Heritability and Quantitative Trait Loci for Popping Characteristics in Sorghum Grain

Popped sorghum (Sorghum bicolor, L. Moench) is becoming increasingly popular with niche consumers. However, sorghum has not undergone the years of intensive selective breeding that popcorn has. This study measured popping characteristics and grain traits to estimate heritability, the relative effect of environment and genotype x environment interactions on these traits and to identify quantitative trait loci (QTL) for popping quality. Using a heated-air popping methodology, a recombinant inbred line population was phenotyped for popping characteristics in grain from three environments in Texas. Entry-mean heritability of popping efficiency (PE) ranged from 0.595 – 0.755 and the heritability of expansion ratio (ER) ranged from 0.617 – 0.769 across environments. ANOVA indicate that both environment and genotype x environment interactions were significant sources of variation. Using genome sequence mapping technology, five QTL were identified for popping efficiency and four were identified for expansion ratio. Additionally QTL for endosperm color, kernel diameter, kernel weight, and kernel hardness were found, and several of those were consistent across multiple production environments. These results indicate that popping quality a complex quantitative trait in sorghum, but improvement of popping efficiency, expansion ratio, and other kernel characteristics via marker-assisted selection is possible

Examination scheduling using the ant system.

This work is concerned with heuristic approaches to examination timetabling. It is demonstrated that a relatively new evolutionary method, the Ant System, can be the basis of a successful two-phase solution method. The first phase exploits ant feedback in order both to produce large volumes of feasible timetables and to optimise secondary objectives. The second phase acts as a repair facility where solution quality is improved further while maintaining feasibility. This is accomplished without increasing computational effort to unrealistic levels. The work builds on an existing implementation for the graph colouring problem, the natural model for examination scheduling. It is demonstrated that by adjusting the graph model to allow the accommodation of several side constraints as well incorporating enhancement techniques within the algorithm itself, the Ant System algorithm becomes very effective at producing feasible timetables. The enhancements include a diversification function, new reward functions and trail replenishment tactics. It is observed that the achievement of second-order objectives can be enhanced through a variety of means. A modified elitist strategy (ERF) significantly improves the performance of the Ant System due to the extra emphasis on second-order feedback. It is also shown that through the incorporation of the ERF, trail limits and, in particular, 19th century evolutionary theory the area of the solution space explored by the ants during the infancy of the search can be reduced. In addition, a good level of exploration is maintained as the search matures. This balance between exploration and exploitation is the main determinant of solution quality. The use of a repair facility, as is common practice with evolutionary algorithms, encourages fitter solutions. The interaction between Lamarckian evolution and searching in an extended neighbourhood through the graph theoretic concept of Kempe chains leads to better overall solutions

Evaluation and Implementation of Proximal and Remote Sensing Techniques in a Sorghum Breeding Program

Plant breeders must improve the efficiency of their programs to meet the needs of a rising world population and a rapidly changing climate. Proximal and remote sensing technologies stand as an attractive option for breeders, as they can help to alleviate the phenotyping bottleneck in most programs. Sorghum (Sorghum bicolor, L. Moench) stands as an excellent crop for researchers to test these technologies. Traits such as biomass yield, plant height, and anthracnose resistance are all important traits to sorghum breeders. In addition, spatial variability is often of chief concern in sorghum breeding trials. For biomass yield and plant height, we utilized Canopy Volume/Canopy Coverage estimates and structure-from-motion (SfM)-derived plant height estimates, respectively. It was determined that Canopy Volume is effective at teasing out the most genotypic variation, while minimizing error, when compared to Canopy Coverage as an estimate of biomass. Additionally, the ninety-fifth percentile (P95) of SfM height estimate was shown to be more strongly correlated with ground-truth estimates of plant height. For estimation of spatial variability, we utilized soil apparent electrical conductivity (ECa) grids to test three different linear models for their ability to account for spatial autocorrelation in various trials via a Moran’s I test. We found that in most situations it is unnecessary to use blocking or soil ECva grids, but that in situations where it is necessary there is usually a superior choice. Thus, it is probably best to use both methods and determine which is the best for each situation by finding which model removes spatial autocorrelation. Finally, we tested normalized difference vegetation index (NDVI) for its ability to estimate the incidence and severity of anthracnose (Colletotrichum sublineola) disease in a sorghum breeding population. We find that NDVI is highly effective at delineating genotypic variation for anthracnose resistance later in the season but is inferior to ground-truth methods early on. There are many other traits and aspects of sorghum breeding that have yet to be tested, but these examples serve as an indicator that remote and proximal sensing will be an incredibly valuable tool in the future

Extracellular chloride is required for efficient activation of secondary signalling pathways during platelet aggregation

Anion channels perform a diverse range of functions and have been implicated in ATP release, volume regulation and phosphatidylserine exposure. Platelets have been shown to express several anion channels however their function is incompletely understood. Due to a paucity of specific pharmacological blockers, we investigated the global effect of extracellular chloride substitution on platelet activation using aggregometry and flow cytometry. In the absence of extracellular chloride we observed a modest effect on the maximum aggregation response to thrombin or collagen-related peptide. Although the rate of aggregation was substantially reduced in a manner that was dependent on the extracellular chloride concentration, aggregation in the absence of chloride was noticeably biphasic, indicative of impaired secondary signalling. This was further investigated by targeting secondary agonists with aspirin and apyrase or by blockade of the ADP receptor P2Y12. Under these conditions, the rates of aggregation were comparable to those recorded in the absence of extracellular chloride. Finally, we assessed platelet granule release by flow cytometry and report a chloride-dependent element of alpha, but not dense, granule secretion. Taken together these data support a role for anion channels in the efficient induction of platelet activation, likely via enhancement of secondary signalling pathways

Three-coordinate iron(II) expanded ring N-heterocyclic carbene complexes

A sterically demanding seven-membered expanded ring N-heterocyclic carbene (NHC) ligand allows access to rare examples of three-coordinate iron(II)-NHC complexes incorporating only halide coligands of the general formula [Fe(NHC)X 2 ] (NHC = 7-DiPP; X = Br (1) Cl (2)). Reducing the steric influence of the ancillary NHC ligand through modulation of the N-aryl substituents leads to either four- or three-coordinate complexes of the general formula [Fe(NHC)Br 2 (THF)] (3) or [Fe(NHC)Br 2 ] (4) (NHC = 7-Mes), dependent upon the solvent of recrystallization. The further reduction of NHC steric influence results in four-coordinate geometries at iron in the form of the dimeric species [Fe(NHC)Br(μ-Br)] 2 (5) or [Fe(NHC)Br 2 (THF)] (6) (NHC = SDiPP), again dependent upon the solvent of recrystallization. Compounds 1-6 have been analyzed by 1 H NMR spectroscopy, X-ray crystallography, elemental microanalysis, Mössbauer spectroscopy (for 1 and 3-5), and Evans method magnetic susceptibility. In addition to these measurements the three-coordinate species 1 and 4 have been further analyzed by SQUID magnetometry and CASSCF calculations, which show significant magnetic anisotropy that is extremely sensitive to the coordination geometry

Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations

The inosine triphosphate pyrophosphatase (ITPA) protein is responsible for removing noncanonical purine nucleoside triphosphates from intracellular nucleotide pools. Absence of ITPA results in genomic instability and increased levels of inosine in DNA and RNA. The proline to threonine substitution at position 32 (P32T) affects roughly 15% of the global population and can modulate treatment outcomes for cancer, lupus, and hepatitis C patients. The substitution of arginine with cysteine at position 178 (R178C) is extremely uncommon and has only been reported in a small cohort of early infantile encephalopathy patients suggesting that a functional ITPA protein is required for life in humans. Here we present molecular dynamic simulations that describe the structure and dynamics of the wild-type ITPA homodimer and two of its clinically relevant mutants, P32T and R178C. The simulation results indicate that both the P32T and R178C mutations alter the structure and dynamic properties of the protein and provide a possible explanation of the experimentally observed effect of the mutations on ITPA activity. Specifically, the mutations increased the overall flexibility of the protein and changed the dominant collective motions of the top lobe as well as the helix 2 of the lower lobe. Moreover, we have identified key active-site residues that are classified as essential or intermediate for inosine triphosphate (ITP) hydrolyzing activity based on their hydrogen bond occupancy. Here we also present biochemical data indicating that the R178C mutant has very low ITP hydrolyzing activity

Extracellular chloride is required for efficient platelet aggregation.

Anion channels perform a diverse range of functions and have been implicated in ATP release, volume regulation, and phosphatidylserine exposure. Platelets have been shown to express several anion channels but their function is incompletely understood. Due to a paucity of specific pharmacological blockers, we investigated the effect of extracellular chloride substitution on platelet activation using aggregometry and flow cytometry. In the absence of extracellular chloride, we observed a modest reduction of the maximum aggregation response to thrombin or collagen-related peptide. However, the rate of aggregation was substantially reduced in a manner that was dependent on the extracellular chloride concentration and aggregation in the absence of chloride was noticeably biphasic, indicative of impaired secondary signaling. This was further investigated by targeting secondary agonists with aspirin and apyrase or by blockade of the ADP receptor P2Y12. Under these conditions, the rates of aggregation were comparable to those recorded in the absence of extracellular chloride. Finally, we assessed platelet granule release by flow cytometry and report a chloride-dependent element of alpha, but not dense, granule secretion. Taken together these data support a role for anion channels in the efficient induction of platelet activation, likely via enhancement of secondary signaling pathways

Dissemination of Registered COVID-19 Clinical Trials (DIRECCT): a cross-sectional study

Background The results of clinical trials should be completely and rapidly reported during public health emergencies such as COVID-19. This study aimed to examine when, and where, the results of COVID-19 clinical trials were disseminated throughout the first 18 months of the pandemic. Methods Clinical trials for COVID-19 treatment or prevention were identified from the WHO ICTRP database. All interventional trials with a registered completion date ≤ 30 June 2021 were included. Trial results, published as preprints, journal articles, or registry results, were located using automated and manual techniques across PubMed, Google Scholar, Google, EuropePMC, CORD-19, the Cochrane COVID-19 Study Register, and clinical trial registries. Our main analysis reports the rate of dissemination overall and per route, and the time from registered completion to results using Kaplan–Meier methods, with additional subgroup and sensitivity analyses reported. Results Overall, 1643 trials with completion dates ranging from 46 to 561 days prior to the start of results searches were included. The cumulative probability of reporting was 12.5% at 3 months from completion, 21.6% at 6 months, and 32.8% at 12 months. Trial results were most commonly disseminated in journals (n = 278 trials, 69.2%); preprints were available for 194 trials (48.3%), 86 (44.3%) of which converted to a full journal article. Trials completed earlier in the pandemic were reported more rapidly than those later in the pandemic, and those involving ivermectin were more rapidly reported than other common interventions. Results were robust to various sensitivity analyses except when considering only trials in a “completed” status on the registry, which substantially increased reporting rates. Poor trial registry data on completion status and dates limits the precision of estimates. Conclusions COVID-19 trials saw marginal increases in reporting rates compared to standard practice; most registered trials failed to meet even the 12-month non-pandemic standard. Preprints were common, complementing journal publication; however, registries were underutilized for rapid reporting. Maintaining registry data enables accurate representation of clinical research; failing to do so undermines these registries’ use for public accountability and analysis. Addressing rapid reporting and registry data quality must be emphasized at global, national, and institutional levels

The Mission Accessible Near-Earth Objects Survey: Four years of photometry

Over 4.5 years, the Mission Accessible Near-Earth Object Survey (MANOS) assembled 228 Near-Earth Object (NEO) lightcurves. We report rotational lightcurves for 82 NEOs, constraints on amplitudes and periods for 21 NEOs, lightcurves with no detected variability within the image signal to noise and length of our observing block for 30 NEOs, and 10 tumblers. We uncovered 2 ultra-rapid rotators with periods below 20s; 2016MA with a potential rotational periodicity of 18.4s, and 2017QG$_{18}$ rotating in 11.9s, and estimate the fraction of fast/ultra-rapid rotators undetected in our project plus the percentage of NEOs with a moderate/long periodicity undetectable during our typical observing blocks. We summarize the findings of a simple model of synthetic NEOs to infer the object morphologies distribution using the measured distribution of lightcurve amplitudes. This model suggests a uniform distribution of axis ratio can reproduce the observed sample. This suggests that the quantity of spherical NEOs (e.g., Bennu) is almost equivalent to the quantity of highly elongated objects (e.g., Itokawa), a result that can be directly tested thanks to shape models from Doppler delay radar imaging analysis. Finally, we fully characterized 2 NEOs as appropriate targets for a potential robotic/human mission: 2013YS$_{2}$ and 2014FA$_{7}$ due to their moderate spin periods and low $\Delta v$.Comment: Accepted for Publication, The Astrophysical Journal Supplement Serie