NatSurFact: Progress in commercializing rhamnolipids

NatSurFact is a rhamnolipid-based biosurfactant ingredient for the cosmetics industry developed by Logos Technologies. Rhamnolipids are a member of the glycolipid class of biosurfactants. They are made up of a rhamnose sugar head group and medium chain length 3-hydroxy fatty acid tails. Their structure was first elucidated in 1949 and they have been studied for myriad applications both academically and commercially since. While their properties as an anionic surfactant in the salt form are attractive – natural, mild, high foaming, high cleansing – they are not sold yet in appreciable commercial quantities. To bring rhamnolipids to market, Logos has focused on efficient and cost effective manufacturing. We will present some interesting characteristics of NatSurFact rhamnolipids product grades and discuss our process of production. We are working with a variety of downstream partners and academics to develop personal care formulations, including cosmetics, and our efforts will be detailed. Finally, we will talk about the future of rhamnolipids and NatSurFact as the market for biosurfactants begins to mature

Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress

Matrix metalloproteinases (MMPs) are zinc-dependent endo-peptidases that in mammals are known to be involved in remodeling the extracellular matrix (ECM) in developmental and pathological processes. In this study, we report At5-MMP of Arabidopsis thaliana to be important for root development and root bacterial communities. At5-MMP is mainly localized in the root vasculature and lateral root, an At5-MMP T-DNA insertion mutant (mmp5 KO) showed reduced root growth and a lower number of root apexes, causing reduced water uptake from the soil. Subsequently, mmp5 KO is sensitive to drought stress. Inhibited auxin transport was accompanied with resistance to indole-3-acetic acid (IAA), 2, 4-dichlorophenoxyacetic acid (2, 4-D), and 1-naphthaleneacetic acid (NAA). The content of endogenous abscisic acid (ABA) was lower in roots of mmp5 KO than in wild type. Genes responsive to ABA as well as genes encoding enzymes of the proline biosynthesis were expressed to a lower extent in mmp5 KO than in wild type. Moreover, drought stress modulated root-associated bacterial communities of mmp5 KO: the number of Actinobacteria increased. Therefore, At5-MMP modulates auxin/ABA signaling rendering the plant sensitive to drought stress and recruiting differential root bacterial communities

Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences

Introns are a ubiquitous feature of eukaryotic genomes, and the dynamics of intron evolution between species has been extensively studied. However, comparatively few analyses have focused on the evolutionary forces shaping patterns of intron variation within species. To better understand the population genetic characteristics of introns, we performed an extensive population genetics analysis on key intron splice sequences obtained from 38 strains of Saccharomyces cerevisiae. As expected, we found that purifying selection is the dominant force governing intron splice sequence evolution in yeast, formally confirming that intron-containing alleles are a mutational liability. In addition, through extensive coalescent simulations, we obtain quantitative estimates of the strength of purifying selection (2Nes ≈ 19) and use diffusion approximations to provide insights into the evolutionary dynamics and sojourn times of newly arising splice sequence mutations in natural yeast populations. In contrast to previous functional studies, evolutionary analyses comparing the prevalence of introns in essential and nonessential genes suggest that introns in nonribosomal protein genes are functionally important and tend to be actively maintained in natural populations of S. cerevisiae. Finally, we demonstrate that heritable variation in splicing efficiency is common in intron-containing genes with splice sequence polymorphisms. More generally, our study highlights the advantages of population genomics analyses for exploring the forces that have generated extant patterns of genome variation and for illuminating basic biological processes

Terrestrial Very-Long-Baseline Atom Interferometry:Workshop Summary

This document presents a summary of the 2023 Terrestrial Very-Long-Baseline Atom Interferometry Workshop hosted by CERN. The workshop brought together experts from around the world to discuss the exciting developments in large-scale atom interferometer (AI) prototypes and their potential for detecting ultralight dark matter and gravitational waves. The primary objective of the workshop was to lay the groundwork for an international TVLBAI proto-collaboration. This collaboration aims to unite researchers from different institutions to strategize and secure funding for terrestrial large-scale AI projects. The ultimate goal is to create a roadmap detailing the design and technology choices for one or more km-scale detectors, which will be operational in the mid-2030s. The key sections of this report present the physics case and technical challenges, together with a comprehensive overview of the discussions at the workshop together with the main conclusions

The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance

While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

<div><p>The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel <em>h2a.z</em> loss-of-function line in <em>Arabidopsis thaliana.</em> Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.</p> </div

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information

Genes with H2A.Z gene body enrichment are misregulated in <i>h2a.z</i>.

<p>(A) Fold enrichment of the top 19 over-represented GO categories in the 1,800 upregulated genes in the <i>h2a.z</i> mutant, all of which are response-related. For simplicity, all categories have had “Response to” removed from their names, with the exception of “Immune response” and “Defense response”. All categories have P-values for over-representation less than 1×10⁻⁵, and each P-value is indicated within the respective bar. GO terms that also appear as overrepresented in similar analyses done with genes upregulated in at least two of the three <i>h2a.</i>z, <i>pie1</i>, and <i>hta9;hta11</i> mutant datasets are marked with a red asterisk. (B) Box plots of Responsiveness Score for all genes partitioned by the degree of up and downregulation in the <i>h2a.z</i> mutant. Genes are grouped into bins based on increasing log₂ (<i>h2a.z</i>/WT) expression level, ranging from −8.6 to 9.8; a separate bin shows the Responsiveness Score for all genes. The red and green triangles below the X-axis respectively represent decreased and increased expression in the mutant over WT. (C) Kernel density plots for transcriptional changes in the <i>h2a.z</i> mutant (log₂ (<i>h2a.z</i>/WT) transcription) for housekeeping genes (blue, n = 384) and hypervariable genes (red, n = 123). (D) Box plots of H2A.Z body-enrichment (IP - input) for all genes with H2A.Z body enrichment scores (n = 12,237) partitioned by degree of up and downregulation. Genes are grouped as in (B). (E) Box plots for responsiveness, broken down by subcategory, in the 2-fold upregulated genes (n = 1,800, shown in green) and the least misregulated genes (less than 1.4-fold up or down regulated, n = 9,300, shown in grey and labeled “No change”). Subcategories and associated responsiveness scores are from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002988#pgen.1002988-Aceituno1" target="_blank">[70]</a>, and represent the three major types of stimuli: developmental (tissue), abiotic, and biotic.</p