Genetic control of kernel compositional variation in a maize diversity panel

Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which, over time, has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants; however, much of the underlying genetic control of these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g., carbohydrates, protein, and starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g., dent, sweetcorn, and popcorn) were explored, and significant differences and meaningful correlations were detected. In total, 22.9-71.0% of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole-genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 72 statistically significant SNPs for 11 compositional traits. This study provides valuable insights in the phenotypic variation and genetic control underlying compositional traits that can be used in breeding programs for improving maize grain quality.

Genetic control of kernel compositional variation in a maize diversity panel

Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which, over time, has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants; however, much of the underlying genetic control of these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g., carbohydrates, protein, and starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g., dent, sweetcorn, and popcorn) were explored, and significant differences and meaningful correlations were detected. In total, 22.9-71.0% of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole-genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 72 statistically significant SNPs for 11 compositional traits. This study provides valuable insights in the phenotypic variation and genetic control underlying compositional traits that can be used in breeding programs for improving maize grain quality.

Predicting moisture content during maize nixtamalization using machine learning with NIR spectroscopy

Moisture content during nixtamalization can be accurately predicted from NIR spectroscopy when coupled with a support vector machine (SVM) model, is strongly modulated by the environment, and has a complex genetic architecture. Lack of high-throughput phenotyping systems for determining moisture content during the maize nixtamalization cooking process has led to difficulty in breeding for this trait. This study provides a high-throughput, quantitative measure of kernel moisture content during nixtamalization based on NIR scanning of uncooked maize kernels. Machine learning was utilized to develop models based on the combination of NIR spectra and moisture content determined from a scaled-down benchtop cook method. A linear support vector machine (SVM) model with a Spearman's rank correlation coefficient of 0.852 between wet laboratory and predicted values was developed from 100 diverse temperate genotypes grown in replicate across two environments. This model was applied to NIR spectra data from 501 diverse temperate genotypes grown in replicate in five environments. Analysis of variance revealed environment explained the highest percent of the variation (51.5%), followed by genotype (15.6%) and genotype-by-environment interaction (11.2%). A genome-wide association study identified 26 significant loci across five environments that explained between 5.04% and 16.01% (average = 10.41%). However, genome-wide markers explained 10.54% to 45.99% (average = 31.68%) of the variation, indicating the genetic architecture of this trait is likely complex and controlled by many loci of small effect. This study provides a high-throughput method to evaluate moisture content during nixtamalization that is feasible at the scale of a breeding program and provides important information about the factors contributing to variation of this trait for breeders and food companies to make future strategies to improve this important processing trait.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.

Self-reported cognitive problems predict employment trajectory in patients with bipolar I disorder

BACKGROUND

Cognitive impairment in bipolar disorder has been associated with poor functional outcomes. We examined the relation of self-reported cognitive problems to employment trajectory in patients diagnosed with bipolar I disorder.

METHODS

154 bipolar I disorder patients were followed for 15-43months at the Bipolar Disorders Center for Pennsylvanians. Using a multinomial logistic regression we examined predictors of employment group including self-reported cognitive problems, mood symptoms, education and age. Cognitive functioning was measured via 4 self-report items assessing memory/concentration at baseline and termination. Employment status was recorded at baseline and termination. Employment was categorized as working (full-time, part-time, homemaker, volunteer) or not working (leave of absence, disability, unemployed, no longer volunteering) at each time point. Patients were categorized as good stable, improving, worsening and poor stable.

RESULTS

Baseline self-reported concentration problems and years of education significantly predicted employment trajectory.

LIMITATIONS

Post-hoc analyses of existing clinical data.

CONCLUSIONS

Self-reported concentration problems assessed in the context of specific areas of functioning may serve as a sensitive predictor of functional outcome in patients diagnosed with bipolar I disorder.

Hot Stars and Cool Clouds: The Photodissociation Region M16

We present high-resolution spectroscopy and images of a photodissociation region (PDR) in M16 obtained during commissioning of the near-infrared spectrometer (NIRSPEC) on the Keck II telescope. PDRs play a significant role in regulating star formation, and M16 offers the opportunity to examine the physical processes of a PDR in detail. We simultaneously observe both the molecular and ionized phases of the PDR and resolve the spatial and kinematic differences between them. The most prominent regions of the PDR are viewed edge-on. Fluorescent emission from nearby stars is the primary excitation source, although collisions also preferentially populate the lowest vibrational levels of H2. Variations in density-sensitive emission-line ratios demonstrate that the molecular cloud is clumpy, with an average density n=3x105 cm-3. We measure the kinetic temperature of the molecular region directly and find that TH2=930 K. The observed density, temperature, and UV flux imply a photoelectric heating efficiency of 4%. In the ionized region, ni=5x103 cm-3 and THii=9500 K. In the brightest regions of the PDR, the recombination line widths include a nonthermal component, which we attribute to viewing geometry.

J-Band Infrared Spectroscopy of a Sample of Brown Dwarfs Using NIRSPEC on Keck II

Near-infrared spectroscopic observations of a sample of very cool, low-mass objects are presented with higher spectral resolution than in any previous studies. Six of the objects are L dwarfs, ranging in spectral class from L2 to L8/9, and the seventh is a methane or T dwarf. These new observations were obtained during commissioning of the near-infrared spectrometer (NIRSPEC), the first high-resolution near-infrared cryogenic spectrograph for the Keck II 10 m telescope on Mauna Kea, Hawaii. Spectra with a resolving power of R approximately 2500 from 1.135 to 1.360 µm (approximately J band) are presented for each source. At this resolution, a rich spectral structure is revealed, much of which is due to blending of unresolved molecular transitions. Strong lines due to neutral potassium (K i) and bands due to iron hydride (FeH) and steam (H2O) change significantly throughout the L sequence. Iron hydride disappears between L5 and L8, the steam bands deepen, and the K i lines gradually become weaker but wider because of pressure broadening. An unidentified feature occurs at 1.22 µm that has a temperature dependence like FeH but has no counterpart in the available FeH opacity data. Because these objects are 3-6 mag brighter in the near-infrared compared with the I band, spectral classification is efficient. One of the objects studied (2MASSW J1523+3014) is the coolest L dwarf discovered so far by the 2 Micron All-Sky Survey (2MASS), but its spectrum is still significantly different from the methane-dominated objects such as Gl 229B or SDSS 1624+0029.

Infrared Spectroscopy of a Massive Obscured Star Cluster in the Antennae Galaxies (NGC 4038/9) with NIRSPEC

We present infrared spectroscopy of the Antennae galaxies (NGC 4038/9) with the near-infrared spectrometer (NIRSPEC) at the W. M. Keck Observatory. We imaged the star clusters in the vicinity of the southern nucleus (NGC 4039) with 0&farcs;39 seeing in the K band using NIRSPEC's slit-viewing camera. The brightest star cluster revealed in the near-IR [MK&parl0;0&parr0; approximately -17.9] is insignificant optically but is coincident with the highest surface brightness peak in the mid-IR (12-18 µm) Infrared Space Observatory image presented by Mirabel et al. We obtained high signal-to-noise ratio 2.03-2.45 µm spectra of the nucleus and the obscured star cluster at R approximately 1900. The cluster is very young ( approximately 4 Myr), massive (M approximately 16x106 M middle dot in circle), and compact (with a density of approximately 115 M middle dot in circle pc-3 within a 32 pc half-light radius), assuming a Salpeter initial mass function (0.1-100 M middle dot in circle). Its hot stars have a radiation field characterized by Teff approximately 39,000 K, and they ionize a compact H ii region with ne approximately 104 cm-3. The stars are deeply embedded in gas and dust (AV approximately 9-10 mag), and their strong far-ultraviolet field powers a clumpy photodissociation region with densities nH greater, similar105 cm-3 on scales of approximately 200 pc, radiating LH21-0S&parl0;1&parr0;=9600 L middle dot in circle.

2 Micron Spectroscopy within 0&farcs;3 of Sagittarius A*

We present moderate- (R approximately 2700) and high-resolution (R approximately 22,400) 2.0-2.4 µm spectroscopy of the central 0.1 arcsec2 of the Galaxy obtained with the facility near-infrared spectrometer (NIRSPEC) for the Keck II telescope. The composite spectra do not have any features attributable to the brightest stars in the central cluster; i.e., after background subtraction, W12CO&parl0;2-0&parr0;<2 Å. This stringent limit leads us to conclude that the majority, if not all, of the stars are hotter than typical red giants. Coupled with previously reported photometry, we conclude that the sources are likely OB main-sequence stars. In addition, the continuum slope in the composite spectrum is bluer than that of a red giant and is similar to that of the nearby hot star IRS 16NW. It is unlikely that they are late-type giants stripped of their outer envelopes because such sources would be much fainter than those observed. Given their inferred youth (tauage<20 Myr), we suggest the possibility that the stars have formed within 0.1 pc of the supermassive black hole. We find a newly identified broad-line component (VFWHM approximately 1000 km s-1) toward the 2.2178 µm [Fe iii] line located within a few arcseconds of Sagittarius A*. A similar component is not seen in the Brgamma emission.

The Rest-Frame Optical Spectrum of MS 1512-cB58

Moderate-resolution, near-IR spectroscopy of MS 1512-cB58 is presented, obtained during commissioning of the near-infrared spectrometer (NIRSPEC) on the Keck II telescope. The strong lensing of this z=2.72 galaxy by the foreground cluster MS 1512+36 makes it the best candidate for detailed study of the rest-frame optical properties of Lyman-break galaxies. In 80 minutes of on-source integration, we have detected Halpha, [N ii] lambdalambda6583, 6548, [O i] lambda6300, He i lambda5876, [O iii] lambdalambda5007, 4959, Hbeta, Hgamma, [O ii] lambda3727, and a strong continuum signal in the range of 1.29-2.46 µm. A redshift of z=2.7290+/-0.0007 is inferred from the emission lines, in contrast to the z=2.7233 calculated from UV observations of interstellar absorption lines. Using the Balmer line ratios, we find an extinction of E(B-V) = 0.27. Using the line strengths, we infer a star formation rate (SFR) of 620+/-18 M middle dot in circle yr-1 (H0=75, q0=0.1, and Lambda=0), which is a factor of 2 higher than that measured from narrowband imaging observations of the galaxy but is a factor of almost 4 lower than the SFR inferred from the UV continuum luminosity. The width of the Balmer lines yields a mass of Mvir=1.2x1010 M middle dot in circle. We find that the oxygen abundance is 13 solar, in good agreement with other estimates of the metallicity. However, we infer a high nitrogen abundance, which may argue for the presence of an older stellar population.

Discovery of an Obscured Broad-Line Region in the High-Redshift Radio Galaxy MRC 2025-218

This Letter presents infrared spectra taken with the newly commissioned near-infrared spectrometer (NIRSPEC) on the Keck II telescope of the high-redshift radio galaxy MRC 2025-218 (z=2.63). These observations represent the deepest infrared spectra of a radio galaxy to date and have allowed for the detection of Hbeta, [O iii] lambdalambda4959, 5007, [O i] lambda6300, Halpha, [N ii] lambdalambda6548, 6583, and [S ii] lambdalambda6716, 6713. The Halpha emission is very broad (FWHM=9300 km s-1) and luminous (2.6x1044 ergs s-1), and it is very comparable to the line widths and strengths of radio-loud quasars at the same redshift. This strongly supports active galactic nucleus unification models linking radio galaxies and quasars, although we discuss some of the outstanding differences. The line [O iii] lambda5007 is extremely strong and has extended emission with large relative velocities toward the nucleus. We also derive that if the extended emission is due to star formation, each knot has a star formation rate comparable to a Lyman-break galaxy at the same redshift.

Design and SAR of novel potassium channel openers targeted for urge urinary incontinence. 2. Selective and potent benzylamino cyclobutenediones

A novel series of benzylamine, potassium channel openers (KCOs) is presented as part of our program toward designing new, bladder-selective compounds for the treatment of urge urinary incontinence (UUI). We have found that the in vitro potency of (R)-4-[3,4-dioxo-2-(1,2, 2-trimethyl-propylamino)-cyclobut-1-enylamino]-3-ethyl-benzo nitrile 1 in the relaxation of precontracted rat detrusor strips can also be obtained with cyanobenzylamine derivative 4 (IC(50) = 0.29 microM) (Figure 3). Addition of a 2-Cl substituted benzylamine moiety and changing the alkylamino substituent of 4 to a t-Bu amine gives 31 (IC(50) = 0.14 microM)-a compound with similar in vitro potency as 4 as well as relaxant activity on bladder smooth muscle in vivo when administered orally (31, ED(50) = 3 mg/kg) in a rodent model of bladder instability. Further modifications, particularly the replacement of the t-Bu amino substituent with a tert-amylamine, gave a similarly active compound 60 (IC(50) = 0.10 microM) which shows excellent in vivo efficacy (ED(50) = 0.6 mg/kg). Moreover, 60, 3-(2,4-dichloro-6-methyl-benzylamino)-4-(1, 1-dimethyl-propylamino)-cyclobut-3-ene-1,2-dione (WAY-151616), shows excellent tissue selectivity for bladder K channels over arterial tissue (60, MAP ED(20) = 100 mg/kg; selectivity: MAP ED(20)/bladder ED(50) = 166). Other manipulations of the benzylamino cyclobutenediones, acylation of the benzylamine, conversion of the benzylamine substituent to a benzamide, homologation of the benzylamine to a phenethylamine, and incorporation of a methyl group at the benzyl carbon, all led to substantial loss of in vitro activity, although some in vivo activity was maintained in the acylated analogues. Compound 60 represents an attractive candidate for development in the treatment of UUI.

Novel and selective calcitonin-inducing agents

A series of xanthine sulfonamides is presented as a class of calcitonin (CT) inducers - a potentially new method for treating diseases associated with postmenopausal bone loss such as osteoporosis. We have found that certain di-n-butylxanthine sulfonamides 4 upregulate CT transcription in a CT-luciferase reporter gene assay (CT-luci) and increase the production and release of CT in a CT secretion/RIA assay (CTS). In addition, these compounds do not have potent PDE4 inhibitory activity as do the related xanthine methylene ketones such as denbufyllene (2). One compound in particular (9) shows a transcription activation ratio (TAR) of 2.1 in CT-luci, a CTS increase of 3.6-fold, and a PDE4 (phosphodiesterase type IV) IC(50) = 4.1 microM. In addition, this compound showed a statistically significant 47% trabecular bone protection in ovariectomized-induced osteopenia (OVX) rats as determined by assay when administered for 4 weeks at 30 mg/kg/day, i. p. by quantitative computed tomography (QCT). When administered p.o., compound 9 shows 50% trabecular bone protection when administered for 3 weeks at 50 mg/kg/day, i.p. This compared with salmon CT which shows 62% trabecular bone protection when administered at 50 IU/kg/day for 4 weeks.

The assessment of lamotrigine, an antiepileptic drug, in the treatment of tinnitus

OBJECTIVE

Tinnitus is an extremely prevalent condition that currently has no satisfactory clinical treatment. Development of therapy has been hampered by the diversity of underlying conditions that give rise to the symptom of tinnitus. A drug that has multiple actions may have an improved chance of being effective. One such drug is lamotrigine, a recently developed antiepileptic agent that has both glutamate release inhibition and sodium channel antagonist activity.

STUDY DESIGN

Lamotrigine was evaluated in a double-blind, placebo-controlled, crossover clinical trial. Patients initially were tested with an intravenous infusion of lidocaine (10 mg/mL) to a maximum of 100 mg or until a reduction in tinnitus. Lamotrigine or placebo tablets were taken once daily (25 mg) for 2 weeks, 50 mg for 2 weeks, and 100 mg for 4 weeks.

SETTING

Patients were chosen from among volunteers from the tinnitus clinic in the local hospital without reference to underlying pathology.

PATIENTS

Those patients whose tinnitus had been present for less than 6 months or whose tinnitus was likely to vary spontaneously were excluded.

INTERVENTIONS

Perceived intensity and intrusiveness of tinnitus was assessed before entry onto the trial and at 4-week intervals throughout the trial.

MAIN OUTCOME MEASURES

Assessment comprised questionnaires, visual analog scales, and a battery of audiologic measurements.

RESULTS

There was no correlation between the response to lidocaine and the response to lamotrigine. There was good agreement between the questionnaires and visual analog scales in the reporting of perceived changes; however, this was not reflected as changes in the audiologic tests.

CONCLUSIONS

Of the 31 participants who completed the trial, questionnaires indicated that lamotrigine was effective in a very few of these persons.

Identification and analysis of a class 2 alpha-mannosidase from Aspergillus nidulans

A Class 2 alpha-mannosidase gene was cloned and sequenced from the filamentous fungus Aspergillus nidulans. A portion of the gene was amplified using degenerate oligonucleotide primers which were designed based on similarity between the Saccharomyces cerevisiae vacuolar and rat ER/cytosolic Class 2 protein sequences. The PCR amplification product was used to isolate the full length gene, and DNA sequencing revealed a 3383 bp coding region containing three introns. The predicted 1049 amino acid reading frame contained six potential N-glycosylation sites and encoded a protein of 118 kDa. The protein sequence did not appear to encode a typical fungal signal sequence or membrane spanning domain. Although the cellular location of the A.nidulans mannosidase was not determined, experimental evidence suggested that it was located within a subcellular organelle. The Matchbox sequence similarity matrix indicated that the A.nidulans protein sequence was more highly similar to the rat ER/cytosolic (Rij = 0.33) and S.cerevisiae vacuolar alpha-mannosidases (Rij = 0.43) than the rat and yeast sequences were to each other (Rij = 0.29). These three enzymes were found to be distantly related to other Class 2 sequences, and compose a third subgroup of Class 2 alpha-mannosidases, as shown by ClustalW sequence alignment.

Variations in the uptake of beta-carotene in the oral mucosa of individuals after 3 days of supplementation

Variations in the response of individuals to beta-carotene supplementation were studied by measuring the accumulation of beta-carotene in oral mucosa cells. Beta-carotene was administered orally to 178 individuals for 3 consecutive days, exfoliated oral mucosa cells were collected by brushing the entire oral mucosa on the 7th day following supplementation, and the beta-carotene content was measured by HPLC analysis of the pronase-treated cells. The rise in beta-carotene levels in the oral mucosa following supplementation varied considerably. Significant differences in mean beta-carotene levels in the oral mucosa were observed in 4 population groups. After supplementation, beta-carotene levels increased by factors of 10.3 (100 Mile House), 7.8 (Williams Lake), 6.9 (Lytton) and 3.4 (Vancouver), respectively. This difference in mean beta-carotene values is due to there being different proportions of weak and strong responders in the various population groups. Neither peak levels nor increases in beta-carotene levels were correlated with base-line concentrations of beta-carotene in the pre-supplementation samples. A second supplementation was given to 54 individuals several months after the initial supplementation. Of 17 weak responders in the first supplementation study, 10 (58.8%) individuals again showed only a small increase. A time-course study revealed that low responders showed no significant changes in beta-carotene levels over the 21 days following supplementation. Particular attention should be paid to weak responders when results of intervention trials using beta-carotene are interpreted.

Defective production of leucocytic endogenous mediator (interleukin 1) by peripheral blood leucocytes of patients with systemic sclerosis, systemic lupus erythematosus, rheumatoid arthritis and mixed connective tissue disease

Leucocytic endogenous mediator is one of the activities ascribed to the cytokine or family of cytokines known as interleukin 1. In this study we have examined the ability of circulating blood leucocytes from patients with rheumatic diseases to produce this mediator in vitro. Leucocytic endogenous mediator production was found to be significantly decreased below normal values (mean 107 units, s.e.m. +/- 25) in systemic sclerosis (-6 units +/- 18), systemic lupus erythematosus (-25 units +/- 13), rheumatoid arthritis (-3 units +/- 13) and mixed connective tissue disease (-4 units +/- 40). A control group of ill patients with cancer produced 57 units +/- 8.