4.1 software and stepwise regression analysis. The main results are as follows:1. 19 additive QTLs and 2 dominant QTLs about plant height were detected in four introgression lines, and 7, 4, 5, 5 QTLs related plant height in ZPH1388-IL, ZPH5-IL, Dong237-ILand Chang7-2-IL. Among the 21 plant height QTLs, the largest contribution to phenotypic variation was QTLqPHa12 from Dong237-IL population, which evaluated 43.44% of the phenotypic variation of plant height . Followed by qPHa3 from ZPH1388-IL, the phenotypic contribution rate was 20% 2. Sixteen QTLs related ear height were detected in the population of the 4 introgression lines, of which there were 15 additive and 1 dominant QTLs. In addition, 9, 3, and 4 QTLs were detected in ZPH1388-IL, ZPH5-IL and Dong237-IL respectively. Among the 16 ear height QTLs, the largest contribution to phenotypic variation was QTL (qEHa1) from the ZPH1388 IL, which recorded the phenotypic variation of ear height by 26.01%. Next the phenotype contribution rates were 22.05% and 21.46%, respectively for qEHa13 and qEHa15 from Dong237-IL. Fourteen QTLs related leaf angle was detected in the population of the introgression lines, of which there were 5 additive QTLs and 9 dominant QTLs. Moreover, 2, 9, and 3 QTLs were detected in ZPH1388-IL, ZPH5-IL, Dong237-IL, respectively. Among the 14 leaf angle QTLs, the largest contribution to phenotypic variation was QTL (qLAa4) from the Dong237-IL then qLAa3 from ZPH5-IL, detecting the phenotypic variation of leaf angle of 28.56% and 24.08%, respectively.The results showed that the QTL locus was characterized by uneven chromosome distribution. The chromosome 1, 2, 5, and 7 are the regions with the QTL concentrated distribution of plant type traits. The QTL of plant type also showed QTL concentrated distribution in some regions of chromosomes. For example, there are three QTLs about plant height and ear height in the region of chromosome bin1.02, three QTLs about plant and ear heights, as well as leaf angle in the region of chromosome bin 2.02. These areas are QTL enrichment region (or the hot spots) of the pleiotropic gene loci related the plant type and ear traits.

Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other.

A considerable number of deposited variants has provided new possibilities for knowledge discovery in different types of prostate cancer. Here, we analyzed variants located on 3'UTR, 5'UTR, CDs, Intergenic, and Intronic regions in castration-resistant prostate cancer (8496 variants), familial prostate cancer (3241 variants), metastatic castration-resistant prostate cancer (3693 variants), and prostate cancer (16599 variants). Chromosome regions 10p15-p14 and 2p13 were highly enriched (P < 0.00001) for variants located in 3'UTR, 5'UTR, CDs, intergenic, and intronic regions in castration-resistant prostate cancer. In contrast, 10p15-p14, 10q23.3, 12q13.11, 13q12.3, 1q25, and 8p22 regions were enriched (P < 0.001) in familial prostate cancer. In metastatic castration-resistant prostate cancer, 10p15-p14, 10q23.3, 11q22-q23, 14q21.1, and 14q32.13 were highly variant regions (P < 0.001). Chromosome 2 and chromosome 1 hosted many enriched variant regions. AKR1C3, BRCA1, BRCA2, CHGA, CYP19A1, HOXB13, KLK3, and PTEN contained the highest number of 3'UTR, 5'UTR, CDs, Intergenic, and Intronic variants. Network analysis showed that these genes are upstream of important functions including prostate gland development, tumor recurrence, prostate cancer-specific survival, tumor progression, cancer mortality, long-term survival, cancer recurrence, angiogenesis, and AR. Interestingly, all of EGFR, JAK2, NR3C1, PDZD2, and SEMA3C genes had single nucleotide polymorphisms (SNP) in castration-resistant prostate cancer, consistent with high selection pressure on these genes during drug treatment and consequent resistance. High occurrence of variants in 3'UTRs suggests the importance of regulatory variants in different types of prostate cancer; an area that has been neglected compared with coding variants. This study provides a comprehensive overview of genomic regions contributing to different types of prostate cancer.

An abnormal meta-stable nanoscale eutectic reaction revealed by in-situ observations

Phase selection and growth of materials far from equilibrium provides fertile ground for novel phases and morphologies since a multitude of different pathways may be energetically accessible. In this study, a complex metastable devitrification of Al60Sm11 (ε-phase) from its amorphous precursor is discovered using a combination of in-situ high-energy X-ray diffraction (HEXRD), providing insight into the average bulk behavior, and in-situ aberration corrected scanning transmission electron microscopy, revealing the atomic scale mechanisms of growth and their dynamics. We have found that non-equilibrium chemical partitioning disrupts the nominal planer growth by formation of nanoscale Al enriched regions inhomogeneously segregated at the ε/glass interface, to locally balance the compositionally dependent driving force and the associated diffusional burden imposed on its grain growth. These Al-rich regions form fcc-Al-rich nanocrystallites epitaxially with the ε-phase, modifying ε/glass interface mobility and creating a crenulated growth front. This new mechanism offers a pathway for fabricating alloy structures with nanoprecipitate dispersions through a meta-stable phase transition.