Transformation ländlicher Räume aus institutioneller Perspektive. Sozio-ökonomische Entwicklung und Landnutzungswandel in Xishuangbanna, Südwest-China.

Landscapes and societies in Xishuangbanna Dai Autonomous Prefecture in Southwest China have undergone unprecedented changes over the last 60 years. These transformations within the landscapes manifest themselves as land cover change, for example intensification of traditional land use systems and introduction of monocultures leading to deforestation, loss of biodiversity and other forms of environmental degradation. At the same time, communities and societies within these landscapes have experienced a certain degree of economic development, mainly through exploitation of natural resources. Through changing of political and economic frameworks, they have also profound transformations within their social and socio-cultural configurations. Based on the outcomes of field work in Xishuangbanna between 2006 and 2010, this study examines institutions, institutional voids and institutional change concerning land-use in the Naban River Watershed National Nature Reserve. Combining socio-economic and ecological data, patterns of land-use change and their interrelation to local communities are explored. With the emergence of the rubber-line, a socio-ecological frontier, disparities between upland and lowland landscapes and communities are intensifying.Wie viele andere Regionen weltweit haben Landschaften und Gesellschaften Xishuangbannas, einer Präfektur im Südwesten Chinas in den letzten 60 Jahren rasante Veränderungen erfahren. Auf Landschaftsebene manifestieren sich diese Transformationen als Landnutzungswandel, z. B. durch Intensivierung traditioneller Landnutzungspraktiken und Modernisierung der Landwirtschaft. Besonders die Einführung von Monokulturen führt zu Entwaldung, Verlust der biologischen Diversität und anderen Arten von Umweltdegradation und -zerstörung. Zur gleichen Zeit haben Dorfgemeinschaften und Gesellschaften zu einem gewissen Grad durch wirtschaftliche Entwicklung von der Ausbeutung der natürlichen Ressourcen profitiert, einhergehend mit tiefgreifenden Veränderungen ihrer sozialen und sozioökonomischen Gefüge. Besonders über die Zusammenhänge zwischen ökologischen und sozialen Veränderungen ist bisher wenig bekannt. Die Möglichkeit zur Feldforschung in und über eine abgelegene, aber gleichzeitig diverse und dynamische Region wie Xishuangbanna bot eine wertvolle Gelegenheit, Mensch-Umweltbeziehungen näher zu erforschen. Die Forschung für diese Doktorarbeit erfolgte im Rahmen eines multidisziplinären Forschungsprojektes mit dem Titel "Erhaltung von Kulturlandschaften durch Diversifizierung der Ressourcen-Nutzung, Strategien und Technologien für Agrar-Ökosystemen im bergigen Südwesten Chinas", auch bekannt als "Living Landscapes China" (LILAC)

Finding approximate gene clusters with GECKO 3

Winter S, Jahn K, Wehner S, et al. Finding approximate gene clusters with GECKO 3. Nucleic Acids Research. 2016;44(20):9600-9610.Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min

Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins

Background Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requires the development of genetic tools to study polymorphism, differentiation, and stock structure. This study aimed to investigate genomic polymorphism through ddRAD sequencing, in order to identify a panel of single nucleotide polymorphisms (SNPs) and to simultaneously assess genetic diversity and structure in wild (from rivers Amazon, Solimões, Tocantins and Araguaia) and captive populations. Results Compared to many other teleosts, the degree of polymorphism in A. gigas was low with only 2.3% of identified RAD-tags (135 bases long) containing SNPs. A panel of 393 informative SNPs was identified and screened across the five populations. Higher genetic diversity indices (number of polymorphic loci and private alleles, Shannon’s Index and HO) were found in populations from the Amazon and Solimões, intermediate levels in Tocantins and Captive, and very low levels in the Araguaia population. These results likely reflect larger population sizes from less urbanized environments in the Amazon basin compared to Araguaia. Populations were significantly differentiated with pairwise FST values ranging from 0.086 (Amazon × Solimões) to 0.556 (Amazon × Araguaia). Mean pairwise relatedness among individuals was significant in all populations (P

Identification of proteins from the secretory/excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus (Linnaeus, 1758) reveals unique secreted proteins amongst haematophagous ecdysozoa

Background It is hypothesised that being a blood-feeding ectoparasite, Argulus foliaceus (Linnaeus, 1758), uses similar mechanisms for digestion and host immune evasion to those used by other haematophagous ecdysozoa, including caligid copepods (e.g. sea louse). We recently described and characterised glands associated with the feeding appendages of A. foliaceus using histological techniques. The work described in the present study is the first undertaken with the objective of identifying and partially characterising the components secreted from these glands using a proteomic approach. Methods Argulus foliaceus parasites were sampled from the skin of rainbow trout (Oncorhynchus mykiss), from Loch Fad on the Isle of Bute, Scotland, UK. The proteins from A. foliaceus secretory/excretory products (SEPs) were collected from the supernatant of artificial freshwater conditioned with active adult parasites (n = 5–9 per ml; n = 560 total). Proteins within the SEPs were identified and characterised using LC-ESI-MS/MS analysis. Data are available via ProteomeXchange with identifier PXD016226. Results Data mining of a protein database translated from an A. foliaceus dataset using ProteinScape allowed identification of 27 predicted protein sequences from the A. foliaceus SEPs, each protein matching the criteria of 2 peptides with at least 4 contiguous amino acids. Nine proteins had no matching sequence through OmicsBox (Blast2GO) analysis searches suggesting that Argulus spp. may additionally have unique proteins present in their SEPs. SignalP 5.0 software, identified 13 proteins with a signal sequence suggestive of signal peptides and supportive of secreted proteins being identified. Notably, the functional characteristics of identified A. foliaceus proteins/domains have also been described from the salivary glands and saliva of other blood-feeding arthropods such as ticks. Identified proteins included: transporters, peroxidases, metalloproteases, proteases and serine protease inhibitors which are known to play roles in parasite immune evasion/induction (e.g. astacin), immunomodulation (e.g. serpin) and digestion (e.g. trypsin). Conclusions To our knowledge, the present study represents the first proteomic analysis undertaken for SEPs from any branchiuran fish louse. Here we reveal possible functional roles of A. foliaceus SEPs in digestion and immunomodulation, with a number of protein families shared with other haematophagous ectoparasites. A number of apparently unique secreted proteins were identified compared to other haematophagous ecdysozoa

Characterisation of the First Bovine Parainfluenza Virus 3 Isolate Detected in Cattle in Turkey

A respiratory disease outbreak on a cattle farm in northern Turkey produced respiratory tract symptoms and severe pneumonia symptoms in 20 calves. Eight calves died, and a lung specimen from one carcass was analysed for bacteria and for viruses of the Bovine respiratory diseases complex. Bacteriological analysis was negative, but antigen detection ELISA and RT-PCR results indicated the presence of Bovine parainfluenza virus (BPIV). Virus isolation succeeded on Madin-Darby Bovine Kidney cells, and subsequent whole genome sequencing and phylogenetic analysis identified BPIV-3c. This is the first report of BPIV-3c isolation from cattle in Turkey, indicating the need for more virological and epidemiological studies

Development of SNP and microsatellite markers for goldsinny wrasse (Ctenolabrus rupestris) from ddRAD sequencing data

Wrasse (Labridae) species have been used as parasite cleaners in Atlantic salmon farming since the 1980s. However, their use has recently escalated, with millions now being introduced into salmon cages each year. Most fish are of wild origin, their exploitation potentially impacting native populations. Genetic information is urgently required to inform management decisions. We identified 174 microsatellite and 149 SNP markers from ddRAD sequence data. From these, 17 and 48 microsatellite and SNP markers, respectively, were validated by genotyping 150 goldsinny wrasse collected from five locations along the Norwegian and Swedish coasts. Two to 30 alleles were identified at the microsatellite loci, while gene diversity (He) ranged 0.101&ndash;0.907. All SNP loci were biallelic, with averagedHeper locus ranging between 0.063 and 0.495

Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology

The Gram-positive bacterium Listeria monocytogenes&nbsp;is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. L. monocytogenes&nbsp;causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. Listeriosis has one of the highest mortality rates (up to 30%) of all food-borne infections. This human pathogenic bacterium is an important model organism for biomedical research to investigate cell-mediated immunity. L. monocytogenes&nbsp;is also one of the best characterised bacterial systems for the molecular analysis of intracellular parasitism. Recently several transcriptomic studies have also made the ubiquitous distributed bacterium as a model to understand mechanisms of gene regulation from the environment to the infected host on the level of mRNA and non-coding RNAs (ncRNAs). We have used semiconductor sequencing technology for RNA-seq to investigate the repertoire of listerial ncRNAs under extra- and intracellular growth conditions. Furthermore, we applied a new bioinformatic analysis pipeline for detection, comparative genomics and structural conservation to identify ncRNAs. With this work, in total, 741 ncRNA locations of potential ncRNA candidates are now known for L. monocytogenes, of which 611 ncRNA candidates were identified by RNA-seq. 441 transcribed ncRNAs have never been described before. Among these, we identified novel long non-coding antisense RNAs with a length of up to 5,400 nt e.g. opposite to genes coding for internalins, methylases or a high-affinity potassium uptake system, namely the kdpABC&nbsp;operon, which were confirmed by qRT-PCR analysis. RNA-seq, comparative genomics and structural conservation of L. monocytogenes&nbsp;ncRNAs illustrate that this human pathogen uses a large number and repertoire of ncRNA including novel long antisense RNAs, which could be important for intracellular survival within the infected eukaryotic host

Genomewide comparison and novel ncRNAs of Aquificales

Background&nbsp; The Aquificales&nbsp;are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae&nbsp;and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism.&nbsp; Results&nbsp; In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales&nbsp;based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins.&nbsp; Combining severalin silicofeatures (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo&nbsp;dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium.&nbsp; Conclusions&nbsp; We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico&nbsp;analysis with dRNA-seq data of A. aeolicus&nbsp;we predict nearly 100 novel ncRNA candidates

Detection of Chikunguny a virus by RT-LAMP

Background A single-tube one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of chikungunya virus (CHIKV) targeting the conserved 6K-E1 target region was developed. The assay was validated with sera collected from a CHIKV outbreak in Senegal in 2015. Methodology/Principal findings A novel design approach by combining Principal Component Analysis and phylogenetic analysis of 110 available CHIKV sequences and the LAMP oligonucleotide design software LAVA was used. The assay was evaluated with an External Quality Assessment panel from the European Network for Diagnostics of "Imported" Viral Diseases and was shown to be sensitive and specific and did not cross-detect other arboviruses. The limit of detection as determined by probit analysis, was 163 molecules, and 100% reproducibility in the assays was obtained for 103 molecules (7/8 repetitions were positive for 102 molecules). The assay was validated using 35 RNA samples extracted from sera, and results were compared with those obtained by quantitative RT-PCR carried out at the Institut Pasteur Dakar, demonstrating that the RT-LAMP is 100% sensitive and 80% specific, with a positive predictive value of 97% and negative predictive value of 100%. Conclusions/Significance The RT-LAMP appeared to show superior performance with material stored for months compared to qRT-PCR and can be therefore recommended for use in infrastructures with poor settings

Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV) the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982-2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59% of the IPNV isolates belonged to the persistent type and 32% to the low virulent type and only one highly pathogenic strain0 (1.79%) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Underrepresentation of CpG dinucleotides in the IPNV genome to minimise detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes together with the assumption of adaptation and immune escape indicates that IPNV is evolving with the host