Improvement in the Production of L-Lysine by Overexpression of Aspartokinase (ASK) in C. glutamicum ATCC 21799

Purpose: To clone Corynebacterium glutamicum ATCC21799 aspartokinase gene (EC 2.7.2.4) using shuttle expression vector pEKEx2 in order to increase lysine production.Methods: C. glutamicum DNA was extracted and used for amplification of aspartokinase gene (ask) by cloning into an E. coli/C. glutamicum shuttle expression vector, pEKEx2. Initially, the recombinant vector transformed into E. coli DH5á and then into C. glutamicum.Results: Electrophoresis of recombinant protein by SDS-PAGE showed that the molecular weight of the recombinant protein was 42 KD. The induction of recombinant vector by IPTG had an inhibitory effect on cell growth due to over-expression of the cloned gene. The results of lysine assay by Chinard method showed that lysine production increased about two-fold, compared with the parent strain, as a result of increased copy numbers of lysC gene in recombinant strain.Conclusion: A two-fold increase in lysine production was observed by cloning of the ASK gene in C. glutamicum rather than in E. coli, due to the presence of lysine exporter channel which facilitates lysine extraction.Keywords: LysC gene, Corynebacterium glutamicum, L- lysine, Cloning, Aspartokinase, E. col

The structures underpinning vulnerability: examining landscape-society interactions in a smallholder coffee agroforestry system

Smallholder farmers dependent on rain-fed agriculture are particularly vulnerable to extreme climate events and, therefore, it is necessary to identify adaptive measures that would increase farmer resilience to these shocks. The management options in a low-input system, like forest coffee (Coffea arabica), are limited and there are several factors out of farmers' control driving their vulnerability to changing climatic conditions. These can relate to social structures and landscape factors, which can interact to reduce farmers' adaptive capacity, creating a state of contextual vulnerability. We explored the potential synergies of this interaction across elevation, patch area and shade management gradients for smallholder coffee farms around the UNESCO Yayu Coffee Forest Biosphere Reserve in Ethiopia before, during and immediately following the 2015/16 El Niño. We documented a dramatic collapse in coffee yields across all farms, resulting in coffee incomes 29.5 ± 18.0 % and 19.5 ± 10.0 % of 2014 incomes in 2015 and 2016, respectively. We identified farms at elevations between 1500-1600 m with canopy openness between 40-45 % as being consistently low yielding over our study period. We found these farmers had the highest rates of income diversification and, therefore, were already exhibiting adaptive capacity. Farmers with the largest income losses were spatially concentrated between 1600-1700 m, located in larger patch areas with lower canopy openness. Farmers at this elevation have access to poor infrastructure, restrictions on shade management and reported higher dependence on income from coffee, indicating an interaction of biotic and social factors exacerbating their vulnerability. Unfortunately, due to a nationally declared state of emergency, we were unable to survey farmers on the adaptive measures they undertook; therefore, we are limited in assessing their resilience. However, we do show the importance of considering both biotically and socially-mediated influences for assessing smallholder vulnerability, particularly barriers to diversifying incomes

Biodiversity–production feedback effects lead to intensification traps in agricultural landscapes

Intensive agriculture with high reliance on pesticides and fertilizers constitutes a major strategy for ‘feeding the world’. However, such conventional intensification is linked to diminishing returns and can result in ‘intensification traps’—production declines triggered by the negative feedback of biodiversity loss at high input levels. Here we developed a novel framework that accounts for biodiversity feedback on crop yields to evaluate the risk and magnitude of intensification traps. Simulations grounded in systematic literature reviews showed that intensification traps emerge in most landscape types, but to a lesser extent in major cereal production systems. Furthermore, small reductions in maximal production (5–10%) could be frequently transmitted into substantial biodiversity gains, resulting in small-loss large-gain trade-offs prevailing across landscape types. However, sensitivity analyses revealed a strong context dependence of trap emergence, inducing substantial uncertainty in the identification of optimal management at the field scale. Hence, we recommend the development of case-specific safety margins for intensification preventing double losses in biodiversity and food security associated with intensification traps

Pursuing climate resilient coffee in Ethiopia – a critical review

This paper provides a multi-scalar examination of the Ethiopian coffee sector and its pursuit of climate resilience. Concern is growing about the potential impact of climate change on Arabica coffee in Ethiopia and the 25 million livelihoods it supports. Arabica coffee has a relatively narrow envelope of climatic suitability and recent studies suggest that the area of bioclimatically suitable space for the species in its native Ethiopia could decline dra- matically in the coming decades. We adopt a critical perspective on resilience that reflects on the situated nature of the ecology/science of coffee and climate change and the operation of social, economic, and discursive power across scales, paying particular attention to the differentiated impacts of climate change and associated resi- lience strategies. This analysis begins by reviewing Ethiopia’s Climate Resilient Green Economy strategy and argues that the current lack of attention to coffee is inappropriate considering the coffee sector’s vulnerability to climate change, economic importance and association with forests. The paper then examines the contemporary coffee sector which provides the context for reflecting on three potential responses to the threat climate change poses; a spatial response from farmers, adaptive farm management responses such as changing shade levels and the development of the country’s genetic resources to cultivate improved varieties. The analysis explores the disconnect between the interventions emerging from national and international institutions and the local con- text. The multi-scale approach highlights the presence of complex normative trade-offs associated with pursing climate resilience strategies and reinforces the importance of appreciating the dynamics which influence deci- sion-making in the country

Standard of insurance procedures and risk assessment manual for cold water fish culture regarding management and natural disasters

The total production of Rainbow trout fish aquaculture in 2009 had been 72515 t which was significantly increased (91519 t) in 2010. Despite of increasing trout fish production during last decade, absence conformity between suitable cultural and proliferation district of this fish species and geographical one, faced this industry harmfully to natural disasters such as flood, overflow and so on, and mismanagement due to human injustices. Hence insurance and supporting concept of can be having a determinant role in efflorescence and increasing production of this fish. The aim of this project is performing an insurance policy based on risk analysis model in propagation and cultural phases of rainbow trout aquaculture, separately. In this study, pay attention to standards in trout fish aquaculture procedure and determination of critical parameters on, are the first research step and recognition of risk factors in different aquaculture phases due to natural disasters and mismanagement, from the brood stock maintenance till reach to 3-5 g fingerling and finally market size fishes, are the following research steps. After determination of proportion percentages of each parameters regarding to arise the risk, analysis risks and risk management were done for trout fish aquaculture. Three provinces, Fars, Mazandaran and Charmahal Bakhtiary as poles production of trout fish were chosen as delegates of the whole Iran and insurance ability of trout fish hatcheries and aquaculture farms were done. Trout aquaculture standardization were obtained, natural disasters and mismanagement affected on aquaculture activities were recognized (Chapters 1 and 3) and due to importance of health and disease of trout fish, mortality causes and audit signs of also determined and analyzed (Chapter 2) . In Chapter 4, trout farms degraded and fix and natural disasters for trout fish brood stock, propagation hatcheries and cultural farms were analyzed and accounted. Finally, premium and recompense were accounted for hatchery and farm separately

Responsible aquaculture: warm water fish preparation management and preparation of guidelines

Responsible aquaculture is a new concept in Iran but in some countries there are good historical performances. In fact this concept is as the spacial challenge for developing countries in order to improvement of aquaculturist livelihood. In bangladesh, near to 60% of the people, which the most of are villagers, live under the poor line. Developing the NGOs and their activities to reach the responsible aquaculture objectives were so effective, since this activity has been knew as profitable acuaculture and many international workshops, symposiums and conferences have been held in this regard all the world. In this project, a complex of parameters affected on preparing management of warmwater fish farms have been studied with using previous studies and experiments of different countries and executive guidelines of four modules prepared including: -Guidline of preparing of warmwater fish ponds -Guidline of water enrichment and using fertilization in warmwater fish ponds -Guidline of using aeration in warmwater fish ponds -Guidline of stocking method in warmwater fish pond

Quantitative evaluation and identification of fungi in Shahid Rajaeii Dam Lake, Mazandaran Province (Sari)

The present study is carried out to investigate the fungal species present in water of Shahid Rajaeii damlake in Sari, (Mazandaran province). Samples were taken from five stations including, Station 1: Input of Shirinrud river, station 2: Input of Sefidrud river, Station 3: The confluence of the two branches, Station 4: dam crest and stations 5: Output dam from June to February 2012. Every sample was diluted by sterile saline (10-1 and 10-2) and 0.5 mL from each dilution was cultured on SD and incubated at 27-30°C for 3-5 days. Finally, the number of colonies wasrecorded as (colony forming unit = CFU) per 100 mL. Identification of fungal agents were conducted by slide culture preparation and stained in lacto-phenol blue. The results showed that in August and February were significantly highest and lowest rates of fungal colonies were isolated from water in different stations respectively. Moreover, the number of fungal colonies in the crown and the output was significantly higher than other stations. The frequency of identified fungi were: Aspergillus species (31.4%), various types of yeast (mainly Candida) (24.2%), Penicillium sp. (19.3%), Cladosporium sp.(10.3%), Mucor sp. (5.4%), Fusarium sp. (2.9%), sterile hype (2.8%), Alternaria sp. (2.3%) and Paecilomyces sp. (1.4%)

Optimum management of warmwater fish farms stocking, capacity determination, growth rate and brood stock managements and harvesting

This study was conducted to codify the guideline and indexes of optimal management in warm-water fish farms to attain sustainable aquaculture which they are population density, species diversity, brood stock'smanagements, capacity determination, growth and harvesting managements in cultural ponds. As results, these guideline and indexes were codifies for these fish farms and propagation centers. It's obviously that these sustainable patterns can be used for improving of permanent development for this aquacultural industry

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000–12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural rearrangements in the small dispensable chromosomes, while footprints of positive selection were present in only a small number of protein coding genes