Computational identification of 48 potato microRNAs and their targets

MicroRNAs (miRNAs) are a new family of small RNA molecules known in animals and plants, whose conservation among species suggests that they bear conserved biological functions. So far, little is known about miRNA in Solanum tuberosum species. Using previously known miRNAs from Arabidopsis, rice and other plant species against expressed sequence tags (ESTs), genomic survey sequence (GSS) and nucleotide databases, we identified 48 potential miRNAs in S. tuberosum. These potato miRNAs may regulate 186 potential targets, which are involved in floral, leaf, root, and stem development, signal transduction, metabolism pathways, and stress responses. To validate the prediction of miRNAs in potato, we performed a RT-PCR analysis and found that potato miRNAs have diverse expression patterns during development.     

Highly sensitive analysis strategies of microRNAs based on electrochemiluminescence

The ultrasensitive detection of microRNAs (miRNAs) is currently pursued for the diagnosis of diseases. Due to its outstanding sensitivity, electrochemiluminescence (ECL) is expected to be very effective toward the above goal. In this short review, bioanalytical strategies currently employed in ECL detections of miRNAs are summarized. ECL sensors based on electrochemiluminescent resonance energy transfer (ERET), hybridization chain reaction (HCR), strand displacement reaction (SDR), and other strategies, have an extremely low detection limit of 10^?18 M miRNA. In particular, the establishment of miniaturized ECL sensors has shown great potential for point-of-need testing of diseases.     

Simultaneous photoelectrochemical detection of dual microRNAs by capturing CdS quantum dots and methylene blue based on target-initiated strand displaced amplification

Herein,we propose a novel photoelectrochemical(PEC) biosensor for dual microRNAs(miRNAs) highly sensitive and simultaneous biosensing based on strand displaced amplification(SDA) reaction.The recognition of H_(miR-21) and H_(let-7 a) by microRNA-21 and let-7 a leads to their change in hairpin structures,subsequently initiating the immobilization of abundant CdS quantum dots(CdS QD s) and methylene blue(MB) based on SDA reaction.The immobilized CdS QDs and MB produce both high PEC currents under430 nm light and 627 nm light illumination,respectively,and the generated PEC currents are closely relied on target miRNAs amounts.Thus,highly sensitive and simultaneous detection of microRNA-21 and let-7 a was readily achieved with detection limit at 6.6 fmol/L and 15.4 fmol/L based on 3σ,respectively.Further,this PEC biosensor was applied in simultaneous analysis of miRNA-21 and let-7 a in breast cancer patient's serum with acceptable results.We expect this biosensor will find more useful application in diagnosis of miRNA-related diseases.     

The importance of reference materials in doping-control analysis

Polyamidoamine (PAMAM) dendrimers and water-soluble 3-mercaptopropionic acid (MPA)-capped CdSe quantum dots (QDs) were combined to produce a new gel containing supramolecular complexes of QDs/PAMAM dendrimers. The formation of the QDs/PAMAM supramolecular complexes was confirmed by high resolution electron microscopy and Fourier transform infrared (FTIR) analyses. Molecular dynamics simulations corroborated the structure of the new QDs/PAMAM-based supramolecular compound. Finally, on the basis of the prominent fluorescent properties of the supramolecular complexes, PAMAM dendrimer was functionalized with folic acid to produce a new QDs/PAMAM-folate derivative that showed an efficient and selective performance as a marker for gastric cancer cells.     

The importance of GC and GC-MS in perfume analysis

Gas chromatography (GC) and mass spectrometry (MS) are by far the most important analytical techniques in the perfume industry. Both perfume houses (the suppliers) and the home and personal-care companies (the clients) rely primarily on GC and GC-MS for unraveling the composition of perfumes (i.e. perfume formulation), quality control, competitor analysis and trace analysis on substrates and in the headspace. State-of-the-art perfume formulation is based on perfume-specific Kovats Index (KI) and MS databases. By applying FID (flame-ionization detector) response-correction factors, the accuracy of the perfume-formulation process can be further improved. Because of the complexity of perfumes, use is made of GC columns and conditions that offer maximum resolution rather than minimum analysis time. Mass-spectral deconvolution tools can be very useful in identifying perfume ingredients from GC-MS data in cases of co-elution or strong matrix interference. By applying the MS detector in the selected ion monitoring (SIM) mode, GC-MS is very suitable for trace analysis of perfume ingredients, thus enabling the study of perfume efficacy during use of home and personal-care products. Recent developments in the field of comprehensive GC (i.e. GC×GC) also seem very promising for perfume analysis.     

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program, we identified 50 potential microRNAs (miRNAs) in Giardia lamblia, one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs, currently known in other species, were not found in G. lamblia. This suggests that miRNA biogenesis and miRNA-mediated gene regulation pathway may evolve independently, especially in evolutionarily distant lineages. A majority (43) of the predicted miRNAs are located at one single locus; however, some miRNAs have two or more copies in the genome. Among the 58 miRNA genes, 28 are located in the intergenic regions whereas 30 are present in the anti-sense strands of the protein-coding sequences. Five predicted miRNAs are expressed in G. lamblia trophozoite cells evidenced by expressed sequence tags or RT-PCR. Thirty-seven identified miRNAs may target 50 protein-coding genes, including seven variant-specific surface proteins (VSPs). Our findings provide a clue that miRNA-mediated gene regulation may exist in the early stage of eukaryotic evolution, suggesting that it is an important regulation system ubiquitous in eukaryotes.     

Electrochemical analysis of microRNAs with hybridization chain reaction-based triple signal amplification

Selective and sensitive detection of trace microRNA is important for early diagnosis of diseases due to its expression level related to diseases. Herein, a triple signal amplification strategy is developed for trace microRNA-21 (miRNA-21) detection by combining with target-triggered cyclic strand displacement reaction (TCSDR), hybridization chain reaction (HCR) and enzyme catalytic amplification. Four DNA hairpins (H1, H2, H3, H4) are employed to form an ultralong double-strand DNA (dsDNA) structure, which is initiated by target miRNA-21. As H3 and H4 are labeled with horseradish peroxidase (HRP), numerous HRPs are loaded on the long dsDNA, producing significantly enhanced electrocatalytic signals in the hydrogen peroxide (H₂O₂) and 3,3′,5,5′-tetramethylbenzidine (TMB) reaction strategy. Compared with single signal amplification, the triple signal amplification strategy shows higher electrochemical response, wider dynamic range and lower detection limit for miRNA-21 detection with excellent selectivity, reproducibility and stability. Taking advantage of the triple signal amplification strategy, the proposed electrochemical biosensor can detect miRNA-21 in 10 HeLa cell lysates, suggesting that it is a promising method for fruitful assay in clinical diagnosis.     

The importance of aspect ratio in profile analysis tensiometry

The latest developments in profile analysis tensiometry (PAT) for determining surface tension and interfacial viscoelastic parameters involve the determination of a digital interface profile and its best fit with the Young–Laplace equation. In this short communication, we show that the results for surface tension and other interfacial parameters determined by PAT are extremely sensitive to the (aspect) ratio of length to width of a pixel. Fine calibration (to five decimal digits) for the aspect ratio required to obtain physically consistent results is not always achieved with conventional numerical procedures due to nanometer resolution limit of optical imaging devices but can be manually adjusted using the known surface tension of pure water and/or surfactant solutions at reference temperature.     

Technical challenges in applying capillary electrophoresis-single strand conformation polymorphism for routine genetic analysis

Recent and future advances in population genetics will have a significant impact on health care practices and the economics of health care provision only if a spectrum of patient-tailored, effective methods of DNA screening for sequence alterations has been developed. Genetic screening by capillary electrophoresis-single strand conformation polymorphism (CE-SSCP), which is based upon the differences in electrophoretic mobilities of wild-type and mutant DNA species, offers an important complement to other presently available techniques such as Sanger sequencing and DNA hybridization arrays due to its simplicity, versatility, and low cost of analysis. A two-part review of CE-SSCP that discusses its advantages and limitations is presented. Emphasis is placed on technological aspects of CE-SSCP (including such rarely addressed issues as sample preparation protocols and the nature of the polymeric DNA separation matrix) as well as on the potential of CE-SSCP for routine genetic analysis. An attempt is made to organize and present the information in sufficient detail to allow the use of SSCP for routine genetic screening even by those inexperienced in CE. Some discussion of CE-based heteroduplex analysis (HA) is also presented.     

Application of polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) to identification of flatfish species.

A method of DNA analysis based on polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) was developed to verify the authenticity of labeled raw and frozen fillets of some flatfish species. PCR was used to amplify a short fragment (201 bp) of the mitochondrial cytochrome b gene, which was denatured and analyzed by polyacrylamide gel electrophoresis for detection of SSCPs. Species-specific patterns of DNA bands were obtained for sole (Solea solea), European plaice (Pleuronectes platessa), flounder (Platichthys flesus), and Greenland halibut (Reinhardtius hippoglossoides).     

The importance of the geometrical factor in nuclear activation analysis

When a beam of radiation is used as a probe in order to study the elemental composition of an object, the factors involved in obtaining maximum detection sensitivity include target homogeneity, beam uniformity and the solid angle subtended between target and detector. Here we have investigated, both theoretically and experimentally, the significance of these factors in an experimental facility for in-vitro prompt gamma-ray neutron activation analysis and an arrangement used in in-vivo activation analysis. The correction factor to the solid angle, to account for non-uniformity, and the optimisation of reaction rate and solid angle are considered.     

The importance of short structural motifs in protein structure analysis

Summary Proteins tend to use recurrent structural motifs on all levels of organization. In this paper we first survey the topics of recurrent motifs on the local secondary structure level and on the global fold level. Then, we focus on the intermediate level which we call the short structural motifs. We were able to identify a set of structural building blocks that are very common in protein structure. We suggest that these building blocks can be used as an important link between the primary sequence and the tertiary structure. In this framework, we present our latest results on the structural variability of the extended strand motifs. We show that extended strands can be divided into three distinct structural classes, each with its own sequence specificity. Other approaches to the study of short structural motifs are reviewed.     

Vector analysis of multi-measurements identification

Summary Vector analysis is suggested for any identification problem which involves the comparison of “unknown” with standards and which requires several experiments in order to enable the identification. It is shown that the method of least geometric distance and the method of scalar product (spectral contact angle) are the same if the distance is measured for points on a hypersphere with unit radius. Any one of these methods can be used. It is important to normalize each vector to unit length.     

In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species

MicroRNAs are a recently identified class of small regulatory RNAs that target more than 30% protein-coding genes. Elevating evidence shows that miRNAs play a critical role in many biological processes, including developmental timing, tissue differentiation, and response to chemical exposure. In this study, we applied a computational approach to analyze expressed sequence tags, and identified 32 miRNAs belonging to 22 miRNA families, in three earthworm species Eisenia fetida, Eisenia andrei, and Lumbricus rubellus. These newly identified earthworm miRNAs possess a difference of 2-4 nucleotides from their homologous counterparts in Caenorhabditis elegans. They also share similar features with other known animal miRNAs, for instance, the nucleotide U being dominant in both mature and pre-miRNA sequences, particularly in the first position of mature miRNA sequences at the 5' end. The newly identified earthworm miRNAs putatively regulate mRNA genes that are involved in many important biological processes and pathways related to development, growth, locomotion, and reproduction as well as response to stresses, particularly oxidative stress. Future efforts will focus on experimental validation of their presence and target mRNA genes to further elucidate their biological functions in earthworms.     

In silico analysis of proteins and microRNAs related to human African trypanosomiasis in tsetse fly

Human African trypanosomiasis (HAT), also known as sleeping sickness, causes millions of deaths worldwide. HAT is primarily transmitted by the vector tsetse fly (Glossina morsitans). Early diagnosis remains a key objective for treating this disease. MicroRNAs (miRNAs) are evolutionarily conserved small non-coding RNAs that play key roles in vector-borne diseases. To date, the roles of proteins and miRNAs in HAT disease have not been thoroughly elucidated. In this study, we have re-annotated the function of protein-coding genes and identified several miRNAs based on a series of bioinformatics tools. A batch of 81.1 % of tsetse fly proteins could be determined homology in mosquito genome, suggesting their probable similar mechanisms in vector-borne diseases. A set of 11 novel salivary proteins and 14 midgut proteins were observed in the tsetse fly, which could be applied to the development of vaccine candidates for the control of HAT disease. In addition, 35 novel miRNAs were identified, among which 10 miRNAs were found to be unique in tsetse fly. Pathway analysis of these 10 miRNAs indicated that targets of miR-15a-5p were significantly enriched in the HAT-related neurotrophin signaling pathway. Besides, topological analysis of the miRNA-gene network indicated that miR-619-5p and miR-2490-3p targeted several genes that respond to trypanosome infection, including thioester-containing protein Tep1 and heat shock protein Hsp60a. In conclusion, our work helps to elucidate the function of miRNAs in tsetse fly and establishes a foundation for further investigations into the molecular regulatory mechanisms of HAT disease.