Structures and stability of N<Subscript>13</Subscript><Superscript>+</Superscript> and N<Subscript>13</Subscript><Superscript>−</Superscript> clusters

The structures and stabilities of eleven N₁₃ ⁺ and N₁₃ ^– isomers have been investigated with second-order Møller–Plesset (MP2) and density functional theory (DFT) methods. Five N₁₃ ⁺ isomers and six N₁₃ ^– isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N₁₃ ⁺ cation is structure C-2 with C_2v symmetry, which contains a pentazole ring and two N₄ open chains. It is different from those of the N₇ ⁺ and N₉ ⁺ clusters, but similar to the N₁₁ ⁺ cluster. Meanwhile, the most stable N₁₃ ^– structure A-2 is composed of a pentazole ring and a six-membered ring connected by two nitrogen atoms. It is not only different from those of the N₇ ^– and N₉ ^– clusters, but also from the N₁₁ ^– cluster. The decomposition pathways of structures C-2 and A-2 were investigated at the B3LYP/(aug)-cc-pVDZ level. From the barrier heights of the structures C-2 and A-2 decomposition processes, it is suggested that C-2 is difficult to observe experimentally and A-2 may be observed as a short-lived species. Figure Optimized geometrical parameters of N₁₃ ⁺ isomer C-2      

Biomining — biotechnologies for extracting and recovering metals from ores and waste materials

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Interactions between oestrogen and 1α,25(OH)<Subscript>2</Subscript>-vitamin D<Subscript>3</Subscript> signalling and their roles in spermatogenesis and spermatozoa functions

Oestrogens and 1α,25(OH)₂-vitamin D₃ (1,25-D₃) are steroids that can provide effects by binding to their receptors localised in the cytoplasm and in the nucleus or the plasma membrane respectively inducing genomic and non-genomic effects. As confirmed notably by invalidation of the genes, coding for their receptors as tested with mice with in vivo and in vitro treatments, oestrogens and 1,25-D₃ are regulators of spermatogenesis. Moreover, some functions of ejaculated spermatozoa as viability, DNA integrity, motility, capacitation, acrosome reaction and fertilizing ability are targets for these hormones. The studies conducted on their mechanisms of action, even though not completely elicited, have allowed the demonstration of putative interactions between their signalling pathways that are worth examining more closely. The present review focuses on the elements regulated by oestrogens and 1,25-D₃ in the testis and spermatozoa as well as the interactions between the signalling pathways of both hormones.     

α<Subscript>2A</Subscript>- and α<Subscript>2C</Subscript>-Adrenoceptors as Potential Targets for Dopamine and Dopamine Receptor Ligands

The poor norepinephrine innervation and high density of Gi/o-coupled α_2A- and α_2C-adrenoceptors in the striatum and the dense striatal dopamine innervation have prompted the possibility that dopamine could be an effective adrenoceptor ligand. Nevertheless, the reported adrenoceptor agonistic properties of dopamine are still inconclusive. In this study, we analyzed the binding of norepinephrine, dopamine, and several compounds reported as selective dopamine D₂-like receptor ligands, such as the D₃ receptor agonist 7-OH-PIPAT and the D₄ receptor agonist RO-105824, to α₂-adrenoceptors in cortical and striatal tissue, which express α_2A-adrenoceptors and both α_2A- and α_2C-adrenoceptors, respectively. The affinity of dopamine for α₂-adrenoceptors was found to be similar to that for D₁-like and D₂-like receptors. Moreover, the exogenous dopamine receptor ligands also showed high affinity for α_2A- and α_2C-adrenoceptors. Their ability to activate Gi/o proteins through α_2A- and α_2C-adrenoceptors was also analyzed in transfected cells with bioluminescent resonance energy transfer techniques. The relative ligand potencies and efficacies were dependent on the Gi/o protein subtype. Furthermore, dopamine binding to α₂-adrenoceptors was functional, inducing changes in dynamic mass redistribution, adenylyl cyclase activity, and ERK1/2 phosphorylation. Binding events were further studied with computer modeling of ligand docking. Docking of dopamine at α_2A- and α_2C-adrenoceptors was nearly identical to its binding to the crystallized D₃ receptor. Therefore, we provide conclusive evidence that α_2A- and α_2C-adrenoceptors are functional receptors for norepinephrine, dopamine, and other previously assumed selective D₂-like receptor ligands, which calls for revisiting previous studies with those ligands.     

Mitochondria and peroxisomes: Are the ‘Big Brother’ and the ‘Little Sister’ closer than assumed?

Mitochondria and peroxisomes are essential subcellular organelles in mammals. Despite obvious differences, both organelles display certain morphological and functional similarities. Recent studies have elucidated that these highly dynamic and plastic organelles share components of their division machinery. Mitochondria and peroxisomes are metabolically linked organelles, which are cooperating and cross-talking. This review addresses the dynamics and division of mitochondria and peroxisomes as well as their functional similarities to provide insight as to why these organelles share the fission machinery in evolutionary aspects.     

Electronic and optical properties of C<Subscript>24</Subscript>, C<Subscript>12</Subscript>X<Subscript>6</Subscript>Y<Subscript>6</Subscript>, and X<Subscript>12</Subscript>Y<Subscript>12</Subscript> (X = B,Al and Y = N,P)

Utilizing first-principles calculations, we studied the electronic and optical properties of C₂₄, C₁₂X₆Y₆, and X₁₂Y₁₂ fullerenes (X?=?B, Al; Y?=?N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C₂₄ may be tuned by doping, and the B₁₂N₁₂ fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices. They could also be used in solar cells and LEDs due to their low reflectivities.

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Graphical abstract Possible applications of doped C₂₄ fullerene

     

Transport of nitrogen and zinc to rhodes grass by arbuscular mycorrhiza and roots as affected by different nitrogen sources (NH<Subscript>4</Subscript><Superscript>+</Superscript>-N and NO<Subscript>3</Subscript><Superscript>−</Superscript>-N)

We investigated the effect of mineral nitrogen forms on transfer of nitrogen (N) and zinc (Zn) from attached compartments to rhodes grass (Chloris gayana) colonised with arbuscular mycorrhizal fungi (AMF). After being pre-cultivated in substrates with adequate nutrient supply and either AMF inoculated (+AM) or left non-inoculated (?AM), rhodes grass was positioned adjacent to an outer compartment holding a similar substrate but applied with labelled nitrogen (¹⁵N) either as ammonium (NH₄ ⁺) or nitrate (NO₃ ^?), and a high supply of Zn (150 mg kg^?1 DS). Plant roots together with fungal mycelium were either allowed to explore the outer compartment (with root access) or only mycorrhizal hyphae were allowed (without root access). Within each access treatment, biomasses of rhodes grass were not significantly affected by AMF inoculation or N form. AMF contribution to plant ¹⁵N uptake was about double in NH₄ ⁺ compared with NO₃ ^?-supplied treatments while the mycorrhizal influence on plant Zn uptake was insignificant. Without root access, the shoot ¹⁵N/Zn concentration ratio was up to ten-fold higher in +AM than –AM treatments and this ratio increase was clearly more pronounced in NH₄ ⁺ than NO₃ ^?-supplied treatments. In conclusion, rhodes grass in symbiosis with the tested AMF acquired more N when supplied with ammonium. Moreover, there is clear indication that although the AMF have transported both nutrients (N and Zn), N was preferentially transferred as compared to Zn. We confirmed that, while rhodes grass is not able to prevent excessive Zn uptake via roots under conditions of high Zn, mycorrhiza is able to avoid excessive Zn supply to the host plant when the fungus alone has access to contaminated patches.     

Genotype × region and genotype × production level interactions in Holstein cows

The identification of the presence of genotype by environment interaction effects on important traits in Holstein cattle allows for the use of international genetic evaluations and a more efficient design of regional genetic evaluation programmes. The aim of this study was to determine the genotype × environment interaction effects in Chilean Holstein dairy cattle through the analysis of records corresponding to calvings between 1998 and 2015. Herds were classified in the central and southern regions of Chile based on herd location as well as by high and low levels of production environments based on the fat plus protein yield averages per herd within each region. The central region has a Mediterranean climate and a confined production system while the southern region has a humid temperate climate and a production system based on grazing with supplementation. Traits studied were milk yield (MY), fat yield (FY), protein yield (PY), fat content (FC) and protein content (PC) by lactation, age at first calving (AFC) and calving interval (CI). Several four-trait mixed animal models were applied to environmental category data as different traits, which included herd-year-calving season (herd-year-birth season for AFC) and lactation number as fixed effects, and animal additive genetic, sire-herd, permanent environment and residual effects as random effects. Genetic correlations (r_g) for MY, FY, FC, PC and CI were found to decrease as differences between environmental categories increased. The r_g between the most extreme environmental categories considered in this study for AFC (0.26) was the only one found statistically lower than 0.60. Genetic correlation values statistically lower than 0.80 (P < 0.05) were observed for AFC, CI, MY, FY and PY between some environmental categories. If separate genetic evaluations are adopted as practical criteria when the value of r_g is lower than 0.60, the consequence of improving a multi-trait economic breeding objective in this population is likely to be small unless extreme environmental categories are considered. However, a moderate decrease in selection response and re-ranking of selection candidates is expected for AFC, CI and yield traits when selection is performed in different environmental conditions. Genotype × environment interaction effects involving production systems in a Mediterranean climate and confinement vs. Temperate Oceanic climate and grazing with supplementation, and between two fat plus protein yield level categories within each environment, were at most moderate for the studied traits.     

Complementary DNA sequences encoding the rat MHC class II RT1-B<Superscript>u</Superscript> and RT1-D<Superscript>u</Superscript> α and β chains

The rat major histocompatibility complex loci RT1-B and RT1-D are equivalent to the human leucocyte antigens HLA-DQ and HLA-DR respectively. Here we describe the complementary DNA (cDNA) sequence encoding the and chains of both the RT1-B and RT1-D locus genes of the rat RT1^u haplotype. We have found entire sequence identity between five different inbred rat strains of the RT1^u haplotype, which differs from previously published, incomplete sequences. This information is of considerable value for experimental studies of transplantation immunity and autoimmune disease.Nucleotide sequences reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers AJ554214 (RT1-B^ua), AJ554215 (RT1-B^ub) and AJ554216 (RT1-D^ua).     

Correlated motions of C′–N and C<Subscript>α</Subscript>–C<Subscript>β</Subscript> pairs in protonated and per-deuterated GB3

We investigated correlated µs-ms time scale motions of neighboring ¹³C′–¹⁵N and ¹³C_α–¹³C_β nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange. The time scale of motions falls into the intermediate to fast regime (with respect to the chemical shift time scale, 100–400 s^?1 range) for the ¹³C′–¹⁵N pairs and into the slow to intermediate regime for the ¹³C_α–¹³C_β pairs (about 150 s^?1). Comparison of the results obtained for protonated and deuterated GB3 suggests that deuteration has a tendency to reduce these slow scale correlated motions, especially for the ¹³C_α–¹³C_β pairs.     

Cooperation of adenosine and prostaglandin E<Subscript>2</Subscript> (PGE<Subscript>2</Subscript>) in amplification of cAMP–PKA signaling and immunosuppression

INTRODUCTION: We hypothesize that adenosine and PGE(2) could have a complementary immunosuppressive effect that is mediated via common cAMP-PKA signaling. MATERIALS AND METHODS: To test this hypothesis, the effect of adenosine and PGE(2) on the cytotoxic activity and cytokine production of lymphokine activated killer (LAK) cells was investigated. RESULTS: PGE(2) and adenosine inhibited LAK cells cytotoxic activity and production of INF-gamma, GM-CSF and TNF-alpha. In combination they showed substantially higher inhibition than each modality used alone. Using agonists and antagonists specific for PGE(2) and adenosine receptors we found that cooperation of PGE(2) and adenosine in their inhibitory effects are mediated via EP(2) and A(2A) receptors, respectively. LAK cells have 35-fold higher expression of EP(2) than A(2A). Combined PGE(2) and adenosine treatment resulted in augmentation of cAMP production, PKA activity, CREB phosphorylation and inhibition of Akt phosphorylation. Wortmannin and LY294002 enhanced the suppressive effects of adenosine and PGE(2). In contrast, Rp-8-Br-cAMPS, an inhibitor of PKA type I blocked their immunosuppressive effects, suggesting that the inhibitory effects of PGE(2) and adenosine are mediated via common pathway with activation of cAMP-PKA and inhibition of Akt. CONCLUSION: In comparison to other immunosuppressive molecules (TGF-beta and IL-10), adenosine and PGE(2) are unique in their ability to inhibit the executive function of highly cytotoxic cells. High intratumor levels of adenosine and PGE(2) could protect tumor from immune-mediated destruction by inactivation of the tumor infiltrating functionally active immune cells.     

<Superscript>2</Superscript>H–<Superscript>13</Superscript>C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates

Site-specific determination of molecular motion and water accessibility by indirect detection of ²H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization (^RESPIRATIONCP) technique was developed, which allowed efficient transfer of ²H magnetization to ¹³C at moderate ²H radiofrequency field strengths available on most commercial MAS probes. In this work, we investigate the ²H–¹³C magnetization transfer characteristics of one-bond perdeuterated CD _n spin systems and two-bond H/D exchanged C–(O)–D and C–(N)–D spin systems in carbohydrates and proteins. Our results show that multi-bond, broadband ²H–¹³C polarization transfer can be achieved using ²H radiofrequency fields of ~50 kHz, relatively short contact times of 1.3–1.7 ms, and with sufficiently high sensitivity to enable 2D ²H–¹³C correlation experiments with undistorted ²H spectra in the indirect dimension. To demonstrate the utility of this ²H–¹³C technique for studying molecular motion, we show ²H–¹³C correlation spectra of perdeuterated bacterial cellulose, whose surface glucan chains exhibit a motionally averaged C6 ²H quadrupolar coupling that indicates fast trans-gauche isomerization about the C5–C6 bond. In comparison, the interior chains in the microfibril core are fully immobilized. Application of the ²H–¹³C correlation experiment to H/D exchanged Arabidopsis primary cell walls show that the O–D quadrupolar spectra of the highest polysaccharide peaks can be fit to a two-component model, in which 74% of the spectral intensity, assigned to cellulose, has a near-rigid-limit coupling, while 26% of the intensity, assigned to matrix polysaccharides, has a weakened coupling of 50 kHz. The latter O–D quadrupolar order parameter of 0.22 is significantly smaller than previously reported C–D dipolar order parameters of 0.46–0.55 for pectins, suggesting that additional motions exist at the C–O bonds in the wall polysaccharides. ²H–¹³C polarization transfer profiles are also compared between statistically deuterated and H/D exchanged GB1.     

Variability and directionality of temporal changes in δ<Superscript>13</Superscript>C and δ<Superscript>15</Superscript>N of aquatic invertebrate primary consumers

Seasonal oscillations in the carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope signatures of aquatic algae can cause seasonal enrichment–depletion cycles in the isotopic composition of planktonic invertebrates (e.g., copepods). Yet, there is growing evidence that seasonal enrichment–depletion cycles also occur in the isotope signatures of larger invertebrate consumers, taxa used to define reference points in isotope-based trophic models (e.g., trophic baselines). To evaluate the general assumption of temporal stability in non-zooplankton aquatic invertebrates, δ¹³C and δ¹⁵N time series data from the literature were analyzed for seasonality and the influence of biotic (feeding group) and abiotic (trophic state, climate regime) factors on isotope temporal patterns. The amplitude of δ¹³C and δ¹⁵N enrichment–depletion cycles was negatively related to body size, although all size-classes of invertebrates displayed a winter-to-summer enrichment in δ¹³C and depletion in δ¹⁵N. Among feeding groups, periphytic grazers were more variable and displayed larger temporal changes in δ¹³C than detritivores. For nitrogen, temporal variability and magnitude of directional change of δ¹⁵N was most strongly related to ecosystem trophic state (eutrophic > mesotrophic, oligotrophic). This study provides evidence of seasonality in the isotopic composition of aquatic invertebrates across very broad geographical and ecological gradients as well as identifying factors that are likely to modulate the strength and variability of seasonality. These results emphasize the need for researchers to recognize the likelihood of temporal changes in non-zooplankton aquatic invertebrate consumers at time scales relevant to seasonal studies and, if present, to account for temporal dynamics in isotope trophic models.     

Comparisons of δ<Superscript>13</Superscript>C of photosynthetic products and ecosystem respiratory CO<Subscript>2</Subscript> and their responses to seasonal climate variability

This study investigated the relationship between ¹³C of ecosystem components, soluble plant carbohydrates and the isotopic signature of ecosystem respired CO₂ (¹³C_R) during seasonal changes in soil and atmospheric moisture in a beech (Fagus sylvatica L.) forest in the central Apennine mountains, Italy. Decrease in soil moisture and increase in air vapour pressure deficit during summer correlated with substantial increase in ¹³C of leaf and phloem sap soluble sugars. Increases in ¹³C of ecosystem respired CO₂ were linearly related to increases in phloem sugar ¹³C (r²=0.99, P0.001) and leaf sugar ¹³C (r²=0.981, P0.01), indicating that a major proportion of ecosystem respired CO₂ was derived from recent assimilates. The slopes of the best-fit lines differed significantly (P0.05), however, and were about 0.86 (SE=0.04) for phloem sugars and about 1.63 (SE=0.16) for leaf sugars. Hence, changes in isotopic signature in phloem sugars were transferred to ecosystem respiration in the beech forest, while leaf sugars, with relatively small seasonal changes in ¹³C, must have a slower turnover rate or a significant storage component. No significant variation in ¹³C was observed in bulk dry matter of various plant and ecosystem components (including leaves, bark, wood, litter and soil organics). The apparent coupling between the ¹³C of soluble sugars and ecosystem respiration was associated with large apparent isotopic disequilibria. Values of ¹³C_R were consistently more depleted by about 4 relative to phloem sugars, and by about 2 compared to leaf sugars. Since no combination of the measured pools could produce the observed ¹³C_R signal over the entire season, a significant isotopic discrimination against ¹³C might be associated with short-term ecosystem respiration. However, these differences might also be explained by substantial contributions of other not measured carbon pools (e.g., lipids) to ecosystem respiration or contributions linked to differences in footprint area between Keeling plots and carbohydrate sampling. Linking the seasonal and inter-annual variations in carbon isotope composition of carbohydrates and respiratory CO₂ should be applicable in carbon cycle models and help the understanding of inter-annual variation in biospheric sink strength.     

Differential growth and yield responses of salt-tolerant and susceptible rice cultivars to individual (Na<Superscript>+</Superscript> and Cl<Superscript>−</Superscript>) and additive stress effects of NaCl

Negative impacts exerted by sodium (Na⁺) and chloride (Cl^?) ions individually as well their possible additive effects (under NaCl) were evaluated on growth and yield reductions in rice, besides investigating whether salt-tolerant genotypes respond differentially than their sensitive counterparts. Though both Na⁺ and Cl^? ions get accumulated in plant tissues under NaCl stress, most research has historically been aimed to decipher harmful effects induced by Na⁺ ions. Accordingly, physiological and molecular mechanisms involved in Cl^? toxicity are not clearly understood in crop plants. To address these issues, 65-day-old plants of two rice cultivars, Panvel-3 (tolerant) and Sahyadri-3 (sensitive) were subjected to Cl^?, Na⁺ and NaCl (each with 100 mM concentration and electrical conductivity of ≈10 dS m^?1) stress using soil-based systems. Stress conditions were maintained till harvesting of mature (128-day-old) plants. All three treatments induced substantial antagonistic effects on growth, dry mass, yield components (number of grains per panicle, length, width, thickness and weight of grain, along with the percentage of grains filled) and overall crop yield, with greater impacts under NaCl than its constituent ions. Salinity treatments caused an imbalance in reducing sugars, protein, starch and proline contents, with the greatest magnitude under NaCl. A negative correlation between Cl^?/Na⁺ accumulation and crop yield was witnessed, with higher severity on the sensitive cultivar. The overall magnitude of toxicity was observed highest in NaCl followed by Na⁺ and Cl^?, respectively, suggesting additive effects of constituent ions under NaCl. Both cultivars responded similarly; however, the tolerant cultivar, unlike the sensitive one, kept Na⁺:K⁺ ratio <1.0 and accumulated proline in response to salinity treatments used in this study.     

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.