Protein complex prediction based on <Emphasis Type="Italic">k</Emphasis>-connected subgraphs in protein interaction network

Background  

Protein complexes play an important role in cellular mechanisms. Recently, several methods have been presented to predict protein complexes in a protein interaction network. In these methods, a protein complex is predicted as a dense subgraph of protein interactions. However, interactions data are incomplete and a protein complex does not have to be a complete or dense subgraph.     

Cytotoxic activity of some marine brown algae against cancer cell lines

The aim of this study was to investigate the in vitro cytotoxic activity of total extract of MeOH (70%) and partition fractions of hexan, chloroform (CHCL3), ethylacetate (EtOAc) and MeOH-H2O of brown algae species (Sargassum swartzii, Cystoseira myrica, Colpomenia sinuosa) found in the Persian Gulf against in different cell lines including HT-29, Caco-2, T47D, MDA-MB468 and NIH 3T3 cell lines by MTT and AnnexinV-PI assay. The hexan fraction of S. swartzii and C. myrica showed selective cytotoxicity against proliferation of Caco-2 cells (IC50 < 100 μg/ml) T47D cell line (IC50<100 μg/ml), respectively. S. swartzii and C. myrica were also observed for increasing apoptosis in Caco-2 and T47D cells. Total extract and fractions of C. sinuosa did not show any significant cytotoxicity against the studied cell lines. MDA-MB468 cells were more sensitive to C. myrica than was T47D (IC50 99.9 ± 8.11 vs. 56.50' ± 0.88). This reflects an estrogen receptor independent mechanism for cytotoxicity of the extract. The IC50 of the hexan fraction of C. myrica on T47D parent cells was lower than it was on T47D-TR cells (IC50 99.9 ± 8.11 vs. 143.15 ± 7.80). This finding suggests a role for the MDR-1 in the development of possible future tolerance to the extract.     

Paleoenvironmental model and sequence stratigraphy of the Asmari Formation in southwest Iran

The Asmari Formation is a thick carbonate succession of the Oligo-Miocene in southwest Iran (Zagros Basin). The Zagros Basin was a continental margin attached to the eastern edge of Africa throughout the Phanerozoic. The foraminiferal limestone from the Asmari Formation has been studied to determine its microfacies, paleoenvironments and sedimentary sequences. Based on analysis of larger benthic foraminiferal assemblages and microfacies features three major depositional environments are identified. These include open marine, barrier and lagoon-lower intertidal. These three are represented by eleven microfacies. A carbonate ramp platform is suggested for the depositional environment of the Asmari Formation. The inner ramp facies are characterized by wackestone-packstone, dominated by various taxa of imperforate foraminifera. The middle ramp facies represented by packstone-grainstone to floatstone with a diverse assemblage of larger hyaline foraminifera. The outer ramp is dominated by argillaceous wackestone, characterized by planktonic foraminifera and larger hyaline foraminifera. Two third-order sequences are identified based on deepening and shallowing patterns in microfacies, staking patterns and the distribution of Oligocene-Miocene foraminifers.     

Distribution of Miogypsinoides in the Zagros Basin,in southwest Iran

In the present study three species of Miogypsinoides are described from the Oligocene–Miocene Asmari Formation of the Zagros Basin in the southwest of Iran. This is the explanation of the morphological recognition and distribution of Miogypsinoides complanatus, Miogypsinoides formosensis (Upper Oligocene, Chattian) and Miogypsinoides dehaartii (Lower Miocene, Aquitanian). Nepionic acceleration is the most important factor for recognition of Miogypsinoides species. Also it is applied in stratigraphic correlation. Examination of samples indicates a decreasing number of nepionic chambers (Mx) as time passes so M. dehaartii with Mx < 10 belong to the Aquitanian age. The study of microfacies shows that these species lived in an open marine environment with normal salinity and medium hydraulic energy in a middle ramp position.     

Efficacy of entomopathogenic nematodes against potato tuber moth,Phthorimaea operculella (Lepidoptera: Gelechiidae) under laboratory conditions

The susceptibility of potato tuber moth, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae) to native and commercial strains of entomopathogenic nematodes (EPNs) was studied under laboratory conditions. Native strains of EPNs were collected from northeastern Iran and characterised as Steinernema feltiae and Heterorhabditis bacteriophora (FUM 7) using classic methods as well as analysis of internal transcribed spacer (ITS) and D2/D3 sequences of 28S genes. Plate assays were performed to evaluate the efficiency of five EPN strains belonging to four species including Steinernema carpocapsae (commercial strain), S. feltiae, Steinernem glaseri and H. bacteriophora (FUM 7 and commercial strains). This initial assessment with 0, 75, 150, 250, 375 and 500 IJs/ml concentrations showed that S. carpocapsae and H. bacteriophora caused the highest mortality in both larval and prepupal stages of P. operculella, PTM. Thereafter, these three strains (i.e. S. carpocapsae, H. bacteriophora FUM 7 and the commercial strains) were selected for complementary assays to determine the effects of soil type (loamy, loamy–sandy and sandy) on the virulence of EPNs against the second (L2) and fourth instar (L4) larvae as well as prepupa. A soil column assay was conducted using 500 and 2000 IJs in 2-ml distilled water. Mortality in the L2 larvae was not affected by the EPN strain or soil type, while there was a significant interactive effect of nematode strains and soil type on larval mortality. The results also showed that EPN strains have higher efficiency in lighter soils and caused higher mortality on early larvae than that in loamy soil. In L4 larvae, mortality of PTM was significantly influenced by nematode strain and applied concentrations of infective juveniles. The larval mortality induced by S. carpocapsae was higher than those caused either by a commercial or the FUM 7 strain of H. bacteriophora. Prepupa were the most susceptible stage.     

An electroosmotically-driven micromixer modified for high miniaturized microchannels using surface micromachining

In order to offer the ability of smaller volumes and high throughput in Lab-On-a-Chip and micro Total Analysis Systems devices, more miniaturized components are needed. Due to a low Reynolds number on the microscale, the mixing process can be particularly troublesome. This problem is compounded by the fact that more miniaturization can be challenging in a microfluidic system. In such a case, electroosmotic (EO) force is an efficient force to perturb low Reynolds number fluid. In this paper, a novel Micro-Electro-Mechanical-Systems (MEMS) based fabrication for microfluidic devices, and a more miniaturized micromixer are presented. The proposed technology process requires the covering of excited electrode patterns by a thin Silicon-Nitride (Si₃N₄) insulator layer. Fabrication parameters such as Low Pressure Chemical Vapor Deposition (LPCVD) Si₃N₄ deposition effect, and height of the Phosphor Silicate Glass (PSG) sacrificial layer were investigated for the electroosmotically-driven mixer. Particle tracing for fluid flow was illustrated, the particles were stretched and folded for a long time, which was a proof of chaotic regime. Finite Element Analysis (FEA) revealed that the mixer with covered electrodes provides the high mixing efficiency of above 90% for a 96 μm long microchannel. Using a silicon nitride insulator layer reduces high electric field gradient at sharp corners and edges of the electrodes, leading to the elimination of unwanted electrolyte effects. Thus, the excitation and geometrical parameters were optimized for the micromixer.     

Electrochemical spectroscopic investigations on the interaction of an ytterbium complex with DNA and their analytical applications such as biosensor

Metal ion-DNA interactions are important in nature, often changing the genetic material's structure and function. A new Yb complex of YbCl₃ (tris(8-hydroxyquinoline-5-sulfonic acid) ytterbium) was synthesized and utilized as an electrochemical indicator for the detection of DNA oligonucleotide based on its interaction with Yb(QS)₃. Cyclic voltammetry (CV) and fluorescence spectroscopy were used to investigate the interaction of Yb(QS)₃ with ds-DNA. It was revealed that Yb(QS)₃ presented an excellent electrochemical activity on glassy carbon electrode (GCE) and could intercalate into the double helix of double-stranded DNA (ds-DNA). The binding mechanism of interaction was elucidated on glassy carbon electrode dipped in DNA solution and DNA modified carbon paste electrode by using differential pulse voltammetry and cyclic voltammetry. The binding ratio between this complex and ds-DNA was calculated to be 1:1. The extent of hybridization was evaluated on the basis of the difference between signals of Yb(QS)₃ with probe DNA before and after hybridization with complementary DNA. With this approach, this DNA could be quantified over the range from 1 × 10⁻⁸ to 1.1 × 10⁻⁷ M. The interaction mode between Yb(QS)₃ and DNA was found to be mainly intercalative interaction. These results were confirmed with fluorescence experiments.