T cell receptor sequence clustering and antigen specificity

There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available. Current efforts in TCR specificity analysis focus on identifying characteristics in immune repertoires which can explain or predict disease outcome or progression, or can be used to monitor the efficacy of disease therapy. In this context, clustering of TCRs by sequence to reflect biological similarity, and especially to reflect antigen specificity have become of paramount importance. We review the main TCR sequence clustering methods and the different similarity measures they use, and discuss their performance and possible improvement. We aim to provide guidance for non-specialists who wish to use TCR repertoire sequencing for disease tracking, patient stratification or therapy prediction, and to provide a starting point for those aiming to develop novel techniques for TCR annotation through clustering

Identification of a cellulose synthase-associated protein required for cellulose biosynthesis

Cellulose synthase-interactive protein 1 (CSI1) was identified in a two-hybrid screen for proteins that interact with cellulose synthase (CESA) isoforms involved in primary plant cell wall synthesis. CSI1 encodes a 2,150-amino acid protein that contains 10 predicted Armadillo repeats and a C2 domain. Mutations in CSI1 cause defective cell elongation in hypocotyls and roots and reduce cellulose content. CSI1 is associated with CESA complexes, and csi1 mutants affect the distribution and movement of CESA complexes in the plasma membrane

The broiler meat system in Nairobi, Kenya: using a value chain framework to understand animal and product flows, governance and sanitary risks

Livestock food systems play key subsistence and income generation roles in low to middle income countries and are important networks for zoonotic disease transmission. The aim of this study was to use a value chain framework to characterize the broiler chicken meat system of Nairobi, its governance and sanitary risks. A total of 4 focus groups and 8 key informant interviews were used to collect cross-sectional data from: small-scale broiler farmers in selected Nairobi peri-urban and informal settlement areas; medium to large integrated broiler production companies; traders and meat inspectors in live chicken and chicken meat markets in Nairobi. Qualitative data were collected on types of people operating in the system, their interactions, sanitary measures in place, sourcing and selling of broiler chickens and products. Framework analysis was used to identify governance themes and risky sanitary practices present in the system. One large company was identified to supply 60% of Nairobi’s day-old chicks to farmers, mainly through agrovet shops. Broiler meat products from integrated companies were sold in high-end retailers whereas their low value products were channelled through independent traders to consumers in informal settlements. Peri-urban small-scale farmers reported to slaughter the broilers on the farm and to sell carcasses to retailers (hotels and butcheries mainly) through brokers (80%), while farmers in the informal settlement reported to sell their broilers live to retailers (butcheries, hotels and hawkers mainly) directly. Broiler heads and legs were sold in informal settlements via roadside vendors. Sanitary risks identified were related to lack of biosecurity, cold chain and access to water, poor hygiene practices, lack of inspection at farm slaughter and limited health inspection in markets. Large companies dominated the governance of the broiler system through the control of day-old chick production. Overall government control was described as relatively weak leading to minimal official regulatory enforcement. Large companies and brokers were identified as dominant groups in market information dissemination and price setting. Lack of farmer association was found to be system-wide and to limit market access. Other system barriers included lack of space and expertise, leading to poor infrastructure and limited ability to implement effective hygienic measures. This study highlights significant structural differences between different broiler chains and inequalities in product quality and market access across the system. It provides a foundation for food safety assessments, disease control programmes and informs policy-making for the inclusive growth of this fast-evolving sector

The Embryonic Transcriptome Of The Red-Eared Slider Turtle (Trachemys Scripta)

The bony shell of the turtle is an evolutionary novelty not found in any other group of animals, however, research into its formation has suggested that it has evolved through modification of conserved developmental mechanisms. Although these mechanisms have been extensively characterized in model organisms, the tools for characterizing them in non-model organisms such as turtles have been limited by a lack of genomic resources. We have used a next generation sequencing approach to generate and assemble a transcriptome from stage 14 and 17 Trachemys scripta embryos, stages during which important events in shell development are known to take place. The transcriptome consists of 231,876 sequences with an N-50 of 1,166 bp. GO terms and EC codes were assigned to the 61,643 unique predicted proteins identified in the transcriptome sequences. All major GO categories and metabolic pathways are represented in the transcriptome. Transcriptome sequences were used to amplify several cDNA fragments designed for use as RNA in situ probes. One of these, BMP5, was hybridized to a T. scripta embryo and exhibits both conserved and novel expression patterns. The transcriptome sequences should be of broad use for understanding the evolution and development of the turtle shell and for annotating any future T. scripta genome sequences

Local Embeddedness and Economic and Social Upgrading in Madagascar's Export Apparel Industry

Over the past decade, several Sub-Saharan African (SSA) countries have developed or expanded export-oriented apparel industries in the context of the Multi-Fibre Arrangement (MFA) quotas and preferential market access, most importantly under the African Growth and Opportunity Act (AGOA). Madagascar is different to the other main SSA low-income country (LIC) apparel exporters - Kenya, Lesotho and Swaziland - given its more diverse end markets and ownership structures and the political instability that led to the loss of AGOA status at the end of 2009. This paper assesses the development of Madagascar's export-oriented apparel industry and economic and social upgrading dynamics in particular in the context of the AGOA loss. It identifies four types of firms and value chains that differ with regard to ownership patterns, end markets and, most importantly, 'local embeddedness', with important implications for both economic upgrading dynamics and possibilities and the sustainability of the industry. The paper concludes that, despite the contraction in the exportoriented apparel industry post-AGOA, Madagascar is still a more successful apparel producer in terms of economic upgrading than the other main apparel-exporting LICs in SSA. The key to this trajectory lies in the differentiation of global value chain (GVC) relationships, local embeddedness and export diversification

Analysing intermediary organisations and their influence on upgrading in emerging agricultural clusters

This paper analyses intermediary organisations in developing economy agricultural clusters. The paper critically engages with a growing narrative in studies of intermediaries that have stressed the ownership structure of intermediaries as a key driver for enabling knowledge transfer, inter-firm learning and upgrading of small producers in clusters. Two case studies of Latin American clusters are presented and discussed. The study suggests that in addition to ownership structure, cluster governance and the embeddedness of intermediaries in clusters are critical factors that need to be taken into account in understanding the influence of intermediaries in the upgrading of small producers in clusters

Local supplier firms in Madagascar’s apparel export industry : Upgrading paths, transnational social relations and regional production networks

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Modelling of regulatory factor and managerial impact assessment in the regional economy sectors: a case-study of the Kaliningrad region (Russia)

This article discusses the methodology of developing tools for assessing regulatory factors and managerial impacts on the regional economy and individual sectors and businesses. The potential of projection models is investigated, including balance models, convergence of regional and sectoral projection and compiling reliable and representative data sets capable of describing the current economic situation. An attempt was made to develop a series of models for several regional economies; to that end, the modelling of managerial and regulatory impact assessment was used in combination with the well-known value chain approach. In the interests of effective public administration, one of the requirements is to create sectoral model formats compatible with the regional projection models. Results of pilot modelling managerial and regulatory impacts on Kaliningrad region’s economies are presented through examples of agribusiness, transport, industry, tourism and recreation. Implementation of regulatory impact modelling in the framework of the suggested approach is proved for other regions. The main advantage of the developed models for the regional management is their ability to reduce uncertainty in decision-making due to obtaining estimates of the impact of the decisions on the changing situation and the conditions for the development of sectors and industries