The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold

Background

An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold.

Methods and results

We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research.

Conclusions

Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.

     

Molecular genetic diversity of Satureja bachtiarica

Fifty-seven genotypes from eight population of Satureja bachtiarica was evaluated using fifteen ISSR and eleven RAPD markers. DNA profiling using RAPD primers amplified 84 loci, among which 81 were polymorphic with an average of 7.36 polymorphic fragments per locus. Also, using RAPD markers maximum and minimum polymorphic bands observed for Semyrom (77.38 %) and Farsan (40.48 %) populations, respectively. Semyrom population recorded the highest unbiased expected heterozygosity (0.259) and Shannon’s Indices (0.38). While, the lowest values of unbiased expected heterozygosity (0.172) and Shannon’s Index (0.245) were recorded for Eghlid and Farsan populations, respectively. On the other hand, ISSR primers produced 136 bands, from which 134 were polymorphic with an average of 9.06 polymorphic fragments per primer (98.52 %). The ISSR markers evaluation revealed that maximum and minimum polymorphic bands observed for Semyrom (66.18 %) and Farsan (31.62 %), respectively. Shahrekorud population recorded the highest unbiased expected heterozygosity (0.211) and Shannon’s Indices (0.301). While, the lowest value of unbiased expected heterozygosity (0.175) observed for Farsan and Yazd populations and the lowest Shannon’s Index (0.191) recorded by Farsan population. The overall results of the study revealed that both ISSR and RAPD markers were effective for evaluation of genetic variation of S. bachtiarica.     

Dynamics of bacterial populations during bench‐scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats

This study describes a bench‐scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture‐independent analysis of seawater from continuous cultures revealed high‐bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate.     

Incremental reductions of positive charge within the S4 region of a voltage-gated K+ channel result in corresponding decreases in gating charge.

The S4 region of voltage-dependent ion channels is involved in the voltage-sensing mechanism of channel activation. Previous studies in fast inactivating channels have used non-steady-state measurements and thus have not allowed the quantitative assessment of activation parameters. Using site-directed mutagenesis and voltage-clamp recordings in a noninactivating channel (RCK1), we demonstrate that stepwise reductions of positive charge within the S4 region correlate with a progressive decrease in the channel's overall gating valence. In addition to testing for electrostatic behavior of individual charged residues, our study was designed to probe nonelectrostatic influences on charge movement. We provide evidence that individual charged residues behave differentially in response to the electric field, so that purely electrostatic influences cannot fully account for the gating movement of certain charges.     

The effect of coagulation factors polymorphisms on abortion

Objective

Recent studies showed coagulation factors play important role in controlling pregnancy duration in addition to controlling homeostasis. Recent studies showed several polymorphisms of coagulation factors genes increase the clot formation and lead to abortion. In this study, we evaluated the polymorphisms of coagulation factors and their effects on the development of the fetus.

Material and Methods

Relevant literature was identified by a PubMed search (1988-2017) of English language papers using the terms Abortion, pregnancy woman, coagulation factor and polymorphism.

Result

Several polymorphisms of coagulation factors disturb the exchange of food and other materials between the fetus and the mother, and impairs the formation of the placenta during embryonic stages.

Discussion

Evaluation of functional polymorphisms in coagulation factors gene during fetal development can be used as a prognostic factor in the prevention of the abortion.

     

Active site inhibitors of HCV NS5B polymerase. The development and pharmacophore of 2-thienyl-5,6-dihydroxypyrimidine-4-carboxylic acid

5,6-Dihydroxypyrimidine-4-carboxylic acids are a promising series of hepatitis C virus (HCV) NS5B polymerase inhibitors that bind at the active site of the enzyme. Here we report a simple 2-thienyl substituted analogue that shows 10-fold improved activity over the original lead, and which allowed us to further delineate the key elements of the pharmacophore of this class of inhibitor. This work led to the identification of a trifluoromethyl acylsulfonamide group as a viable replacement for the C4 carboxylic acid in this series.     

Combining choice modeling estimates and stochastic simulations to assess the potential of new crops—The case of lignocellulosic perennials in Southwestern Germany

In the future, the lignocellulosic perennial crops short rotation coppice (SRC) and miscanthus are supposed to provide renewable raw materials for a bio‐based economy. To assess the potential regional supply of these crops, which are not yet widespread in Baden–Wuerttemberg (Southwest Germany), we used a two‐step approach. In a first step, we conducted a Discrete Choice Experiment (DCE) in regions of Baden–Wuerttemberg that—given their site conditions—are suitable for SRC or miscanthus. The respondents were characterized by significant preference heterogeneity for both (negatively valued) perennial crops and for all presented choice attributes. Thus, it was appropriate to estimate a random parameter logit model (RPL). The attributes average yearly contribution margin, long‐term purchase guarantee and cultivation by colleagues in the neighborhood had a significantly positive effect on the likelihood of cultivation, whereas the attributes contribution margin variability and initial investment need showed a significantly negative effect. In a second step, assuming realistic values for the levels of the attributes considered in the DCE, in stochastic simulations, we randomly draw part‐worth utilities from the multivariate normal distribution of these parameters according to the RPL results. This way, for alternative biomass prices, we derived shares of farmers’ willing to engage in perennial crop production and produced related regional supply functions. Under moderate yield and realistic input and farmland opportunity cost assumptions, the full regional miscanthus potential can only be achieved when farmers are offered either subsidies or price‐risk‐reducing long‐term contracts. Based on empirically determined heterogeneous farmer preferences, our two‐step approach is suitable to yield realistic estimations of any not yet implemented farming practices. We finally note caveats related to our analysis and discuss some policy implications of the major findings.     

Investigation by fluorescence spectroscopy, resonance rayleigh scattering and zeta potential approaches of the separate and simultaneous binding effect of Paclitaxel and estradiol with human serum albumin

Separate and simultaneous binding effects of paclitaxel (a drug with anti-tumor activity) and estradiol (used for treating multiple maladies) with human serum albumin (HSA) were investigated by fluorescence quenching, UV absorption, circular dichroism, zeta potential and molecular dynamic techniques. An extensive fluorescence quenching was observed during the reaction of drugs and HSA and was rationalized in terms of a static quenching mechanism. The molecular distances between the donor (HSA) and acceptors (paclitaxel or estradiol) in binary and ternary systems were estimated according to F?rster's theory of dipole-dipole non-radiation energy transfer. The features of drug-induced structural disturbances of HSA have been studied in detail by synchronous fluorescence and circular dichroism (CD) analysis. The resonance Rayleigh scattering (RRS) intensities were proportional to the paclitaxel and estradiol concentrations in the range of respectively (0-8)×10(-6) and (0-1)×10(-4) mM in binary systems. The critical induced aggregation concentrations (C(CIAC)) of paclitaxel and estradiol for binary and ternary systems were determined by nonlinear relationships between the enhancement of the RRS intensities and the drug concentrations. A comparison between binary and ternary systems for two drugs allowed us to estimate the effect of a drug on the initial formation aggregation of the second drug. The zeta potential results were used to verify the existence of complexation and confirmed the C(CIAC) values obtained by the RRS technique. This phenomenon was supported by a progressive rise of the protein charge to a reversal point as a consequence of drug binding. The quantitative analysis data of circular dichroism (CD) spectra demonstrated that the binding of paclitaxel and/or estradiol to HSA induced conformational changes in HSA. Moreover, the α-helix content in HSA greatly decreased in the presence of paclitaxel as opposed when estradiol was present. Protein-ligand docking suggested that estradiol bound to residues situated in subdomain IIA of HSA. On the other hand, in the ternary system, the presence of the first drug decreased the binding affinity of the second drug to HSA. Therefore binding effects of paclitaxel and estradiol with HSA alone have different behavior than simultaneous interaction.     

Comparative study of ammonium transporters in different organisms by study of a large number of structural protein features via data mining algorithms

Ammonium is an excellent nitrogen source, and ammonium transfer is a fundamental process in most organisms. Membrane transport of ammonium is the key component of nitrogen metabolism mediated by Ammonium Transporter/Methylamine Permease/Rhesus (AMT/MEP/Rh) protein family. Ammonium transporters play different physiological roles in various organisms. Here, we looked at the protein characteristics of ammonium transporters in different organisms to create a link between protein characteristics and the organism. In order to increase the accuracy and precision of the employed models, for the first time, an attempt was made to cover all structural aspects of ammonium transporters in animals, bacteria, fungi, plants, and human by extracting and calculating 874 protein attributes of primary, secondary, and tertiary structures for each ammonium transporter. Then, various weighting and modeling algorithms were applied to determine how structural protein features change between organisms. Considering a large number of protein attributes made it possible to detect key protein characteristics in the structure of ammonium transporters. The results, for the first time, indicated that His-based features including count/frequency of His and frequency/count of Ile-His were the most significant features generating different types of ammonium transporters within organisms. Within different tested models, the C5.0 model was the most efficient and precise model for discrimination of organism type, based on ammonium transporter sequence, with the precision of 94.85%. The determination of protein characteristics of ammonium transporters in different organisms provides a new vista for understanding the evolution of transporters based on the modulation of protein characteristics and facilitates engineering of new transporters. In our point of view, dissecting a large number of structural protein characteristics through data mining algorithms provides a novel functional strategy for studying evolution and phylogeny. This research will serve as a basis for future studies on engineering novel ammonium transporters.