Local examination of skin diffusion using FTIR spectroscopic imaging and multivariate target factor analysis

In the context of trans-dermal drug delivery it is very important to have mechanistic insight into the barrier function of the skin's stratum corneum and the diffusion mechanisms of topically applied drugs. Currently spectroscopic imaging techniques are evolving which enable a spatial examination of various types of samples in a dynamic way. ATR-FTIR imaging opens up the possibility to monitor spatial diffusion profiles across the stratum corneum of a skin sample. Multivariate data analyses methods based on factor analysis are able to provide insight into the large amount of spectroscopically complex and highly overlapping signals generated. Multivariate target factor analysis was used for spectral resolution and local diffusion profiles with time through stratum corneum. A model drug, 4-cyanophenol in polyethylene glycol 600 and water was studied. Results indicate that the average diffusion profiles between spatially different locations show similar profiles despite the heterogeneous nature of the biological sample and the challenging experimental set-up.

Effects of target expansion on selection performance in older computer users

Point and click interactions using a mouse are an integral part of computer use for current desktop systems. Compared with younger users though, older adults experience greater difficulties performing cursor positioning tasks, and this can present limitations to using a computer easily and effectively. Target expansion is a technique for improving pointing performance, where the target dynamically grows as the cursor approaches. This has the advantage that targets conserve screen real estate in their unexpanded state, yet can still provide the benefits of a larger area to click on. This paper presents two studies of target expansion with older and younger participants, involving multidirectional point-select tasks with a computer mouse. Study 1 compares static versus expanding targets, and Study 2 compares static targets with three alternative techniques for expansion. Results show that expansion can improve times by up to 14%, and reduce error rates by up to 50%. Additionally, expanding targets are beneficial even when the expansion happens late in the movement, i.e. after the cursor has reached the expanded target area or even after it has reached the original target area. Participants’ subjective feedback on the target expansion are generally favorable, and this lends further support for the technique.

Analysis of genetic instability during mammary tumor progression using a novel selection-based assay for in vivo mutations in a bacteriophage lambda transgene target.

Genetic instability is thought to be responsible for the numerous genotypic changes that occur during neoplastic transformation and metastatic progression. To explore the role of genetic instability at the level of point mutations during mammary tumor development and malignant progression, we combined transgenic mouse models of mutagenesis detection and oncogenesis. Bitransgenic mice were generated that carried both a bacteriophage lambda transgene to assay mutagenesis and a polyomavirus middle T oncogene, mammary gland-targeted expression of which led to metastatic mammary adenocarcinomas. We developed a novel assay for the detection of mutations in the lambda transgene that selects for phage containing forward mutations only in the lambda cII gene, using an hfl- bacterial host. In addition to the relative ease of direct selection, the sensitivity of this assay for both spontaneous and chemically induced mutations was comparable to the widely used mutational target gene, lambda lacI, making the cII assay an attractive alternative for mutant phage recovery for any lambda-based mouse mutagenesis assay system. The frequencies of lambda cII- mutants were not significantly different in normal mammary epithelium, primary mammary adenocarcinomas, and pulmonary metastases. The cII mutational spectra in these tissues consisted mostly of G/C-->A/T transitions, a large fraction of which occurred at CpG dinucleotides. These data suggest that, in this middle T oncogene model of mammary tumor progression, a significant increase in mutagenesis is not required for tumor development or for metastatic progression.

Analysis of RNA-binding proteins by in vitro genetic selection: identification of an amino acid residue important for locking U1A onto its RNA target.

An in vitro genetic system was developed as a rapid means for studying the specificity determinants of RNA-binding proteins. This system was used to investigate the origin of the RNA-binding specificity of the mammalian spliceosomal protein U1A. The U1A domain responsible for binding to U1 small nuclear RNA was locally mutagenized and displayed as a combinatorial library on filamentous bacteriophage. Affinity selection identified four U1A residues in the mutagenized region that are important for specific binding to U1 hairpin II. One of these residues (Leu-49) disproportionately affects the rates of binding and release and appears to play a critical role in locking the protein onto the RNA. Interestingly, a protein variant that binds more tightly than U1A emerged during the selection, showing that the affinity of U1A for U1 RNA has not been optimized during evolution.

Raman spectroscopic study of vivianites of different origins

Raman spectroscopy has been used to study a selection of vivianites from different origins. A band is identified at around 3480 cm-1 whose intensity is sample dependent. The band is attributed to the stretching vibration of Fe3+ OH units which are formed through the autooxidation of the vivianite minerals either by self-oxidation or by photocatalytic oxidation according to the reaction: (Fe2+)3(PO4)2·8H2O + 1/2O2 (Fe2+)3– x(Fe3+)x(PO4)2(OH)x·(8–x)H2O in which some of the water of crystallization is converted to hydroxyl anions. Complexity of the OH stretching region through the overlap of broad bands is reflected in the water HOH deformation modes at 1660 cm–1. Using the infrared bands at 3281, 3105 and 3025 cm–1, hydrogen bond distances of 2.734(5), 2.675(2) and 2.655(2) Å are calculated. Vivianites are characterised by an intense band at 950 cm–1 assigned to the PO4 symmetric stretching vibration. Low Raman intensity bands are observed at ~1077, ~1050, 1015 and ~ 985 cm–1 assigned to the phosphate PO4 antisymmetric stretching vibrations. Multiple antisymmetric stretching vibrations are due to the reduced tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Two bands are observed at ~ 423 and ~ 456 cm–1 assigned to the2bending modes. For the vivianites four bands are observed at ~ 584, ~ 571, ~ 545 and ~ 525 cm–1 assigned to the 4modes of vivianite.

A spectroscopic comparison of selected Chinese kaolinite, coal bearing kaolinite and halloysite : a mid-infrared and near-infrared study

Mid-infrared (MIR) and near-infrared (NIR) spectroscopy have been compared and evaluated for differentiating kaolinite, coal bearing kaolinite and halloysite. Kaolinite, coal bearing kaolinite and halloysite are the three relative abundant mineral of the kaolin group, especially in China. In the MIR spectra, the differences are shown in the 3000-3600 cm-1 between kaolinite and halloysite. It can not be obviously differentiated the kaolinite and halloysite, let alone kaolinite and coal bearing kaolinite. However, NIR, together with MIR, give us the sufficient evidence to differentiate the kaolinite and halloysite, especially kaolinite and coal bearing kaolinite. There are obvious differences between kaolinite and halloysite in the all range of their spectra, and it also show some difference between kaolinite and coal bearing kaolinite. Therefore, the reproducibility of measurement, signal to noise ratio and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for mineral analysis.

Infrared spectroscopic study of halloysite-potassium acetate intercalation complex

Mid-infrared (MIR) and near-infrared (NIR) spectroscopy have been used to study the molecular structure of halloysite and potassium acetate intercalated halloysite and to determine the structural changes of halloysite through intercalation. The MIR spectra show all fundamental vibrations including the hydroxyl units, basic aluminosilicate framework and water molecules in the structure of halloysite and its intercalation complex. Comparison between halloysite and halloysite-potassium acetate intercalation complex shows almost all bands observed for halloysite are also observed for halloysite-potassium acetate intercalation complex apart from bands observed in the 1700-1300 cm-1 region, but with differences in band intensity. However, NIR, based on MIR spectra, provide sufficient evidence to analyze the structural changes of halloysite through intercalation. There are obvious differences between halloysite and halloysite-potassium acetate intercalation complex in the all spectral ranges. Therefore, the reproducibility of measurement and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for molecular structural analysis.

HMM triangle relative entropy concepts in sequential change detection applied to vision-based dim target manoeuvre detection

The quick detection of abrupt (unknown) parameter changes in an observed hidden Markov model (HMM) is important in several applications. Motivated by the recent application of relative entropy concepts in the robust sequential change detection problem (and the related model selection problem), this paper proposes a sequential unknown change detection algorithm based on a relative entropy based HMM parameter estimator. Our proposed approach is able to overcome the lack of knowledge of post-change parameters, and is illustrated to have similar performance to the popular cumulative sum (CUSUM) algorithm (which requires knowledge of the post-change parameter values) when examined, on both simulated and real data, in a vision-based aircraft manoeuvre detection problem.

The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes

In Arabidopsis thaliana (Arabidopsis), DICER-LIKE1 (DCL1) functions together with the double-stranded RNA binding protein (dsRBP), DRB1, to process microRNAs (miRNAs) from their precursor transcripts prior to their transfer to the RNA-induced silencing complex (RISC). miRNA-loaded RISC directs RNA silencing of cognate mRNAs via ARGONAUTE1 (AGO1)-catalyzed cleavage. Short interefering RNAs (siRNAs) are processed from viral-derived or transgene-encoded molecules of doublestranded RNA (dsRNA) by the DCL/dsRBP partnership, DCL4/DRB4, and are also loaded to AGO1-catalyzed RISC for cleavage of complementary mRNAs. Here, we use an artificial miRNA (amiRNA) technology, transiently expressed in Nicotiana benthamiana, to produce a series of amiRNA duplexes with differing intermolecular thermostabilities at the 5′ end of duplex strands. Analyses of amiRNA duplex strand accumulation and target transcript expression revealed that strand selection (amiRNA and amiRNA*) is directed by asymmetric thermostability of the duplex termini. The duplex strand possessing a lower 59 thermostability was preferentially retained by RISC to guide mRNA cleavage of the corresponding target transgene. In addition, analysis of endogenous miRNA duplex strand accumulation in Arabidopsis drb1 and drb2345 mutant plants revealed that DRB1 dictates strand selection, presumably by directional loading of the miRNA duplex onto RISC for passenger strand degradation. Bioinformatic and Northern blot analyses of DCL4/DRB4-dependent small RNAs (miRNAs and siRNAs) revealed that small RNAs produced by this DCL/dsRBP combination do not conform to the same terminal thermostability rules as those governing DCL1/DRB1-processed miRNAs. This suggests that small RNA processing in the DCL1/DRB1-directed miRNA and DCL4/DRB4-directed sRNA biogenesis pathways operates via different mechanisms.

A new plasmid display technology for the in vitro selection of functional phenotype–genotype linked proteins

Background: Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype–genotype link between the displayed protein and the encoding gene. Results: A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50–DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein–plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype–genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions: A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins

Background Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype-genotype link between the displayed protein and the encoding gene. Results A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50-DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein-plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype-genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

Identification of optimal epitopes for Plasmodium falciparum rapid diagnostic tests that target histidine-rich proteins 2 and 3

Rapid diagnostic tests (RDTs) represent important tools to diagnose malaria infection. To improve understanding of the variable performance of RDTs that detect the major target in Plasmodium falciparum, namely, histidine-rich protein 2 (HRP2), and to inform the design of better tests, we undertook detailed mapping of the epitopes recognized by eight HRP-specific monoclonal antibodies (MAbs). To investigate the geographic skewing of this polymorphic protein, we analyzed the distribution of these epitopes in parasites from geographically diverse areas. To identify an ideal amino acid motif for a MAb to target in HRP2 and in the related protein HRP3, we used a purpose-designed script to perform bioinformatic analysis of 448 distinct gene sequences from pfhrp2 and from 99 sequences from the closely related gene pfhrp3. The frequency and distribution of these motifs were also compared to the MAb epitopes. Heat stability testing of MAbs immobilized on nitrocellulose membranes was also performed. Results of these experiments enabled the identification of MAbs with the most desirable characteristics for inclusion in RDTs, including copy number and coverage of target epitopes, geographic skewing, heat stability, and match with the most abundant amino acid motifs identified. This study therefore informs the selection of MAbs to include in malaria RDTs as well as in the generation of improved MAbs that should improve the performance of HRP-detecting malaria RDTs.