Metabolic fuels along the nephron: Pathways and intracellular mechanisms of interaction

Substrates in large numbers are removed from the blood by the kidney in linear relationship to their arterial concentrations [1, 2]. At normal arterial blood levels, the kidney utilizes significant amounts of free fatty acids, lactate, glutamine, 3-hydroxybutyrate, and citrate. Furthermore, the kidney removes substrates like pyruvate, α-ketoglutarate, glycerol, proline, and some other amino acids of low arterial concentrations. However, when blood levels of these substances increase, their renal uptake rates likewise increase [1, 2]. Metabolic fates of these substrates in the kidney are related intimately to major functions of the kidney including excretion of waste materials, reabsorption of life conserving substances and water, and other important endocrine and metabolic functions.When studied in vitro, the capacity of renal tissue to take up substrates was shown to be far in excess of the rates occurring under in vivo conditions [2]. This indicates that saturation is not reached in vivo due to suboptimal substrate concentrations. For lactate, pyruvate, glutamine, proline, fatty acids, and ketone bodies, normal arterial levels are below or around the half-maximal concentration kinetically determined in in vitro uptake studies [3–8]. However, even under this nonsaturating condition, the rates of substrate uptake in vivo exceed the quantities of fuel needed to meet the energy demands of the kidney as calculated from oxygen uptake [1, 9]. Table 1 summarizes the calculated oxygen uptake and ATP formation rates for some substrates. From the theoretical and the experimental data on substrate uptake rates and measurements of oxygen consumption [1, 2], it becomes clear that the kidney takes up more substrates than could be accounted for by oxidation.The term “incomplete oxidation” was introduced by Cohen [1] to explain this phenomenon. For example, 3-hydroxybutyrate taken up by the kidney is partially released as acetoacetate [8]. On the other hand, no net product release was found for other substrates taken up in excess. From recent in vitro studies, it was concluded that the kidney can utilize substrates by metabolic pathways that do not lead to their oxidation [2–7]. Thus, lactate, glycerol, glutamine, and other substrates are in part converted to glucose through the gluconeogenic pathway, whereas fatty acids which cannot be converted to glucose are recovered mainly as triacylglycerol [5, 10].Two major questions may be raised at this point: (1) What nephron cells are responsible for the substrate uptake rates observed? (2) What are the mechanisms regulating intracellular interactions of various substrates?This review will briefly summarize some recent findings on intercellular heterogeneity and intracellular regulatory mechanisms that may help explain the metabolic balances observed in vivo

Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions

Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long‐read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein‐coding genes and 6,747 non‐coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (P. persica) diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions/kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). TEs have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. TEs may also be at the origin of important phenotypic differences between both species, and in particular, for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.info:eu-repo/semantics/publishedVersio

Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

Background: Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results: Using an almond intraspecific cross between ‘Nonpareil’ and ‘Lauranne’ (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P < 0.05. Due to the large number of skewed markers in the linkage group 7, the potential existence of deleterious gene(s) was assessed in the group. Integrated maps produced by two different mapping methods using JoinMap® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions: We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.Iraj Tavassolian, Gholmereza Rabiei, Davina Gregory, Mourad Mnejja, Michelle G Wirthensohn, Peter W Hunt, John P Gibson, Christopher M Ford, Margaret Sedgley, and Shu-Biao W

Direct application of compound-specific radiocarbon analysis of leaf waxes to establish lacustrine sediment chronology

Author Posting. © Springer, 2007. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Paleolimnology 39 (2008): 43-60, doi:10.1007/s10933-007-9094-1.This study demonstrates use of compound-specific radiocarbon analysis (CSRA) for dating Holocene lacustrine sediments from carbonate-hosted Ordy Pond, Oahu, Hawaii. Long-chain odd-numbered normal alkanes (n-alkanes), biomarkers characteristic of terrestrial higher plants, were ubiquitous in Ordy Pond sediments. The δ13C of individual n-alkanes ranged from −29.9 to −25.5‰, within the expected range for n-alkanes synthesized by land plants using the C3 or C4 carbon fixation pathway. The 14C ages of n-alkanes determined by CSRA showed remarkably good agreement with 14C dates of rare plant macrofossils obtained from nearby sedimentary horizons. In general, CSRA of n-alkanes successfully refined the age-control of the sediments. The sum of n-alkanes in each sample produced 70–170 μg of carbon (C), however, greater age errors were confirmed for samples containing less than 80 μg of C. The 14C age of n-alkanes from one particular sedimentary horizon was 4,155 years older than the value expected from the refined age-control, resulting in an apparent and arguable age discrepancy. Several lines of evidence suggest that this particular sample was contaminated by introduction of 14C-free C during preparative capillary gas chromatography. This study simultaneously highlighted the promising potential of CSRA for paleo-applications and the risks of contamination associated with micro-scale 14C measurement of individual organic compounds.This project was funded by Petroleum Research Fund (PRF #40088-ACS) and in part by Sigma Xi, The Scientific Research Society (Grants in aid of research, 2003)

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

[ES]: Reducir la pérdida de variabilidad genética es un reto en los programas de mejora debido al repetido uso de un escaso número de genotipos. Para estudiar la variabilidad genética del almendro en su mejora a nivel mundial se utilizaron datos genealógicos de 222 variedades y selecciones provenientes de Argentina, Australia, Francia, Grecia, Israel, Italia, Rusia, España y EE. UU. Se calculó la consanguinidad, las relaciones por parejas y la contribución genética para todos los genotipos. Los resultados señalan dos principales líneas de mejora basadas en tres cultivares ‘Tuono’–‘Cristomorto’ y ‘Nonpareil’. Existen 75 descendientes directos (compartiendo 30) de ‘Tuono’ o ‘Cristomorto’ mientras que ‘Nonpareil’ tiene 72 descendientes directos. El coeficiente medio de consanguinidad de los genotipos analizados fue 0,036, con 13 presentando una elevada consanguinidad. Los programas de mejora de EE. UU. (0,06), Francia (0,05) y España (0,03) mostraron consanguinidad. De acuerdo con su contribución genética, las variedades modernas de Israel, Francia, EE. UU., España y Australia, se basan en seis, cinco, cuatro, cuatro y dos genotipos fundadores principales respectivamente. Entre el grupo de 65 genotipos con el alelo Sf de autocompatibilidad, el coeficiente medio de relación fue de 0,133, con ‘Tuono’ como principal fundador (23,75% de la contribución genética total).[EN]: Loss of genetic variability is a challenge increasing when breeding due to the repeated use of a reduced number of founders. Pedigree data of 222 almond cultivars and selections were used to study worldwide genetic variability in modern programs from Argentina, Australia, France, Greece, Israel, Italy, Russia, Spain and USA. Inbreeding coefficients, pairwise relatedness and genetic contribution were calculated. The results reveal two mainstream breeding lines based in three cultivars: ‘Tuono’–‘Cristomorto’ and ‘Nonpareil’. Direct descendants from ‘Tuono’ or ‘Cristomorto’ account to 75 (sharing 30 descendants), while ‘Nonpareil’ has 72 direct descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.036, with 13 genotypes presenting a high inbreeding coefficient. Breeding programs from USA (0.06), France (0.05) and Spain (0.03) showed inbreeding. According to their genetic contribution, modern cultivars from Israel, France, USA, Spain and Australia, trace back to six, five, four, four and two main founders respectively. Among the group of 65 genotypes with the Sf allele for self–compatibility, the mean relatedness coefficient was 0.133, with ‘Tuono’ as main founder (23.75% of total genetic contribution).Peer reviewe

The Almond Tree Genome

Editors: Raquel Sánchez-Pérez, Angel Fernandez i Marti, Pedro Martinez-GomezThis book brings together the latest information on almond genomics and transcriptomics, with a particular focus on cutting-edge findings, tools, and strategies employed in genome sequencing and analysis with regard to the most important agronomic traits. Cultivated almond [(Prunus dulcis (Miller) D. A. Webb, syn. Prunus amygdalus Batsch., Amygdalus communis L., Amygdalus dulcis Mill.)] is a tree crop producing seeds of great economic interest, and adapted to hot and dry climates. Domesticated in Southeast Asia, its small diploid genome and phenotypic diversity make it an ideal model to complement genomics studies on peach, generally considered to be the reference Prunus species. Both represent consanguineous species that evolved in two distinct environments: warmer and more humid in the case of peach, and colder and xerophytic for almond. The advent of affordable whole-genome sequencing, in combination with existing Prunus functional genomics data, has now made it possible to leverage the novel diversity found in almond, providing an unmatched resource for the genetic improvement of this speciesPeer reviewe