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Transcription factors play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene regulatory networks to predict the regulatory targets for each transcription factor, such as yeast-1-hybrid screens and gene co-expression network analysis. Here we identified potential transcription factor targets and used a reverse genetics approach to test the predictions of several gene regulatory networks in maize. Loss-of-function mutant alleles were isolated for 22 maize transcription factors. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on yeast-1-hybrid screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from gene co-expression network-based methods found significant enrichments for prediction sets of some transcription factors, but most predicted targets did not exhibit altered expression. This could result from false-positive gene co-expression network predictions, a transcription factor with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other transcription factors. Collectively, these findings suggest that loss-of-function for single uncharacterized transcription factors might have limited phenotypic impacts but can reveal subsets of gene regulatory network predicted targets with altered expression.

 

We here address the problem of fairly allocating indivisible goods or chores to n agents with weights that define their entitlement to the set of indivisible resources. Stemming from well-studied fairness concepts such as envy-freeness up to one good (EF1) and envy-freeness up to any good (EFX) for agents with equal entitlements, we present, in this study, the first set of impossibility results alongside algorithmic guarantees for fairness among agents with unequal entitlements.Within this paper, we expand the concept of envy-freeness up to any good or chore to the weighted context (WEFX and XWEF respectively), demonstrating that these allocations are not guaranteed to exist for two or three agents. Despite these negative results, we develop a WEFX procedure for two agents with integer weights, and furthermore, we devise an approximate WEFX procedure for two agents with normalized weights. We further present a polynomial-time algorithm that guarantees a weighted envy-free allocation up to one chore (1WEF) for any number of agents with additive cost functions. Our work underscores the heightened complexity of the weighted fair division problem when compared to its unweighted counterpart.

 

One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is not enough. Carbon dioxide removal (CDR) will also be needed to avoid the catastrophic effects of global warming. Although the drawdown and storage of CO2 occur naturally via the coupling of the silicate and carbonate cycles, they operate over geological timescales (thousands of years). Here, we suggest that microbes can be used to accelerate this process, perhaps by orders of magnitude, while simultaneously producing potentially valuable by-products. This could provide both a sustainable pathway for global drawdown of CO2 and an environmentally benign biosynthesis of materials. We discuss several different approaches, all of which involve enhancing the rate of silicate weathering. We use the silicate mineral olivine as a case study because of its favorable weathering properties, global abundance, and growing interest in CDR applications. Extensive research is needed to determine both the upper limit of the rate of silicate dissolution and its potential to economically scale to draw down significant amounts (Mt/Gt) of CO2. Other industrial processes have successfully cultivated microbial consortia to provide valuable services at scale (e.g., wastewater treatment, anaerobic digestion, fermentation), and we argue that similar economies of scale could be achieved from this research. 

For any subset$Z \subseteq {\mathbb {Q}}$, consider the set$S_Z$of subfields$L\subseteq {\overline {\mathbb {Q}}}$which contain a co-infinite subset$C \subseteq L$that is universally definable inLsuch that$C \cap {\mathbb {Q}}=Z$. Placing a natural topology on the set${\operatorname {Sub}({\overline {\mathbb {Q}}})}$of subfields of${\overline {\mathbb {Q}}}$, we show that ifZis not thin in${\mathbb {Q}}$, then$S_Z$is meager in${\operatorname {Sub}({\overline {\mathbb {Q}}})}$. Here,thinandmeagerboth mean “small”, in terms of arithmetic geometry and topology, respectively. For example, this implies that only a meager set of fieldsLhave the property that the ring of algebraic integers$\mathcal {O}_L$is universally definable inL. The main tools are Hilbert’s Irreducibility Theorem and a new normal form theorem for existential definitions. The normal form theorem, which may be of independent interest, says roughly that every$\exists $-definable subset of an algebraic extension of${\mathbb Q}$is a finite union of single points and projections of hypersurfaces defined by absolutely irreducible polynomials.

 

Abstract. We study the extent to which curves over finite fields are characterized by their zeta functions and the zeta functions of certain of their covers. Suppose C and C ′ are curves over a finite field K, with K-rational base points P and P ′ , and let D and D ′ be the pullbacks (via the Abel–Jacobi map) of the multiplication-by-2 maps on their Jacobians. We say that (C, P) and (C ′ , P ′ ) are doubly isogenous if Jac(C) and Jac(C ′ ) are isogenous over K and Jac(D) and Jac(D ′ ) are isogenous over K. For curves of genus 2 whose automorphism groups contain the dihedral group of order eight, we show that the number of pairs of doubly isogenous curves is larger than na¨ıve heuristics predict, and we provide an explanation for this phenomenon. 

Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping‐by‐sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.

 

Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated forde novogenome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.

 

Abstract It is unclear how mobile DNA sequences (transposable elements, hereafter TEs) invade eukaryotic genomes and reach stable copy numbers, as transposition can decrease host fitness. This challenge is particularly stark early in the invasion of a TE family at which point hosts may lack the specialized machinery to repress the spread of these TEs. One possibility (in addition to the evolution of host regulation of TEs) is that TE families may evolve to preferentially insert into chromosomal regions that are less likely to impact host fitness. This may allow the mean TE copy number to grow while minimizing the risk for host population extinction. To test this, we constructed simulations to explore how the transposition probability and insertion preference of a TE family influence the evolution of mean TE copy number and host population size, allowing for extinction. We find that the effect of a TE family’s insertion preference depends on a host’s ability to regulate this TE family. Without host repression, a neutral insertion preference increases the frequency of and decreases the time to population extinction. With host repression, a preference for neutral insertions minimizes the cumulative deleterious load, increases population fitness, and, ultimately, avoids triggering an extinction vortex.