Drying–Rewetting Cycles Affect Fungal and Bacterial Growth Differently in an Arable Soil

Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying–rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6–10 repetitions of a drying–rewetting cycle. Drying–rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying–rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying–rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.     

Plasmonic Circular Dichroism Study of DNA–Gold Nanoparticles Bioconjugates

Plasmonic circular dichroism (CD) responses of hybrid nanostructures containing noble metal nanoparticles and chiral molecules have received increasing interest with various applications in nanophotonics. Chiral biomolecules show strong CD signals typically found in the ultraviolet region, whereas, in the visible range, they produce a weak signal. Strengthening the CD signal in the visible region is of high importance, which could be achieved through fabrication of novel hybrid nanostructures. Herein, gold nanoparticles (GNPs) have been assembled via DNA linker to investigate the possibility of enhancing plasmonic CD signal in the visible range. DNA-linked assemblies with pre- and postannealed conditions were characterized by ultraviolet–visible spectroscopy, dynamic light scattering (DLS), and CD spectropolarimetry. In the presence of DNA linker with sticky ends, the aggregation phenomenon was traced by red shifts of surface plasmon resonance of nanoparticles. Time-dependent hybridization of single-stranded “sticky ends” with DNA-conjugated GNPs and increased probability of hydrogen bond formation lead to enhancement of CD signals in the ultraviolet region. Complexation of biomolecule and nanoparticle assemblies induced enhanced CD signals in the visible range, which was noticed both before and after purification. DLS characterization of the assemblies also confirmed the difference in the size of aggregates, which could be controlled by the linker molecules. This investigation encourages possibility of utilizing plasmonic CD technique as a tool for tracing fabricated nanostructure assemblies with enhanced characterization possibility.     

Haemodynamic analysis of femoral artery bifurcation models under different physiological flow waveforms

Thrombus in a femoral artery may form under stagnant flow conditions which vary depending on the local arterial waveform. Four different physiological flow waveforms – poor (blunt) monophasic, sharp monophasic, biphasic and triphasic – can exist in the femoral artery as a result of different levels of peripheral arterial disease progression. This study aims to examine the effect of different physiological waveforms on femoral artery haemodynamics. In this regard, a fluid–structure interaction analysis was carried out in idealised models of bifurcated common femoral artery. The results showed that recirculation zones occur in almost all flow waveforms; however, the sites at where these vortices are initiated, the size and structure of vortices are highly dependent on the type of flow waveform being used. It was shown that the reverse diastolic flow in biphasic and triphasic waveforms leads to the occurrence of a retrograde flow which aids in ‘washout’ of the disturbed flow regions. This may limit the likelihood of thrombus formation, indicating the antithrombotic role of retrograde flow in femoral arteries. Furthermore, our data revealed that the flow particles experience considerably higher residence time under blunt and sharp monophasic waveforms than under biphasic and triphasic waveforms. This confirms that the risk of atherothrombotic plaque initiation and development in femoral arteries is higher under blunt and sharp monophasic waveforms than under biphasic and triphasic flow waveforms.     

Bioinformatics prediction and experimental validation of a novel microRNA: hsa-miR-B43 within human CDH4 gene with a potential metastasis-related function in breast cancer

As a class of short noncoding RNAs, microRNAs (miRNAs) play a key role in the modulation of gene expression. Although, the regulatory roles of currently identified miRNAs in various cancer types including breast cancer have been well documented, there are many as yet undiscovered miRNAs. The aim of the current study was to bioinformatically reanalyze a list of 189 potentially new miRNAs introduced in a previously published paper (PMID: 21346806) and experimentally explore the existence and function of a candidate one: hsa-miR-B43 in breast cancer cells. The sequences of 189 potential miRNAs were re-checked in the miRbase database. Genomic location and conservation of them were assessed with the University of California Santa Cruz (UCSC) genome browser. SSC profiler, RNAfold, miRNAFold, MiPred, and FOMmiR bioinformatics tools were furthermore utilized to explore potential hairpin structures and differentiate real miRNA precursors from pseudo ones. hsa-miR-B43 was finally selected as one of the best candidates for laboratory verification. The expression and function of hsa-miR-B43 were examined by real-time polymerase chain reaction, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, and wound-healing assays. DIANA-microT, RNAhybrid and Enrichr tools were used to predict the miRNA target genes and for further enrichment analysis. We could detect the exogenous and endogenous expression of hsa-miR-B43, as a real novel miRNA, in cancer cell lines. Gene Ontology enrichment, pathway analysis and wound-healing assay results furthermore confirmed that a metastasis-related function may be assigned to hsa-miR-B43. Our results introduced hsa-miR-B43, as a novel functional miRNA, which might play a role in the metastatic process. Further studies will be necessary to completely survey the existence and function of hsa-miR-B43 in other cancer types.     

<Emphasis Type="Italic">Trans</Emphasis>-chalcone: a novel small molecule inhibitor of mammalian alpha-amylase

Trans-chalcone (1,3-diphenyl-2-propen-1-one), a biphenolic core structure of flavonoids precursor was tested for inhibitory activity toward alpha-amylase. Porcine pancreatic alpha-amylase was observed to be effectively inhibited by this compound, which showed competitive behavior with a K _i of 48 μM. Soluble starch (the natural substrate of the enzyme) was used in this study in order to obtain more realistic results. The possible binding mode of the compound was assessed in silico, and the two residues Trp59, and Tyr62 were proposed as main interacting residues with trans-chalcone. In conclusion, this compound could be used to design effective inhibitors of alpha-amylase.