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Total and orbital electron densities of molecules are explored for the effect of the long-range correction (LC) for density functional theory (DFT) exchange functionals by comparing to the effect of the ab initio coupled cluster singles and doubles (CCSD) method. Calculating the LC effect on the total electron densities shows that the LC stabilizes the electrons around the long-range interaction regions of kinetic energy density, which are assumed to be electrons other than free electrons and self-interacting electrons, while the CCSD method stabilizes the electrons in the long-range interaction regions in the vertical molecular planes. As a more precise test, the LC effect on orbital densities are compared to the CCSD effect on Dyson orbital densities. Surprisingly, these effects are similar for the unoccupied orbitals, indicating that the LC covers the effects required to reproduce the CCSD Dyson unoccupied orbitals. For exploring the discrepancies between these effects on the occupied orbitals, the photoionization cross sections are calculated as a direct test for the shapes of the HOMOs to investigate the differences between these effects on the occupied orbitals. Consequently, the LC clearly produces the canonical HOMOs close to the CCSD Dyson and experimental ones, except for the HOMO of benzene molecule that mixes with the HOMO - 1 for the CCSD Dyson orbitals. This indicates that the orbital analyses using the photoionization cross sections are available as a direct test for the quality of DFT functionals., (© 2023 Wiley Periodicals LLC.)

It is established that the reactive orbital energy theory (ROET) theoretically reproduces the rule-based electronic theory diagrams of organic chemistry by a comparative study on the charge transfer natures of typical organic carbon-carbon and carbon-heteroatom bond formation reactions: aldol, Mannich, α-aminooxylation, and isogyric reactions. The ROET, which is an expansion of the reaction electronic theories (e.g., the frontier orbital theory) in terms of orbital energies, elucidates the reactive orbitals driving reactions and the charge transferability indices of the reactions. Performing the ROET analyses of these reactions shows that the charge transfer directions given in the rule-based diagrams of the electronic theory are reproduced even for the functional groups of charge transfer destinations in all but only two processes for 38 reaction processes. The ROET analyses also make clear the detailed orbital-based pictures of these bond formation reactions: that is, the use of the out-of-plane antibonding π orbitals in acidic conditions (enol-mode) and in-plane antibonding π orbitals in basic conditions (enolate-mode), which explain the experimentally assumed mechanisms such as the π-bond formations in acidic conditions and σ-bond formations at α-carbons in basic conditions. Furthermore, the ROET analyses explicate that the methyl group initially accepts electrons and then donates them to the bond formations in the target reactions. It is, consequently, suggested that the ROET serves a theoretical foundation for the electronic theory of organic chemistry., (© 2022 Wiley Periodicals LLC.)

Proteins bearing nuclear export signals (NESs) are translocated to the cytoplasm from the nucleus mainly through the CRM1-dependent pathway. However, the NES consensus sequence remains poorly defined, and there are currently no high-throughput methods for identifying NESs. In this study, we report the development of an efficient yeast selection system for detecting nuclear export activity as well as several reliable NES consensus sequences identified using this method. Our selection system is based on the nuclear export-dependent rescue of Tys1p, an essential cytoplasmic protein that has been artificially localized to the nucleus in a haploid Delta tys1 knockout strain. A screen of a random peptide library revealed 101 distinct CRM1-dependent NESs, which were classified into six patterns according to the conserved hydrophobic spacing. By combining mutational analyses, we have defined new NES consensus sequences with more specific and redundant residues than the traditional consensus sequence, which are consistent with most experimentally confirmed NESs. These NES consensus sequences should help identify functional NESs, and our selection system can be used to identify other targeting signals or proteins imported to specific subcellular compartments.

In order to specify phylogenetic positions of the genera of Tofieldiaceae (Tofieldia, Triantha, Pleea, Harperocallis, Isidrogalvia), and to suggest reasonable circumscription of the family and genera of Tofieldiaceae, we determined DNA sequences of matK and rbcL for each genus of the family, and analyzed them phylogenetically with the 45 families and 113 genera of the monocots other than Tofieldiaceae, whose matK and rbcL sequences have already been reported. We found that Tofieldia, Triantha, Pleea, and Harperocallis form the same clade, which receives 100% bootstrap support. This clade can be regarded as corresponding to Tofieldiaceae, and is embedded in the clade of Alismatales (98%). On the other hand, Isidrogalvia is not included in this Tofieldiaceae clade, and positioned as sister to Narthecium (100%), embedded in the clade of Nartheciaceae (Dioscoreales) (100%). In the Tofieldiaceae, Pleea first diverges from the remaining three genera (100%), and then, Harperocallis diverges from the Tofieldia- Triantha complex (100%). In the Tofieldia- Triantha complex, five Tofieldia species form the same clade (100%), and two Triantha species form another clade (100%). Thus, Isidrogalvia should be transferred from Tofieldiaceae to Nartheciaceae. As Isidrogalvia, as well as the Nartheciaceae, have the carpels that are fully connate into a single style, Isidrogalvia fits the Nartheciaceae well with respect to carpel connation. After this transfer, the Tofieldiaceae correspond mainly to plants with almost free carpels and three styles. Pleea is better treated as an independent genus than included in Tofieldia. Triantha can be treated either as an independent genus or as congeneric with Tofieldia.

The sundew genus Drosera consists of carnivorous plants with active flypaper traps and includes nearly 150 species distributed mainly in Australia, Africa, and South America, with some Northern Hemisphere species. In addition to confused intrageneric classification of Drosera, the intergeneric relationships among the Drosera and two other genera in the Droseraceae with snap traps, Dionaea and Aldrovanda, are problematic. We conducted phylogenetic analyses of DNA sequences of the chloroplast rbcL gene for 59 species of Drosera, covering all sections except one. These analyses revealed that five of 11 sections, including three monotypic sections, are polyphyletic. Combined rbcL and 18S rDNA sequence data were used to infer phylogenetic relationships among Drosera, Dionaea, and Aldrovanda. This analysis revealed that all Drosera species form a clade sister to a clade including Dionaea and Aldrovanda, suggesting that the snap traps of Aldrovanda and Dionaea are homologous despite their morphological differences. MacClade reconstructions indicated that multiple episodes of aneuploidy occurred in a clade that includes mainly Australian species, while the chromosome numbers in the other clades are not as variable. Drosera regia, which is native to South Africa, and most species native to Australia, were clustered basally, suggesting that Drosera originated in Africa or Australia. The rbcL tree indicates that Australian species expanded their distribution to South America and then to Africa. Expansion of distribution to the Northern Hemisphere from the Southern Hemispere occurred in a few different lineages.

Background: Glutamine (GLN) plays many important roles for the enterocytes in health and disease, but no liquid enteral products contain GLN because of its instability. We hypothesized that glutamate (GLU) may replace GLN in supplementation to an enteral diet, and compared the metabolic effect of GLU and GLN on the gut to each other., Methods: Rats suffering from a 30% burn received an enteral diet containing 30% GLU (m/w to total amino acids; GLU group), 30% GLN (GLN group), or a standard amino acid formula (CTR group). After a 64-hour feeding period, the small intestine and the portal and arterial blood were harvested to observe portal and arterial amino acid levels, and glutaminase activity and glutathione in the jejunal mucosa. In another study, 3H uptake into the mucosal protein was examined after a massive dose injection of 3H-phenylalanine., Results: Alanine, a product of GLN or GLU catabolism, significantly increased in the portal blood of the GLU group compared with the GLN group. In the gut mucosa of the GLU group, 3H uptake into protein and total glutathione were higher than those of other two groups. GLN did not elevate the glutaminase activity. Arterial GLU levels increased in the GLU group, however remained within safety limits., Conclusions: Enterally delivered GLU may be a preferable fuel for the enterocytes and enhance the mucosal protein synthesis. GLU probably can substitute for GLN in supplementation to an enteral diet regarding many roles GLN plays in the intestinal mucosa under stress situations.

The metabolic impact of infusing a large amount of leucine (Leu) or valine (Val) was examined with regard to the corrective effect of total parenteral nutrition (TPN). Rats recovering from severe sepsis received either Leu- or Val-enriched TPN solution for 30 hours. The in vivo behavior of the amino acids administered was explored by a pulse injection of 14C-labeled Leu or Val. The recovery of 14CO2 from Leu increased by 64% in the septic rats of Leu-TPN group (41% of dose; p less than .01), as compared with control rats receiving the same TPN solution, whereas no significant rise in the 14CO2 recovery from Val occurred in the septic rats given Val-TPN (45% of dose) in comparison with the corresponding controls. The enhancement of Leu catabolism to CO2 in the Leu-TPN group was compatible with the alterations of urinary nitrogen excretion, plasma Leu level, and metabolite contents of liver and muscle. The only difference in metabolite levels observed between the two TPN groups was in hepatic total adenine nucleotides. Plasma amino acid levels were largely unaffected by infusion of these TPN solutions highly enriched with branched-chain amino acids (45%), except for an approximately threefold elevation of the Val level in Val-TPN rats. Thus, when administered in a large quantity during such short-term TPN, Leu can exert its metabolic effect without causing an imbalance in plasma amino acids under severe catabolic conditions.

The effects of two kinds of total parenteral nutrition (TPN) on energy and protein metabolism were examined in rats subjected to 15% full-thickness scald burns in the absence of septic complications. One type of TPN was enriched in branched-chain amino acids (BCAAs), especially leucine (45% BCAA content), and the other was conventional TPN (21% BCAA content). Burned rats received isocaloric and isonitrogeneous TPN solutions for 48 hr after resuscitation by saline infusion for 24 hr. Liver and rectus abdominis muscle were removed from the rats at 7, 24, 48, and 72 hr. The concentrations of adenine nucleotides, RNA, protein, glucose-6-phosphate, hepatic glycogen, muscle phosphocreatine, and 3-methylhistidine were determined. Metabolic alterations occurred during the period of saline resuscitation (0-24 hr). At 48 hr the RNA and protein levels were significantly more improved in the BCAA-TPN group than in the conventional TPN group. At 72 hr, however, the results for the two groups were similar in most metabolite levels. Thus, BCAA-TPN enriched in leucine rapidly stimulated protein synthesis in the liver and muscle. This rapid effect may make it useful during the initial nutritional management of severe trauma patients.