Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds

<p>Abstract</p> <p>Background</p> <p>Soybean (<it>Glycine max </it>[L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their contribution to human health and plant defense systems. However, attempts to modify seed isoflavone contents have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved.</p> <p>Results</p> <p>In this study, a mapping population of RILs with three replicates was analyzed in four different environments (two locations over two years). We found a total of thirty-five main-effect genomic regions and many epistatic interactions controlling genistein, daidzein, glycitein and total isoflavone accumulation in seeds. The use of distinct environments permitted detection of a great number of environment-modulated and minor-effect QTL. Our findings suggest that isoflavone seed concentration is controlled by a complex network of multiple minor-effect loci interconnected by a dense epistatic map of interactions. The magnitude and significance of the effects of many of the nodes and connections in the network varied depending on the environmental conditions. In an attempt to unravel the genetic architecture underlying the traits studied, we searched on a genome-wide scale for genomic regions homologous to the most important identified isoflavone biosynthetic genes. We identified putative candidate genes for several of the main-effect and epistatic QTL and for QTL reported by other groups.</p> <p>Conclusions</p> <p>To better understand the underlying genetics of isoflavone accumulation, we performed a large scale analysis to identify genomic regions associated with isoflavone concentrations. We not only identified a number of such regions, but also found that they can interact with one another and with the environment to form a complex adaptable network controlling seed isoflavone levels. We also found putative candidate genes in several regions and overall we advanced the knowledge of the genetics underlying isoflavone synthesis.</p

The Role of Lipolysis Stimulated Lipoprotein Receptor in Breast Cancer and Directing Breast Cancer Cell Behavior

The claudin-low molecular subtype of breast cancer is of particular interest for clinically the majority of these tumors are poor prognosis, triple negative, invasive ductal carcinomas. Claudin-low tumors are characterized by cancer stem cell-like features and low expression of cell junction and adhesion proteins. Herein, we sought to define the role of lipolysis stimulated lipoprotein receptor (LSR) in breast cancer and cancer cell behavior as LSR was recently correlated with tumor-initiating features. We show that LSR was expressed in epithelium, endothelium, and stromal cells within the healthy breast tissue, as well as in tumor epithelium. In primary breast tumor bioposies, LSR expression was significantly correlated with invasive ductal carcinomas compared to invasive lobular carcinomas, as well as ERα positive tumors and breast cancer cell lines. LSR levels were significantly reduced in claudin-low breast cancer cell lines and functional studies illustrated that re-introduction of LSR into a claudin-low cell line suppressed the EMT phenotype and reduced individual cell migration. However, our data suggest that LSR may promote collective cell migration. Re-introduction of LSR in claudin-low breast cancer cell lines reestablished tight junction protein expression and correlated with transepithelial electrical resistance, thereby reverting claudin-low lines to other intrinsic molecular subtypes. Moreover, overexpression of LSR altered gene expression of pathways involved in transformation and tumorigenesis as well as enhanced proliferation and survival in anchorage independent conditions, highlighting that reestablishment of LSR signaling promotes aggressive/tumor initiating cell behaviors. Collectively, these data highlight a direct role for LSR in driving aggressive breast cancer behavior

Religion as practices of attachment and materiality: the making of Buddhism in contemporary London

This article aims to explore Buddhism’s often-overlooked presence on London’s urban landscape, showing how its quietness and subtlety of approach has allowed the faith to grow largely beneath the radar. It argues that Buddhism makes claims to urban space in much the same way as it produces its faith, being as much about the practices performed and the spaces where they are enacted as it is about faith or beliefs. The research across a number of Buddhist sites in London reveals that number of people declaring themselves as Buddhists has indeed risen in recent years, following the rise of other non-traditional religions in the UK; however, this research suggests that Buddhism differs from these in several ways. Drawing on Baumann’s (2002) distinction between traditionalist and modernist approaches to Buddhism, our research reveals a growth in each of these. Nevertheless, Buddhism remains largely invisible in the urban and suburban landscape of London, adapting buildings that are already in place, with little material impact on the built environment, and has thus been less subject to contestation than other religious movements and traditions. This research contributes to a growing literature which foregrounds the importance of religion in making contemporary urban and social worlds

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Lawmakers\u27 Use of Scientific Evidence Can Be Improved

Core to the goal of scientific exploration is the opportunity to guide future decision-making. Yet, elected officials often miss opportunities to use science in their policymaking. This work reports on an experiment with the US Congress-evaluating the effects of a randomized, dual-population (i.e., researchers and congressional offices) outreach model for supporting legislative use of research evidence regarding child and family policy issues. In this experiment, we found that congressional offices randomized to the intervention reported greater value of research for understanding issues than the control group following implementation. More research use was also observed in legislation introduced by the intervention group. Further, we found that researchers randomized to the intervention advanced their own policy knowledge and engagement as well as reported benefits for their research following implementation

Routes for breaching and protecting genetic privacy

We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here, we technically map threats to genetic privacy and discuss potential mitigation strategies for privacy-preserving dissemination of genetic data.Comment: Draft for comment

Reply to: New Meta- and Mega-analyses of Magnetic Resonance Imaging Findings in Schizophrenia: Do They Really Increase Our Knowledge About the Nature of the Disease Process?

This work was supported by National Institute of Biomedical Imaging and Bioengineering Grant No. U54EB020403 (to the ENIGMA consortium)

Plant Adaptation to Drought --- Interdisciplinary Research at the University of Missouri [abstract]

Only abstract of poster available.Track V: BiomassDrought is the most important cause of crop failure in Missouri and limits plant productivity in large parts of the US and the world. Drought induces severe reductions in average annual crop yields on a regional scale and can have devastating effects at the farm level. Regional droughts can also strikingly reduce net primary productivity of natural ecosystems. Research on plant adaptation to drought is a long-standing, important component of MU faculty members, who comprise a strong, collaborative team of university and USDA-ARS scientists and are among the international leaders in drought research. Group members represent expertise from a broad range of disciplines, including plant physiology, agronomy, forestry, plant breeding, molecular biology, biotechnology, entomology, plant pathology, and soil science. Areas of research span from basic to applied aspects of plant adaptation to drought, fostering the translation of basic discoveries of underlying mechanisms to the delivery of more drought-tolerant crops at the doorsteps of American farmers. In addition to local collaborations, the team interacts with other scientists in the state of Missouri (e.g. Danforth Plant Sciences Center and Washington University in St. Louis) and at the national and international levels (including Australia, England, India, Mexico [CIMMYT], and The Philippines [International Rice Research Institute]). Active research projects conducted by the drought community at MU include research funded by state, federal, commodity group (e.g. Missouri Soybean Merchandising Council, United Soybean Board, Cotton Inc.) and private (Monsanto, Syngenta) sources. Of particular note, members of the group were recently awarded over $1.5 million from the Missouri Life Sciences Research Board to establish “rainout shelters” that will allow control of precipitation under field conditions. The ability to manage the timing, duration, and intensity of water deficit stress under field conditions is essential to examine plant responses to drought and interactions of drought and biotic stresses in mid-western environments. The track record of excellence in drought research and the broad range of expertise of the interdisciplinary group provide fertile grounds for creative and productive research endeavors that are directed to optimize crop and woody plant biomass production

Bordetella pertussis Autotransporter Vag8 Binds Human C1 Esterase Inhibitor and Confers Serum Resistance

Bordetella pertussis employs numerous strategies to evade the immune system, including the ability to resist killing via complement. Previously we have shown that B. pertussis binds a complement regulatory protein, C1 esterase inhibitor (C1inh) to its surface in a Bvg-regulated manner (i.e. during its virulence phase), but the B. pertussis factor was not identified. Here we set out to identify the B. pertussis C1inh-binding factor. Using a serum overlay assay, we found that this factor migrates at approximately 100 kDa on an SDS-PAGE gel. To identify this factor, we isolated proteins of approximately 100 kDa from wild type strain BP338 and from BP347, an isogenic Bvg mutant that does not bind C1inh. Using mass spectrometry and bioinformatics, we identified the autotransporter protein Vag8 as the putative C1inh binding protein. To prove that Vag8 binds C1inh, vag8 was disrupted in two different B. pertussis strains, namely BP338 and 18–323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh. In addition, the passenger domain of Vag8 was expressed and purified as a histidine-tagged fusion protein and tested for C1inh-binding in an ELISA assay. Whereas the purified Vag8 passenger bound C1inh, the passenger domain of BrkA (a related autotransporter protein) failed to do so. Finally, serum assays were conducted to compare wild type and vag8 mutants. We determined that vag8 mutants from both strains were more susceptible to killing compared to their isogenic wild type counterparts. In conclusion, we have discovered a novel role for the previously uncharacterized protein Vag8 in the immune evasion of B. pertussis. Vag8 binds C1inh to the surface of the bacterium and confers serum resistance