Advances in biotechnology: genomics and genome editing

Genomics, the study of genes, their functions and related techniques has become a crucial science for developing understanding of life processes and how they evolve. Since the advent of the human genome project, huge strides have been made in developing understanding of DNA and RNA sequence information and how it can be put to good use in the biotechnology sector. Newly derived sequencing and bioinformatics tools have added to the torrent of new insights gained, so that 'sequence once and query often' type DNA apps are now becoming reality. Genome editing, using tools such as CRISPR/Cas9 nuclease or Cpf1 nuclease, provide rapid methods for inserting, deleting or modifying DNA sequences in highly precise ways, in virtually any animal, plant or microbial system. Recent international discussions have considered human germline gene editing, amongst other aspects of this technology. Whether or not gene edited plants will be considered as genetically modified remains an important question. This will determine the regulatory processes adopted by different groups of nations and applicability to feeding the world's ever growing population. Questions surrounding the intellectual property rights associated with gene editing must also be resolved. Mitochondrial replacement therapy leading to '3-Parent Babies' has been successfully carried out in Mexico, by an international team, to correct mother to child mitochondrial disease transmission. The UK has become the first country to legally allow 'cautious use' of mitochondrial donation in treatment. Genomics and genome editing will continue to advance what can be achieved technically, whilst society determines whether or not what can be done should be applied

The Development of Spatial-Temporal, Probability, and Covariation Information to Infer Continuous Causal Processes

This paper considers how 5- to 11-year-olds’ verbal reasoning about the causality underlying extended, dynamic natural processes links to various facets of their statistical thinking. Such continuous processes typically do not provide perceptually distinct causes and effect, and previous work suggests that spatial–temporal analysis, the ability to analyze spatial configurations that change over time, is a crucial predictor of reasoning about causal mechanism in such situations. Work in the Humean tradition to causality has long emphasized on the importance of statistical thinking for inferring causal links between distinct cause and effect events, but here we assess whether this is also viable for causal thinking about continuous processes. Controlling for verbal and non-verbal ability, two studies (N = 107; N = 124) administered a battery of covariation, probability, spatial–temporal, and causal measures. Results indicated that spatial–temporal analysis was the best predictor of causal thinking across both studies, but statistical thinking supported and informed spatial–temporal analysis: covariation assessment potentially assists with the identification of variables, while simple probability judgment potentially assists with thinking about unseen mechanisms. We conclude that the ability to find out patterns in data is even more widely important for causal analysis than commonly assumed, from childhood, having a role to play not just when causally linking already distinct events but also when analyzing the causal process underlying extended dynamic events without perceptually distinct components

Determination of some major and trace elements in the lower Sakarya River water by ICP-MS

In this paper, water and sediment samples were collected along the Lower Sakarya River basin for a twelve month period between February 2007 and January 2008. The samples were analysed for trace elements (31 elements in sediment and 33 elements in water) using the ICP-MS technique as pollution indicators. The results indicated that the Sakarya River water was polluted by sources of beryllium and thallium which exceeded the limits set by US Environmental Protection Agency (USEPA 2003). Sediments were polluted by Antimony, Tin, Rhodium and Selenium. The results also provide useful data for the conservation of the Black Sea where it is joined by the Sakarya River. (C) 2018 ACG Publications. All rights reserved

Challenges in the Search for Perchlorate and Other Hydrated Minerals With 2.1-μm Absorptions on Mars

A previously unidentified artifact has been found in Compact Reconnaissance Imaging Spectrometer for Mars targeted I/F data. It exists in a small fraction (<0.05%) of pixels within 90% of images investigated and occurs in regions of high spectral/spatial variance. This artifact mimics real mineral absorptions in width and depth and occurs most often at 1.9 and 2.1 μm, thus interfering in the search for some mineral phases, including alunite, kieserite, serpentine, and perchlorate. A filtering step in the data processing pipeline, between radiance and I/F versions of the data, convolves narrow artifacts (“spikes”) with real atmospheric absorptions in these wavelength regions to create spurious absorption-like features. The majority of previous orbital detections of alunite, kieserite, and serpentine we investigated can be confirmed using radiance and raw data, but few to none of the perchlorate detections reported in published literature remain robust over the 1.0- to 2.65-μm wavelength range

Determination of Boron in hazelnut varieties with the addition of sorbitol by using ICP-OES and ultrasonic nebulization after microwave digestion system

Boron is an essential nutrient for plants and an essential element for many organisms, but can be toxic to aquatic and terrestrial organisms above certain concentrations. The aim of this research is determining the Boron content of four varieties of Hazelnut (Corylus avellana L.) from Sakarya. Inductively coupled plasma optical emission spectrometry (ICP-OES) with ultrasonic nebulization (USN) was used for the determination of Boron contents. This method is based on microwave digestion system and reduced memory effect of Boron by using sorbitol. Different conditions were optimized for this method. Four hazelnut varieties, eight soil samples and certificated reference material (NIM-GBW10012) were analyzed. The Boron contents were found as 18.27, 28.3, 38.6, 17.6 mg/kg in Kara, Sivri, Delisava and Tombul hazelnut varieties, respectively. And Boron contents of soil samples were between 30.44 to 196.79 mg/kg. The results revealed that the Turkish hazelnut is a good natural source of Boron. (C) 2018 ACG Publications. All rights reserved

The interaction between ectomycorrhizal fungi and growth promoting bacteria in plant development from in-vitro to the field

There is currently an array of biotechnological tools which may positively influence plant development and establishment. Symbiosis with ectomycorrhizal fungi is known to improve plant health by increasing nutrient and water uptake and alleviating environmental stresses. Some rhizosphere bacteria are also proven to act as plant stimulating agents, health managers and growth promoters. The use of a combined inoculum using both microorganisms has great potential in forestry. Nevertheless, the interaction between fungi and bacteria is highly specific and bacteria are known not only to enhance fungal growth (mycorrhiza promoting bacteria), but also to strongly inhibit it. It is therefore important to evaluate the compatibility between ectomycorrhizal fungi and bacteria and to determine the impact of such combination in plant development when aiming at the use of optimized microbial inoculum for enhancing plant growth. In the present work we investigated the use of a dual inoculation system, consisting of a bacterial strain from the genus Mesorhizobium in combination with ectomycorrhizal fungi, from in-vitro tests to a nursery stage followed by transplantation to the field. Approximately 5000 seedlings were used in these experiments comprising Quercus suber, Quercus robur, Quercus rubra, Pinus pinaster and Pinus pinea. Seedlings were grown for 9 months in a commercial forest greenhouse and then transplanted to 4 locations in Portugal. The first sampling was made before field transplantation. Results showed that the combined use of fungi-bacteria inoculum significantly influenced plant growth and its effect was different from that of each individual microbial partner, emphasizing the strong interaction between microorganisms

A Mutation in Amino Acid Permease AAP6 Reduces the Amino Acid Content of the Arabidopsis Sieve Elements but Leaves Aphid Herbivores Unaffected.

The aim of this study was to investigate the role of the amino acid permease gene AAP6 in regulating phloem amino acid composition and then to determine the effects of this altered diet on aphid performance. A genotype of Arabidopsis thaliana (L.) was produced in which the function of the amino acid permease gene AAP6 (At5g49630) was abolished. Plants homozygous for the insertionally inactivated AAP6 gene had a significantly larger mean rosette width than the wild type and a greater number of cauline leaves. Seeds from the aap6 mutant were also significantly larger than those from the wild-type plants. Sieve element (SE) sap was collected by aphid stylectomy and the amino acids derivatized, separated, and quantified using Capillary Electrophoresis with Laser Induced Fluorescence (CE-LIF). In spite of the large variation across samples, the total amino acid concentration of SE sap of the aap6 mutant plants was significantly lower than that of the wild-type plants. The concentrations of lysine, phenylalanine, leucine, and aspartic acid were all significantly lower in concentration in the aap6 mutant plants compared with wild-type plants. This is the first direct demonstration of a physiological role for an amino acid transporter in regulating SE composition in vivo. The amino acid availability in sieve element sap is thought to be the major limiting factor for aphid growth and reproduction. Despite the changes in their diet, the aphid Myzus persicae(Sulzer) displayed only small changes in feeding behaviour on mutant plants when measured using the Electronic Penetration Graph (EPG) technique. Salivation by the aphid into the SE (E1 phase) was increased on mutant plants but there was no significant effect on other feeding EPG behaviours, or in the rate of honeydew production. Consistent with the small effect on aphid feeding behaviour, there was only a small effect of reduced sieve element amino acid concentration on aphid reproduction. The data are discussed in relation to the regulation of phloem composition and the role of phloem amino acids in regulating aphid performance

Combining ectomycorrhizal fungi and bacteria: a powerful tool to improve tree performance

Ectomycorrhizal fungi are ubiquitous to forest soils and the symbiosis between these microorganisms and plants roots is known to be essential for tree establishment and development, especially in areas of poor soil. Studies have also shown that some rhizosphere bacteria may act as plant stimulating agents and growth promoters. Additionally, bacteria and fungi strongly interact and therefore the analysis of the triangle plant-fungi-bacteria is a vital approach when aiming at the use of microbial inocula to enhance plant performance. To obtain a synergistic combination between microorganisms, a thorough selection is required since bacteria may strongly inhibit fungal growth, and vice versa, incurring in the risk of failed inoculum. In the present work we investigated the use of a dual inoculation system, consisting of a bacterial strain from the genus Mesorhizobium in combination with selected ectomycorrhizal fungi. In vitro tests were performed to assess the dynamic of co-culturing both microorganisms. The inoculum was applied at nursery stage and saplings were then transplanted into the field. Approximately 5000 seedlings were used in this experiment comprising the following species: Quercus suber, Quercus robur, Quercus rubra, Pinus pinaster and Pinus pinea. Seedlings were grown for 9 months in a commercial forest greenhouse and then transplanted to 4 locations in Portugal: Mindelo, Santo Tirso, Vila do Conde and Proença-a-Nova. Samples were taken at the end of nursery phase and 8 months after transplantation. Biometric and mycorrhizal parameters were analyzed and the persistence of the inoculated strains was evaluated. The presence of selected phytohormones was also determined. Results showed that the combined use of fungi-bacteria inoculum can be more effective than the use of each individual microbial partner. The use of ectomycorrhizal fungi and bacteria has great potential in forestry as a biotechnological tool to produce high performance plants at nursery stage and in the field