Comparison principle for stochastic heat equations driven by α\alpha-stable white noises

For a class of non-linear stochastic heat equations driven by $\alpha$-stable white noises for $\alpha\in(1,2)$ with Lipschitz coefficients, we first show the existence and pathwise uniqueness of $L^p$-valued c\`{a}dl\`{a}g solutions to such a equation for $p\in(\alpha,2]$ by considering a sequence of approximating stochastic heat equations driven by truncated $\alpha$-stable white noises obtained by removing the big jumps from the original $\alpha$-stable white noises. If the $\alpha$-stable white noise is spectrally one-sided, under additional monotonicity assumption on noise coefficients, we prove a comparison theorem on the $L^2$-valued c\`{a}dl\`{a}g solutions of such a equation. As a consequence, the non-negativity of the $L^2$-valued c\`{a}dl\`{a}g solution is established for the above stochastic heat equation with non-negative initial function

Existence of weak solutions to stochastic heat equations driven by truncated α\alpha-stable white noises with non-Lipschitz coefficients

We consider a class of stochastic heat equations driven by truncated $\alpha$-stable white noises for $1<\alpha<2$ with noise coefficients that are continuous but not necessarily Lipschitz and satisfy globally linear growth conditions. We prove the existence of weak solution, taking values in two different spaces, to such an equation using a weak convergence argument on solutions to the approximating stochastic heat equations. For $1<\alpha<2$ the weak solution is a measure-valued c\`{a}dl\`{a}g process. However, for $1<\alpha<5/3$ the weak solution is a c\`{a}dl\`{a}g process taking function values, and in this case we further show that for $0<p<5/3$ the uniform $p$-th moment for $L^p$-norm of the weak solution is finite, and that the weak solution is uniformly stochastic continuous in $L^p$ sense and satisfies a flow property

Does epigenetic polymorphism contribute to phenotypic variances in Jatropha curcas L.?

<p>Abstract</p> <p>Background</p> <p>There is a growing interest in <it>Jatropha curcas </it>L. (jatropha) as a biodiesel feedstock plant. Variations in its morphology and seed productivity have been well documented. However, there is the lack of systematic comparative evaluation of distinct collections under same climate and agronomic practices. With the several reports on low genetic diversity in jatropha collections, there is uncertainty on genetic contribution to jatropha morphology.</p> <p>Result</p> <p>In this study, five populations of jatropha plants collected from China (CN), Indonesia (MD), Suriname (SU), Tanzania (AF) and India (TN) were planted in one farm under the same agronomic practices. Their agronomic traits (branching pattern, height, diameter of canopy, time to first flowering, dormancy, accumulated seed yield and oil content) were observed and tracked for two years. Significant variations were found for all the agronomic traits studied. Genetic diversity and epigenetic diversity were evaluated using florescence Amplified Fragment Length Polymorphism (fAFLP) and methylation sensitive florescence AFLP (MfAFLP) methods. Very low level of genetic diversity was detected (polymorphic band <0.1%) within and among populations. In contrast, intermediate but significant epigenetic diversity was detected (25.3% of bands were polymorphic) within and among populations. More than half of CCGG sites surveyed by MfAFLP were methylated with significant difference in inner cytosine and double cytosine methylation among populations. Principal coordinates analysis (PCoA) based on Nei's epigenetic distance showed Tanzania/India group distinct from China/Indonesia/Suriname group. Inheritance of epigenetic markers was assessed in one F1 hybrid population between two morphologically distinct parent plants and one selfed population. 30 out of 39 polymorphic markers (77%) were found heritable and followed Mendelian segregation. One epiallele was further confirmed by bisulphite sequencing of its corresponding genomic region.</p> <p>Conclusion</p> <p>Our study confirmed climate and practice independent differences in agronomic performance among jatropha collections. Such agronomic trait variations, however, were matched by very low genetic diversity and medium level but significant epigenetic diversity. Significant difference in inner cytosine and double cytosine methylation at CCGG sites was also found among populations. Most epigenetic differential markers can be inherited as epialleles following Mendelian segregation. These results suggest possible involvement of epigenetics in jatropha development.</p

Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas

BACKGROUND: Temporal and spatial expression of fatty acid and lipid biosynthetic genes are associated with the accumulation of storage lipids in the seeds of oil plants. In jatropha (Jatropha curcas L.), a potential biofuel plant, the storage lipids are mainly synthesized and accumulated in the endosperm of seeds. Although the fatty acid and lipid biosynthetic genes in jatropha have been identified, the expression of these genes at different developing stages of endosperm has not been systemically investigated. RESULTS: Transmission electron microscopy study revealed that the oil body formation in developing endosperm of jatropha seeds initially appeared at 28 days after fertilization (DAF), was actively developed at 42 DAF and reached to the maximum number and size at 56 DAF. Sixty-eight genes that encode enzymes, proteins or their subunits involved in fatty acid and lipid biosynthesis were identified from a normalized cDNA library of jatropha developing endosperm. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the 68 genes could be collectively grouped into five categories based on the patterns of relative expression of the genes during endosperm development. Category I has 47 genes and they displayed a bell-shaped expression pattern with the peak expression at 28 or 42 DAF, but low expression at 14 and 56 DAF. Category II contains 8 genes and expression of the 8 genes was constantly increased from 14 to 56 DAF. Category III comprises of 2 genes and both genes were constitutively expressed throughout endosperm development. Category IV has 9 genes and they showed a high expression at 14 and 28 DAF, but a decreased expression from 42 to 56 DAF. Category V consists of 2 genes and both genes showed a medium expression at 14 DAF, the lowest expression at 28 or 42 DAF, and the highest expression at 56 DAF. In addition, genes encoding enzymes or proteins with similar function were differentially expressed during endosperm development. CONCLUSION: The formation of oil bodies in jatropha endosperm is developmentally regulated. The expression of the majority of fatty acid and lipid biosynthetic genes is highly consistent with the development of oil bodies and endosperm in jatropha seeds, while the genes encoding enzymes with similar function may be differentially expressed during endosperm development. These results not only provide the initial information on spatial and temporal expression of fatty acid and lipid biosynthetic genes in jatropha developing endosperm, but are also valuable to identify the rate-limiting genes for storage lipid biosynthesis and accumulation during seed development

Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families

Abstract Introduction The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction. Results By processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-score) at least 0.5. Detailed analyses reveal that the abundance of microbial genera in the ocean is highly correlated to the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Tara Oceans genomes in the contact-map prediction and subsequent ab initio folding simulations. Of interesting note, PF15461, which has a majority of members coming from ocean-related bacteria, is identified as an important photosynthetic protein by structure-based function annotations. The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with other metagenomics datasets, which results in 235 families with an estimated TM-score over 0.5. Conclusions These results demonstrate a new avenue to improve the capacity of protein structure and function modeling through marine metagenomics, especially for difficult proteins with few homologous sequences.https://deepblue.lib.umich.edu/bitstream/2027.42/152239/1/13059_2019_Article_1823.pd

A First Generation Microsatellite- and SNP-Based Linkage Map of Jatropha

Jatropha curcas is a potential plant species for biodiesel production. However, its seed yield is too low for profitable production of biodiesel. To improve the productivity, genetic improvement through breeding is essential. A linkage map is an important component in molecular breeding. We established a first-generation linkage map using a mapping panel containing two backcross populations with 93 progeny. We mapped 506 markers (216 microsatellites and 290 SNPs from ESTs) onto 11 linkage groups. The total length of the map was 1440.9 cM with an average marker space of 2.8 cM. Blasting of 222 Jatropha ESTs containing polymorphic SSR or SNP markers against EST-databases revealed that 91.0%, 86.5% and 79.2% of Jatropha ESTs were homologous to counterparts in castor bean, poplar and Arabidopsis respectively. Mapping 192 orthologous markers to the assembled whole genome sequence of Arabidopsis thaliana identified 38 syntenic blocks and revealed that small linkage blocks were well conserved, but often shuffled. The first generation linkage map and the data of comparative mapping could lay a solid foundation for QTL mapping of agronomic traits, marker-assisted breeding and cloning genes responsible for phenotypic variation

High-Performance Elastic Management for Cloud Containers Based on Predictive Message Scheduling

Containerized data centers can improve the computational density of IaaS layers. This intensive high-concurrency environment has high requirements for message scheduling and container processing. In the paper, an elastically scalable strategy for cloud containers based on predictive message scheduling is introduced, in order to reduce the delay of messages and improve the response time of services and the utilization of container resources. According to the busy degree of different containers, a management strategy of multiple containers at message-granularity level is developed, which gives the containers better elasticity. The simulation results show that the proposed strategy improves service processing efficiency and reduces response latency compared with existing solutions

Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis

Protein engineering is actively pursued in industrial and laboratory settings for high thermostability. Among the many protein engineering methods, rational design by bioinformatics provides theoretical guidance without time-consuming experimental screenings. However, most rational design methods either rely on protein tertiary structure information or have limited accuracies. We proposed a primary-sequence-based algorithm for increasing the heat resistance of a protein while maintaining its functions. Using adenylate kinase (ADK) family as a model system, this method identified a series of amino acid sites closely related to thermostability. Single- and double-point mutants constructed based on this method increase the thermal denaturation temperature of the mesophilic Escherichia coli (E. coli) ADK by 5.5 and 8.3 °C, respectively, while preserving most of the catalytic function at ambient temperatures. Additionally, the constructed mutants have improved enzymatic activity at higher temperature

Mobile e-Commerce Recommendation System Based on Multi-Source Information Fusion for Sustainable e-Business

A lack of in-depth excavation of user and resources information has become the main bottleneck restricting the predictive analytics of recommendation systems in mobile commerce. This article provides a method which makes use of multi-source information to analyze consumers’ requirements for e-commerce recommendation systems. Combined with the characteristics of mobile e-commerce, this method employs an improved radial basis function (RBF) network in order to determine the weights of recommendations, and an improved Dempster–Shafer theory to fuse the multi-source information. Power-spectrum estimation is then used to handle the fusion results and allow decision-making. The experimental results illustrate that the traditional method is inferior to the proposed approach in terms of recommendation accuracy, simplicity, coverage rate and recall rate. These achievements can further improve recommendation systems, and promote the sustainable development of e-business