Genome-wide inference of regulatory networks in Streptomyces coelicolor

Background: The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to discover and engineer the pharmacologically important natural products made by these species. The availability of genomic tools and access to a large warehouse of transcriptome data for the model organism, Streptomyces coelicolor, provides incentive to decipher the intricacies of the regulatory cascades and develop biologically meaningful hypotheses. Results: In this study, more than 500 samples of genome-wide temporal transcriptome data, comprising wild-type and more than 25 regulatory gene mutants of Streptomyces coelicolor probed across multiple stress and medium conditions, were investigated. Information based on transcript and functional similarity was used to update a previously-predicted whole-genome operon map and further applied to predict transcriptional networks constituting modules enriched in diverse functions such as secondary metabolism, and sigma factor. The predicted network displays a scale-free architecture with a small-world property observed in many biological networks. The networks were further investigated to identify functionally-relevant modules that exhibit functional coherence and a consensus motif in the promoter elements indicative of DNA-binding elements. Conclusions: Despite the enormous experimental as well as computational challenges, a systems approach for integrating diverse genome-scale datasets to elucidate complex regulatory networks is beginning to emerge. We present an integrated analysis of transcriptome data and genomic features to refine a whole-genome operon map and to construct regulatory networks at the cistron level in Streptomyces coelicolor. The functionally-relevant modules identified in this study pose as potential targets for further studies and verification.

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145

Dietary nutrient manipulation to improve the performance and tibia characteristics of broilers fed oak acorn (Quercus Brantii Lindl)

An experiment was conducted to evaluate the effects of dietary nutrients (protein, methionine, and choline) manipulation on the performance and tibia characteristics of broilers fed diets containing 15% oak acorn. A completely randomized design with five treatments and four replicates of 15 chicks each, was used. One group was fed a diet based on corn (without oak acorn) as control and other four groups were fed diets containing oak acorn with one of the following nutrient manipulation: without nutrient manipulation, high level of methionine (100% more than NRC), high level of CP (10% more than NRC), and addition of 0.2% choline. Starter and finisher diets were fed from one to 21 and 22 to 42 d of age, respectively. The results indicated that group fed diet without nutrient manipulation presented higher feed intake and worse feed conversion ratio (p<0.05) compared with the control group throughout the experiment. Elevated levels of methionine, protein, and choline had significant beneficial effects on feed conversion ratio during starter phase. Feeding oak acorn negatively influenced tibia bone characteristics (bone ash and strength) both at 21 and 42 d of age, whereas the supplementation with protein, methionine and choline prevented those negative effects. In conclusion, dietary inclusion of 15% oak acorn had negative effects on broiler performance and tibia characteristics. Detrimental effects of oak acorn, particularly on tibia bone, were reduced or prevented by increasing the dietary levels of choline, methionine, and protein

Rapid Isolation and Molecular Detection of Streptomycin-Producing Streptomycetes

Introduction: Streptomyces species are mycelial, aerobic gram-positive bacteria that are isolated from soil and produce a diverse range of antibiotics. Streptomyces griseus produces the antibiotic, streptomycin and forms spores even in a liquid culture. The gene cluster for the production of Streptomycin antibiotic contains strR gene that encodes StrR, a pathway-specific regulator. Then, this pathway-specific regulator induces transcription of other streptomycin production genes in the gene cluster. The overall aim of this work was rapid isolation and molecular detection of streptomycin-producing Streptomycetes, especially S. griseus, from Iranian soils in order to manipulate them for increased production of streptomycin. Methods: This research used new initiative half-specific medium for isolation of Streptomycetes from natural environments, called FZmsn. The fifty colonies of Streptomyces strains grown on the surface of FZmsn medium isolated from environmental samples were defined on the basis of their morphological characteristics and light microscope studies. A set of primers was designed to detect strR by OLIGO software. Results: In colony-PCR reactions followed by gel electrophoresis, 6 colonies from Streptomyces strains colonies were detected as S. griseus colonies. Conclusion: These native Streptomyces strains will be used for genetic manipulation of S. griseus in order to increase production levels of streptomycin

Application of Allele Specific Oligonucleotide (ASO) PCR in Determination of Rh Antigens in Thalassemic Patients

Background and Aim: Thalassemia is a genetic disease whit relative or complete lack of alpha or beta globin chain. Patients with moderate and severe form need to have multitransfusion in early life. Occurrence of all immunization against blood group antigens in patients with thalassemia is relatively high and may have difficulties in treatment and transfusion. Antibody production against this blood groups cause lots of problems like preparation of compatible blood for transfusion. Correct diagnosis of blood group phenotype due to existence of dual population of donor and patient RBC would be difficult.Materials and Methods: In this study, randomly from 40 thalassemic patients, before blood transfusion, 4cc of peripheral blood collected in tubes containing EDTA. Also, 10 healthy individuals who had no history of blood transfusion were in the study as control for serological (agglutination) and molecular results . Phenotyping of patients and control group was done by tube agglutination method by commercial antibody. For molecular test, Allele Specific Primer Amplification (ASPA) PCR was performed for each antigens in separate micro tubes. Results: In this study' we could set up a method that can amlify any of Rh C c E and E gene separately by a pair of specific primer in a same thermal conditions.Comparison of results of two methods showed that in the control group with no transfusion history. Similar results in phenotyping and genotyping was observed. But in patients, results of two methods had lots of differences.Discussion and Conclusion: The advantage of this method over PCR-RFLP method is that' all four genes can be amplified the in a same concentration and temperature conditions, and ability to determine the individual's antigen, immediately by electrophoresis. Therefore, Since the above method is simple and inexpensive for medical and research centers it is recommended

Synthesis and structural characterization of new lead(II) discrete and infinite cage-like framework: a precursor to produce pure phase nano-sized lead(II) oxide

A novel Pb(II) complex, {[Pb2(tpmba)2(NO3)4]·MeOH} n (1), was obtained by the reaction of a tripodal ligand, N,N′,N″-tris(pyrid-3-ylmethyl)-1,3,5-benzenetricarboxamide (tpmba), with Pb(NO3)2. The structure of complex was determined by X-ray crystallography. The results of structural analysis of the complex reveal that 1 is a M2L2 cage-like with a methanol molecule beside the cage. An entirely different structure and topology between 1 and similar complexes indicate that the nature of organic ligands affects the structure of assemblies. The results indicate that the framework of this complex is predominated by the nature of the organic ligand, anions, solvent and geometric need of the metal ions. It was found that the coordination number of PbII ions is eight, (PbN3O5) has a stereo-chemically active electron lone pair and the coordination sphere is hemi-directed. PbO nanoparticles are obtained by thermolysis of 1 at 180 °C with oleic acid as a surfactant. Scanning electron microscopy shows that the size of the PbO particles is ~30 nm.Gholam Hossein Shahverdizadeh, Fateme Hakimi, Babak Mirtamizdoust, Aliakbar Soudi, Pejman Hojati-Talem

Chemical-physical properties of spinel CoMn(2)O(4) nano-powders and catalytic activity in the 2-propanol and toluene combustion: effect of the preparation method

Spinel-type CoMn(2)O(4)nano-powders are prepared using sol-gel auto combustion (SGC) and co-precipitation (CP) methods and their catalytic activities are evaluated in combustion of 2-propanol and toluene. The chemical-physical properties of the oxides are characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), N(2)-adsorption-desorption, temperature programmed reduction (TPR) and scanning electron microscopy (SEM). After calcination at 700°C, CoMn(2)O(4)-SGC shows higher amounts of the normal-type spinel phase and is more crystalline than CoMn(2)O(4)-CP. Higher calcination temperatures (850°C) do not affect very much the weight percentage of the normal-type spinel phase; although the crystal size slightly increased. The TPR analysis evidences a large number of Mn(3+) cations in CoMn(2)O(4)-SGC compared to CoMn(2)O(4)-CP. This difference, together with the higher surface area, could justify the higher activity of CoMn(2)O(4)-SGC in both the investigated reactions.Seyed Ali Hosseini, Dariush Salari, Aligholi Niaei, Francesca Deganello, Giuseppe Pantaleo, Pejman Hojat

On the benefit of melatonin in protection against ouabain-induced arrhythmia through modulation of oxidative stress factors in isolated rat atria

Considering the cardioprotective and antioxidant properties of melatonin, in the present experiment, we investigated the possible involvement of oxidative stress factors in antiarrhythmic effects of melatonin in ouabain-induced arrhythmia in isolated rat atria. Male rats were divided into two groups, receiving either of melatonin (2 mg/kg) or vehicle, orally once daily for three weeks. Rats were anesthetized, and atria were isolated and incubated with ouabain in an organ bath. Time of onset of arrhythmia and asystole as well as atrial beating rate and contractile force were recorded. We also measured the activity of superoxide dismutase (SOD) and levels of thiobarbituric acid reactive substances (TBARS) in atria after injection of ouabain to animals. Pretreatment of animals with melatonin could significantly postpone the onset of arrhythmia and asystole compared with vehicle-treated group (P � 0.001). Incubation of ouabain boosted the atrial beating rate in vehicle-treated group (P � 0.01), while this response in melatonin-treated group was not significant (P > 0.05). Injection of ouabain decreased the activity of SOD and increased the levels of TBARS in atria (P � 0.001, P � 0.01, respectively), while pretreatment of animals with melatonin reversed these effects (P � 0.05). It is concluded that melatonin possesses antiarrhythmic properties, and oxidative stress factors might mediate this response. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group