Cloning and expression of codon-optimized recombinant darbepoetin alfa in Leishmania tarentolae T7-TR

Darbepoetin alfa is an engineered and hyperglycosylated analog of recombinant human erythropoietin (EPO) which is used as a drug in treating anemia in patients with chronic kidney failure and cancer. This study desribes the secretory expression of a codon-optimized recombinant form of darbepoetin alfa in Leishmania tarentolae T7-TR. Synthetic codon-optimized gene was amplified by PCR and cloned into the pLEXSY-I-blecherry3 vector. The resultant expression vector, pLEXSYDarbo, was purified, digested, and electroporated into the L. tarentolae. Expression of recombinant darbepoetin alfa was evaluated by ELISA, reverse-transcription PCR (RT-PCR), Western blotting, and biological activity. After codon optimization, codon adaptation index (CAI) of the gene raised from 0.50 to 0.99 and its GC content changed from 56 to 58. Expression analysis confirmed the presence of a protein band at 40 kDa. Furthermore, reticulocyte experiment results revealed that the activity of expressed darbepoetin alfa was similar to that of its equivalent expressed in Chinese hamster ovary (CHO) cells. These data suggested that the codon optimization and expression in L. tarentolae host provided an efficient approach for high level expression of darbepoetin alfa. © 2015 Elsevier Ltd. All rights reserved

Size Control in the Nanoprecipitation Process of Stable Iodine (127I) Using Microchannel Reactor—Optimization by Artificial Neural Networks

In this study, nanosuspension of stable iodine (127I) was prepared by nanoprecipitation process in microfluidic devices. Then, size of particles was optimized using artificial neural networks (ANNs) modeling. The size of prepared particles was evaluated by dynamic light scattering. The response surfaces obtained from ANNs model illustrated the determining effect of input variables (solvent and antisolvent flow rate, surfactant concentration, and solvent temperature) on the output variable (nanoparticle size). Comparing the 3D graphs revealed that solvent and antisolvent flow rate had reverse relation with size of nanoparticles. Also, those graphs indicated that the solvent temperature at low values had an indirect relation with size of stable iodine (127I) nanoparticles, while at the high values, a direct relation was observed. In addition, it was found that the effect of surfactant concentration on particle size in the nanosuspension of stable iodine (127I) was depended on the solvent temperature. © 2015, American Association of Pharmaceutical Scientists

Laser-induced radial birefringence and spin-to-orbital optical angular momentum conversion in silver-doped glasses

Samples of Ag$^+$/Na$^{+}$ ion-exchanged glass that have been subject to intense laser irradiation may develop novel optical properties, as a consequence of the formation of patterns of silver nanoparticles and other structures. Here, we report the observation of a laser-induced permanent transverse birefringence, with the optical axis forming a radial pattern, as revealed by the spin-to-orbital angular momentum conversion occurring in a probe light beam. The birefringence pattern can be modeled well as resulting from thermally-induced stresses arising in the silver-doped glass during laser exposure, although the actual mechanism leading to the permanent anisotropy is probably more complex.Comment: 3 pages, 3 figure

Comparison of antibacterial activities of Ircinia mutans extracts in two different seasons from Kish Island, Persian Gulf, Iran

Sponges, which constitute the phylum Porifera, are the most primitive of the multicellular animals, among all marine organisms screened. Marine sponges produce the largest number of structurally diversified natural products. In this study we investigated in vitro antimicrobial activity of Ircinia mutans collected from the Kish Island in the Persian Gulf against strains of bacteria Escherichia coli (ATCC 15224), Pseudomonas aeruginosa (ATCC 25619), Staphylococcus aureus (ATCC 1764), and Bacillus subtilis spizizenii (ATCC 6633). Diethyl etter, methanol and aqueous extracts of sponge were evaluated by using the Bacterial Broth Dilution Method. The results showed that the aqueous extracts didn’t have any antibacterial activity. Minimum Inhibitory Concentrations (MIC) of the winter diethyl etter extract was 2 mg/ml for E.coli and 20 mg/ml for P. aeruginosa, whereas the summer diethyl etter extract and both of methanol extracts did not show any activity. The MIC and MBC (Minimum Bacterial Concentration) of summer diethyl etter extracts were 2 mg/ml and 3mg/ml against S. aureus; and 5mg/ml and 10mg/ml when tested on B. subtilis. The MIC and MBC of winter diethyl etter extracts were measured as 1.5 mg/ml and 2mg/ml against S. aurous; and 5mg/ml and 10mg/ml when examined on B. subtilis. Summer and winter methanol and aqueous extracts of I. mutans did not show any activity against these bacteria. Therefore secondary metabolite solutions in diethyl etter contain components with antibacterial properties and can be used as antibiotics products

Tularemia and Plague Survey in Rodents in Earthquake Zones in Southeastern Iran

OBJECTIVES: Earthquakes are one the most common natural disasters that lead to increased mortality and morbidity from transmissible diseases, partially because the rodents displaced by an earthquake can lead to an increased rate of disease transmission. The aim of this study was to evaluate the prevalence of plague and tularemia in rodents in the earthquake zones in southeastern Iran. METHODS: In April 2013, a research team was dispatched to explore the possible presence of diseases in rodents displaced by a recent earthquake magnitude 7.7 around the cities of Khash and Saravan in Sistan and Baluchestan Province. Rodents were trapped near and in the earthquake zone, in a location where an outbreak of tularemia was reported in 2007. Rodent serums were tested for a serological survey using an enzyme-linked immunosorbent assay. RESULTS: In the 13 areas that were studied, nine rodents were caught over a total of 200 trap-days. Forty-eight fleas and 10 ticks were obtained from the rodents. The ticks were from the Hyalomma genus and the fleas were from the Xenopsylla genus. All the trapped rodents were Tatera indica. Serological results were negative for plague, but the serum agglutination test was positive for tularemia in one of the rodents. Tatera indica has never been previously documented to be involved in the transmission of tularemia. CONCLUSIONS: No evidence of the plague cycle was found in the rodents of the area, but evidence was found of tularemia infection in rodents, as demonstrated by a positive serological test for tularemia in one rodent

Population genetic structure of the white sardine, Sardinella albella, in the Persian Gulf and Sea of Oman by analysis of mitochondrial control region

Several studies on the white sardine: Sardinella albella, have focused on the identification of stock composition and behavior. In this study population genetic structure and historical demography of S. albella along the cost of the Persian Gulf and Sea of Oman were investigated with a 500-bp segment of mt-DNA control region. In total 40 samples were collected from 3 locations: Jask in Sea of Oman, Qeshm in Strait of Hormuz and Lengeh in the Persian Gulf during 2012-2013. 33 haplotype were obtained none of which were presented in all sampling sites. Analysis of molecular variance (AMOVA) indicated low genetic differentiation among regions (F_ST=0.024, p<0.05). The average pair wise differences between regional population were small but significant (0.0158-0.165). Molecular variance explained by differences among three regions was significantly different from zero but the F_ST did not show clear phylogeographic isolation. This observation can support the conclusion that S. albella has a widespread dispersal potential

Induced spermiation of rainbow trout, Oncorhynchus mykiss, using a GnRh analogue

In this study, the benefits of using the first Iranian made GnRHa[D-Ala6 des Gly10] mGnRH ethylamide, to induce spermiation in male rainbow trout, Oncorhynchus mykiss, were evaluated, In addition, its effect on acceleration and synchronization, quality and quantity of milt and the plasma Testosterone (T) fluctuations were examined. For these purposes, 40 non-spermiating male rainbow trouts were injected with a mammalian gonadotropin releasing hormone analog (GnRHa) preparations of 0 (control), 30, 40 and 80 μg/kg B.W. or vehicle (propylene glycol). Spermiation was very synchronous and accelerated in treated groups. Six days after first injection, the cumulative spermiation rates reached respectively 40, 49 and 79% in injected groups (i.e. 30 to 80 μg/kg B.W.) while none of the control fish was spermiated. GnRHa injections advanced spermiation and reduced the average time to spermiation from 16 3.67 days for control group to 14.3± 2.2, 9.2 ±0.75 and 6.6± 0.29 days for treated groups, respectively (p0.05). Circulating levels of testosterone (T) prior to the GnRHa treatment were relatively low in all groups. Treatment with GnRHa induced significant increase in plasma T after 12 h, increasing it to 43.43±5.82, 38.66±5.63, 39.72±5.07 ng/ml in groups 2 to 4, respectively, which were higher than T levels for control (i.e. 24.58±7.13 ng/ml) p<0.05. These levels remained high up until 48 h in treated groups; but after this time, T levels reduced to the basal levels of time 0, except in 4 which had received its second GnRHa injection at time 48

Entropic forces drive self-organization and membrane fusion by SNARE proteins

SNARE proteins are the core of the cell’s fusion machinery and mediate virtually all known intracellular membrane fusion reactions on which exocytosis and trafficking depend. Fusion is catalyzed when vesicle-associated v-SNAREs form trans-SNARE complexes (“SNAREpins”) with target membrane-associated t-SNAREs, a zippering-like process releasing ∼65 kT per SNAREpin. Fusion requires several SNAREpins, but how they cooperate is unknown and reports of the number required vary widely. To capture the collective behavior on the long timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE properties such as the zippering energy landscape and the surface charge distribution. In simulations the ∼65-kT zippering energy was almost entirely dissipated, with fully assembled SNARE motifs but uncomplexed linker domains. The SNAREpins self-organized into a circular cluster at the fusion site, driven by entropic forces that originate in steric–electrostatic interactions among SNAREpins and membranes. Cooperative entropic forces expanded the cluster and pulled the membranes together at the center point with high force. We find that there is no critical number of SNAREs required for fusion, but instead the fusion rate increases rapidly with the number of SNAREpins due to increasing entropic forces. We hypothesize that this principle finds physiological use to boost fusion rates to meet the demanding timescales of neurotransmission, exploiting the large number of v-SNAREs available in synaptic vesicles. Once in an unfettered cluster, we estimate ≥15 SNAREpins are required for fusion within the ∼1-ms timescale of neurotransmitter release

Transcriptome analysis reveals differential splicing events in IPF lung tissue

Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%), and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%). We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10) and POSTN (RNA-Seq adjusted pval = 2.06e-09), which encode the extracellular matrix proteins collagen alpha-3(VI) and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF. © 2014 Nance et al

Multitask Hopfield Networks

Multitask algorithms typically use task similarity information as a bias to speed up and improve the performance of learning processes. Tasks are learned jointly, sharing information across them, in order to construct models more accurate than those learned separately over single tasks. In this contribution, we present the first multitask model, to our knowledge, based on Hopfield Networks (HNs), named HoMTask. We show that by appropriately building a unique HN embedding all tasks, a more robust and effective classification model can be learned. HoMTask is a transductive semi-supervised parametric HN, that minimizes an energy function extended to all nodes and to all tasks under study. We provide theoretical evidence that the optimal parameters automatically estimated by HoMTask make coherent the model itself with the prior knowledge (connection weights and node labels). The convergence properties of HNs are preserved, and the fixed point reached by the network dynamics gives rise to the prediction of unlabeled nodes. The proposed model improves the classification abilities of singletask HNs on a preliminary benchmark comparison, and achieves competitive performance with state-of-the-art semi-supervised graph-based algorithms.Comment: 16 pages, 1 figure