Resistance to natural and synthetic gene drive systems

Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general.

Genetic Biocontrol for Invasive Species

Invasive species are increasingly affecting agriculture, food, fisheries, and forestry resources throughout the world. As a result of global trade, invasive species are often introduced into new environments where they become established and cause harm to human health, agriculture, and the environment. Prevention of new introductions is a high priority for addressing the harm caused by invasive species, but unfortunately efforts to prevent new introductions do not address the economic harm that is presently manifested where invasive species have already become established. Genetic biocontrol can be defined as the release of organisms with genetic methods designed to disrupt the reproduction of invasive populations. While these methods offer the potential to control or even eradicate invasive species, there is a need to ensure that genetic biocontrol methods can be deployed in a way that minimizes potential harm to the environment. This review provides an overview of the state of genetic biocontrol, focusing on several approaches that were the subject of presentations at the Genetic Biocontrol for Invasive Species Workshop in Tarragona, Spain, March 31st, 2019, a workshop sponsored by the OECD’s Co-operative Research Program on Biological Resource Management for Sustainable Agricultural Systems. The review considers four different approaches to genetic biocontrol for invasive species; sterile-release, YY Males, Trojan Female Technique, and gene drive. The different approaches will be compared with respect to the efficiency each affords as a genetic biocontrol tool, the practical utility and cost/benefits associated with implementation of the approach, and the regulatory considerations that will need to be addressed for each. The opinions expressed and arguments employed in this publication are the sole responsibility of the authors and do not necessarily reflect those of the OECD or of the governments of its Member countries.

Adipose transcriptome analysis provides novel insights into molecular regulation of prolonged fasting in northern elephant seal pups

The physiological and cellular adaptations to extreme fasting in northern elephant seals ( Mirounga angustirostris, NES) are remarkable and may help to elucidate endocrine mechanisms that regulate lipid metabolism and energy homeostasis in mammals. Recent studies have highlighted the importance of thyroid hormones in the maintenance of a lipid-based metabolism during prolonged fasting in weaned NES pups. To identify additional molecular regulators of fasting, we used a transcriptomics approach to examine changes in global gene expression profiles before and after 6-8 wk of fasting in weaned NES pups. We produced a de novo assembly and identified 98 unique protein-coding genes that were differentially expressed between early and late fasting. Most of the downregulated genes were associated with lipid, carbohydrate, and protein metabolism. A number of downregulated genes were also associated with maintenance of the extracellular matrix, consistent with tissue remodeling during weight loss and the multifunctional nature of blubber tissue, which plays both metabolic and structural roles in marine mammals. Using this data set, we predict potential mechanisms by which NES pups sustain metabolism and regulate adipose stores throughout the fast, and provide a valuable resource for additional studies of extreme metabolic adaptations in mammals.

Cryptic female choice enhances fertilization success and embryo survival in chinook salmon

In this study, we investigated two potentially important intersexual postcopulatory gametic interactions in a population of chinook salmon (Oncorhynchus tshawytscha): (i) the effect of female ovarian fluid (OF) on the behaviour of spermatozoa during fertilization and (ii) the effects of multilocus heterozygosity (MLH) (as an index of male quality) and female-male genetic relatedness on sperm behaviour and male fertilization success when there is sperm competition in the presence of that OF. To do this, we conducted a series of in vitro competitive fertilization experiments and found that, when ejaculates from two males are competing for access to a single female's unfertilized eggs, fertilization success was significantly biased towards the male whose sperm swam fastest in the female's OF. Embryo survival--a measure of fitness--was also positively correlated with both sperm swimming speed in OF and male MLH, providing novel evidence that cryptic female choice is adaptive for the female, enhancing the early survival of her offspring and potentially influencing her fitness.

Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations.

Measuring telomere length and telomere dynamics in evolutionary biology and ecology

Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, independent of chronological age.

Several different methods have been developed to measure TL, each offering its own technical challenges. The aim of this review is to provide an overview of the advantages and drawbacks of each method for researchers, with a particular focus on issues that are likely to face ecologists and evolutionary biologists collecting samples in the field or in organisms that may never have been studied in this context before.

We discuss the key issues to consider and wherever possible try to provide current consensus view regarding best practice with regard to sample collection and storage, DNA extraction and storage, and the five main methods currently available to measure TL.

Decisions regarding which tissues to sample, how to store them, how to extract DNA, and which TL measurement method to use cannot be prescribed, and are dependent on the biological question addressed and the constraints imposed by the study system. What is essential for future studies of telomere dynamics in evolution and ecology is that researchers publish full details of their methods and the quality control thresholds they employ.

Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements

Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context.

Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model

Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites.

Detecting short tandem repeats from genome data: opening the software black box

Short tandem repeats, specifically microsatellites, are widely used genetic markers, associated with human genetic diseases, and play an important role in various regulatory mechanisms and evolution. Despite their importance, much is yet unknown about their mutational dynamics. The increasing availability of genome data has led to several in silico studies of microsatellite evolution which have produced a vast range of algorithms and software for tandem repeat detection. Documentation of these tools is often sparse, or provided in a format that is impenetrable to most biologists without informatics background. This article introduces the major concepts behind repeat detecting software essential for informed tool selection. We reflect on issues such as parameter settings and program bias, as well as redundancy filtering and efficiency using examples from the currently available range of programs, to provide an integrated comparison and practical guide to microsatellite detecting programs.

Novel monosaccharides as potent inhibitors of cell proliferation

The effects of several novel monosaccharides upon thymidine incorporation into both normal and tumour cells were investigated. The monosaccharide 2-deoxy-3-[1-(R)-(ethoxycarbonyl)ethyl]- alpha-D-allo-pyranose had the most inhibitory effect on proliferation, with the (S)-enantiomer having less inhibitory effects. The chiral centre at carbon-7 was found to be an important part of the molecule, as 2-deoxy-3-[methoxycarbonyl methyl]-alpha-D-allo-pyranose had greatly decreased anti-proliferative properties in comparison with the parent compound. In addition, the 2-deoxy structure at carbon-2 was also found to be important, as 3-[1-(S)-(ethoxycarbonyl)ethyl]-alpha-D-allo-hexopyranose had greatly decreased inhibitory properties in comparison with the parent compound. The results indicate that these novel monosaccharides possess potent anti-proliferative properties, related to their chiral carbon-7 and 2-deoxy carbon-2 structure and suggest that further substitutions of the functional group at carbon-7 may improve these properties and possibly produce inhibitor selectivity for tumour cells in preference to normal cells.

Evaluating the impacts of human capital stocks and accumulation on economic growth: some new evidence

"Various hypotheses have been put forward in recent years concerning the contribution of human capital to economic growth. This paper argues that school enrolment rates--by far the most commonly used human capital measure in growth regressions attempting to test these hypotheses--conflate human capital stock and accumulation effects and lead to misinterpretations of the role of labour force growth. An alternative education-related human capital measure is constructed which is capable of distinguishing between stocks and flows. Applying this measure to samples of developed and less developed countries during the 1960-85 period suggests not only that there are important growth effects associated both with 'initial' stocks of, and subsequent growth in, human capital, but also that this new measure out-performs the simple school enrolment rates used in previous analyses."