Numerical characterization of protein sequences based on the generalized Chou\u27s pseudo amino acid composition

The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical-chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a (21+λ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins

The Spatial and Temporal Characteristics of the Urban Thermal Environment in East Africa: Implications for Sustainable Urban Development

Targeting cities in East Africa, where urbanisation and climate change are posing unprecedented threats to livelihoods and ecosystems, this thesis focuses on the combined effects of rapid urbanisation and climate change on Land Surface Temperature (LST), Surface Urban Heat Island (SUHI) effects and the role of Blue Green infrastructure (BGI) and vegetation dynamics. The aim of this thesis is to advance understanding of the urban thermal environment and the role of factors such as climate, vegetation and urbanisation patterns that add to its complexity. Through the use of satellite and remote sensing data (e.g., Google Earth Engine), spatial and statistical analyses, conducted in ArcGIS, Geoda and R, this thesis provides analyses of temporal trends between 2003 and 2017, and spatial differences in LST and SUHI in five East African cities (Khartoum, Addis Ababa, Kampala, Nairobi, Dar es Salaam). It advances understanding of how the configuration of urban areas affects the urban thermal environment, the amount of vegetation and surface water, and demonstrates the influence of urban density on the changes in SUHI intensity in both space and time. By linking the findings from the three results chapters and placing this in the context of the broader literature, corresponding policy implications and solutions are presented. The urgent need to provide a more detailed understanding of urban thermal environments, including macroclimate differences, seasonal variation and urban morphological characteristics, is highlighted. Recommendations emphasise the use of cloud-based analysis methods to overcome data scarcity, while the results point towards the utility of nature-based solutions for urban sustainable development. The methods and lessons emerging from this study can also be applied in other rapidly urbanising cities, where climate change is posing an unprecedented threat to livelihoods and ecosystems, and where resources are limited

2-Iodo-3-meth­oxy-6-methyl­pyridine

The title compound, C7H8INO, which crystallizes with three independent mol­ecules in the asymmetric unit, was prepared by the reaction of 3-meth­oxy-6-methyl­pyridine with KI and I2 in tetra­hydro­furan solution. In the crystal structure, the three independent mol­ecules are arranged in a similar orientation with the three polar meth­oxy groups aligned on one side and the three non-polar methyl groups on the other side. The three mol­ecules, excluding methyl H atoms, are essentially planar, with r.m.s. deviations of 0.0141 (1), 0.0081 (1) and 0.0066 (2)Å. The three pyridine rings make dihedral angles of 58.09 (3) 66.64 (4) and 71.5 (3)°. The crystal structure features rather weak inter­molecular C—H⋯O hydrogen bonds, which link two mol­ecules into dimers, and short I⋯N contacts [4.046 (3) Å]

Involvement of TIP60 acetyltransferase in intracellular Salmonella replication

<p>Abstract</p> <p>Background</p> <p><it>Salmonella </it>enterica is a facultative intracellular pathogen that replicates within a membrane-bound compartment termed <it>Salmonella </it>containing vacuole (SCV). The biogenesis of SCV requires <it>Salmonella </it>type III protein secretion/translocation system and their effector proteins which are translocated into host cells to exploit the vesicle trafficking pathways. SseF is one of these effectors required for SCV formation and Intracellular <it>Salmonella </it>replication through unknown mechanisms.</p> <p>Results</p> <p>In an attempt to identify host proteins that interact with SseF, we conduct a yeast two-hybrid screening of human cell cDNA library using SseF as the bait. We identified that TIP60, an acetyltransferase, interacts with SseF. We showed that the TIP60 acetylation activity was increased in the presence of SseF, and TIP60 was upregulated upon <it>Salmonella </it>infection. In addition, TIP60 is required for efficient intracellular <it>Salmonella </it>replication in macrophages.</p> <p>Conclusion</p> <p>Taken together, our data suggest that <it>Salmonella </it>may use SseF to exploit the host TIP60 acetyltransferase activity to promote efficient <it>Salmonella </it>replication inside host cells.</p

Characterization and antitumor activity of camptothecin from endophytic fungus Fusarium solani isolated from Camptotheca acuminate

Background: Camptothecin (CPT) is a potent drug against cancers, originally from plants. The endophytic fungi could produce the secondary metabolite same as the host and is used as medicine.Objectives: The aim of this paper was to investigate an endophytic fungal CPT with anti-neoplastic activity.Methods: Endophytic fungi were isolated from Camptotheca acuminata in China. CPT from strain S-019 was characterized by TLC, HPLC and EI-MS analysis. Anti-tumor activity of fungal CPT was detected by MTT and fluorescent dye methods using Vero and PC-3 cells.Results: A total of 94 endophytic fungi strains were isolated from tissues of C. acuminata and 16 fungi strains displayed cytotoxic activity on Vero or PC3 cells. Of which, the fungal strain S-019, classified as Fusarium solani, displayed impressive cytotoxic activity on cancer cells and was found to produce CPT by analysis of TLC, HPLC and EI-MS methods. Bioassay studies confirmed that the fungi CPT had potent cytotoxicity on Vero cells and induced apoptosis of Vero cells.Conclusion: The endophytic fungi from camptotheca trees are a reliable source for natural anticancer compounds. The endophytic fungi could produce CPT same as plant. The fungal CPT exhibited effective activity at inhibiting cell growth and inducing apoptosis on Vero cells.Keywords: Endophytic fungi, camptothecin, anti-tumor, Camptotheca acuminat

The nuclear factor-κB inhibitor pyrrolidine dithiocarbamate reduces polyinosinic-polycytidilic acid-induced immune response in pregnant rats and the behavioral defects of their adult offspring

<p>Abstract</p> <p>Background</p> <p>Epidemiological studies have indicated that maternal infection during pregnancy may lead to a higher incidence of schizophrenia in the offspring. It is assumed that the maternal infection increases the immune response, leading to neurodevelopmental disorders in the offspring. Maternal polyinosinic-polycytidilic acid (PolyI:C) treatment induces a wide range of characteristics in the offspring mimicking some schizophrenia symptoms in humans. These observations are consistent with the neurodevelopmental hypothesis of schizophrenia.</p> <p>Methods</p> <p>We examined whether suppression of the maternal immune response could prevent neurodevelopmental disorders in adult offspring. PolyI:C or saline was administered to early pregnant rats to mimic maternal infection, and the maternal immune response represented by tumor necrosis factor alpha (TNF-α) and interleukin-10 (IL-10) levels was determined by enzyme-linked immunosorbent assays (ELISA). The NF-κB inhibitor pyrrolidine dithiocarbamate (PDTC) was used to suppress the maternal immune response. Neurodevelopmental disorders in adult offspring were examined by prepulse inhibition (PPI), passive avoidance, and active avoidance tests.</p> <p>Results</p> <p>PolyI:C administration to early pregnant rats led to elevated serum cytokine levels as shown by massive increases in serum TNF-α and IL-10 levels. The adult offspring showed defects in prepulse inhibition, and passive avoidance and active avoidance tests. PDTC intervention in early pregnant rats suppressed cytokine increases and reduced the severity of neurodevelopmental defects in adult offspring.</p> <p>Conclusions</p> <p>Our findings suggest that PDTC can suppress the maternal immune response induced by PolyI:C and partially prevent neurodevelopmental disorders of adult offspring.</p

APOA-I: a possible novel biomarker for metabolic side effects in first episode schizophrenia

The purpose of this study was to investigate the change in plasma protein expression in first episode schizophrenia after an 8-week treatment with risperidone, and to explore potential biomarkers for metabolic side effects associated with risperidone treatment. Eighty first-episode schizophrenia patientswere enrolled in the study. Fifteen of the 80 patients were randomly selected to undergo proteomic analysis. Plasma proteins were obtained before and after the 8-week risperidone treatment, and measured using two-dimensional gel electrophoresis (2-DE), Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry(MALDI-TOF/TOF) and peptide mass fingerprinting.Proteins with the highest fold changes after risperidone treatment were then measured for all 80 patients using enzyme linked immunosorbent assay (ELISA). The relationship between changes in plasma protein levels and changes in metabolic parameters after risperidone treatment was examined. In 15 randomly selected patients, approximately 1,500 protein spots were detected in each gel by 2-DE. Of those proteins, 22 spots showed significant difference in abundance after risperidone treatment (p\u27s \u3c 0.05). After MALDI-TOF peptide mass fingerprinting, apolipoprotein A-I (APOA-I) and Guanine Nucleotide Binding Protein, Alpha Stimulating (GNAS), were found to have the highest fold changes.The content of APOA-I was significantly increased, and the content of GNAS was significantly decreased after risperidone treatment (p\u27s\u3c0.05). The analysis in the entire study sample showed similar findings in changes of APOA-I and GNAS after risperidone treatment. Further analysis showed significant relationships between changesin APOA-1 and changes in triglyceride, total cholesterol, and body mass index after controlling for age, gender and family history of diabetes. Similar analysis showed a trend positive relationship between changes in GNAS and changes in BMI. Using proteomic analysis, the study suggested that APOA-I might be a novel biomarkers related to metabolic side effects in first episode schizophrenia treated with risperidone