Genomic comparison between members of the Salinibacteraceae family,and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano

The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability. Altogether, the results indicated an open pan-genome for the family Salinibacteraceae, as well as the codification of relevant traits such as diverse rhodopsin genes, CRISPR-Cas systems and spacers, and one T6SS secretion system that could give ecological advantages to an EHB-2 isolate. For the new Salinibacter species, we propose the name Salinibacter altiplanensis sp. nov. (the designated type strain is AN15^T = CECT 9105^T = IBRC-M 11031^T).     

CECT: computationally efficient congestion-avoidance and traffic engineering in software-defined cloud data centers

The proliferation of cloud data center applications and network function virtualization (NFV) boosts dynamic and QoS dependent traffic into the data centers network. Currently, lots of network routing protocols are requirement agnostic, while other QoS-aware protocols are computationally complex and inefficient for small flows. In this paper, a computationally efficient congestion avoidance scheme, called CECT, for software-defined cloud data centers is proposed. The proposed algorithm, CECT, not only minimizes network congestion but also reallocates the resources based on the flow requirements. To this end, we use a routing architecture to reconfigure the network resources triggered by two events: (1) the elapsing of a predefined time interval, or, (2) the occurrence of congestion. Moreover, a forwarding table entries compression technique is used to reduce the computational complexity of CECT. In this way, we mathematically formulate an optimization problem and define a genetic algorithm to solve the proposed optimization problem. We test the proposed algorithm on real-world network traffic. Our results show that CECT is computationally fast and the solution is feasible in all cases. In order to evaluate our algorithm in term of throughput, CECT is compared with ECMP (where the shortest path algorithm is used as the cost function). Simulation results confirm that the throughput obtained by running CECT is improved up to 3× compared to ECMP while packet loss is decreased up to 2×.     

Infrared microspectroscopy: Sampling heterogeneity in plant cell wall composition and architecture

The use of probes such as monoclonal and polyclonal antibodies to specific cell wall components, at both the light and electron microscope levels, has demonstrated the diversity in cell wall composition between species, between tissues, between different regions of the cell surface, and even within a single wall. Traditional methods of cell wall analysis have provided valuable information on wall composition and architecture, but, by having to rely on the use of bulk samples, have averaged out this intrinsic heterogeneity. Fourier Transform Infrared (FTIR) microspectroscopy addresses this problem by providing chemical information from an area as small as 10×10 μm of a single cell wall fragment or area of a tissue section that has been imaged with a microscope accessory.
We have used FTIR microspectroscopy as a powerful and extremely rapid assay for wall components and putative cross-links in muro. The spectra are sensitive to polymer conformation, and the use of polarisers in the microscope accessory allows the orientation of particular functional groups to be determined, with respect to the long axis of elongating cells. The spectra constitute species and tissue-specific 'fingerprints', and the use of classical discriminant analysis may provide the opportunity for correlating spectral features with chemical, architectural or rheological wall properties. Spectral mapping of an area of a specimen allows the morphological features resulting from cell growth and differentiation to be characterised chemically at the single cell level.     

Kani: a QoS-aware hypervisor-level scheduler for cloud computing environments

Cloud computing environments (CCEs) are expected to deliver their services with qualities in service level agreements. On the other hand, they typically employ virtualization technology to consolidate multiple workloads on the same physical machine, thereby enhancing the overall utilization of physical resources. Most existing virtualization technologies are, however, unaware of their delivered quality of services (QoS). For example, the Xen hypervisor merely focuses on fair sharing of processor resources. We believe that CCEs have got married with traditional virtualization technologies without many traits in common. To bridge the gap between these two technologies, we have designed and implemented Kani, a QoS-aware hypervisor-level scheduler. Kani dynamically monitors the quality of delivered services to quantify the deviation between desired and delivered levels of QoS. Using this information, Kani determines how to allocate processor resources among running VMs so as to meet the expected QoS. Our evaluations of Kani scheduler prototype in Xen show that Kani outperforms the default Xen scheduler namely the Credit scheduler. For example, Kani reduces the average response time to requests to an Apache web server by up to \(93.6\,\%\); improves its throughput by up to \(97.9\,\%\); and mitigates the call setup time of an Asterisk media server by up to \(96.6\,\%\).     

Cryptic Caribbean species of Scorpaena (Actinopterygii: Scorpaeniformes) suggested by cytogenetic and molecular data

Cytogenetic and molecular analyses enabled identification of two cytotypes among individuals of the spotted scorpion fish Scorpaena plumieri from Margarita Island, Venezuela. Cytotype 1 was characterized by 48 subtelo‐acrocentric chromosomes and fundamental number (number of chromosome arms; FN) equalled 48, while cytotype 2 was characterized by two metacentric and 46 subtelo‐acrocentric chromosomes and FN was 50. These cytotypes also differed in the location of the ribosomal gene clusters and in the distribution of the constitutive heterochromatin. Moreover, fish from the cytotypes 1 and 2 were found to belong to distinct mitochondrial lineages. The presence of two S. plumieri cytotypes from two lineages separated by high genetic distance suggests that they correspond to sympatric cryptic species.     

Synthesis,Characterization, Molecular Modeling,and DNA Interaction Studies of Copper Complex Containing Food Additive Carmoisine Dye

A copper complex of carmoisine dye; [Cu(carmoisine)₂(H₂O)₂]; was synthesized and characterized by using physico-chemical and spectroscopic methods. The binding of this complex with calf thymus (ct) DNA was investigated by circular dichroism, absorption studies, emission spectroscopy, and viscosity measurements. UV-vis results confirmed that the Cu complex interacted with DNA to form a ground-state complex and the observed binding constant (2× 10⁴ M^?1) is more in keeping with the groove bindings with DNA. Furthermore, the viscosity measurement result showed that the addition of complex causes no significant change on DNA viscosity and it indicated that the intercalation mode is ruled out. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the reaction. The results of circular dichroism (CD) suggested that the complex can change the conformation of DNA from B-like form toward A-like conformation. The cytotoxicity studies of the carmoisine dye and its copper complex indicated that both of them had anticancer effects on HT-29 (colon cancer) cell line and they may be new candidates for treatment of the colon cancer.     

Heterogeneity of KRAS Mutation Status in Rectal Cancer

IntroductionAnti-EGFR targeted therapy is of increasing importance in advanced colorectal cancer and prior KRAS mutation testing is mandatory for therapy. However, at which occasions this should be performed is still under debate. We aimed to assess in patients with locally advanced rectal cancer whether there is intra-specimen KRAS heterogeneity prior to and upon preoperative chemoradiotherapy (CRT), and if there are any changes in KRAS mutation status due to this intervention.ResultsFor 20 (43%) out of the 47 patients, a KRAS mutation was detected. With 12 out of 20, the majority of these mutations affected codon 35. We did not obtained evidence that CRT results in changes of the KRAS mutation pattern. In addition, no intratumoral heterogeneity in the KRAS mutational status could be proven. This was true for both the biopsies prior to CRT and the resection specimens thereafter. The discrepancy observed in some samples when using the SNaPshot™ assay was due to insufficient sensitivity of this technique upon massive tumor regression by CRT as application of the therascreen® KRAS test revealed concordant results.ConclusionOur results indicate that the KRAS mutation status at the primary tumor site of rectal cancer is homogenous. Its assessment for therapeutic decisions is feasible in pre-therapeutic biopsies as well as in post-therapeutic resected specimens. The amount of viable tumor cells seems to be an important determinant for assay sensitivity and should thus be considered for selection of the analytical method.