Isolation of human NURF: a regulator of Engrailed gene expression

The modification of chromatin structure is an important regulatory mechanism for developmental gene expression. Differential expression of the mammalian ISWI genes, SNF2H and SNF2L, has suggested that they possess distinct developmental roles. Here we describe the purification and characterization of the first human SNF2L-containing complex. The subunit composition suggests that it represents the human ortholog of the Drosophila nucleosome-remodeling factor (NURF) complex. Human NURF (hNURF) is enriched in brain, and we demonstrate that it regulates human Engrailed, a homeodomain protein that regulates neuronal development in the mid-hindbrain. Furthermore, we show that hNURF potentiates neurite outgrowth in cell culture. Taken together, our data suggess a role for an ISWI complex in neuronal growth.     

Photoreactive bicyclic amino acids as substrates for mutant Escherichia coli phenylalanyl-tRNA synthetases

Unnatural amino acids carrying reactive groups that can be selectively activated under non-invasive biologically benign conditions are of interest in protein engineering as biological tools for the analysis of protein-protein and protein-nucleic acids interactions. The double ring system phenylalanine analogues benzofuranylalanine and benzotriazolylalanine were synthesized, and their photolability was tested by UV irradiation at 254, 320, and 365 nm. Although both showed photo reactivity, benzofuranylalanine appeared as the most promising compound because this amino acid was activated by UVA (long wavelength) irradiation. These amino acids were also tested for in vitro charging of tRNA(Phe) and for protein mutagenesis via the phenylalanyl-tRNA synthetase variant alphaA294G that is able to facilitate in vivo protein synthesis using a range of para-substituted phenylalanine analogues. The results demonstrate that benzofuranylalanine, but not benzotriazolylalanine, is a substrate for phenylalanine tRNA synthetase alphaA294G, and matrix-assisted laser desorption ionization time-of-flight analysis showed it to be incorporated into a model protein with high efficiency. The in vivo incorporation into a target protein of a bicyclic phenylalanine analogue, as described here, demonstrates the applicability of phenylalanine tRNA synthetase variants in expanding the scope of protein engineering.     

Multipotent drugs with cholinergic and neuroprotective properties for the treatment of Alzheimer and neuronal vascular diseases. I. Synthesis,biological assessment,and molecular modeling of simple and readily available 2-aminopyridine-, and 2-chloropyridine-3,5-dicarbonitriles

The synthesis, molecular modeling, and pharmacological analysis of new multipotent simple, and readily available 2-aminopyridine-3,5-dicarbonitriles (3–20), and 2-chloropyridine-3,5-dicarbonitriles (21–28), prepared from 2-amino-6-chloropyridine-3,5-dicarbonitrile (1) and 2-amino-6-chloro-4-phenylpyridine-3,5-dicarbonitrile (2) is described. The biological evaluation showed that some of these molecules were modest inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), in the micromolar range. The 2-amino (3, 4), and 2-chloro derivatives 21–23, 25, 26 were AChE selective inhibitors, whereas 2-amino derivatives 5, 14 proved to be selective for BuChE. Only inhibitor 24 was equipotent for both cholinesterases. Kinetic studies on compound 23 showed that this compound is a mixed-type inhibitor of AChE showing a K_i of 6.33 μM. No clear SAR can be obtained form these data, but apparently, compounds bearing small groups such as the N,N′-dimethylamino or the pyrrolidino, regardless of the presence of a 2-amino, or 6-chloro substituent in the pyridine ring, preferentially inhibit AChE. Molecular modeling on inhibitors 4, 5, 22, and 23 has been carried out to give a better insight into the binding mode on the catalytic active site (CAS), and peripheral anionic site (PAS) of AChE. The most important differences in the observed binding relay on the modifications of the group at C2, as the amino group forms two hydrogen bonds that direct the binding mode, while in the case of compounds with a chlorine atom, this is not possible. The neuroprotective profile of these molecules has been investigated. In the LDH test, only compounds 26, 3, 22, and 24 showed neuroprotection with values in the range 37.8–31.6% in SH-SY5Y neuroblastoma cells stressed with a mixture of oligomycin-A/rotenone, but in the MTT test only compound 17 (32.9%) showed a similar profile. Consequently, these compounds can be considered as attractive multipotent therapeutic molecules on two key pharmacological receptors playing key roles in the progress of Alzheimer, that is, cholinergic dysfunction and oxidative stress, and neuronal vascular diseases.     

Analysis of Nedd8-associated polypeptides: a model for deciphering the pathway for ubiquitin-like modifications

Ubiquitin-like proteins modify target proteins, altering their activities or causing them to be slated for degradation. These modifications are used to efficiently regulate key events in the cell. To explore the set of proteins modified by a small ubiquitin-like protein, we have developed a proteomic approach. Affinity purification of an epitope-tagged Nedd8 allowed the identification of the majority of proteins known to be involved with the neddylation pathway. This purification not only isolated the known targets of neddylation but also the constellation of enzymes and complexes known to regulate neddylation and deneddylation, including the COP9 signalosome, Nub1, and enzymes in the neddylation cascade. This purification scheme can be applied to other small ubiquitin-like proteins, especially those with limited protein targets such as the SUMOs (1, 2, and 3), Isg15, or FAT10.     

Heavy metal contamination and health risk assessment in drinking water of Sistan and Baluchistan,Southeastern Iran

Access to safe and clean drinking water is an essential element of healthy life also known as the primary human needs. The present study was conducted to investigate heavy metal (HM) concentrations of drinking water. Excess health risk of HM (Cr, Pb, and Cd) intake is related to the drinking water consumption in local population. HMs concentrations were analyzed by using graphite furnace atomic absorption spectrometer and were compared with permissible limits regulated by country and World Health Organization (WHO). The hazard quotient (HQ) and Excess Lifetime Cancer Risk (ELCR) were determined to show the carcinogenic and non-carcinogenic effects of HMs, respectively. HQs were found in the order of Pb > Cd > Cr and subsequently HI index was also estimated for all HM in two age groups (children and adults). The comparisons indicate no possibility of non-carcinogenic effects to the local population. The values for ELCR were found in the order of Cr > Cd > Pb. The ELCR index was found above acceptable risk levels for chromium and cadmium in both children and adults groups. Furthermore, intermetal correlation results revealed that heavy metals have common sources resulting from geogenic and anthropogenic activities and these are major sources of water contamination in Sistan and Baluchestan province.     

Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies

Poly(ADP-ribose) polymerase-1 (PARP-1) enzyme has critical roles in DNA replication repair and recombination. Thus, PARP-1 inhibitors play an important role in the cancer therapy. In the current study, we have performed combination of in silico and in vitro studies in order to discover novel inhibitors against PARP-1 target. Structure-based virtual screening was carried out for an available small molecules database. A total of 257,951 ligands from Otava database were screened at the binding pocket of PARP-1 using high-throughput virtual screening techniques. Filtered structures based on predicted binding energy results were then used in more sophisticated molecular docking simulations (i.e. Glide/standard precision, Glide/XP, induced fit docking – IFD, and quantum mechanics polarized ligand docking – QPLD). Potential high binding affinity compounds that are predicted by molecular simulations were then tested by in vitro methods. Computationally proposed compounds as PARP-1 inhibitors (Otava Compound Codes: 7111620047 and 7119980926) were confirmed by in vitro studies. In vitro results showed that compounds 7111620047 and 7119980926 have IC₅₀ values of 0.56 and 63 μM against PARP-1 target, respectively. The molecular mechanism analysis, free energy perturbation calculations using long multiple molecular dynamics simulations for the discovered compounds which showed high binding affinity against PARP-1 enzyme, as well as structure-based pharmacophore development (E-pharmacophore) studies were also studied.     

DPD simulation of non-Newtonian electroosmotic fluid flow in nanochannel

We use the dissipative particle dynamics (DPD) method to simulate the non-Newtonian electroosmotic flow (EOF) through nanochannels. Contrary to a large amount of past computational efforts dedicated to the study of EOF profile, this work pays attention to the EOF of non-Newtonian fluids, which has been rarely touched in past publications. Practically, there are many MEMS/NEMS devices, in which the EOF behaviour should be treated assuming both non-continuum and non-Newtonian conditions. Therefore, our concern in this work is to simulate the EOF through nanochannels considering both non-Newtonian fluid properties and non-continuum flow conditions. We have chosen DPD as our working tool because it provides several important advantages comparing with the classical time consuming molecular dynamics method. Using the DPD method, we explore the effect of a few important fluid properties and nanochannel parameters on the EOF behaviour and the resulting flow rate magnitudes. Our investigation will result in a number of findings, which have not been reported in past research works.     

Association of the costimulatory molecule gene polymorphisms and active cytomegalovirus infection in hematopoietic stem cell transplant patients

Determinative associations may exist between costimulatory molecule gene polymorphisms with a variety of post hematopoietic stem cell transplantation (HSCT) viral related clinical outcomes especially acute graft versus host disease (aGVHD). Therefore in this study the associations between costimulatory molecule gene polymorphisms including: cytotoxic T-lymphocyte antigen-4 (CTLA4), programmed cell death-1 (PD-1), inducible T cell costimulator (ICOS), and cluster differentiation 28 (CD28) with active cytomegalovirus (CMV) infection were evaluated in HSCT patients. The 72 allogeneic HSCT patients with and without aGVHD were enrolled in this cross sectional study between years: 2004–2011. The single nucleotide polymorphisms in loci of the costimulatory molecules including: CTLA4 gene (?318 C/T, 1722 T/C, 1661 A/G, +49 A/G), PD-1 gene (PD-1.3 A/G, PD-1.9 C/T), ICOS gene (1720 C/T), and CD28 gene (+17 C/T) were analyzed in studied HSCT patients by PCR-RFLP methods. The active CMV infection was evaluated in fresh EDTA-treated blood samples of each allogeneic HSCT patients by CMV antigenemia kit according to manufacturer’s instruction. Active CMV infection was found in 11 of 72 (15.27 %) of allogeneic HSCT patients. The T allele and TT genotype of the CD28 +17 C/T were significantly higher frequency in active CMV infected allogeneic HSCT patients experienced aGVHD. The G allele and GG genotype of the CTLA4 ?1661 A/G were significantly higher frequent in active CMV infected allogeneic HSCT patients experienced low grade of aGVHD. Finally, finding of significant associations between CD28 +17 C/T and CTLA4 ?1661 A/G genotypes with CMV active infection in allogeneic HSCT patients experienced aGVHD emphasize on the importance of the genetic pattern of costimulatory genes in outcomes of active CMV infection in HSCT patients needs completed studies.     

Rearing larval stages of Hippodamia variegata Goeze (Col.: Coccinellidae) on artificial diet

The ladybird Hippodamia variegata Goeze is a widespread species found in many parts of the world. It is an efficient predator which feeds on a wide range of pests, specially aphids and other sap feeders. Mass rearing of this predator, in order to use in biological control programmes, entails a great deal of difficulties, among which are the aspects associated with nutrition. Applying artificial diets is of a great importance in mass rearing of biological control agents. We investigated the use of 15 artificial diets that included three separated experiments, in order to rear larval stages of this ladybird. The survival rate and developmental time were assessed on each treatment. The survival rate of the larvae on best diet was 53.30, 93.33, and 93.33% in different experiments. The developmental time in the experiment 1, 2 and 3 for the larva fed on the Aphis fabae was 15.59, 15.51 and 15.94, respectively, but when nourished by the best artificial diets, this factor was 26.59, 26.60 and 20.59, respectively. Developmental time for the larvae fed on A. fabae was significantly shorter than developmental time of larvae on artificial diets. Our results showed that artificial diets have the capacity to support the larval development to adulthood.