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ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
To quantify the ChIP signal we will firstly construct 1-kilobase-wide tilling windows over the genome, and subsequently count the number of reads in each window, for each experiment. We will then normalize the counts, to account for a different total number of reads in each experiment, and finally calculate the correlation between all pairs of samples. Although this procedure represents a crude way of data quantification, it provides sufficient information to ascertain the data quality.
The transformation and fragmentation of Canadian agriculture
Published in Alan Hall, The Subjectivities and Politics of Occupational Risk, 2020
While adding substantially to the pesticide bill, there were substantial savings in time, fertilizer and fuel costs, since tilling is by its very nature a slow and fuel-intensive process. The farmers could also often dispense with the larger, more powerful tractors needed for plowing, although the planting drills were heavier and more expensive than regular planters so the cost savings on machinery and fuel balance out to some extent. However, there was also a need for more careful management of timing for planting to ensure proper seeding. A greater sensitivity to wet weather often complicated things considerably in terms of seed germination and mould problems, and consequently, accentuated production and timing pressures. On the other hand, no-till crops tended to weather drought conditions better (OMAF, 1993a). Although no-till could reduce the amount of time farmers and their workers spent in a given field area, in practice no-till was partly encouraged by the government and agri-food industry as a way of expanding the amount of land farmed by a given operator. Several case-study adopters claimed that they were working harder and longer hours as a result (see also Hall, 1998b)
Genetically Engineered Food
Published in David Lightsey, The Myths about Nutrition Science, 2019
Let me highlight just a few of the positive points genetic engineering (GE) has to offer the food production process: Developing varieties which are more pest and pathogen resistant which will decrease the use of pesticides.Developing varieties which tolerate heat and drought.Reducing the acreage used for food production because yield per acre will be greater.Reducing soil erosion due to less tilling.Improving water quality due to a reduced need for insecticides and herbicides.Allowing the poor to eat by expanding food production in areas that were once less tolerant to a crop due to marginal soil or environmental factors.Increasing yield per acre at a decreased cost.Yielding nutritionally enhanced crops for regional use.Increasing shelf life of food.
Application of HMTL and novel IWQI models in rural groundwater quality assessment: a case study in Nigeria
Published in Toxin Reviews, 2022
Daniel A. Ayejoto, Johnbosco C. Egbueri, Monday T. Enyigwe, Osita I. Chiaghanam, Peter D. Ameh
Ameka and its surrounding rural communities in southeastern Nigeria were chosen as the study region for this assessment. This area lies between 6°8′N and 6°13′N latitudes and 8°5′E and 8°10′E longitudes (Figure 1). The vast majority of the people who live in this area work in open-pit mines. Some of the locals still work in salt mines. Since it is a rural region, many of these miners are uneducated, and as a result, they violate certain environmental regulations that govern mining in Nigeria. In other words, many of the miners are involved in illicit and indiscriminate mining practices. Furthermore, for food security and economic benefit, residents of Ameka and its environs rely heavily on small, medium, and large-scale agricultural activities. The region is naturally endowed with fertile soils, which boost agricultural productivity. As a result, farmers seldom use inorganic fertilizers in their farming. However, continuous tilling of agricultural lands (soils) is thought to dissociate ore deposits in the region, allowing some associated PTEs to become free and ready to transit into water systems. When released into water, the PTEs in water end up posing health and environmental threats to water users who mostly do not treat their water before drinking. In general, it is thought that the high level of mining and agricultural activities and volumes of wastes produced in this region pollute the available rural water supplies.
Nutrition Provides the Essential Foundation for Optimizing Mental Health
Published in Evidence-Based Practice in Child and Adolescent Mental Health, 2021
Julia J. Rucklidge, Jeanette M. Johnstone, Bonnie J. Kaplan
Several causes of nutrient depletion of our food have been identified. Modern agriculture has sought to increase the yield for many crops to increase financial margins, which creates a “dilution effect” of lower nutrient levels (Marles, 2017). Many years of tilling the soil, even with rotating crops, depletes minerals. Food producers use fertilizer, the primary components of which are nitrogen, phosphorous, and potassium (NPK). While these three are important, plants require 15–16 essential minerals for best growth, defense against insects, and the ability to synthesize vitamins (Datnoff et al., 2007).
Understanding neurobehavioral genetics of zebrafish
Published in Journal of Neurogenetics, 2020
Sergey V. Cheresiz, Andrey D. Volgin, Alexandra Kokorina Evsyukova, Alim A.O. Bashirzade, Konstantin A. Demin, Murilo S. de Abreu, Tamara G. Amstislavskaya, Allan V. Kalueff
Despite the need for efficient gene KO to produce LOF phenotypes, such reverse genetics approaches have originally been unavailable in zebrafish (Hisano, Ota, & Kawahara, 2014). While mouse KO uses homologous recombination and electroporation into embryonic stem cells (ESC), this approach is impossible in zebrafish because they lack ESC (Hisano et al.,2014; Kurowska et al.,2011). The TILLING approach to the target-selected KO, instead, used a hybrid technique based on ENU mutagenesis (as in zebrafish forward genetics screens) combined with mutant screening by amplification of genes and cleavage of only mutant heteroduplexes with the surveyor endonuclease CEL-I. However, the problem with TILLING is that the carrier of a target mutation in the gene of interest is likely to harbor other simultaneous ENU-induced mutations at other loci (Kurowska et al.,2011), complicating linking the observed phenotype to a specific mutation. Albeit gradually replaced by artificial site-specific endonuclease-based approaches (e.g. Zn-finger nucleases ZFNs, TALENs, and CRISPR/Cas9), TILLING remains useful in zebrafish neurogenetics. For example, TILLING-generated KO of the fragile X mental retardation (fmr1) gene in the Fragile X syndrome (FXS) zebrafish model recapitulates intellectual disability, anxiety, autism and other clinical behavioral deficits (den Broeder et al.,2009). Likewise, the zebrafish KO model of superoxide dismutase (SOD)-related ALS produced by TILLING is better than current murine models, since fish express mutant Sod1 at physiological levels (as in ALS patients), unlike its overexpression in transgenic mice (Da Costa et al.,2014). Thus, less efficient than the artificial site-specific endonuclease-based approaches in generating KO, TILLING can still be used for the targeted selection of point or short indel mutants with complex physiological roles in zebrafish disease models.