Spatiotemporal food web dynamics along a desert riparian–upland transition

Increased awareness of spatiotemporal variation in species interactions has motivated the study of temporally-resolved food web dynamics at the landscape level. Empiricists have focused attention on cross-habitat flows of materials, nutrients, and prey, largely ignoring the movement of predators between habitats that differ in productivity (and how predators integrate pulses in resource availability over time). We set out to study seasonal variation in food web interactions between mammalian carnivores and their rodent prey along a riparian–upland gradient in semi-arid southeastern Arizona which features both spatial and temporal heterogeneity in resource availability. Specifically, we tested whether mammalian carnivores spill over from productive, near-river habitats into adjacent, desert-scrub habitats; and if they do, to document the effects of this spillover on rodent communities. Furthermore, we examined seasonal variation in top-down effects by measuring changes in carnivore diet and distribution patterns and rodent populations over time. The results indicate that carnivores track seasonally-abundant resources across the landscape, varying both their diet and movement patterns. In turn, desert-scrub rodent population dynamics track seasonal shifts in carnivore habitat use but not resource availability, suggesting that predation plays a role in structuring rodent communities along the San Pedro River. Further evidence comes from data on rodent community composition, which differs between desert-scrub habitats near and far from the river, despite similarities in resource availability. Our data also suggest that seasonal omnivory helps predators survive lean times, increasing their effects on prey populations. Taken together, these results underscore the importance of spatiotemporal variation in species interactions, highlighting the complexity of natural systems and the need for further detailed studies of food web dynamics.     

The effects of NOS3 Glu298Asp variant on colorectal cancer risk and progression in Turkish population

Endothelial nitric oxide synthase (eNOS), coded by the gene NOS3, may play an important role in uncontrollable cellular growth in several cancer types. Our study was performed to test the association between Glu298Asp polymorphisms in the NOS3 gene and colorectal cancer risk and progression. In this study, NOS3 Glu298Asp polymorphism was genotyped in 84 patients with colorectal cancer and 99 healthy subjects using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis. There were significant differences in the distribution of NOS3 genotypes and frequencies of the alleles between colorectal cancer patients and controls (P = 0.016, P = 0.006, respectively). The increased frequency of NOS3 Glu298Asp homozygotes genotypes in patients who had advanced tumour stage was statistically significant (P = 0.042). Our findings have suggested that NOS3 Glu298Asp polymorphism might be associated with the risk and progression of colorectal cancer in Turkish population.     

Utilizing inherent fluorescence of therapeutics to analyze real-time uptake and multi-parametric effector kinetics

The precise detection of pharmaceutical drug uptake and knowledge of a drug's efficacy at the single-cell level is crucial for understanding a compound's performance. Many pharmaceutical drugs, like the model substances Doxorubicin, Mitoxantrone or Irinotecan, have a distinctive natural fluorescence that can be readily exploited for research purposes. Utilizing this respective natural fluorescence, we propose a method analyzing simultaneously in real-time the efficiency, effects and the associated kinetics of compound-uptake and efflux in mammalian cells by flow cytometry. We show that real-time flow cytometric quantification of compound-uptake is reliably measured and that analyzing their respective uptake kinetic provides additional valuable information which can be used for improving drug dosage and delivery. Exploiting the native fluorescence of natural compounds is clearly advantageous compared to the usage of non-related fluorescent uptake-reporter substances, possibly yielding in unphysiological data. Flow cytometric analysis allows live-dye based multi-parametric high-throughput screening of pharmaceutical compound activity, improving cytotoxicity testing by combining several assays into a single, high resolution readout. This approach can be a useful tool identifying potential inhibitors for multiple drug resistance (MDR), representing a major challenge to the targeted treatment of various diseases.     

Direct upstream motility in Escherichia coli

We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 μm/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio.     

IRAK1 deletion disrupts cardiac Toll/IL-1 signaling and protects against contractile dysfunction

Myocardial contractile dysfunction accompanies both systemic and cardiac insults. Septic shock and burn trauma can lead to reversible contractile deficits, whereas ischemia and direct inflammation of the heart can precipitate transient or permanent impairments in contractility. Many of the insults that trigger contractile dysfunction also activate the innate immune system. Activation of the innate immune response to infection is coordinated by the conserved Toll/interleukin-1 (IL-1) signal transduction pathway. Interestingly, components of this pathway are also expressed in normal and failing hearts, although their function is unknown. The hypotheses that Toll/IL-1 signaling occurs in the heart and that intact pathway function is required for contractile dysfunction after different insults were tested. Results from these experiments demonstrate that lipopolysaccharides (LPS) activate Toll/IL-1 signaling and IL-1 receptor-associated kinase-1 (IRAK1), a critical pathway intermediate in the heart, indicating that the function of this pathway is not limited to immune system tissues. Moreover, hearts lacking IRAK1 exhibit impaired LPS-triggered downstream signal transduction. Hearts from IRAK1-deficient mice also resist acute LPS-induced contractile dysfunction. Finally, IRAK1 inactivation enhances survival of transgenic mice that develop severe myocarditis and lethal heart failure. Thus the Toll/IL-1 pathway is active in myocardial tissue and interference with pathway function, through IRAK1 inactivation, may represent a novel strategy to protect against cardiac contractile dysfunction.     

Micronuclei,nuclear lesions and interphase silver-stained nucleolar organizer regions (AgNORs) as cyto-genotoxicity indicators in Oreochromis niloticus exposed to textile mill effluent

In this study, cyto-genotoxic effects of a textile mill effluent on fish Oreochromis niloticus were investigated using the micronucleus (MN) test and methods to analyze interphase silver-stained nucleolar organizer regions (AgNORs). Fishes were exposed to three different concentrations of textile mill effluent (5, 10 and 20%(v/v)) for 3, 6 and 9 days. Cyclophosphamide (2mg/l) was used as a positive control. Micronucleus frequencies were examined in peripheral blood erythrocytes and gill cells. Nuclear abnormalities (NA) other than micronuclei such as binuclei, lobed nuclei, blebbed nuclei and notched nuclei were also evaluated in peripheral erythrocytes. Interphase AgNOR parameters were examined in epithelial cells obtained from the edge of caudal fins after 90 and 180min of exposure. As a result, dose-dependent increases in the frequencies of micronuclei and other NA in erythrocytes were observed. MN frequencies in gill cells also significantly increased, while the interphase AgNOR parameters in fin cells decreased, as a result of textile effluent and cylophosphamide treatments.     

Cytogenetic analysis of a Mediterranean Gobiid fish Gobius paganellus L., 1758 from Turkey

In this study, cytogenetic analysis of Gobius paganellus, a Mediterranean Gobiid fish from the southern coast of Turkey, was carried out by modified air-dried technique. Phytohemaglutinine pretreatment was performed before the conventional air-dried technique to increase the mitotic index. Chromosomes were obtained using gill tissue. As a result, it was determined that the diploid chromosome number of Gobius paganellus is 2n = 44 (NF = 45), comprising one large metacentric and 43 acrocentric chromosomes.     

Saccharomyces cerevisiae C1D is implicated in both non-homologous DNA end joining and homologous recombination

C1D is a gamma-irradiation inducible nuclear matrix protein that interacts with and activates the DNA-dependent protein kinase (DNA-PK) that is essential for the repair of the DNA double-strand breaks and V(D)J recombination. Recently, it was demonstrated that C1D can also interact with TRAX and prevent the association of TRAX with Translin, a factor known to bind DNA break-point junctions, and that over expression of C1D can induce p53-dependent apoptosis. Taken together, these findings suggest that mammalian C1D could be involved in maintenance of genome integrity by regulating the activity of proteins involved in DNA repair and recombination. To obtain direct evidence for the biological function of C1D that we show is highly conserved between diverse species, we have analysed the Saccharomyces cerevisiae C1D homologue. We report that the disruption of the YC1D gene results in a temperature sensitivity and that yc1d mutant strains exhibit defects in non-homologous DNA end joining (NHEJ) and accurate DNA repair. In addition, using a novel plasmid-based in vivo recombination assay, we show that yc1d mutant strains are also defective in homologous recombination. These results indicate that YC1D is implicated in both homologous recombination and NHEJ pathways for the repair of DNA double-strand breaks.     

Increased frequency of the S-allele of the L-myc oncogene in breast cancer

BACKGROUND: Association between restriction fragment length polymorphisms (RFLP) of known oncogenes and a predisposition to develop cancer have been postulated. The L-myc gene is a potential molecular marker associated with cancer susceptibility as well as metastasis, prognosis, and adverse survival. Our aim was to test the hypothesis that there was an association between L-myc S allele in breast cancer and a predisposition to the disease. MATERIALS AND METHODS: The distribution of L-myc polymorphism in 56 patients with breast cancer was determined by polymerase chain reaction-based restriction fragment length polymorphism and compared with that of 51 healthy control subjects. RESULTS: The allele frequencies of L and S in breast cancer patients were 0.70 and 0.30, respectively and those in normal individuals were 0.54 and 0.46, respectively. This difference was primarily the result of a high frequency of the S allele among breast cancer patients compared to controls. The frequency of S allele was significantly higher in breast cancer patients than in normal individuals (p < 0.01). No correlation was observed between the presence of L-myc S allele and several parameters of each patient's history or characteristics of tumor. CONCLUSION: Our results suggested that L-myc polymorphism may be significant in an individual's susceptibility to breast cancer in Turkey and may be useful for identifying patients at high risk of developing breast cancer.     

Ensuring performance and provider profit through data replication in cloud systems

Cloud computing is a relatively recent computing paradigm that is often the answer for dealing with large amounts of data. Tenants expect the cloud providers to keep supplying an agreed upon quality of service, while cloud providers aim to increase profits as it is a key ingredient of any economic enterprise. In this paper, we propose a data replication strategy for cloud systems that satisfies the response time objective for executing queries while simultaneously enables the provider to return a profit from each execution. The proposed strategy estimates the response time of the queries and performs data replication in a way that the execution of any particular query is still estimated to be profitable for the provider. We show with simulations that how the proposed strategy fulfills these two criteria.