Exploring the Brainpeps database

Since the discovery that peptides can cross the blood-brain barrier (BBB), doors have been opened to new therapeutics for CNS diseases and pain management. Recently, we have constructed the Brainpeps database (brainpeps.ugent.be) to give an overview of the available BBB transport data of peptides, which are scattered in the literature [1]. One possible application of the Brainpeps database is the study of structure-property relationships (QSPRs). Before peptides can be used as drugs, their impurity profile needs to be examined as part of the International Conference on Harmonization (ICH) risk assessment of peptide drugs. Compared to small molecules, no in-silico predictive programs are available for toxicity screening of the different peptide impurities towards passing the BBB. To predict the BBB-behaviour of peptides as well as their impurities, we explored the Brainpeps database. During this presentation, the first results of the modelling experiments are presented. Our starting hypothesis is that the interactions of peptides at the blood-brain barrier are comparable with those of peptides in HPLC systems. Therefore, we determined the retention characteristics on different fused-core HPLC systems of a set of model peptides selected from the Brainpeps database and explored the relationship between the chromatographic characteristics and their BBB-influx properties [2]. In conclusion, using the Brainpeps database and experimental HPLC data, a first step towards in-silico profiling of peptides, including their impurities, at the blood-brain barrier level is taken. More chromatographic analyses of BBB peptides and harmonization on testing the BBB transport of peptides are future challenges to validate and unify this model. References [1] Van Dorpe S., Bronselaer A., Nielandt J., Stalmans S., Wynendaele E., Audenaert K., Van de Wiele C., Burvenich C., Peremans K., Hsuchou H., De Tré G., De Spiegeleer B. Brainpeps: the blood-brain barrier peptide database. Brain Struct Funct (2012), DOI: 10.1007/s00429-011-0375-0. [2] D’Hondt M., Van Dorpe S., Gevaert B., Wynendaele E., Stalmans S., Peremans K., Burvenich C., De Spiegeleer B. Fused-core RP-HPLC modelling of peptides. Journal of Pharmaceutical Analysis (2012), Accepted for publication

Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats : a comparison between bidirectional pyrosequencing and cultivation

The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1–22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1–V2 and V3–V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity

Quorumpeps database : chemical space, microbial origin and functionality of quorum sensing peptides

Quorum-sensing (QS) peptides are biologically attractive molecules, with a wide diversity of structures and prone to modifications altering or presenting new functionalities. Therefore, the Quorumpeps database (http://quorumpeps.ugent.be) is developed to give a structured overview of the QS oligopeptides, describing their microbial origin (species), functionality (method, result and receptor), peptide links and chemical characteristics (3D-structure-derived physicochemical properties). The chemical diversity observed within this group of QS signalling molecules can be used to develop new synthetic bio-active compounds

Diversity and Habitat Specificity of Free-Living Protozoa in Commercial Poultry Houses

Despite stringent biosecurity measures, infections by bacterial food pathogens such as Campylobacter are a recurrent problem in industrial poultry houses. As the main transmission route remains unclear, persistence of these infections has been linked to bacterial survival and possibly multiplication within protozoan vectors. To date, however, virtually no information is available on the diversity and occurrence of free-living protozoa in these environments. Using a combination of microscopic analyses of enrichment cultures and molecular methods (denaturing gradient gel electrophoresis [DGGE]) on natural samples, we show that, despite strict hygiene management, free-living protozoa are common and widespread throughout a 6-week rearing period in both water and dry samples from commercial poultry houses. Protozoan communities were highly diverse (over 90 morphotaxa and 22 unique phylotypes from sequenced bands) and included several facultative pathogens and known bacterial vectors. Water samples were consistently more diverse than dry ones and harbored different communities, mainly dominated by flagellates. The morphology-based and molecular methods yielded markedly different results: amoebic and, to a lesser degree, ciliate diversity was seriously underestimated in the DGGE analyses, while some flagellate groups were not found in the microscopic analyses. Some recommendations for improving biosecurity measures in commercial poultry houses are suggested

Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta

Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated

The effectiveness of a fundamental motor skill intervention in pre-schoolers with motor problems depends on gender but not environmental context

This study evaluated the effect of a 10-week fundamental motor skill programme in pre-schoolers with motor problems. Alongside the general effect of the intervention, we also explored possible gender differences and the role of the environmental context (living community, socio-economic status, and recreational space inside/outside the house). The intervention group (n=47; 20 ♂ and 27 ♀) received twenty 60-min motor skill sessions (2 per week) in addition to the regular physical education curriculum for pre-schoolers; the control group (n=46; 21 ♂ and 25 ♀) did not receive additional practice. General motor competence, and locomotor and object control subscales, were assessed before and after the intervention using the Test of Gross Motor Development 2nd edition (TGMD-2). Data regarding environmental factors were gathered through a questionnaire. A Group×Gender×Time ANOVA revealed that the intervention group benefited significantly from the intervention and scored better than the control group at the post-test for general motor competence and both sub-categories (locomotor and object control skill). Moreover, the intervention programme was found to be effective in helping 49% of the intervention group to achieve an average motor skill level, according to the TGMD-2 norms, while a further decline in motor competence was observed in the control group. Interestingly, the effect appeared to be gender-specific, since object control skill improved only in girls of the intervention group. Considering the environmental context, none of the above-mentioned factors was found to have an influence on the effectiveness of the intervention. The present study highlights the need for an early motor skill programme with a gender-specific approach in order to help low skilled boys and girls master a diverse set of motor skills

Large-scale wearable data reveal digital phenotypes for daily-life stress detection

Physiological signals have shown to be reliable indicators of stress in laboratory studies, yet large-scale ambulatory validation is lacking. We present a large-scale cross-sectional study for ambulatory stress detection, consisting of 1002 subjects, containing subjects' demographics, baseline psychological information, and five consecutive days of free-living physiological and contextual measurements, collected through wearable devices and smartphones. This dataset represents a healthy population, showing associations between wearable physiological signals and self-reported daily-life stress. Using a data-driven approach, we identified digital phenotypes characterized by self-reported poor health indicators and high depression, anxiety and stress scores that are associated with blunted physiological responses to stress. These results emphasize the need for large-scale collections of multi-sensor data, to build personalized stress models for precision medicine

Aberrant binding of mutant HSP47 affects posttranslational modification of type I collagen and leads to osteogenesis imperfecta

Heat shock protein 47 (HSP47), encoded by the SERPINH1 gene, is a molecular chaperone essential for correct folding of collagens. We report a homozygous p.(R222S) substitution in HSP47 in a child with severe osteogenesis imperfecta leading to early demise. p.R222 is a highly conserved residue located within the collagen interacting surface of HSP47. Binding assays show a significantly reduced affinity of HSP47-R222S for type I collagen. This altered interaction leads to posttranslational overmodification of type I collagen produced by dermal fibroblasts, with increased glycosylation and/or hydroxylation of lysine and proline residues as shown by mass spectrometry. Since we also observed a normal intracellular folding and secretion rate of type I collagen, this overmodification cannot be explained by prolonged exposure of the collagen molecules to the modifying hydroxyl- and glycosyltransferases, as is commonly observed in other types of OI. We found significant upregulation of several molecular chaperones and enzymes involved in procollagen modification and folding on Western blot and RT-qPCR. In addition, we showed that an imbalance in binding of HSP47-R222S to unfolded type I collagen chains in a gelatin sepharose pulldown assay results in increased binding of other chaperones and modifying enzymes. The elevated expression and binding of this molecular ensemble to type I collagen suggests a compensatory mechanism for the aberrant binding of HSP47-R222S, eventually leading to overmodification of type I collagen chains. Together, these results illustrate the importance of HSP47 for proper posttranslational modification and provide insights into the molecular pathomechanisms of the p.(R222S) alteration in HSP47, which leads to a severe OI phenotype. Author summary Heat shock protein 47 (HSP47) is essential for correct collagen folding. We report a homozygous p.(R222S) substitution in HSP47 in a child with severe osteogenesis imperfecta. The highly conserved p.R222 residue is located within the collagen interacting surface and HSP47-R222S shows a significantly reduced affinity for type I collagen. This altered interaction leads to posttranslational overmodification of type I collagen. In contrast to other types of OI, this overmodification is not caused by prolonged exposure of collagen to modifying enzymes, since the intracellular folding rate of type I collagen appears to be normal. We show significant upregulation of several molecular chaperones and collagen-modifying enzymes and increased binding of several of these molecules to unfolded type I collagen chains upon abnormal HSP47-R222S binding. This suggests a compensatory mechanism for aberrant HSP47-R222S binding, eventually leading to overmodification of type I collagen chains, and underscores the importance of HSP47 for proper posttranslational modification

Gambaran Persepsi Pasien tentang Pelaksanaan Pemenuhan Kebutuhan Personal Hygiene oleh Perawat di RSUD Ungaran Semarang Tahun 2016

Kebutuhan personal hygiene pada pasien yang harus terpenuhi selama di rumah sakit adalah mandi dan berpakaian, menggosok gigi, mencuci rambut, membersihkan kuku, toileting, dan membersihkan perineum. Salah satu dampak fisik yang terjadi apabila tidak dilakukan personal hygiene adalah dermatitis. Penelitian ini bertujuan untuk mengetahui gambaran persepsi pasien tentang pelaksanaan pemenuhan kebutuhan personal hygiene pada pasien rawat inap di RSUD Ungaran Semarang Tahun 2016. Penelitian ini menggunakan jenis penelitian kuantitatif dengan desain penelitian deskriptif eksploratif. Teknik pengambilan sampel menggunakan teknik purposive sampling yang berjumlah 133 orang sesuai kriteria inklusi. Analisa data yang digunakan adalah dengan distribusi frekuensi. Berdasarkan hasil analisa data statistik diperoleh, sebagian besar pasien menjawab tidak baik terhadap pelaksanaan mandi dan berpakaian sebesar 87 orang (65,4%), perawatan kuku tangan dan kaki baik sebesar 81 orang (56,4%), perawatan rambut tidak baik sebesar 89 orang (66,9%), perawatan gigi dan mulut tidak baik sebesar 104 orang (78,2%), toileting tidak baik sebesar 88 orang (66,2%), dan perawatan perineum tidak baik sebesar 112 (84,2%). Hasil penelitian secara keseluruhan menunjukkan bahwa, pelaksanaan personal hygiene tidak baik sebesar 80 orang (60,2%) dan baik 53 orang (39,8%). Berdasarkan hasil penelitian, disarankan agar perawat dapat meningkatkan pelaksanaan personal hygiene dengan memberikan edukasi dan informasi kepada keluarga pasien