Whole genome analysis of the plant growth-promoting Rhizobacteria Bacilllus amyloliquefaciens FZB42 with focus on its secondary metabolites

Bacillus amyloliquefaciens FZB42 besitzt einen beeindruckenden Effekt zur Verbesserung des Pflanzenwachstums. Um die Mechanismen, vor allem auf molekularer Ebene, zu verstehen, wurde das komplette Genom von FZB42 in dieser Arbeit sequenziert. Abwesenheit von der weit verbreiteten Phagen-verwandten Genen im Genom von B. subtilis 168, der in enger Verwandtschaft zum FZB42 steht, ist ein besonderes Merkmal. Dagegen enthält das Genom von FZB42 viele DNA-Inseln, in denen unikale Gene in FZB42 als Cluster gefunden wurden. Viele Gene, die möglicherweise zur Pflanzenwachstumsförderung beitragen, wurden in dieser Arbeit identifiziert. B. amyloliquefaciens FZB42 ist natürlich kompetent. Das kompetente Stadium in FZB42 kommt früher als in B. subtilis 168, nämlich während der späten exponentiellen Wachstumsphase. Das FZB42-Genom enthält den kompletten Satz von Genen, die für die Entwicklung der genetischen Kompetenz nötig sind. Ausgenommen von Gene für Quorum-Sensing-System ist die Mehrzahl der Kompetenz-Gene von FZB42 sehr ähnlich zu denen in B. subtilis 168. Das FZB42 Genom birgt ein enormes Potential zur Produktion von sekundären Metaboliten. Genetische Manipulationen wurden durchgeführt, um die Funktionen der trans-AT Domänen und der Modifikationsdomänen in den PKS-Gen-Clustern zu erklären. Mit Ausnahme von fünf Gen-Clustern in B. subtilis 168 (Surfactin, Fengycin, Bacillibactin, Bacillaene und Bacilysin), sind Bacillomycin D, Difficidin, Macrolactin und ein hypothetisches Tripeptid einzigartig im Genom der FZB42. FZB42 kann kein bekanntes ribosomal synthetisiertes Bacteriocin produzieren kann. Gleichzeitig beinhaltet sein Genom ein Gen-Cluster, das wahrscheinlich für die Produktion eines neuartigen Bacteriocins verantwortlich ist. Die eindrucksvolle genetische Kapazität zur Herstellung von antagonistischen sekundären Metaboliten ermöglicht es FZB42, nicht nur erfolgreich neben konkurrierenden Organismen innerhalb seiner natürlichen Umgebung zu überleben, sondern auch Pflanzen gegen pathogene Bakterien und Pilze zu schützen.Bacillus amyloliquefaciens FZB42 has an impressive effect to improve plant growth. In order to understand the mechanisms, especially at the molecular biological level, the whole genome of FZB42 was sequenced in this work. The absence of extended phage insertions which are typical for the closely related B. subtilis 168 genome is a particular feature. On the other hand, several DNA islands where unique genes in FZB42 were found clustered. Many candidate genes that may contribute to the plant growth promotion were identified in this works. B. amyloliquefaciens FZB42 is naturally competent. FZB42 exhibited its maximal competence earlier than B. subtilis, during late exponential growth. Not surprisingly, the FZB42 genome harbors the complete set of genes necessary for development of genetic competence. The majority of competence genes are highly homologous to their counterparts in B. subtilis 168, excluded from genes for the quorum-sensing system. The FZB42 genome harbors enormous potential for producing secondary metabolites. Genetic manipulation was carried out to investigate the trans-AT domains and some modification domains in the pks gene clusters. With the exception of five gene clusters in B. subtilis 168 (Surfactin, Fengycin, Bacillibactin, Bacillaene and Bacilysin), Bacillomycin D, Difficidin, Macrolactin and a hypothetical tripeptide are unique in the genome of the FZB42. A remarkable feature of the FZB42 genome is that it does not produce any known ribosomally synthesized bacteriocin, whereas a gene cluster probably responsible for production of a new bacteriocin was identified in this work. The impressive genetic capacity to produce antagonistic acting secondary metabolites not only enables FZB42 to cope successfully with competing organisms within its natural environment, but also to protect plants from pathogenic bacteria and fungi

Endogenous Matching and Contractual Choice between Agricultural Processors and Farmers in China

Contracts are widely used by agricultural processors for purchasing inputs not only in developed countries but also in developing countries such as China. The total number of formal, written contracts between farmers and food processors is increasing rapidly in China, and the formal contracts that exist are becoming more complex. Contractual design in China is evolving from simple price-quantity contracts toward more complicated arrangements known as cooperation contracts or joint-stock cooperation contracts, designed to share risk and mitigate opportunistic behaviors by the contracting parties. Due to small farm sizes, the contracted amount in the typical contract in China is very small compared with Western countries, and each processor usually has a large number of contracted farmers. This paper uses data from a 2003 survey of food processing firms by the Chinese Ministry of Agriculture to analyze the determinants of contractual choices between these firms and farmers and the number of farmers that each firm contracts with. An important issue identified in the literature in analyzing the determinants of contractual choices is endogenous matching between parties to a contract and the effects of this endogenous matching on contract choice. We find strong evidence to support endogenous matching. In particular, our results indicate that firms which contract with a larger number of farms are more likely to use cooperation contracts than relational contracts.China, contractual design, endogenous matching, farms, food processing, Agribusiness, Industrial Organization, Q13, L14,

Demolition, Rehabilitation, and Conservation: Heritage in Shanghai’s Urban Regeneration, 1990–2015 [post-print]

Urban heritage sites in central cities are most difficult to protect during rapid and large scale urban (re)development. Rising land values from property development conflict with and constrain heritage preservation. Compared with many cities in developed and developing countries, large Chinese cities have experienced a stronger redevelopment imperative, faster population growth, and a weaker concern for urban heritages over the last three decades. We use Shanghai to examine the contested evolution of heritage preservation against massive urban redevelopment through three stages from 1990 to the present. Using three heritage projects (Xintiandi, Tianzifang, Bugaoli), we focus on: 1) how each project was implemented and the economic and spatial outcomes each has produced; 2) how the mode of each project’s development interacted with the shifting official policies for heritage preservation; and 3) the implications of the findings, theoretical and practical, for more effective urban preservation

Demolition, rehabilitation, and conservation: heritage in Shanghai’s urban regeneration, 1990–2015 [post-print]

Urban heritage sites in central cities are most difficult to protect during rapid and large scale urban (re)development. Rising land values from property development conflict with and constrain heritage preservation. Compared with many cities in developed and developing countries, large Chinese cities have experienced a stronger redevelopment imperative, faster population growth, and a weaker concern for urban heritages over the last three decades. We use Shanghai to examine the contested evolution of heritage preservation against massive urban redevelopment through three stages from 1990 to the present. Using three heritage projects (Xintiandi, Tianzifang, Bugaoli), we focus on: 1) how each project was implemented and the economic and spatial outcomes each has produced; 2) how the mode of each project’s development interacted with the shifting official policies for heritage preservation; and 3) the implications of the findings, theoretical and practical, for more effective urban preservation

Chunk-Based Bi-Scale Decoder for Neural Machine Translation

In typical neural machine translation~(NMT), the decoder generates a sentence word by word, packing all linguistic granularities in the same time-scale of RNN. In this paper, we propose a new type of decoder for NMT, which splits the decode state into two parts and updates them in two different time-scales. Specifically, we first predict a chunk time-scale state for phrasal modeling, on top of which multiple word time-scale states are generated. In this way, the target sentence is translated hierarchically from chunks to words, with information in different granularities being leveraged. Experiments show that our proposed model significantly improves the translation performance over the state-of-the-art NMT model.Comment: Accepted as a short paper by ACL 201

On Content-centric Wireless Delivery Networks

The flux of social media and the convenience of mobile connectivity has created a mobile data phenomenon that is expected to overwhelm the mobile cellular networks in the foreseeable future. Despite the advent of 4G/LTE, the growth rate of wireless data has far exceeded the capacity increase of the mobile networks. A fundamentally new design paradigm is required to tackle the ever-growing wireless data challenge. In this article, we investigate the problem of massive content delivery over wireless networks and present a systematic view on content-centric network design and its underlying challenges. Towards this end, we first review some of the recent advancements in Information Centric Networking (ICN) which provides the basis on how media contents can be labeled, distributed, and placed across the networks. We then formulate the content delivery task into a content rate maximization problem over a share wireless channel, which, contrasting the conventional wisdom that attempts to increase the bit-rate of a unicast system, maximizes the content delivery capability with a fixed amount of wireless resources. This conceptually simple change enables us to exploit the "content diversity" and the "network diversity" by leveraging the abundant computation sources (through application-layer encoding, pushing and caching, etc.) within the existing wireless networks. A network architecture that enables wireless network crowdsourcing for content delivery is then described, followed by an exemplary campus wireless network that encompasses the above concepts.Comment: 20 pages, 7 figures,accepted by IEEE Wireless Communications,Sept.201