Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo).

Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled and integrated with phenotypic characterization of genetic diversity. We developed a multi-parental framework for trait dissection in melon (Cucumis melo), leveraging a novel pan-genome constructed for this highly variable cucurbit crop. A core subset of 25 diverse founders (MelonCore25), consisting of 24 accessions from the two widely cultivated subspecies of C. melo, encompassing 12 horticultural groups, and 1 feral accession was sequenced using a combination of short- and long-read technologies, and their genomes were assembled de novo. The construction of this melon pan-genome exposed substantial variation in genome size and structure, including detection of ~300 000 structural variants and ~9 million SNPs. A half-diallel derived set of 300 F2 populations, representing all possible MelonCore25 parental combinations, was constructed as a framework for trait dissection through integration with the pan-genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color intensity and pattern, fruit sugar content, and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.

Mutations on the N-terminal edge of the DELSEED loop in either the α or ß subunit of the mitochondrial F1-ATPase enhance ATP hydrolysis in the absence of the central γ rotor.

F(1)-ATPase is a rotary molecular machine with a subunit stoichiometry of α(3)ß(3)γ(1)δ(1)ε(1). It has a robust ATP-hydrolyzing activity due to effective cooperativity between the three catalytic sites. It is believed that the central γ rotor dictates the sequential conformational changes to the catalytic sites in the α(3)ß(3) core to achieve cooperativity. However, recent studies of the thermophilic Bacillus PS3 F(1)-ATPase have suggested that the α(3)ß(3) core can intrinsically undergo unidirectional cooperative catalysis (T. Uchihashi et al., Science 333:755-758, 2011). The mechanism of this γ-independent ATP-hydrolyzing mode is unclear. Here, a unique genetic screen allowed us to identify specific mutations in the α and ß subunits that stimulate ATP hydrolysis by the mitochondrial F(1)-ATPase in the absence of γ. We found that the F446I mutation in the α subunit and G419D mutation in the ß subunit suppress cell death by the loss of mitochondrial DNA (ρ(o)) in a Kluyveromyces lactis mutant lacking γ. In organello ATPase assays showed that the mutant but not the wild-type γ-less F(1) complexes retained 21.7 to 44.6% of the native F(1)-ATPase activity. The γ-less F(1) subcomplex was assembled but was structurally and functionally labile in vitro. Phe446 in the α subunit and Gly419 in the ß subunit are located on the N-terminal edge of the DELSEED loops in both subunits. Mutations in these two sites likely enhance the transmission of catalytically required conformational changes to an adjacent α or ß subunit, thereby allowing robust ATP hydrolysis and cell survival under ρ(o) conditions. This work may help our understanding of the structural elements required for ATP hydrolysis by the α(3)ß(3) subcomplex.

Design and Realization of Polymeric Waveguide/Microring Structures for Telecommunication Domain.

Polymer-based micro-optical components are very important for applications in optical communication. In this study, we theoretically investigated the coupling of polymeric waveguide and microring structures and experimentally demonstrated an efficient fabrication method to realize these structures on demand. First, the structures were designed and simulated using the FDTD method. The optical mode and loss in the coupling structures were calculated, thereby giving the optimal distance for optical mode coupling between two rib waveguide structures or for optical mode coupling in a microring resonance structure. Simulations results then guided us in the fabrication of the desired ring resonance microstructures using a robust and flexible direct laser writing technique. The entire optical system was thus designed and manufactured on a flat base plate so that it could be easily integrated in optical circuits.

Rice-shrimp ecosystems in the Mekong Delta: Linking water quality, shrimp and their natural food sources.

Aquatic ecosystems are used for extensive rice-shrimp culture where the available water alternates seasonally between fresh and saline. Poor water quality has been implicated as a risk factor for shrimp survival; however, links between shrimp, water quality and their main food source, the natural aquatic biota inhabiting these ponds, are less well understood. We examined the aquatic biota and water quality of three ponds over an entire year in the Mekong Delta, Vietnam, where the growing season for the marine shrimp Penaeus monodon has been extended into the wet season, when waters freshen. The survival (30-41%) and total areal biomass (350-531 kg ha-1) of shrimp was constrained by poor water quality, with water temperatures, salinity and dissolved oxygen concentrations falling outside known optimal ranges for several weeks. Declines in dissolved oxygen concentration were matched by declines in both shrimp growth rates and lipid content, the latter being indicative of nutritional condition. Furthermore, as the dry season transitioned into the wet, shifts in the taxonomic composition of phytoplankton and zooplankton were accompanied by declines in the biomass of benthic algae, an important basal food source in these systems. Densities of the benthic invertebrates directly consumed by shrimp also varied substantially throughout the year. Overall, our findings suggest that the survival, condition and growth of shrimp in extensive rice-shrimp ecosystems will be constrained when poor water quality and alternating high and low salinity negatively affect the physiology, growth and composition of the natural aquatic biota. Changes in management practices, such as restricting shrimp inhabiting ponds to the dry season, may help to address these issues and improve the sustainable productivity and overall condition of these important aquatic ecosystems.

The genetic requirements of fatty acid import by Mycobacterium tuberculosis within macrophages.

Mycobacterium tuberculosis (Mtb) imports and metabolizes fatty acids to maintain infection within human macrophages. Although this is a well-established paradigm, the bacterial factors required for fatty acid import are poorly understood. Previously, we found that LucA and Mce1 are required for fatty acid import in Mtb (Nazarova et al., 2017). Here, we identified additional Mtb mutants that have a reduced ability to import a fluorescent fatty acid substrate during infection within macrophages. This screen identified the novel genes as rv2799 and rv0966c as be necessary for fatty acid import and confirmed the central role for Rv3723/LucA and putative components of the Mce1 fatty acid transporter (Rv0200/OmamB, Rv0172/Mce1D, and Rv0655/MceG) in this process.

Rv3723/LucA coordinates fatty acid and cholesterol uptake in Mycobacterium tuberculosis.

Pathogenic bacteria have evolved highly specialized systems to extract essential nutrients from their hosts. Mycobacterium tuberculosis (Mtb) scavenges lipids (cholesterol and fatty acids) to maintain infections in mammals but mechanisms and proteins responsible for the import of fatty acids in Mtb were previously unknown. Here, we identify and determine that the previously uncharacterized protein Rv3723/LucA, functions to integrate cholesterol and fatty acid uptake in Mtb. Rv3723/LucA interacts with subunits of the Mce1 and Mce4 complexes to coordinate the activities of these nutrient transporters by maintaining their stability. We also demonstrate that Mce1 functions as a fatty acid transporter in Mtb and determine that facilitating cholesterol and fatty acid import via Rv3723/LucA is required for full bacterial virulence in vivo. These data establish that fatty acid and cholesterol assimilation are inexorably linked in Mtb and reveals a key function for Rv3723/LucA in in coordinating thetransport of both these substrates.