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Acute myeloid leukemia (AML) cells require BRD9 to regulate MYC gene expression and prevent myeloid differentiation. Selective inhibition of BRD9 using a chemical probe that was validated using a resistant bromodomain-swap allele of BRD9 limits AML cell growth. Here we show that acute myeloid leukemia (AML) cells require the BRD9 subunit of the SWI−SNF chromatin-remodeling complex to sustain MYC transcription, rapid cell proliferation and a block in differentiation. Based on these observations, we derived small-molecule inhibitors of the BRD9 bromodomain that selectively suppress the proliferation of mouse and human AML cell lines. To establish these effects as on-target, we engineered a bromodomain-swap allele of BRD9 that retains functionality despite a radically altered bromodomain pocket. Expression of this allele in AML cells confers resistance to the antiproliferative effects of our compound series, thus establishing BRD9 as the relevant cellular target. Furthermore, we used an analogous domain-swap strategy to generate an inhibitor-resistant allele of EZH2 . To our knowledge, our study provides the first evidence for a role of BRD9 in cancer and reveals a simple genetic strategy for constructing resistance alleles to demonstrate on-target activity of chemical probes in cells.

The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be “undruggable,” between switch I and II on RAS; 1 is mechanistically distinct from covalent KRASG12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.

Tomato ( Solanum lycopersicum ) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles. Cell-type transcriptome profiling greatly elucidate organismal development. Here, the authors report a spatiotemporally resolved comprehensive transcriptome analysis of tomato fruit ontogeny and suggest a new model of fruit maturation which initiates in internal tissues then radiates outwards.

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans 1 , 2 . However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis 3 , 4 . Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host’s native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families—a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases—from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure–activity relationship, and will thus enable the rational design of potent vaccine adjuvants. QS-21—an FDA-approved vaccine adjuvant—and several structural analogues of QS-21 can be synthesized in engineered yeast strains, and this process is much less laborious compared with the conventional mode of extraction from the Chilean soapbark tree.

Mapping of a mutation in a tomato deficient in the plant cuticle component cutin yields the first cutin synthase, as shown via accumulation of polymer precursors and in vitro oligomerization of synthetic substrates. A hydrophobic cuticle consisting of waxes and the polyester cutin covers the aerial epidermis of all land plants, providing essential protection from desiccation and other stresses. We have determined the enzymatic basis of cutin polymerization through characterization of a tomato extracellular acyltransferase, CD1, and its substrate, 2-mono(10,16-dihydroxyhexadecanoyl)glycerol. CD1 has in vitro polyester synthesis activity and is required for cutin accumulation in vivo , indicating that it is a cutin synthase.

Martin et al . describe a protocol to use laser microdissection to isolate specific cells or tissues from tomato fruit. This can be used to perform cell type–specific transcriptome studies in fleshy fruits, as well as in other plant tissues. This protocol enables transcriptome profiling of specific cell or tissue types that are isolated from tomato using laser microdissection (LM). To prepare tissue for LM, fruit samples are first fixed in optimal cutting temperature (OCT) medium and frozen in molds. The tissue is then sectioned using a cryostat before being dissected using an LM instrument. The RNAs contained in the harvested cells are purified and subjected to two rounds of amplification to yield sufficient quantities of RNA to generate cDNA libraries. Unlike several other techniques that are used to isolate specific cell types, LM has the advantage of being readily applied to any plant species without having to generate transgenic plants. Using the protocols described here, LM-mediated cell-type transcriptomic analysis of two samples requires ∼8 d from tissue harvest to RNA sequencing (RNA-seq), whereas each additional sample, up to a total of 12 samples, requires ∼1 additional day for the LM step. RNA obtained using this method has been successfully used for deep-coverage transcriptome profiling, which is a particularly effective strategy for identifying genes that are differentially expressed between cell or tissue types.

The period from conception to 24 months of age is a crucial window for nutrition interventions. Personalized maternal counseling may improve childbirth outcomes, growth, and health. We assessed the effectiveness of facility-based personalized maternal nutrition counseling (from pregnancy to 18 months after birth) in improving child growth and health in rural Burkina Faso. We conducted a paired cluster randomized controlled trial in a rural district of Burkina Faso with 12 primary health centers (clusters). Healthcare providers in the intervention centers received patient-centered communication and nutrition counseling training. Pregnant women in the third trimester living in the center catchment areas and intending to stay for the next 2 years were prospectively included. We followed 2253 mother-child pairs quarterly until the child was aged 18 months. Women were interviewed about counseling experiences, dietary practices during pregnancy, and their child's feeding practices and morbidity history. Anthropometric measurements were taken at each visit using standardized methods. The primary outcomes were the cumulative incidence of wasting, and changes in child weight-for-height z-score (WHZ). Secondary outcomes were the women's prenatal dietary practices, early breastfeeding practices, exclusive breastfeeding, timely introduction of complementary food, child's feeding frequency and dietary diversity, children's mean birth weight, endpoint prevalence of stunting, and cumulative incidence of diarrhea, fever, and acute respiratory infection. All analyses were by intention-to-treat using mixed effects models. The intervention and control arms each included six health centers. Mothers in the intervention arm had a significantly higher exposure to counseling with 11.2% for breastfeeding techniques to 75.7% for counseling on exclusive breastfeeding. Mothers of infants below 6 months of age in the intervention arm were more likely to exclusively breastfeed (54.3% vs 42.3%; Difference of Proportion (DP) 12.8%; 95% CI: 2.1, 23.6; p = 0.020) as compared to the control arm. Between 6 and 18 months of age, more children in the intervention arm benefited from the required feeding frequency (68.8% vs 53.4%; DP 14.1%; 95% CI: 9.0, 19.2; p<0.001) and a larger proportion had a minimum dietary diversity (28.6% vs 22.0%; DP 5.9%; 95% CI: 2.7, 9.2; p<0.001). Birth weight of newborns in the intervention arm was on average 84.8 g (p = 0.037) larger compared to the control arm. However, we found no significant differences in child anthropometry or morbidity between study arms. Facility-based personalized maternal nutrition counseling was associated with an improved prenatal dietary practices, Infant and Young Child Feeding practices, and child birth weight. Complementary strategies are warranted to obtain meaningful impact on child growth and morbidity. This includes strategies to ensure good coverage of facility-based services and effective nutrition/care practices in early childhood.

Next generation DNA sequencing technologies are driving increasingly rapid, affordable and high resolution analyses of plant transcriptomes through sequencing of their associated cDNA (complementary DNA) populations; an analytical platform commonly referred to as RNA-sequencing (RNA-seq). Since entering the arena of whole genome profiling technologies only a few years ago, RNA-seq has proven itself to be a powerful tool with a remarkably diverse range of applications, from detailed studies of biological processes at the cell type-specific level, to providing insights into fundamental questions in plant biology on an evolutionary time scale. Applications include generating genomic data for heretofore unsequenced species, thus expanding the boundaries of what had been considered \"model organisms,\" elucidating structural and regulatory gene networks, revealing how plants respond to developmental cues and their environment, allowing a better understanding of the relationships between genes and their products, and uniting the \"omics\" fields of transcriptomics, proteomics, and metabolomics into a now common systems biology paradigm. We provide an overview of the breadth of such studies and summarize the range of RNA-seq protocols that have been developed to address questions spanning cell type-specific-based transcriptomics, transcript secondary structure and gene mapping.

Measurements of the status and trends of key indicators for the ocean and marine life are required to inform policy and management in the context of growing human uses of marine resources, coastal development, and climate change. Two synergistic efforts identify specific priority variables for monitoring: Essential Ocean Variables (EOVs) through the Global Ocean Observing System (GOOS), and Essential Biodiversity Variables (EBVs) from the Group on Earth Observations Biodiversity Observation Network (GEO BON). Both systems support reporting against internationally agreed conventions and treaties. GOOS, established under the auspices of the Intergovernmental Oceanographic Commission (IOC), plays a leading role in coordinating global monitoring of the ocean and in the definition of EOVs. GEO BON is a global biodiversity observation network that coordinates observations to enhance management of the world’s biodiversity and promote both the awareness and accounting of ecosystem services. Convergence and agreement between these two efforts are required to streamline existing and new marine observation programs to advance scientific knowledge effectively and to support the sustainable use and management of ocean spaces and resources. In this context, the Marine Biodiversity Observation Network (MBON), a thematic component of GEO BON, is collaborating with GOOS, the Ocean Biogeographic Information System (OBIS), and the Integrated Marine Biosphere Research (IMBeR) project to ensure that EBVs and EOVs are complementary, representing alternative uses of a common set of scientific measurements. This work is informed by the Joint Technical Commission for Oceanography and Marine Meteorology (JCOMM), an intergovernmental body of technical experts that helps international coordination on best practices for observing, data management and services, combined with capacity development expertise. Characterizing biodiversity and understanding its drivers will require incorporation of observations from traditional and molecular taxonomy, animal tagging and tracking efforts, ocean biogeochemistry, and ocean observatory initiatives including the deep ocean and seafloor. The partnership between large-scale ocean observing and product distribution initiatives (MBON, OBIS, JCOMM, and GOOS) is an expedited, effective way to support international policy-level assessments (e.g., the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services or IPBES), along with the implementation of international development goals (e.g., the United Nations Sustainable Development Goals).