Phylogenetic analysis based on full genome sequencing of Italian tomato spotted wilt virus isolates identified in “Roggianese” sweet pepper and chilli pepper

A study aimed at defining population structure of Italian tomato spotted wilt virus (TSWV) isolates was performed. Full genome sequencing of six TSWV isolates found in two Italian regions (two from Latium: Lazio 17 and Tarquinia; and four from Calabria: PepCal 10, 12, 22 and 24) were assembled. Identity percentages in nucleotide sequence among these TSWV isolates are here provided. The six full length genome sequences were compared with other two Italian isolates (p105 and p202/3WT) already fully sequenced, as well as full TSWV genomes that could be retrieved from GenBank. Phylogenetic analysis, performed in concatenated sequences and for each gene of each genome segment (L, M and S), confirmed the presence of two clades, namely A-like and D-like. In particular, the phylogenetic tree based on segment L grouped all the newly sequenced TSWV isolates in D-like clade. In the M segment phylogenetic tree, all our TSWV isolates shifted in the A-like clade. Isolates separation was not correlated to their geographical origin in phylogenetic study of distinct ORFs encoded by the RNA S segment. In fact, in nucleocapsid-encoding phylogenetic tree, PepCal 10 and 22 grouped in an A-like clade with p105, PepCal 12 and 24 in a D-like clade with p202/3WT, whereas Lazio 17 and Tarquinia in a third well distinct group. NSs tree displayed only PepCal 10 with p105 in A-like clade, whereas PepCal 12, 22, 24 with p202/3WT in D-like subclade; and isolates from Latium grouped a separated clade adjacent to D-like isolates. Additional analysis on putative reassortment events showed that TSWV Calabrian isolates likely originated from a reassortment event in M RNA and other in S RNA with p105 as major parent. Recombination events were detected in isolates from Latium in L and S RNAs with Chinese isolates as putative major parent.     

Both mature miR-17-5p and passenger strand miR-17-3p target TIMP3 and induce prostate tumor growth and invasion

MicroRNAs (miRNA) precursor (pre-miRNA) molecules can be processed to release a miRNA/miRNA* duplex. In the canonical model of miRNA biogenesis, one strand of the duplex is thought to be the biologically active miRNA, whereas the other strand is thought to be inactive and degraded as a carrier or passenger strand called miRNA* (miRNA star). However, recent studies have revealed that miRNA* strands frequently play roles in the regulatory networks of miRNA target molecules. Our recent study indicated that miR-17 transgenic mice could abundantly express both the mature miR-17-5p and the passenger strand miR-17-3p. Here, we showed that miR-17 enhanced prostate tumor growth and invasion by increasing tumor cell proliferation, colony formation, cell survival and invasion. miRNA target analysis showed that both miR-17-5p and miR-17-3p repressed TIMP metallopeptidase inhibitor 3 (TIMP3) expression. Silencing with small interfering RNA against TIMP3 promoted cell survival and invasion. Ectopic expression of TIMP3 decreased cell invasion and cell survival. Our results demonstrated that mature miRNA can function coordinately with its passenger strand, enhancing the repressive ability of a miRNA by binding the same target. Within an intricate regulatory network, this may be among the mechanisms by which miRNA can augment their regulatory capacity.     

Peripheral CD8+ T cell proliferation is prognostic for patients with advanced thoracic malignancies

There is a complex interplay between the immune system and a developing tumor that is manifest in the way that the balance of T cell subsets in the local tumor environment reflects clinical outcome. Tumor infiltration by CD8⁺ T cells and regulatory T cells (Treg) is associated with improved and reduced survival, respectively, in many cancer types. However, little is known of the prognostic value of immunological parameters measured in peripheral blood. In this study, peripheral CD8⁺ T cells and Treg from 43 patients with malignant mesothelioma or advanced non-small-cell lung cancer scheduled to commence palliative chemotherapy were assessed by flow cytometry and evaluated for association with patient survival. Patients had a higher proportion of peripheral Treg, proliferating CD8⁺ T cells and CD8⁺ T cells with an activated effector phenotype compared with age-matched healthy controls. Higher proportions of Treg and proliferating CD8⁺ T cells were both associated with poor survival in univariate analyses (hazard ratio [HR] 3.81, 95 % CI 1.69–8.57; p < 0.01 and HR 2.86, 95 % CI 1.26–6.50; p < 0.05, respectively). CD8⁺ T cell proliferation was independently predictive of reduced survival in multivariate analysis (HR 2.58, 95 % CI 1.01–6.61; p < 0.05). These findings suggest that peripheral CD8⁺ T cell proliferation can be a useful prognostic marker in patients with thoracic malignancies planned for palliative chemotherapy.     

Environmental drivers of the bryophyte propagule bank and its comparison with forest-floor assemblage in Central European temperate mixed forests

Species richness, composition and abundance of the bryophyte diaspore bank of Central European temperate mixed forests were compared with the forest-floor bryophyte assemblage. The impact of environmental variables and anthropogenic disturbances, including tree species composition, stand structure, microclimate, light conditions, soil and litter properties, management history, and landscape properties, potentially influencing bryophyte diaspore bank assemblages were explored. Thirty-four, 70–100 years old mixed stands with differing tree species composition were examined in the ?rség National Park, Western Hungary. The diaspore bank was studied by soil collection and cultivation, and data were analysed by multivariate methods. Contrary to the forest-floor bryophyte assemblage, where substrate availability, tree species composition and stand structure were the most influential environmental variables, the composition and abundance of the diaspore bank was mainly affected by site conditions (microclimate, litter and soil properties). Species richness of the bryophyte diaspore bank was lower than that of the forest-floor bryophyte assemblage. Short-lived mosses (colonists, short-lived shuttles) were dominant in the diaspore bank, as opposed to the forest-floor bryophyte community, where perennial mosses dominated. In the studied forests, the importance of the bryophyte diaspore bank was relatively low in the regeneration and maintenance of the forest-floor bryophyte vegetation.     

Doing Sovereignty in Native North America: Anishinaabe Counter-Mapping and the Struggle for Land-Based Self-Determination

Beginning with the premise that sovereignty may be most constructively contemplated not as a definable object or objective but instead as a process, this article examines counter-mapping as a way for contemporary indigenous citizens to “do” sovereignty. It surveys three Anishinaabe/Ojibwe communities’ recent use of geographical techniques to communicate their own territorial claims and counter the competing claims of others. In a 21^st century context characterized by urgent extractive-industrial threats to indigenous landbases and lifeways, the cases presented here demonstrate that counter-mapping can serve as a powerful positive tool. Yet because the prevailing methods available to safeguard land-based self-determination also have the potential to undermine it, I conclude by considering some of the pitfalls that complicate counter-mapping’s ability to promote the sovereignty process. I suggest that indigenous people who choose to enact their sovereignty in this manner are indeed empowered, but only within an existing—and inequitable—socio-political system.     

Conformational Equilibria of Bridled Chiroporphyrins in Solution Investigated by Vibrational Circular Dichroism

A series of bridled chiroporphyrins (BCP) and their metal complexes were prepared, in which two n‐methylene straps connect adjacent meso substituents by ester linkages. These compounds can exist as four atropisomers (αααα, αβαβ, αααβ, or ααββ) depending on the position of the meso groups relative to the macrocycle (α when above and β when below). We characterized the conformation of these chiral porphyrins and their metal (Zn, Ni, Mn) complexes by vibrational circular dichroism (VCD) associated with ab initio calculations. VCD spectra of the three metalloporphyrins were recorded in CDCl₃ and benzene solutions and ab initio calculations of their four atropoisomers were performed at the Density Functional Theory (DFT) level. The bridled chiroporphyrin with the longer straps (9 CH₂) and its nickel(II) complex can be isolated as the αβαβ atropisomer in the solid state and were found with the same conformation in CDCl₃ and benzene solutions. The bridled chiroporphyrin with the shortest straps (8 CH₂) and its zinc(II) complex can be isolated as the αααα atropisomer in the solid state, but in solution they are subject to atropisomeric equilibria, resulting in atropisomer distributions that are strongly solvent‐dependent. Comparison of the experimental VCD spectra with the predicted spectra of the four atropisomers allowed the quantification of these distributions. Finally, the manganese(III) complex also exhibits an atropisomeric equilibria in solution which is slightly solvent‐dependent. Chirality 25:480–486, 2013. © 2013 Wiley Periodicals, Inc.     

Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies

In this study, by applying a combined approach of NMR measurements and molecular modelling, the conformations and the interactions with membrane-like environment of five arginine vasopressin (AVP) or oxytocin (OT) analogues modified with Cα-disubstituted cis-1-amino-4-phenylcyclohexane-1-carboxylic acid in position 2 have been determined. In addition, the AVP analogues were prepared in N-acylated forms with various bulky acyl groups. All of the peptides studied interacted with the mixed dodecylphosphocholine:sodium dodecyl sulphate micelle, providing a model of biological membrane. A different polarities of the AVP- and OT-like peptides resulted in their different position relative to the micelle surface. Thus, the arrangement of the former was nearly perpendicular, whereas the latter was rather parallel to the micelle's surface. Moreover, the results of our studies have shown that the binding sites for antagonists may be overlapped with that for agonists, as well as it may be quite different. Nevertheless, the aromatic–aromatic contacts represent the most important interactions for antagonists, whereas the hydrophilic interactions seem to be crucial for agonists.     

Thermoregulatory effects of melatonin in relation to sleepiness

Thermoregulatory processes have long been implicated in the initiation of human sleep. In this paper, we review our own studies conducted over the last decade showing a crucial role for melatonin as a mediator between the thermoregulatory and arousal system in humans. Distal heat loss, via increased skin temperature, seems to be intimately coupled with increased sleepiness and sleep induction. Exogenous melatonin administration during the day when melatonin is essentially absent mimics the endogenous thermophysiological processes occurring in the evening and induces sleepiness. Using a cold thermic challenge test, it was shown that melatonin‐induced sleepiness occurs in parallel with reduction in the thermoregulatory set‐point (threshold); thus, melatonin may act as a circadian modulator of the thermoregulatory set‐point. In addition, an orthostatic challenge can partially block the melatonin‐induced effects, suggesting an important role of the sympathetic nervous system as a link between the thermoregulatory and arousal systems. A topographical analysis of finger skin temperature with infrared thermometry revealed that the most distal parts of the fingers, i.e., fingertips, represent the important skin regions for heat loss regulation, most probably via opening the arteriovenous anastomoses, and this is clearly potentiated by melatonin. Taken together, melatonin is involved in the fine‐tuning of vascular tone in selective vascular beds, as circulating melatonin levels rise and fall throughout the night. Besides the role of melatonin as “nature's soporific”, it can also serve as nature's nocturnal vascular modulator.     

Global dynamics of two-compartment models for cell production systems with regulatory mechanisms

We present a global stability analysis of two-compartment models of a hierarchical cell production system with a nonlinear regulatory feedback loop. The models describe cell differentiation processes with the stem cell division rate or the self-renewal fraction regulated by the number of mature cells. The two-compartment systems constitute a basic version of the multicompartment models proposed recently by Marciniak-Czochra and collaborators [25] to investigate the dynamics of the hematopoietic system. Using global stability analysis, we compare different regulatory mechanisms. For both models, we show that there exists a unique positive equilibrium that is globally asymptotically stable if and only if the respective reproduction numbers exceed one. The proof is based on constructing Lyapunov functions, which are appropriate to handle the specific nonlinearities of the model. Additionally, we propose a new model to test biological hypothesis on the regulation of the fraction of differentiating cells. We show that such regulatory mechanism is incapable of maintaining homeostasis and leads to unbounded cell growth. Potential biological implications are discussed.     

It is risky out there: the costs of emergence and the benefits of prolonged dormancy

Prolonged dormancy is a stage in herbaceous perennial plants in which some individuals remain alive below ground for one or more growing seasons instead of emerging. Prolonged dormancy is puzzling, because foregoing opportunities for growth and reproduction seems costly. However, studies have shown that it buffers plants from the negative consequences associated with environmental stochasticity, suggesting that dormancy is a beneficial strategy to avoid the risks of stress above ground. If so, emergence during unfavorable conditions should have significant costs. Here, we test the hypothesis that emergence during times of stress has negative demographic consequences in a native perennial forb, Astragalus scaphoides, and investigate the potential underlying physiological mechanisms. We measured plant responses to a severe seasonal drought and an experimental defoliation to ask: (1) How do emergent plants respond to above-ground stress? (2) Do these responses have negative demographic consequences? and (3) Based on these responses, does stress increase the risk of emergence? Plants showed remarkable physiological tolerance to stress in the short term: high temperatures and low moisture did not have a strong effect on photosynthesis rates, and neither drought nor defoliation significantly impacted stored resources. However, stress did result in demographic costs for emergent plants relative to plants experiencing more favorable conditions. Drought resulted in decreased flowering probabilities relative to the long-term average and defoliation significantly increased mortality rates. These results demonstrate that the risk of emerging and experiencing stress entails considerable costs, supporting the hypothesis that prolonged dormancy is a beneficial strategy to avoid such risk.