A Preliminary Study on the Chiral Vector Approach in Determining the Optimum Structure of Carbon Nanotubes and its Correlation to the Chemical Potential Energy Using Avogadro

In this study, the following quantitative properties of carbon nanotubes were explored: the chiral vectors, which are numbers that describe the carbon nanotubes’ structure, and properties such as chemical potential energy. The objective of this study is to simulate various carbon nanotube structures with chiral vectors that range from (0-3) and find a relation between these chiral vectors and the chemical potential energy. Using the software Avogadro, 12 carbon nanotubes with different chiral vectors (n, m) were simulated. These carbon nanotubes were of different lengths to keep the number of atoms in the molecules as close to 100 as possible. Avogadro was also used to calculate the theoretical chemical potential energy of these molecules. Using multiple correlation to analyze the simulations’ data, an R2 value of 0.632 was obtained, which indicates a small positive linear association between them

Cyanoprokaryota of the Salt Marshes at the Pryazov National Natural Park, Ukraine

Cyanoprokaryota of salt marshes were investigated at three scientific sites: in the upper Utlyuk Estuary, on the coast of Lake Sivashik, and at Fedotov Spit. Data on species composition, systematic structure, leading families, and genera are provided. In total, 71 species of cyanoprokaryotes representing 3 orders, 10 families, and 22 genera. The dominant complex included representatives of the genera Schizothrix Kützing ex Gomont, Phormidium Kützing ex Gomont, Lyngbya C.Agardh ex Gomont, Leptolyngbya (Gomont) Anagnostidis & Komárek, Trichormus (Ralfs ex Bornet & Flahault) Komárek & Anagnostidis, Nostoc Vaucher ex Bornet & Flahault, and Nodularia Mert. ex Born. & Flah. The identified species are analyzed for their biotopic nature and their valence to the level of environmental salinity. The distribution of the identified species within the Ukrainian territory is considered

Use of soil biota in the assessment of the ecological potential of urban soils

In assessing the ecological conditions and classification of urban soils, data about soil biota should be taken into account. The environment of urban territories is characterized by significant changes compared to their surrounding environments. It is established that the algal flora of urban soils lose their zonal features and features associated with the edification influence of higher plants. Specific biotopes with a definite species structure are formed in urboecosystems. Fifty 50 algae species have been recorded in the soils of the Henichesk urboecosystems (Kherson region, Ukraine): Cyanoprocaryota – 21, Chlorophyta – 13, Charophyta – 2, Eustigmatophyta – 1, Xanthophyta – 11, Bacillariophyta – 2. Among dominant and subdominant species were Cyanoprocaryota and Chlorophyta. The other phyla were represented by Klebsormidium dissectum, K. flaccidum, Hantzschia amphioxys, Eustigmatos magnus, Botrydiopsis eriensis. Compared with the surrounding environment, the urbanized flora of Henichesk has a low species richness, and is characterized by prevalence of Cyanoprocaryota and Chlorophyta species. The coefficient that takes into account the percentage of preservation of species richness in a particular urban area compared to the background indicators of species richness can be used to evaluate the urban transformation of soil biota. The degree of degradatory changes in the composition of living organisms and the direction of these changes depends on the specificity and intensity of exploitation of the territory of the urban ecosystem. The most diverse composition of algae species within the the city of Henichesk was noted in the recreational, residential, and transport zones, in comparison with the industrial zone and the zone of special use. Different functional areas of the city are distinguished not only by the algae species richness, but also by the composition of dominants. Among the dominants and subdominants of the recreational and transport zones were species of different phyla. The dominants and subdominants of the residential and industrial zones were Cyanoprocaryota species, in the zone of special use – representatives of Chlorophyta. The distribution of species richness of algae along the soil profile in the city acquires an atypical character. The species richness increases not in the most superficial layers of soil, but in the lower, aphotic parts of the soil profile. The soil biota, on the one hand, depends on the ecological conditions of soil, and on the other as a result of its life activity, changes the ecological functions of the soil, strengthening or weakening them. The reduction in the species richness of the soil algae of the urboecosystem Henichesk shows the limitations of ecological functions of urban soils. It is established that changes in the composition of algae in soils of urban ecosystems are one of the indicators of the presence and severity of transformation processes. These processes occur with the soil biota and soil as a whole under the conditions of urban ecosystems and can be used as indicators in the environmental assessment of urban soils, in the development and subsequent examination of ways to reduce negative expression of urbanization

HIV gp120 Induces, NF-κB Dependent, HIV Replication that Requires Procaspase 8

HIV envelope glycoprotein gp120 causes cellular activation resulting in anergy, apoptosis, proinflammatory cytokine production, and through an unknown mechanism, enhanced HIV replication.We describe that the signals which promote apoptosis are also responsible for the enhanced HIV replication. Specifically, we demonstrate that the caspase 8 cleavage fragment Caspase8p43, activates p50/p65 Nuclear Factor kappaB (NF-kappaB), in a manner which is inhibited by dominant negative IkappaBalpha. This caspase 8 dependent NF-kappaB activation occurs following stimulation with gp120, TNF, or CD3/CD28 crosslinking, but these treatments do not activate NF-kappaB in cells deficient in caspase 8. The Casp8p43 cleavage fragment also transactivates the HIV LTR through NF-kappaB, and the absence of caspase 8 following HIV infection greatly inhibits HIV replication.Gp120 induced caspase 8 dependent NF-kappaB activation is a novel pathway of HIV replication which increases understanding of the biology of T-cell death, as well as having implications for understanding treatment and prevention of HIV infection

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Infected Cell Killing by HIV-1 Protease Promotes NF-κB Dependent HIV-1 Replication

Acute HIV-1 infection of CD4 T cells often results in apoptotic death of infected cells, yet it is unclear what evolutionary advantage this offers to HIV-1. Given the independent observations that acute T cell HIV-1 infection results in (1) NF-κB activation, (2) caspase 8 dependent apoptosis, and that (3) caspase 8 directly activates NF-κB, we questioned whether these three events might be interrelated. We first show that HIV-1 infected T cell apoptosis, NF-κB activation, and caspase 8 cleavage by HIV-1 protease are coincident. Next we show that HIV-1 protease not only cleaves procaspase 8, producing Casp8p41, but also independently stimulates NF-κB activity. Finally, we demonstrate that the HIV protease cleavage of caspase 8 is necessary for optimal NF-κB activation and that the HIV-1 protease specific cleavage fragment Casp8p41 is sufficient to stimulate HIV-1 replication through NF-κB dependent HIV-LTR activation both in vitro as well as in cells from HIV infected donors. Consequently, the molecular events which promote death of HIV-1 infected T cells function dually to promote HIV-1 replication, thereby favoring the propagation and survival of HIV-1

Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area

Seeking Clarity within Cloudy Effluents: Differentiating Fungal from Bacterial Peritonitis in Peritoneal Dialysis Patients

Fungal peritonitis is a serious complication of peritoneal dialysis (PD) therapy with the majority of patients ceasing PD permanently. The aims of this study were to identify risk factors and clinical associations that may discriminate between fungal from bacterial peritonitis.We retrospectively identified episodes of fungal peritonitis from 2001-2010 in PD patients at Liverpool and Westmead Hospitals (Australia). Fungal peritonitis cases were matched in a 1:2 ratio with patients with bacterial peritonitis from each institution's dialysis registry, occurring closest in time to the fungal episode. Patient demographic, clinical and outcome data were obtained from the medical records.Thirty-nine episodes of fungal peritonitis (rate of 0.02 episodes per patient-year of dialysis) were matched with 78 episodes of bacterial peritonitis. Candida species were the commonest pathogens (35/39; 90% episodes) with Candida albicans (37%), Candida parapsilosis (32%) and Candida glabrata (13%) the most frequently isolated species. Compared to bacterial peritonitis, fungal peritonitis patients had received PD for significantly longer (1133 vs. 775 catheter-days; p = 0.016), were more likely to have had previous episodes of bacterial peritonitis (51% vs. 10%; p = 0.01), and to have received prior antibacterial therapy (51% vs. 10%; p = 0.01). Patients with fungal peritonitis were less likely to have fever and abdominal pain on presentation, but had higher rates of PD catheter removal (79% vs. 22%; p<0.005), and permanent transfer to haemodialysis (87% vs. 24%; p<0.005). Hospital length of stay was significantly longer in patients with fungal peritonitis (26.1 days vs. 12.6 days; p = 0.017), but the all-cause 30-day mortality rate was similar in both groups. Fluconazole was a suitable empiric antifungal agent; with no Candida resistance detected.Prompt recognition of clinical risk factors, initiation of antifungal therapy and removal of PD catheters are key considerations in optimising outcomes

Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics

Bacteria are able to sense and respond to a variety of external stimuli, with responses that vary from stimuli to stimuli and from species to species. The best-understood is chemotaxis in the model organism Escherichia coli, where the dynamics and the structure of the underlying pathway are well characterised. It is not clear, however, how well this detailed knowledge applies to mechanisms mediating responses to other stimuli or to pathways in other species. Furthermore, there is increasing experimental evidence that bacteria integrate responses from different stimuli to generate a coherent taxis response. We currently lack a full understanding of the different pathway structures and dynamics and how this integration is achieved. In order to explore different pathway structures and dynamics that can underlie taxis responses in bacteria, we perform a computational simulation of the evolution of taxis. This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria better able to localise with favourable conditions gain a selective advantage. We find that a certain dynamics evolves consistently under different model assumptions and environments. These dynamics, which we call non-adaptive dynamics, directly couple tumbling probability of the cell to increasing stimuli. Dynamics that are adaptive under a wide range of conditions, as seen in the chemotaxis pathway of E. coli, do not evolve in these evolutionary simulations. However, we find that stimulus scarcity and fluctuations during evolution results in complex pathway dynamics that result both in adaptive and non-adaptive dynamics depending on basal stimuli levels. Further analyses of evolved pathway structures show that effective taxis dynamics can be mediated with as few as two components. The non-adaptive dynamics mediating taxis responses provide an explanation for experimental observations made in mutant strains of E. coli and in wild-type Rhodobacter sphaeroides that could not be explained with standard models. We speculate that such dynamics exist in other bacteria as well and play a role linking the metabolic state of the cell and the taxis response. The simplicity of mechanisms mediating such dynamics makes them a candidate precursor of more complex taxis responses involving adaptation. This study suggests a strong link between stimulus conditions during evolution and evolved pathway dynamics. When evolution was simulated under conditions of scarce and fluctuating stimulus conditions, the evolved pathway contained features of both adaptive and non-adaptive dynamics, suggesting that these two types of dynamics can have different advantages under distinct environmental circumstances

Activation of PPARγ in Myeloid Cells Promotes Lung Cancer Progression and Metastasis

Activation of peroxisome proliferator-activated receptor-γ (PPARγ) inhibits growth of cancer cells including non-small cell lung cancer (NSCLC). Clinically, use of thiazolidinediones, which are pharmacological activators of PPARγ is associated with a lower risk of developing lung cancer. However, the role of this pathway in lung cancer metastasis has not been examined well. The systemic effect of pioglitazone was examined in two models of lung cancer metastasis in immune-competent mice. In an orthotopic model, murine lung cancer cells implanted into the lungs of syngeneic mice metastasized to the liver and brain. As a second model, cancer cells injected subcutaneously metastasized to the lung. In both models systemic administration of pioglitazone increased the rate of metastasis. Examination of tissues from the orthotopic model demonstrated increased numbers of arginase I-positive macrophages in tumors from pioglitazone-treated animals. In co-culture experiments of cancer cells with bone marrow-derived macrophages, pioglitazone promoted arginase I expression in macrophages and this was dependent on the expression of PPARγ in the macrophages. To assess the contribution of PPARγ in macrophages to cancer progression, experiments were performed in bone marrow-transplanted animals receiving bone marrow from Lys-M-Cre+/PPARγflox/flox mice, in which PPARγ is deleted specifically in myeloid cells (PPARγ-Macneg), or control PPARγflox/flox mice. In both models, mice receiving PPARγ-Macneg bone marrow had a marked decrease in secondary tumors which was not significantly altered by treatment with pioglitazone. This was associated with decreased numbers of arginase I-positive cells in the lung. These data support a model in which activation of PPARγ may have opposing effects on tumor progression, with anti-tumorigenic effects on cancer cells, but pro-tumorigenic effects on cells of the microenvironment, specifically myeloid cells