Wright-Fisher diffusion bridges

The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time $t\in (0,T)$. In a bridge with allele frequencies of 0 at times 0 and $T$ the coalescence structure is that the population coalesces in two directions from $t$ to $0$ and $t$ to $T$ such that there is just one lineage of the allele under consideration at times $0$ and $T$. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time $t\in (0,T)$. The density of the frequency of an allele at time $t$ is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching P\'olya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting. This paper is dedicated to the memory of Paul Joyce

Presentation1_Cooperate or not with knowledge-advantaged ENGO: Motivating supplier environmental responsibility of competitive core enterprises.pdf

Recently, core enterprises are compelled to invest in the environmental responsibility of upstream suppliers, since their brand image and market share will be significantly impacted when suppliers fail to comply with environmental regulations. However, the effectiveness of the core enterprises’ investment efficiency is limited by insufficient environmental knowledge. Although cooperating with the knowledge-advantaged environmental non-governmental organization (ENGO) may be an effective solution, we observe from the recent examples that not all core enterprises are willing to cooperate in a competitive market. Within this context, we develop a theoretical model to investigate whether competitive core enterprises can benefit from cooperating with the knowledge-advantaged ENGO to motivate the supplier’s environmental responsibility. Our results show that cooperation incentivizes core enterprises’ investments in the supplier’s environmental responsibility, which in turn motivates better environmental responsibility of the supplier. However, we illustrate that cooperation is not necessarily the optimal strategy for core enterprises in the duopoly scenario. Specifically, as the knowledge absorption ability increases, a core enterprise may free-ride on another’s investment, shifting its strategic preference from cooperating to not cooperating. In addition, competition may stimulate the core enterprises’ investments and cooperation motivation, thus improving the total environmental effort and supply chain members’ profits. Our findings provide insights into the competitive core enterprises’ strategic choice regarding suppliers’ environmental responsibility management.</p

Manipulations of glucose/lipid metabolism and gut microbiota of resistant starch encapsulated Ganoderma lucidum spores in T2DM rats

Our team previously demonstrated that Ganoderma lucidum spores (GLS) and resistant starch (RS) had hypoglycemic effects separately on type 2 diabetic mellitus (T2DM) rats. This work was to explore the effects of administering encapsulated GLS within RS (referred to as EGLS) in the T2DM rats, which were induced by streptozotocin (STZ). The EGLS was orally administered to rats for 28 days. The parameters of glycometabolism and lipometabolism were evaluated, and fecal microbiota composition was investigated. The results showed that EGLS significantly enhanced glycometabolism and lipometabolism parameters in T2DM rats, which might be associate with the enhancement of the glucose and lipid metabolism, insulin secretion, and glycogen synthesis and reduced lipogenesis. Furthermore, the intervention of EGLS also reduced the Proteobacteria community and improved dysfunctional gut microbiota. This study indicated EGLS may be a potential candidate for dietary intervention to modulate diabetes

Manipulations of glucose/lipid metabolism and gut microbiota of resistant starch encapsulated Ganoderma lucidum spores in T2DM rats

Our team previously demonstrated that Ganoderma lucidum spores (GLS) and resistant starch (RS) had hypoglycemic effects separately on type 2 diabetic mellitus (T2DM) rats. This work was to explore the effects of administering encapsulated GLS within RS (referred to as EGLS) in the T2DM rats, which were induced by streptozotocin (STZ). The EGLS was orally administered to rats for 28 days. The parameters of glycometabolism and lipometabolism were evaluated, and fecal microbiota composition was investigated. The results showed that EGLS significantly enhanced glycometabolism and lipometabolism parameters in T2DM rats, which might be associate with the enhancement of the glucose and lipid metabolism, insulin secretion, and glycogen synthesis and reduced lipogenesis. Furthermore, the intervention of EGLS also reduced the Proteobacteria community and improved dysfunctional gut microbiota. This study indicated EGLS may be a potential candidate for dietary intervention to modulate diabetes

Distribution of putative single nucleotide polymorphisms (SNP) in the transcriptome of <i>L. aurea</i>.

<p>Distribution of putative single nucleotide polymorphisms (SNP) in the transcriptome of <i>L. aurea</i>.</p

<i>De novo</i> Sequence Assembly and Characterization of <i>Lycoris aurea</i> Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing

<div><p>Background</p><p><i>Lycoris aurea</i>, also called Golden Magic Lily, is an ornamentally and medicinally important species of the Amaryllidaceae family. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed <i>de novo</i> transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for <i>L. aurea</i> using high-throughput sequencing technology.</p><p>Methodology and Principal Findings</p><p>Total RNA was isolated from leaves with sodium nitroprusside (SNP), salicylic acid (SA), or methyl jasmonate (MeJA) treatment, stems, and flowers at the bud, blooming, and wilting stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, a total of 937,990 high quality reads (308.63 Mb) with an average read length of 329 bp were generated. Clustering and assembly of these reads produced a non-redundant set of 141,111 unique sequences, comprising 24,604 contigs and 116,507 singletons. All of the unique sequences were involved in the biological process, cellular component and molecular function categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literatures, many putative genes involved in Amaryllidaceae alkaloids synthesis, including <i>PAL</i>, <i>TYDC OMT</i>, <i>NMT</i>, <i>P450</i>, and other potentially important candidate genes, were identified for the first time in this <i>Lycoris</i>. Furthermore, 6,386 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset.</p><p>Conclusions</p><p>The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in <i>L. aurea</i>. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will provide useful information for functional genomic research in future.</p></div

Additional file 4: Table S3. of Identification and differential regulation of microRNAs in response to methyl jasmonate treatment in Lycoris aurea by deep sequencing

Conserved miRNA and miRNA families identified by similarity. (XLSX 105 kb

KEGG metabolism pathway categories assigned with <i>L. aurea</i> unigenes.

<p>KEGG metabolism pathway categories assigned with <i>L. aurea</i> unigenes.</p

Additional file 6: Table S5. of Identification and differential regulation of microRNAs in response to methyl jasmonate treatment in Lycoris aurea by deep sequencing

Validation and comparative relative expression of differentially expressed miRNAs between the CK and MJ100 libraries in L. aurea. (XLSX 19 kb

Selected genes of interest for Amaryllidaceae-type alkaloids biosynthesis in the <i>L. aurea</i> transcriptome, including the contigs and singletons.

<p>Selected genes of interest for Amaryllidaceae-type alkaloids biosynthesis in the <i>L. aurea</i> transcriptome, including the contigs and singletons.</p