Biodiversity and community structure of Late Pleistocene foraminifera from Kish Island, Persian Gulf (Iran)

The raised coral reef sequences at Kish Island provide a rare window into the depositional setting and paleoenvironment of a high-latitude, shallow-water coral reef that developed under turbid conditions in the Persian Gulf during Marine Isotope Stage 7 (~200 to 250?ka). Six sedimentary facies and eight foraminiferal assemblages can be identified throughout the sequence. A ninth assemblage can be defined for the modern subtidal realm. At the base of the sequence is a marl rich in hyaline foraminifera (Elphidium, Ammonia, Asterorotalia, Bulimina, Nonion, and Quinqueloculina) and ostracods, which was deposited in about 30–40?m water depth in a turbid deltaic setting. Shallowing resulted in the marl becoming sandy, and changing to a mollusc-rich facies with rare foraminifera (mostly smaller miliolid taxa) that formed the substrate for coral recruitment. The coral marl layer contains many large corals embedded in situ in an aggregate and coralline algae-rich marl. Two abundance peaks in the foraminifera occur at the base and mid-way through this layer, which also correspond to a change from Murrayinella-dominated to Placopsilina-dominated assemblages, indicating deepening and more open-marine conditions, but elevated turbidity. Towards the top of the layer, abundance of foraminifera decreases and miliolid foraminifera become dominant. The top-most layer is dominated by coral and mollusc fragments and has an Amphistegina-rich reef-related assemblage. Of the Late Pleistocene foraminiferal assemblages, the Murrayinella-, Pararotalia-, and Placopsilina-dominated assemblages are no longer present in the modern gulf for unknown reasons. Of the other five assemblages, only the Amphistegina assemblage is found within proximity to the modern Kish Island. The Elphidium and Asterorotalia-Bulimina assemblages are from deeper areas of the gulf. The Ammonia and Quinqueloculina assemblages occur in lagoonal sediments on the Arabian side of the gulf. Like the modern Persian Gulf, the diversity of foraminifera was low (~80 common species) during the Pleistocene and does not correlate with foraminiferal abundance.     

Maintenance of membrane integrity and increase of taxanes production in hazel (Corylus avellana L.) cells induced by low-intensity ultrasound

Suspension-cultured hazel cells were ultrasonicated at power densities of 4 and 455 mW for 4–40 min. Both treatments stimulated the production of major taxanes: Taxol, 10-deacetylbaccatin, and baccatin III. The highest amounts of these taxanes (0.46, 0.26, and 0.07 mg/l, respectively) were obtained at 8 and 20 min of the treatment at 455 mW. Ultrasound had no adverse effects on cell viability, growth, or membrane integrity. Increased release of taxanes by ultrasound resulted not from increased membrane permeability but more likely from stimulation of taxanes biosynthesis.     

Synthesis and characterization of pyruvate-isoniazid analogs and their copper complexes as potential ICL inhibitors

Currently used anti-tubercular drugs target actively growing Mycobacterium tuberculosis (Mtb) but there are no current therapies targeting persistent mycobacteria. Isocitrate lyase (ICL) is an important enzyme of the glyoxylate shunt pathway used by Mtb for sustaining intracellular infection in inflammatory macrophages under conditions of stress such as nutrient depletion and anaerobic metabolism. Since the humans do not possess this enzyme it constitutes an attractive target for selective drug design. Present work describes synthesis and structural characterization of pyruvate-isoniazid conjugates and their copper complexes with potent anti-tubercular activities against M. tuberculosis H37Rv.     

Disruption of tubulin polymerization and cell proliferation by 1-naphthylarsonic acid

Arsenical compounds exhibit a differential toxicity to cancer cells. Microtubules are a primary target of a number of anticancer drugs, such as arsenical compounds. The interaction of 1-NAA (1-naphthylarsonic acid) has been investigated on microtubule polymerization under in vitro and cellular conditions. Microtubules were extracted from sheep brain. Transmission electron microscopy was used to show microtubule structure in the presence of 1-NAA. Computational docking method was applied for the discovery of ligand-binding sites on the microtubular proteins. Proliferation of HeLa cells and HF2 (human foreskin fibroblasts) was measured by the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide] assay method following their incubation with 1-NAA. Fluorescence microscopic labelling was done with the help of α-tubulin monoclonal antibody and Tunel kit was used to investigate the apoptotic effects of 1-NAA on the HeLa cells. 1-NAA inhibits the tubulin polymerization by the formation of abnormal polymers having high affinity to the inner cell wall.     

Immunization with M2e-Displaying T7 Bacteriophage Nanoparticles Protects against Influenza A Virus Challenge

Considering the emergence of highly pathogenic influenza viruses and threat of worldwide pandemics, there is an urgent need to develop broadly-protective influenza vaccines. In this study, we demonstrate the potential of T7 bacteriophage-based nanoparticles with genetically fused ectodomain of influenza A virus M2 protein (T7-M2e) as a candidate universal flu vaccine. Immunization of mice with non-adjuvanted T7-M2e elicited M2e-specific serum antibody responses that were similar in magnitude to those elicited by M2e peptide administered in Freund’s adjuvant. Comparable IgG responses directed against T7 phage capsomers were induced following vaccination with wild type T7 or T7-M2e. T7-M2e immunization induced balanced amounts of IgG₁ and IgG_2a antibodies and these antibodies specifically recognized native M2 on the surface of influenza A virus-infected mammalian cells. The frequency of IFN-γ-secreting T cells induced by T7-M2e nanoparticles was comparable to those elicited by M2e peptide emulsified in Freund’s adjuvant. Emulsification of T7-M2e nanoparticles in Freund’s adjuvant, however, induced a significantly stronger T cell response. Furthermore, T7-M2e-immunized mice were protected against lethal challenge with an H1N1 or an H3N2 virus, implying the induction of hetero-subtypic immunity in our mouse model. T7-M2e-immunized mice displayed considerable weight loss and had significantly reduced viral load in their lungs compared to controls. We conclude that display of M2e on the surface of T7 phage nanoparticles offers an efficient and economical opportunity to induce cross-protective M2e-based immunity against influenza A.     

Comparative modeling of DszC, an enzyme in biodesulfurization, and performing in silico point mutation for increasing tendency to oil

Desulfurization protein named DszC from Rhodococcus erythropolis is the key enzyme for biodesulforization of dibenzothiophene (DBT) in 4S pathway, which is a pathway with four enzymes. DszC enzyme biodesulfurizes DBT and its derivatives in oil components and biphasic systems. It functions well at the oil- water interface. In this study point mutation performed in DszC enzyme regarding to increase protein hydrophobicity and stability for application in immobilized form. 3D model of DszC predicted using Phyre2, SAM-T08 and M4t servers. I-Mutant 2 server used to determine potential spots for point mutation, and Molegro Virtual Docker (MVD) used for performing point mutation on 3D model. Hydrophobicity plots generated by Bioedit version 7.0.8.0 in Kyte-Doolittle scale indicated that protein hydrophobicity is increased after mutation. Also protein stability increased 26.11 units in scale of DDC2.     

Homology modeling and molecular dynamics simulation of odonthubuthus doriae (Od1) scorpion toxin in comparison to the BmK M1

All of the α-subgroups share similarity in their sequence and structure but different in the toxicity to various voltage-gated sodium channels (VGSCs). We modeled the first 3D structural model of the Od1 based on BmK M1 using homology modeling. The reliability of model for more investigation and compare to BmK M1 has been examined and confirmed. Then the model structure is further refined by energy minimization and molecular dynamics methods. The purpose of this modeling and simulation is comparison toxicity of two mentioned toxins by investigation structural feature of functional regions including core domain, 5-turn and C-terminal which make NC domain. In the one hand, it is intriguing that Od1 in comparison to BmK M1 shows same solvent accessible surface area (SASA) in 5-turn region but a little more exposed and feasibility (more SASA) in C-terminal region and key functional residues of C-terminal such as positive residues Arg58, lys62 and Arg (His)64. These data suggested that Od1 has similarity with BmK M1 but has more toxicity to sodium channel. In the other hand 5-turn proximity of C-terminal to 5-turn in BmK M1with cis peptide bond is less than Od1 without cis peptide bond which is a confirmation with experimental data about BmK M1.A better understanding of the 3-D structure of Od1and comparison to BmK M1 will be helpful for more investigation of functional characters action of natural toxins with a specialized role for VGSCs.     

First report of molecular diagnosis of Tunisian hemophiliacs A: identification of 8 novel causative mutations

ABSTRACT: INTRODUCTION: Hemophilia A is an X linked recessive hemorrhagic disorder caused by mutations in the F8 gene that lead to qualitative and/or quantitative deficiencies of coagulation factor VIII (FVIII). Molecular diagnosis of hemophilia A is challenging because of the high number of different causative mutations that are distributed throughout the large F8 gene. Molecular studies of these mutations are essential in order to reinforce our understanding of their pathogenic effect responsible for the disorder. Aim In this study we have performed molecular analysis of 28 Tunisian hemophilia A patients and analyzed the F8 mutation spectrum. METHODS: We screened the presence of intron 22 and intron 1 inversion in severe hemophilia A patients by southern blotting and polymerase chain reaction (PCR). Detection of point mutations was performed by dHPLC/sequencing of the coding F8 gene region. We predict the potential functional consequences of novel missense mutations with bioinformatics approaches and mapping of their spatial positions on the available FVIII 3D structure. RESULTS: We identified 23 different mutations in 28 Tunisian hemophilia A patients belonging to 22 unrelated families. The identified mutations included 5 intron 22 inversions, 7 insertions, 4 deletions and 7 substitutions. In total 18 point mutations were identified, of which 9 are located in exon 14, the most mutated exonic sequence in the F8 gene. Among the 23 mutations, 8 are novel and not deposited in the HAMSTeRS database nor described in recently published articles. CONCLUSION: The mutation spectrum of Tunisian hemophilia A patients is heterogeneous with the presence of some characteristic features. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1693269827490715.     

Dynamics of adaptation of stomatal behaviour to moderate or high relative air humidity in Tradescantia virginiana

Chlorophyll fluorescence imaging was used to measure stomatalclosure in response to desiccation of Tradescantia virginianaleaves grown under high (90%) and moderate (55%) relative humidities(RHs), or transferred between these humidities. Stomata in leavesgrown at high RH were less responsive to desiccation than thoseof leaves grown at moderate RH. Stomata of plants transferredfrom moderate RH conditions to high RH showed the same diminishedclosure in response to desiccation as did stomata that developedat high RH. This response was found both when the leaves werefully expanded and when still actively expanding during themoderate RH pre-treatment. Four days of exposure to high RHwas the minimal exposure time to induce the diminished closureresponse. When leaves were grown in high RH prior to a 10 dmoderate RH treatment, the reduced stomatal closure responseto desiccation was only reversed in leaves (regions) which wereactively expanding during moderate RH treatment. This indicatesthat with respect to stomatal responses to desiccation, highRH leaf regions have a limited capacity to adapt to moderateRH conditions. The decrease in responsiveness to desiccationof the stomata, induced by long-term exposure to high RH, wasnot due to osmotic adjustment in the leaves. Within 1 d aftertransferring moderate RH-grown plants to a high RH, the abscisicacid (ABA) concentration of their leaves decreased to the lowlevel of ABA found in high RH-grown leaves. The closure responsein leaves exposed to high RH for 5 d, however, could not befully restored by the application of ABA. Transferring plantsfrom high to moderate RH resulted in increased ABA levels within2 d without a recovery of the stomatal closing response. Itis discussed that the diminished stomatal closure in plantsexposed to high RH could be due to changes in the signallingpathway for ABA-related closure of stomata or to an increasedsequestration of ABA by mesophyll tissue or the symplast inthe epidermis, induced by a longer period (several days) ofa low ABA level. Key words: Abscisic acid, desiccation, PSII efficiency, relative water content, stomatal closure, vapour pressure deficit, water potential Received 8 October 2007; Revised 5 November 2007 Accepted 9 November 2007     

Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks

In this study, membrane proteins were classified using the information hidden in their sequences. It was achieved by applying the wavelet analysis to the sequences and consequently extracting several features, each of them revealing a proportion of the information content present in the sequence. The resultant features were made normalized and subsequently fed into a cascaded model developed in order to reduce the effect of the existing bias in the dataset, rising from the difference in size of the membrane protein classes. The results indicate an improvement in prediction accuracy of the model in comparison with similar works. The application of the presented model can be extended to other fields of structural biology due to its efficiency, simplicity and flexibility.