A comparative analysis of metal transportomes from metabolically versatile Pseudomonas

<p>Abstract</p> <p>Background</p> <p>The availability of complete genome sequences of versatile <it>Pseudomonas </it>occupying remarkably diverse ecological niches enabled to gain insights into their adaptative assets. The objective of this study was to analyze the complete genetic repertoires of metal transporters (metal transportomes) from four representative <it>Pseudomonas </it>species and to identify metal transporters with "Genomic Island" associated features.</p> <p>Methods</p> <p>A comparative metal transporter inventory was built for the following four <it>Pseudomonas </it>species: <it>P</it>.<it>putida (Ppu) </it>KT2440, <it>P.aeruginosa </it>(<it>Pae</it>) PA01, <it>P.fluorescens </it>(<it>Pfl</it>) Pf-5 and <it>P.syringae </it>(<it>Psy</it>)<it>pv.tomato DC3000 </it>using TIGR-CMR and Transport DB. Genomic analysis of essential and toxic metal ion transporters was accomplished from the above inventory. Metal transporters with "Genomic Island" associated features were identified using Islandpath analysis.</p> <p>Results</p> <p>Dataset cataloguing has been executed for 262 metal transporters from the four spp. Additional metal ion transporters belonging to NiCoT, Ca P-type ATPase, Cu P-type ATPases, ZIP and MgtC families were identified. In <it>Psy </it>DC3000, 48% of metal transporters showed strong GI features while it was 45% in <it>Ppu </it>KT2440. In <it>Pfl </it>Pf-5 and <it>Pae </it>PA01 only 26% of their metal transporters exhibited GI features.</p> <p>Conclusion</p> <p>Our comparative inventory of 262 metal transporters from four versatile <it>Pseudomonas </it>spp is the complete suite of metal transportomes analysed till date in a prokaryotic genus. This study identified differences in the basic composition of metal transportomes from <it>Pseudomonas </it>occupying diverse ecological niches and also elucidated their novel features. Based on this inventory we analysed the role of horizontal gene transfer in expansion and variability of metal transporter families.</p

Understanding Cell Biology

The cell is the structural and functional unit of all living organisms and is sometimes called the "building block of life.” All living things are made from one or more cells. A cell is the simplest unit of life and they are responsible for keeping an organism alive and functioning. Almost every different type of cell contains genetic material, a membrane and cytoplasm. The most basic categorization of Earth’s organisms is determined by different types of cells. All cells can be divided into one of two classifications: prokaryotic cells and eukaryotic cells. Prokaryotic cells are found in bacteria and archaea. Eukaryotic cells are found in organisms from the domain Eukaryota which includes animals, plants, fungi and protists. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Cells were discovered by Robert Hooke in 1665, who named them for their resemblance to cells inhabited by Christian monks in a monastery. Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms, and that all cells come from pre-existing cells. Cells emerged on Earth at least 3.5 billion years ago. The study of cells is called cell biology or cellular biology

Solid Waste management from Steel Melting Shop

- Production of steel in steel Industry is accomplice for the generation of solid waste materials like sludge, slag, dust etc. In recent days most part of wastes are generated from steelmaking process which is a focus point now-a-days. The solid waste generation, presently in Indian steel industry is in the range of 400 - 500 kg/t of crude steel and recycling rate varies between 40 - 70 % which lead to higher production costs, lower productivity and further environmental degradation. It is very essential not only for recycling of the waste valuable metals and mineral resources but also to protect the environment. I Solid waste management in steel industry is broadly classified in “4 R” i.e. reduce, reuse, recycle and restore the materials. The aim of the paper is to explore the various developments for total recycling of solid waste generated from steel industry, so that the vision for making “clean &amp; green steel with zero waste” can be achieved for survival and growth of steel business in future. Keywords—Steel, Reuse, recycle, solid waste, sustainable development

Genotoxic effects of culture media on human pluripotent stem cells

Culture conditions play an important role in regulating the genomic integrity of Human Pluripotent Stem Cells (HPSCs). We report that HPSCs cultured in Essential 8 (E8) and mTeSR, two widely used media for feeder-free culturing of HPSCs, had many fold higher levels of ROS and higher mitochondrial potential than cells cultured in Knockout Serum Replacement containing media (KSR). HPSCs also exhibited increased levels of 8-hydroxyguanosine, phospho-histone-H2a.X and p53, as well as increased sensitivity to γ-irradiation in these two media. HPSCs in E8 and mTeSR had increased incidence of changes in their DNA sequence, indicating genotoxic stress, in addition to changes in nucleolar morphology and number. Addition of antioxidants to E8 and mTeSR provided only partial rescue. Our results suggest that it is essential to determine cellular ROS levels in addition to currently used criteria i.e. pluripotency markers, differentiation into all three germ layers and normal karyotype through multiple passages, in designing culture media

Mathematical deconvolution of CAR T-cell proliferation and exhaustion from real-time killing assay data.

Chimeric antigen receptor (CAR) T-cell therapy has shown promise in the treatment of haematological cancers and is currently being investigated for solid tumours, including high-grade glioma brain tumours. There is a desperate need to quantitatively study the factors that contribute to the efficacy of CAR T-cell therapy in solid tumours. In this work, we use a mathematical model of predator-prey dynamics to explore the kinetics of CAR T-cell killing in glioma: the Chimeric Antigen Receptor T-cell treatment Response in GliOma (CARRGO) model. The model includes rates of cancer cell proliferation, CAR T-cell killing, proliferation, exhaustion, and persistence. We use patient-derived and engineered cancer cell lines with an in vitro real-time cell analyser to parametrize the CARRGO model. We observe that CAR T-cell dose correlates inversely with the killing rate and correlates directly with the net rate of proliferation and exhaustion. This suggests that at a lower dose of CAR T-cells, individual T-cells kill more cancer cells but become more exhausted when compared with higher doses. Furthermore, the exhaustion rate was observed to increase significantly with tumour growth rate and was dependent on level of antigen expression. The CARRGO model highlights nonlinear dynamics involved in CAR T-cell therapy and provides novel insights into the kinetics of CAR T-cell killing. The model suggests that CAR T-cell treatment may be tailored to individual tumour characteristics including tumour growth rate and antigen level to maximize therapeutic benefit

Inflammation and dietary protein intake exert competing effects on serum albumin and creatinine in hemodialysis patients

Inflammation and dietary protein intake exert competing effects on serum albumin and creatinine in hemodialysis patients.BackgroundCross-sectional studies have shown an inverse correlation between serum C-reactive protein (CRP) and serum albumin concentration in hemodialysis patients. The net effects of inflammation and dietary protein intake on nutritional markers over time are unknown.MethodsTo explore the effects of CRP and normalized protein catabolic rate (nPCR) on serum albumin and creatinine, we analyzed six consecutive months of laboratory data from 364 hemodialysis patients, using a multivariable Mixed model with conservative biases.ResultsThe overall trend over time in serum albumin was slightly positive (0.039 g/dL/month) and in serum creatinine slightly negative (-0.052 mg/dL/month). With increasing CRP, serum albumin declined significantly (-0.124 g/dL/month per unit increase in log CRP, adjusted for age, gender, race, diabetes, and nPCR, P < 0.0001). Serum albumin increased with increasing nPCR (0.021 g/dL/month per 0.1 g/kg/day, P < 0.0001). The effect of CRP on albumin was attenuated in African Americans and at a higher nPCR. Corresponding values for creatinine mirrored those for albumin. With increasing CRP, creatinine declined significantly [-0.142 mg/dL/month per unit increase in log CRP, adjusted for age, gender, race, diabetes (time since initiation of dialysis; vintage), Kt/V, and nPCR, P = 0.002]. Serum creatinine increased with increasing nPCR (0.183 mg/dL/month per g/kg/day, P < 0.0001).ConclusionsProxies of inflammation and dietary protein intake exert competing effects on serum albumin and creatinine in hemodialysis patients. These data provide a rationale for prospective testing of dietary protein supplementation in hemodialysis patients with biochemical evidence of ongoing inflammation and “malnutrition.

Towards a quality metric for dense light fields.

Light fields become a popular representation of three-dimensional scenes, and there is interest in their processing, resampling, and compression. As those operations often result in loss of quality, there is a need to quantify it. In this work, we collect a new dataset of dense reference and distorted light fields as well as the corresponding quality scores which are scaled in perceptual units. The scores were acquired in a subjective experiment using an interactive light-field viewing setup. The dataset contains typical artifacts that occur in light-field processing chain due to light-field reconstruction, multi-view compression, and limitations of automultiscopic displays. We test a number of existing objective quality metrics to determine how well they can predict the quality of light fields. We find that the existing image quality metrics provide good measures of light-field quality, but require dense reference light-fields for optimal performance. For more complex tasks of comparing two distorted light fields, their performance drops significantly, which reveals the need for new, light-field-specific metrics

Towards reconstructing HDR light fields by combining 2D and 3D CNN architectures

High dynamic range imaging has recently become a technological trend, with numerous attempts to reconstruct HDR images and videos from low-dynamic-range data. The reconstruction of light field images is analogous to the reconstruction of HDR videos, within which consecutive frames are temporally coherent. For light field images, many similarities exist between the adjacent views, since they visualize the same scene from different angular perspectives. In this paper, we investigate the theoretical possibilities of combining CNN architectures utilized for HDR images and videos in order to enhance the outputs of HDR light field image reconstruction