DFT conformation and energies of amylose fragments at atomic resolution. Part 2: ‘band-flip’ and ‘kink’ forms of α-maltotetraose

In Part 2 of this series of DFT optimization studies of α-maltotetraose, we present results at the B3LYP/6-311++G∗∗ level of theory for conformations denoted ‘band-flips’ and ‘kinks’. Recent experimental X-ray studies have found examples of amylose fragments with conformations distorted from the usual syn forms, and it was of interest to examine these novel structural motifs by the same high-level DFT methods used in Part 1. As in Part 1, we have examined numerous hydroxymethyl rotamers (gg, gt, and tg) at different locations in the residue sequence, and include the two hydroxyl rotamers, the clockwise ‘c’ and counterclockwise ‘r’ forms. A total of fifty conformations were calculated and energy differences were found to attempt to identify those sources of electronic energy that dictate stressed amylose conformations. Most stressed conformations were found to have relative energies considerably greater (i.e., ∼4 to 12 kcal/mol) than the lowest energy syn forms. Relative energy differences between ‘c’ and ‘r’ forms are somewhat mixed with some stressed conformations being ‘c’ favored and some ‘r’ favored, with the lowest energy ‘kink’ form being an all-gg-r conformation with the ‘kink’ in the bc glycosidic dihedral angles. Comparison of our calculated structures with experimental results shows very close correspondence in dihedral angles.     

Establishment and application of a microsatellite-based parentage identification method for Oreochromis niloticus,O. aureus,and O. niloticus × O. aureus

In genetic fish breeding research, clear pedigree information is of great significance for breeding and parental management. In order to establish a stable, highly accurate, and widely applicable parentage identification method for tilapia, 13 highly polymorphic microsatellite loci within populations of Oreochromis niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population were screened. Four groups of fluorescent-labeled multiple capillary electrophoresis were established for allelic genotyping. The assignment success rate reached 100% when 7, 9, 8 and 12 loci were used in the population of O. niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population, respectively. All 175 progeny individuals of “Yuemin No. 1” tilapia were exclusively assigned to their parental pairs when the 12 loci for the mixed population were used. This study established a fluorescent-labeled microsatellite-based parentage assignment method for O. niloticus, O. aureus, O. niloticus × O. aureus, and their mixed population with high identification accuracy and efficiency, which lays a foundation for pedigree information and population genetic management in tilapia breeding.     

Redescriptions of Nereis oligohalina (Rioja, 1946) and N. garwoodi González-Escalante & Salazar-Vallejo, 2003 and description of N. confusa sp. n. (Annelida,Nereididae)

Type material of several polychaete species described by Enrique Rioja from Mexican coasts are lost, and the current status of some species is doubtful. Nereis oligohalina (Rioja, 1946) was described from the Gulf of Mexico, but it has been considered a junior synonym of Nereis occidentalis Hartman, 1945, or regarded as a distinct species with an amphiamerican distribution. On the other hand, Nereis garwoodi González-Escalante & Salazar-Vallejo, 2003, described from Chetumal Bay, Caribbean coasts, could be confused with Nereis oligohalina. In order to clarify these uncertainties, Nereis oligohalina is redescribed based on specimens from the Mexican Gulf of Mexico, including a proposed neotype; further, Nereis garwoodi is redescribed including the selection of lectotype and paralectotypes, and Nereis confusa sp. n. is described with material from the Gulf of California. A key for the identification of similar species and some comments about speciation in nereidid polychaetes are also included.     

Differentiation of F1 hybrids P. nigra J. F. Arnold × P. sylvestris L., P. nigra J. F. Arnold × P. densiflora Siebold et Zucc., P. nigra J. F. Arnold × P. thunbergiana Franco and their parental species by needle volatile composition

The volatile composition of needles from three F₁ hard pine hybrids produced by the controlled hybridization and their parental species were researched with gas chromatography (GC) and gas chromatography/mass spectrometry (GC/MS) in order to explore the utility of terpenes in hybrid identification (their differentiation from the parental species) as well as confirmation of hybridity. The analysed hybrids were: 1. Pinus nigra J. F. Arnold × Pinus sylvestris L. (= nisy), 2. P. nigra × Pinus densiflora Siebold et Zucc. (= nide) and 3. P. nigra × Pinus thunbergiana Franco (= nith). A total of 55 compounds were identified. All identified compounds were terpenes, except trans-2-hexenal.Three analysed F₁ hybrids showed the same qualitative pattern of the needle volatile composition as their parental species. However, there were quantitative differences in several major terpenes. The volatile composition of the needles from the hybrids nisy were equally similar to both parents, the hybrids nide were more similar to the female parent (P. nigra), whereas the hybrids nith were more similar to the male parent (P. thunbergiana). According to the content of germacrene D, as the specific component of P. nigra (female parent of the three analysed F₁ hybrids), all hybrids were intermediary in relation to the parental species. The content of Δ-3-carene (the specific component of P. sylvestris) in the hybrids nisy was also intermediary. The hybrids nide had a higher content of thunbergol (specific component of P. densiflora) than the other analysed hybrids. In view of the content of β-pinene, the specific component of P. thunbergiana, the hybrids nith were intermediary to the parental species and that content was considerably higher than in the other analysed hybrids. The intermediary quality of F₁ hybrids for these specific components in relation to the parental species confirms their hybrid character.The needle volatile composition analysis as well as the previous morphometric analysis confirm the hybrid character of three F₁ hybrids, whose female parent is P. nigra, and male parents are P. sylvestris, P. densiflora, i.e. P. thunbergiana.     

Structure of Ecologo-Climatic Niches of <Emphasis Type="Italic">Poa palustris</Emphasis> L. and <Emphasis Type="Italic">P. nemoralis</Emphasis> L. (Роасеае) in Asian Russia

In addition to a specific morphotype, each species has a unique ecologo-climatic niche and a geographical area. The study of ecologo-climatic and geographical divergence may significantly contribute to the comprehension of species genesis and amount. The aim of this work is to compare ecologo-climatic niches of Poa palustris L., P. nemoralis L., and populations combining the features of both species (assigned in this work to the hybridogenic complex of P. intricata Wien), as well as reveal their identity. As a result of these researches, the areas of the both species were verified. The ecologo-climatic niches were determined with the use of GIS technologies and on the basis of their coordinates. Then potential areas of species—the regions where climatic conditions are favorable for their growth—were determined on the basis of six independent bioclimatic variables. A comparison of the ecologo-climatic niches calculated by MaxEnt software has shown that their distinctions are statistically significant.     

Comparative morphological and genetic analysis of populations and species of the genus <Emphasis Type="Italic">Daphnia</Emphasis> O.F. Müller, 1785 (Crustacea; Daphniidae) from Lake Glubokoe and Lake Chany

The results of analysis of the variability of body shape of different Daphnia galeata morphs from geographically distinct populations—Lake Glubokoe (Moscow oblast) and Lake Chany (Novosibirsk oblast) are given. The morphological analysis was combined with the analysis of the variability of fragments of the 16S and 12S genes of the mitochondrial DNA (mtDNA) and the internal transcribed spacer 2 (ITS2) of the nuclear DNA. A reconstruction of the phylogenetic relationships between species of the genus Daphnia has been performed using a combined fragment of the 16S and 12S genes of the mtDNA. An inconsistency in the distribution of the 12S- and ITS2-haplotypes for the species D. galeata has been revealed, which indicates the introgression of mtDNA in the Lake Chany population.     

Effect of desiccation on physiological and biochemical indicators associated with the germination and vigor of cryopreserved seeds of <Emphasis Type="Italic">Nicotiana tabacum</Emphasis> L. cv. Sancti Spíritus 96

Cryopreservation is a valuable technique for the long-term conservation of plant germplasm and complementary to traditional seed storage methods. However, critical factors such as seed moisture content should be optimized before using this technique as a safe strategy for storing seeds such as those of Nicotiana spp. This study aimed to determine the effect of desiccation on physiological and biochemical indicators associated with germination and vigor in cryopreserved seeds of Nicotiana tabacum cv. Sancti Spíritus 96 (SS-96). The germination and vigor of seeds with a range of moisture content were assessed using electrolyte leakage and accelerated aging tests. In addition, these physiological indicators were related to the oxidative state of the seeds, in terms of the rate of O₂ ^·? generation and the H₂O₂ content, and the activity of enzymatic antioxidants superoxide dismutase and catalase. The cryopreserved seeds of N. tabacum SS-96 with a moisture content of 2.1% exhibited higher vigor probably due to the retention of membrane integrity, reflected by lower levels of lipid peroxidation and electrolyte leakage associated with the absence of oxidative stress. The results suggest 2.1% as the optimal moisture content for the storage of seeds of this cultivar, both at cryogenic temperatures and at 5°C.     

Membranotropic effects of ω-hydroxypalmitic acid and Ca<Superscript>2+</Superscript> on rat liver mitochondria and lecithin liposomes. Aggregation and membrane permeabilization

The paper examines membranotropic Ca²⁺-dependent effects of ω-hydroxypalmitic acid (HPA), a product of ω-oxidation of fatty acids, on the isolated rat liver mitochondria and artificial membrane systems (liposomes). It was established that in the presence of Ca²⁺, HPA induced aggregation of liver mitochondria, which was accompanied by the release of cytochrome c from the organelles. It was further demonstrated that the addition of Ca²⁺ to HPA-containing liposomes induced their aggregation and/or fusion. Ca²⁺ also caused the release of the fluorescent dye sulforhodamine B from liposomes, indicating their permeabilization. HPA was shown to induce a high-amplitude swelling of Ca²⁺-loaded mitochondria, to decrease their membrane potential, to induce the release of Ca²⁺ from the organelles and to result in the oxidation of the mitochondrial NAD(P)H pool. Those effects of HPA were not blocked by the MPT pore inhibitor CsA, but were suppressed by the mitochondrial calcium uniporter inhibitor ruthenium red. The effects of HPA were also observed when Ca²⁺ was replaced with Sr²⁺ (but not with Ba²⁺ or Mg²⁺). A supposition is made that HPA can induce a Ca²⁺-dependent aggregation of mitochondria, as well as Ca²⁺dependent CsA-insensitive permeabilization of the inner mitochondrial membrane – with the subsequent lysis of the organelles.     

Enzymatic transformation of biologically active 1,3;1,6-β-D-glucan. Structure and activity of resulting fragments

The fragmentation of the biologically active 1,3;1,6-beta-D-glucan Antivir by endo-1,3-beta-D-glucanase LIV from crystalline styles of the marine mollusk Spisula sachalinensis was carried out. It was found that low molecular mass oligomers possessing a stabilizing effect on membranes and anti-viral activity against tobacco mosaic virus appeared in the process of enzymatic hydrolysis of Antivir. Biological activity of 1,3;1,6-beta-D-glucooligo- and polysaccharides was found to be associated with molecular mass (polymerization degree (n) not less than 14) and with presence of intralinked beta-1,6-connected monosaccharide residues. Probably, decrease in molecular mass is compensated by increase in number of intralinked beta-1,6-connected monosaccharide residues.     

Micropropagation of <Emphasis Type="Italic">Vitis vinifera</Emphasis> L. cv. ‘Malagouzia’ and ‘Xinomavro’

The effects of six basal media on in vitro shoot proliferation of the greek grapevines Vitis vinifera L. cv. ‘Malagouzia’ and ‘Xinomavro’ were investigated. Galzy and Zlenco proved to be the most effective for ‘Malagouzia’ and ‘Xinomavro’, respectively. If only BA was present in the medium, shoot development was poor and the plantlets were chlorotic. When the medium was supplemented with BA and NAA, growth was enhanced. The best ratio (in μM) of growth regulators was 0.5/0.3 for ‘Malagouzia’, and 0.1/0.03 for ‘Xinomavro’, which resulted in the highest number of microshoots per explant and greatest proliferation rate. The development of ‘Malagouzia’ and ‘Xinomavro’ explants at 21±2 and 26±2°C was also investigated, revealing the higher temperature to be more effective. Regarding rooting, 0.5 μM IBA improved root formation at 26°C for ‘Malagouzia’ and 0.5 μM IBA at 21°C for ‘Xinomavro’. Moreover, 0.5 μM IBA resulted in a higher rooting percentage (>95%) and proved to be more beneficial for the overall morphological appearance of the plantlets of ‘Malagouzia’. After acclimatization, survival of microshoots cultivated in media with IBA was higher than those in NAA.     

Influence of growth regulators and elicitors on cell growth and α-tocopherol and pigment productions in cell cultures of <Emphasis Type="Italic">Carthamus tinctorius</Emphasis> L.

The present study examined the effects of plant growth hormones, incubation period, biotic (Trametes versicolor, Mucor sp., Penicillium notatum, Rhizopus stolonifer, and Fusarium oxysporum) and abiotic (NaCl, MgSO₄, FeSO₄, ZnSO₄, and FeCl₃) elicitors on cell growth and α-tocopherol and pigment (red and yellow) productions in Carthamus tinctorius cell cultures. The cell growth and α-tocopherol and pigment contents improved significantly on Murashige and Skoog (MS) liquid medium containing 50.0 μM α-naphthalene acetic acid (NAA) and 2.5 μM 6-Benzyladenine (BA) at 28 days of incubation period. Incorporation of T. versicolor (50 mg l⁻¹) significantly enhanced the production of α-tocopherol (12.7-fold) and red pigment (4.24-fold). Similarly, supplementation of 30 mg l⁻¹ T. versicolor (7.54-fold) and 70 mg l⁻¹ Mucor sp. (7.40-fold) significantly increased the production of yellow pigment. Among abiotic elicitors, NaCl (50–70 mg l⁻¹) and MgSO₄ (10–30 mg l⁻¹) significantly improved production of α-tocopherol (1.24-fold) and red pigment (20-fold), whereas yellow pigment content increased considerably by all the abiotic elicitor treatments. Taken together, the present study reports improved productions of α-tocopherol and the pigment as a stress response of safflower cell cultures exposed to these elicitors.     

Analysis of the germination rate,mitotic index and karyotype of Chromolaena barranquillensis (Hieron.) R.M. King & H. Rob.—Asteraceae

Chromolaena barranquillensis (Asteraceae) is an endemic plant of northern Colombia that has garnered economic and medicinal interest, because species from the genus Chromolaena have shown diverse biological activities. This study describes, for the first time, the karyotype, germination and mitotic indices of C. barranquillensis (Hieron.) R.M. King & H. Rob. The germination index was between 34% and 56% with an average germination rate of 1.2 ± 0.4 seeds/day. The mitotic index analysis allowed to determine the cell cycle time (4 h, 10 min) and the mitotic hours (3:00–8:00 h and 17:00 h). The mitosis time was 49 min, equivalent to ~ 20% of the cell cycle. Karyotype analysis showed that C. barranquillensis is a hexaploid species with a chromosomal formula 2n = 6x = 60 = 48 m + 12 sm, and the average chromosomal lengths were 1.7 ± 0.1 μm to 0.9 ± 0.3 μm. The Stebbins asymmetry index was 2B, and the total form percentage was ~ 41%. These results uncover differences between C. barranquillensis and Chromolaena odorata, one of the most abundant species found in the world and the most closely related species to C. barranquillensis.     

Evaluation of in vitro antimicrobial activity of leaf and stem essential oils of <Emphasis Type="Italic">Chloroxylon swietenia</Emphasis> DC.

The essential oils obtained by hydrodistillation of leaves and stems of Chloroxylon swietenia DC. were analysed by GC and GC-MS. The main components in the leaf oil were limonene, pregeijerene, geijerene and germacrene D, while stem oil was rich in limonene, methyl eugenol, pregeijerene and geijerene. The essential oils were evaluated for antimicrobial activity against two gram-positive and two gram-negative bacteria and four pathogenic fungi using agar disc diffusion technique. Subsequently, the minimum inhibitory concentration (MIC) from oils was determined by broth microdilution. Both the oils exhibited moderate to strong activities against all the organisms tested. Bacillus subtilis was most susceptible at 100 μg/ml of leaf and stem oils with inhibition zones of 15.9 and 13.1 mm respectively. Among all the fungi tested, A. niger inhibited effectively with a zone of inhibition of 14.9 and 11.5 mm for leaf and stem oils respectively. The results obtained suggest that the essential oils of the plant possess antimicrobial properties and serve as a biofriendly source of antimicrobial ingredients for the food and pharmaceutical industries.