QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits

The organoleptic quality of tomato fruit involves a set of attributes (flavour, aroma, texture) that can be evaluated either by sensory analyses or by instrumental measures. In order to study the genetic control of this characteristic, a recombinant inbred line (RIL) population was developed from an intraspecific cross between a cherry tomato line with a good overall aroma intensity and an inbred line with medium flavour but bigger fruits. A total of 38 traits involved in organoleptic quality were evaluated. Physical traits included fruit weight, diameter, colour, firmness, and elasticity. Chemical traits were dry matter weight, titratable acidity, pH, and the contents of soluble solids, sugars, lycopene, carotene, and 12 aroma volatiles. A panel of trained assessors quantified sensory attributes: flavour (sweetness and sourness), aroma (overall aroma intensity, together with candy, lemon, citrus fruit, and pharmaceutical aromas) and texture (firmness, meltiness, mealiness, juiciness, and skin difficult to swallow). RILs showed a large range of variation. Molecular markers were used to map a total of 130 quantitative trait loci (QTL) for the 38 traits. They were mainly distributed in a few chromosome regions. Major QTLs (R(2) >30%) were detected for fruit weight, diameter, colour, firmness, meltiness, and for six aroma volatiles. The relationships between instrumental measures and sensory traits were analysed with regard to the QTL map. A special insight was provided about the few regions where QTLs are related to multiple traits. A few examples are shown to illustrate how the simultaneous analysis of QTL segregation for related traits may aid in understanding the genetic control of quality traits and pave the way towards QTL characterization.     

Neutron scattering shows a droplet of oleic acid at the center of the BAMLET complex

The anti‐cancer complex, Bovine Alpha‐lactalbumin Made LEthal to Tumors (BAMLET), has intriguing broad‐spectrum anti‐cancer activity. Although aspects of BAMLET's anti‐cancer mechanism are still not known, it is understood that it involves the oleic acid or oleate component of BAMLET being preferentially released into cancer cell membranes leading to increased membrane permeability and lysis. The structure of the protein component of BAMLET has previously been elucidated by small angle X‐ray scattering (SAXS) to be partially unfolded and dramatically enlarged. However, the structure of the oleic acid component of BAMLET and its disposition with respect to the protein component was not revealed as oleic acid has the same X‐ray scattering length density (SLD) as water. Employing the difference in the neutron SLDs of hydrogen and deuterium, we carried out solvent contrast variation small angle neutron scattering (SANS) experiments of hydrogenated BAMLET in deuterated water buffers, to reveal the size, shape, and disposition of the oleic acid component of BAMLET. Our resulting analysis and models generated from SANS and SAXS data indicate that oleic acid forms a spherical droplet of oil incompletely encapsulated by the partially unfolded protein component. This model provides insight into the anti‐cancer mechanism of this cache of lipid. The model also reveals a protein component “tail” not associated with the oleic acid component that is able to interact with the tail of other BAMLET molecules, providing a plausible explanation of how BAMLET readily forms aggregates. Proteins 2017; 85:1371–1378. © 2017 Wiley Periodicals, Inc.     

Habitat use by early life-history stages of fishes and crustaceans along a changing estuarine landscape: differences between natural and altered shoreline sites

The recent population explosion along the coastal zoneof the southeast United States and the Gulf of Mexicohas accelerated the development rate of waterfrontproperty, and particularly along the Gulf Coast ofMississippi. We compared use of pristine and alteredshoreline habitat by early life-history stages of fishand crustaceans to assess the potential effects ofthis development. Monthly beam trawls were taken at13 sites along shoreline habitats characterized byJuncus/Spartinamarsh, natural beach, and areasaltered by bulkheads and rubble. A total of 52,068fish (n = 48 taxa) and 288,715 crustaceans (n = 24taxa) were collected during a two year study. The mostabundant fish groups included gobiids, sciaenids,clupeids, and engraulids. Crustaceans, excluding thecopepods, were numerically dominated by mysids, bothcaridean and penaeid shrimps, and crabs (Callinectesspp.). Demersal residents were dominatedby Gobiosoma boscand Palaemonetessp.whereas clupeiformes, sciaenids and penaeid shrimpswere dominant among the nektonic and demersaltransient species. These taxa were least abundantalong stretches of shoreline altered with bulkheads orrubble, and were generally most abundant in shorelinehabitats fringed with Juncus/Spartinagrasses.This general pattern in nekton relative abundanceparallel the low diversity (reciprocal of Simpson'sDominance Index) values adjacent to altered marsh tohigh values adjacent to pristine marsh or beachhabitats, suggesting that habitats adjacent to alteredmarsh sites are less frequently used as nurseryhabitat compared to natural sites. These data supportthe hypothesis that shorelines adjacent to marshhabitat are critical to various life history stages ofecologically- and commercially-important species,illustrate the influence of altering natural marshhabitat on resident/transient nekton, and providequantitative data for resource managers in thecontinued efforts to preserve the complex estuarinemarsh landscape.     

Changes in soil moisture drive soil methane uptake along a fire regeneration chronosequence in a eucalypt forest landscape

Disturbance associated with severe wildfires (WF) and WF simulating harvest operations can potentially alter soil methane (CH₄) oxidation in well‐aerated forest soils due to the effect on soil properties linked to diffusivity, methanotrophic activity or changes in methanotrophic bacterial community structure. However, changes in soil CH₄ flux related to such disturbances are still rarely studied even though WF frequency is predicted to increase as a consequence of global climate change. We measured in‐situ soil–atmosphere CH₄ exchange along a wet sclerophyll eucalypt forest regeneration chronosequence in Tasmania, Australia, where the time since the last severe fire or harvesting disturbance ranged from 9 to >200 years. On all sampling occasions, mean CH₄ uptake increased from most recently disturbed sites (9 year) to sites at stand ‘maturity’ (44 and 76 years). In stands >76 years since disturbance, we observed a decrease in soil CH₄ uptake. A similar age dependency of potential CH₄ oxidation for three soil layers (0.0–0.05, 0.05–0.10, 0.10–0.15 m) could be observed on incubated soils under controlled laboratory conditions. The differences in soil CH₄ uptake between forest stands of different age were predominantly driven by differences in soil moisture status, which affected the diffusion of atmospheric CH₄ into the soil. The observed soil moisture pattern was likely driven by changes in interception or evapotranspiration with forest age, which have been well described for similar eucalypt forest systems in south‐eastern Australia. Our results imply that there is a large amount of variability in CH₄ uptake at a landscape scale that can be attributed to stand age and soil moisture differences. An increase in severe WF frequency in response to climate change could potentially increase overall forest soil CH₄ sinks.     

Denitrification in a Sand and Gravel Aquifer

Denitrification was assayed by the acetylene blockage technique in slurried core material obtained from a freshwater sand and gravel aquifer. The aquifer, which has been contaminated with treated sewage for more than 50 years, had a contaminant plume greater than 3.5-km long. Near the contaminant source, groundwater nitrate concentrations were greater than 1 mM, whereas 0.25 km downgradient the central portion of the contaminant plume was anoxic and contained no detectable nitrate. Samples were obtained along the longitudinal axis of the plume (0 to 0.25 km) at several depths from four sites. Denitrification was evident at in situ nitrate concentrations at all sites tested; rates ranged from 2.3 to 260 pmol of N₂O produced (g of wet sediment)⁻¹ h⁻¹. Rates were highest nearest the contaminant source and decreased with increasing distance downgradient. Denitrification was the predominant nitrate-reducing activity; no evidence was found for nitrate reduction to ammonium at any site. Denitrifying activity was carbon limited and not nitrate limited, except when the ambient nitrate level was less than the detection limit, in which case, even when amended with high concentrations of glucose and nitrate, the capacity to denitrify on a short-term basis was lacking. These results demonstrate that denitrification can occur in groundwater systems and, thereby, serve as a mechanism for nitrate removal from groundwater.     

Kinetic Model for NS1643 Drug Activation of WT and L529I Variants of Kv11.1 (hERG1) Potassium Channel

Congenital and acquired (drug-induced) forms of the human long-QT syndrome are associated with alterations in Kv11.1 (hERG) channel-controlled repolarizing I_Kr currents of cardiac action potentials. A mandatory drug screen implemented by many countries led to a discovery of a large group of small molecules that can activate hERG currents and thus may act as potent antiarrhythmic agents. Despite significant progress in identification of channel activators, little is known about their mechanism of action. A combination of electrophysiological studies with molecular and kinetic modeling was used to examine the mechanism of a model activator (NS1643) action on the hERG channel and its L529I mutant. The L529I mutant has gating dynamics similar to that of wild-type while its response to application of NS1643 is markedly different. We propose a mechanism compatible with experiments in which the model activator binds to the closed (C3) and open states (O). We suggest that NS1643 is affecting early gating transitions, probably during movements of the voltage sensor that precede the opening of the activation gate.     

Stretching the immunoglobulin 27 domain of the titin protein: the dynamic energy landscape

Molecular simulations are carried out on the Immunoglobulin 27 domain of the titin protein. The energy landscape is mapped out using an implicit solvent model, and molecular dynamics simulations are run with the solvent explicitly modeled. Stretching a protein is shown to produce a dynamic energy landscape in which the energy minima move in configuration space, change in depth, and are created and destroyed. The connections of these landscape changes to the mechanical unfolding of the Immunoglobulin 27 domain are addressed. Hydrogen bonds break upon stretching by either intrabasin processes associated with the movement of energy minima, or interbasin processes associated with transitions between energy minima. Intrabasin changes are reversible and dominate for flexible interactions, whereas interbasin changes are irreversible and dominate for stiff interactions. The most flexible interactions are Glu-Lys salt bridges, which can act like tethers to bind strands even after all backbone interactions between the strands have been broken. As the protein is stretched, different types of structures become the lowest energy structures, including structures that incorporate nonnative hydrogen bonds. Structures that have flat energy versus elongation profiles become the lowest energy structures at elongations of several Angstroms, and are associated with the unfolding intermediate state observed experimentally.     

Purification, characterization, and subcellular localization of an acid phosphatase from black mustard cell-suspension cultures: comparison with phosphoenolpyruvate phosphatase

An acid phosphatase from Brassica nigra (black mustard) leaf petiole cell-suspension cultures has been purified 1633-fold to a final specific activity of 1225 (mumols orthophosphate produced/min)/mg protein and near homogeneity. The native protein was a glycosylated monomer having a molecular mass of 60 kDa and a pI of 4.5. The enzyme displayed a broad pH optimum of about pH 5.6 and was heat stable. The final preparation hydrolyzed a wide variety of phosphate esters. The highest specificity constants were obtained with 3-phosphoglycerate, 2,3-diphosphoglycerate, PPi, and phosphoenolpyruvate (PEP). The enzyme was activated 1.4-fold by 4 mM Mg2+ or Mn2+, but was strongly inhibited by Mo, Pi, F, and several phosphorylated compounds. Subcellular localization experiments revealed that this nonspecific acid phosphatase is probably a secreted enzyme, localized in the cell wall. By contrast, B. nigra PEP phosphatase appeared to be localized in the cell vacuole. Peptide mapping via CNBr fragmentation was employed to investigate the structural relatedness of the two phosphatases. Their respective CNBr cleavage patterns were dissimilar, suggesting that B. nigra acid and PEP phosphatases are distinct polypeptides. Putative metabolic functions of these two phosphatases are discussed in relation to the biochemical adaptations of B. nigra cell-suspension cultures to nutritional phosphate deprivation.     

The effect of nitrogen on fine white root persistence in cherry (Prunus avium)

The persistence of white roots in cherry (Prunus avium) grown under two levels of nitrogen (high and low), was studied directly using a non-destructive borescope system. Plant growth and nitrogen uptake was increased by the extra nitrogen. Persistence times of white roots were significantly affected by several factors such as nitrogen level, time of appearance and depth in the pot.Suberisation of white roots tended to be late in the growing season, and roots produced in the middle of May persisted as white for significantly longer (5.9 weeks) than those produced in early July (2.5 weeks). Also, roots that appeared at the foot of the pot remained white for longer (5.6 weeks) than roots at the surface of the pot (2.7 weeks). Results also suggest that white root persistence was greater for trees with the lower rate of application of nitrogen (4.5 weeks under low nitrogen compared to 3.6 under high nitrogen).     

Effect of Probe Size on the Concentration of Brain Extracellular Uric Acid Monitored with Carbon Paste Electrodes

Abstract: We have investigated further the anomalously high concentration of brain extracellular uric acid detected with in vivo sampling probes reported recently. The contribution by uric acid and 5-hydroxyindoleacetic acid (5-HIAA) to peak 2 recorded in rat striatum with chronically implanted carbon paste electrodes (CPEs) of different sizes was estimated by comparing peak current densities and the effect of the monoamine oxidase inhibitor pargyline. The concentration of uric acid in the extracellular fluid was some 50 times greater for 320-μm-diameter CPEs than for 160-μm-diameter electrodes, where the urate level was estimated at ∼1 μ M. The concentration of 5-HIAA was similar for 320-, 260-, and 160-μm-diameter CPEs. These data provide an explanation for the previously observed differences in 5-HIAA/urate ratios re corded with 320-μm-diameter CPEs and smaller carbon fibre electrodes. The results also indicate that chronically implanted sampling probes of diameter >160 μm perturb the surrounding tissue, which produces uric acid by a mechanism yet unknown, although preliminary histological data suggest that glial cells may be involved.