Orphan gene finding—an exon assembly approach

This paper introduces an algorithm for finding eukaryotic genes. It particularly addresses the problem of orphan genes, that is of genes that cannot, based on homology alone, be connected to any known gene family and to which it is therefore not possible to apply traditional gene finding methods. To the best of our knowledge, this is also the first algorithm that attempts to compare in an exact way two DNA sequences that contain both coding (i.e. exonic) and non-coding (i.e. intronic and, possibly, intergenic) parts. The comparison is performed following an algorithmical model of a gene that is as close as possible to the biological one (we consider in this paper the “one ORF, one gene” problem only). A gene is seen as a set of exons that are pieces of an assembly and are not independent. The algorithm is efficient enough: although the constants are higher than for usual sequence comparison, its time complexity is proportional to the product of the sequences lengths while its space complexity scales linearly with the length of the smallest sequence.     

Multiplexed-Based Assessment of DNA Damage Response to Chemotherapies Using Cell Imaging Cytometry

The current methods for measuring the DNA damage response (DDR) are relatively labor-intensive and usually based on Western blotting, flow cytometry, and/or confocal immunofluorescence analyses. They require many cells and are often limited to the assessment of a single or few proteins. Here, we used the Celigo^® image cytometer to evaluate the cell response to DNA-damaging agents based on a panel of biomarkers associated with the main DDR signaling pathways. We investigated the cytostatic or/and the cytotoxic effects of these drugs using simultaneous propidium iodide and calcein-AM staining. We also describe new dedicated multiplexed protocols to investigate the qualitative (phosphorylation) or the quantitative changes of eleven DDR markers (H2AX, DNA-PKcs, ATR, ATM, CHK1, CHK2, 53BP1, NBS1, RAD51, P53, P21). The results of our study clearly show the advantage of using this methodology because the multiplexed-based evaluation of these markers can be performed in a single experiment using the standard 384-well plate format. The analyses of multiple DDR markers together with the cell cycle status provide valuable insights into the mechanism of action of investigational drugs that induce DNA damage in a time- and cost-effective manner due to the low amounts of antibodies and reagents required.     

An Overview of the Latest Metabolomics Studies on Atopic Eczema with New Directions for Study

Atopic eczema (AE) is an inflammatory skin disorder affecting approximately 20% of children worldwide and early onset can lead to asthma and allergies. Currently, the mechanisms of the disease are not fully understood. Metabolomics, the analysis of small molecules in the skin produced by the host and microbes, opens a window to observe the mechanisms of the disease which then may lead to new drug targets for AE treatment. Here, we review the latest advances in AE metabolomics, highlighting both the lipid and non-lipid molecules, along with reviewing the metabolites currently known to reside in the skin.     

Object-oriented change detection for the city of Harare,Zimbabwe

Object building and the extraction of homogeneous landscape units on which spatial statistics can be applied is useful in assessing land use and land cover change. Object-oriented processing techniques are becoming more popular compared to traditional pixel-based image analysis. A hierarchical image segmentation approach was adopted to extract the objects from multi-temporal Landsat images over Zimbabwe. The spatial arrangement of t₀ and t₁ objects was independent as the segmentation process was independently applied, although object change of t₁ was based on t₀ boundaries. We applied a Standardized, Object Oriented, Automatic Classification (SOOAC) method based on fuzzy logic. The error matrix for the TM image had an overall accuracy of 95.6% and a KIA value of 94.7%, the ETM showed slightly lower overall accuracy. Various LULC changes were identified over the 13 year period per object and also per class, mainly vegetation decrease. Object-oriented change information is necessary in decision support systems and uncertainty management strategies. This approach addresses some of the major issues in object-based GIS change analysis as it is based on stable object geometry.     

Modified Fluoroquinolones as Antimicrobial Compounds Targeting Chlamydia trachomatis

Chlamydia trachomatis causes the most common sexually transmitted bacterial infection and trachoma, an eye infection. Untreated infections can lead to sequelae, such as infertility and ectopic pregnancy in women and blindness. We previously enhanced the antichlamydial activity of the fluoroquinolone ciprofloxacin by grafting a metal chelating moiety onto it. In the present study, we pursued this pharmacomodulation and obtained nanomolar active molecules (EC₅₀) against this pathogen. This gain in activity prompted us to evaluate the antibacterial activity of this family of molecules against other pathogenic bacteria, such as Neisseria gonorrhoeae and bacteria from the ESKAPE group. The results show that the novel molecules have selectively improved activity against C. trachomatis and demonstrate how the antichlamydial effect of fluoroquinolones can be enhanced.     

Characterization of a Cutibacterium acnes Camp Factor 1-Related Peptide as a New TLR-2 Modulator in In Vitro and Ex Vivo Models of Inflammation

Cutibacterium acnes (C. acnes) has been implicated in inflammatory acne where highly mutated Christie–Atkins–Munch–Petersen factor (CAMP)1 displays strong toll like receptor (TLR)-2 binding activity. Using specific antibodies, we showed that CAMP1 production was independent of C. acnes phylotype and involved in the induction of inflammation. We confirmed that TLR-2 bound both mutated and non-mutated recombinant CAMP1, and peptide array analysis showed that seven peptides (A14, A15, B1, B2, B3, C1 and C3) were involved in TLR-2 binding, located on the same side of the three-dimensional structure of CAMP1. Both mutated and non-mutated recombinant CAMP1 proteins induced the production of C-X-C motif chemokine ligand interleukin (CXCL)8/(IL)-8 in vitro in keratinocytes and that of granulocyte macrophage-colony stimulating factor (GM-CSF), tumor necrosis factor (TNF)-α, IL-1β and IL-10 in ex vivo human skin explants. Only A14, B1 and B2 inhibited the production of CXCL8/IL-8 by keratinocytes and that of (GM-CSF), TNF-α, IL-1β and IL-10 in human skin explants stimulated with rCAMP1 and C. acnes. Following pretreatment with B2, RNA sequencing on skin explants identified the 10 genes displaying the strongest differential expression as IL6, TNF, CXCL1, CXCL2, CXCL3, CXCL8, IL-1β, chemokine ligand (CCL)2, CCL4 and colony stimulating factor (CSF)2. We, thus, identified a new CAMP1-derived peptide as a TLR-2 modulator likely to be a good candidate for clinical evaluation.     

Control of food spoilage fungi by ethanol

This review discusses the effects of ethanol on the inhibition of growth and germination of fungi and on the inactivation of fungal spores. After a brief survey on the impact of spoilage fungi on the economy and food quality, the major applications of ethanol in controlling fruit decay and extending the shelf-life of food products are reviewed. Many parameters including minimum inhibitory concentration (MIC) and D-values for various moulds are included. The thermodynamic relationship between the liquid phase and the headspace and the mode of action of ethanol on fungi are explained. Due to their promising use as a fumigant, special attention is paid to ethanol vapours.     

Biomass production and small-scale testing of freeze-dried lactic acid bacteria starter strains for cassava fermentations

Based on their predominance in Gari fermentations, as well as suitable technological properties, Lactobacillus plantarum, Lactobacillus fermentum, Weissella paramesenteroides and Leuconostoc mesenteroides strains were investigated for their suitability for development as starter strains for this African traditional fermented cassava product. The strains were grown in optimized growth media in 2 L fermenters, harvested and freeze dried, and then tested in lab-scale cassava mash fermentation trials for their ability to ferment the cassava. The strains performed well and rapidly increased the titratable acidity from 1.1 to 1.3% at 24 h to 1.3–1.6% at 48 h. The benefit of including starter cultures was that it lowered the pH of the product much faster and to lower levels than in the uninoculated control fermentation. The results furthermore indicated that especially the L. plantarum-group strains could be produced as starter strains at low cost. Overall, the results of this study showed that starter strains could be easily and economically produced, and thus represent a feasible possibility for further development for application in the field.