Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse subclass of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using nuclear magnetic resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineagespecific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus-the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained similar to 72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated similar to 45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

In angiosperms, double fertilization of an egg cell and a central cell with two sperm cells results in the formation of a seed containing a diploid embryo and a triploid endosperm. The extent to which the embryo sac controls postfertilization events in the seed is unknown. The novel gametophytic maternal-effect maize mutation, baseless1 (bsl1) affects central cell development within the embryo sac, frequently by altering the position of the two polar nuclei. Despite this irregularity, fertilization is as efficient as in wild type. The spatial expression of basal endosperm-specific transcripts is altered in free-nuclear and cellular mutant endosperms. At later stages of seed development, bsl1 predominantly affects development of the basal endosperm transfer layer (BETL). When bsl1/+ diploid plants were pollinated by wild-type tetraploid plants, the BETL abnormalities observed in bsl1/bsl1/+/+ tetraploid endosperms were diverse and of variable severity. Moreover, the frequency of kernels with severely perturbed BETL development correlated with the percentage of severely affected bsl1 central cells. Therefore, BSL1 is likely required in the central cell before fertilization for correct BETL patterning to occur. These findings provide new genetic evidence that a maternal gametophytic component is necessary for correct endosperm patterning.

Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.

We present the first results from a study designed to test whether, given high-quality spectrophotometry spanning the mid-ultraviolet-optical wavelength regime, it is possible to distinguish the metal content and star formation history of individual elliptical galaxies with sufficient accuracy to establish whether their formation history is linked to their detailed morphology and position on the Fundamental Plane.

It is widely believed that ultraluminous infrared (IR) galaxies and active galactic nuclei (AGN) activity are triggered by galaxy interactions and merging, with the peak of activity occurring at z similar to 2, where submillimetre galaxies are thousands of times more numerous than local ULIRGs. In this evolutionary picture, submillimetre galaxies (SMGs) would host an AGN, which would eventually grow a black hole (BH) strong enough to blow off all of the gas and dust leaving an optically luminous QSO. To probe this evolutionary sequence we have focussed on the 'missing link' sources, which demonstrate both strong starburst (SB) and AGN signatures, in order to determine if the SB is the main power source even in SMGs when we have evidence that an AGN is present from their IRAC colours. The best way to determine if a dominant AGN is present is to look for their signatures in the mid-infrared with the Spitzer IRS, since often even deep X-ray observations miss identifying the presence of AGN in heavily dust-obscured SMGs. We present the results of our audit of the energy balance between star-formation and AGN within this special sub-population of SMGs - where the BH has grown appreciably to begin heating the dust emission.

We investigate the stellar populations of Ly alpha emitters (LAEs) at z = 3.1 and 3.7 in 0.65 deg2 of the Subaru/XMM-Newton Deep Field, based on rest-frame ultraviolet-to-optical photometry obtained from the Subaru/XMM-Newton Deep Survey, the UKIRT Infrared Deep Sky Survey/Ultra Deep Survey (UKIDSS/UDS), and the Spitzer legacy survey of the UKIDSS/UDS. Among a total of 302 LAEs (224 for z = 3.1 and 78 for z = 3.7), only 11 are detected in the K band, i.e. brighter than K(3 Sigma) = 24.1 mag. Eight of the 11 K-detected LAEs are spectroscopically confirmed. In our stellar population analysis, we treat K-detected objects individually, while K-undetected objects are stacked at each redshift. We find that the K-undetected objects, which should closely represent the LAE population as a whole, have low stellar masses of similar to 108-108.5 M(circle dot), modest star formation rates (SFRs) of 1-100 M(circle dot) yr-1, and modest dust extinction of E(B - V)(star) < 0.2. The K-detected objects are massive, M(star) similar to 109-1010.5 M(circle dot), and have significant dust extinction with a median of E(B - V)(star) similar or equal to 0.3. Four K-detected objects with the reddest spectral energy distributions, two of which are spectroscopically confirmed, are heavily obscured with E(B - V)(star) similar to 0.65, and their continua resemble those of some local ultraluminous infrared galaxies (ULIRGs). Interestingly, they have large Ly alpha equivalent widths similar or equal to 70-250 A. If these four are excluded, our sample has a weak anticorrelation between Ly alpha equivalent width and M(star). We compare the stellar masses and the specific SFRs (sSFRs) of LAEs with those of Lyman-break galaxies (LBGs), distant red galaxies, submillimetre galaxies, and I- or K-selected galaxies with photometric redshifts of z(phot) similar to 3. We find that the LAE population is the least massive among all the galaxy populations in question, but with relatively high sSFRs, while near-infrared (NIR)-detected LAEs have M(star) and sSFR similar to LBGs. Our reddest four LAEs have very high sSFRs in spite of large M(star), thus occupying a unique region in the M(star) versus sSFR space.

Spitzer spectroscopy has revealed that similar or equal to 80% of submm galaxies (SMGs) are starburst (SB)-dominated in the mid-infrared. Here we focus on the remaining similar or equal to 20% that show signs of harboring powerful active galactic nuclei (AGNs). We have obtained Spitzer-InfraRed Spectrograph spectroscopy of a sample of eight SMGs that are candidates for harboring powerful AGNs on the basis of IRAC color selection (S(8 mu m)/S(4.5 mu m) > 2, i.e., likely power-law mid-infrared spectral energy distributions). SMGs with an AGN dominating (greater than or similar to 50%) their mid-infrared emission could represent the "missing link" sources in an evolutionary sequence involving a major merger. First of all, we detect polycyclic aromatic hydrocarbon (PAH) features in all of the SMGs, indicating redshifts from 2.5 to 3.4, demonstrating the power of the mid-infrared to determine redshifts for these optically faint dusty galaxies. Second, we see signs of both star formation (from the PAH features) and AGN activity (from continuum emission) in our sample: 62% of the sample are AGN-dominated in the mid-infrared with a median AGN content of 56%, compared with <30% on average for typical SMGs, revealing that our IRAC color selection has successfully singled out sources with proportionately more AGN emission than typical SB-dominated SMGs. However, we find that only about 10% of these AGNs dominate the bolometric emission of the SMG when the results are extrapolated to longer infrared wavelengths, implying that AGNs are not a significant power source to the SMG population overall, even when there is evidence in the mid-infrared for substantial AGN activity. When existing samples of mid-infrared AGN-dominated SMGs are considered, we find that S(8 mu m)/S(4.5 mu m) > 1.65 works well at selecting mid-infrared energetically dominant AGNs in SMGs, implying a duty cycle of similar to 15% if all SMGs go through a subsequent mid-infrared AGN-dominated phase in the proposed evolutionary sequence.