Reliability of Intra-Retinal Layer Thickness Estimates

Purpose

Measurement of intra-retinal layer thickness using optical coherence tomography (OCT) has become increasingly prominent in multiple sclerosis (MS) research. Nevertheless, the approaches used for determining the mean layer thicknesses vary greatly. Insufficient data exist on the reliability of different thickness estimates, which is crucial for their application in clinical studies. This study addresses this lack by evaluating the repeatability of different thickness estimates.

Methods

Studies that used intra-retinal layer segmentation of macular OCT scans in patients with MS were retrieved from PubMed. To investigate the repeatability of previously applied layer estimation approaches, we generated datasets of repeating measurements of 15 healthy subjects and 13 multiple sclerosis patients using two OCT devices (Cirrus HD-OCT and Spectralis SD-OCT). We calculated each thickness estimate in each repeated session and analyzed repeatability using intra-class correlation coefficients and coefficients of repeatability.

Results

We identified 27 articles, eleven of them used the Spectralis SD-OCT, nine Cirrus HD-OCT, two studies used both devices and two studies applied RTVue-100. Topcon OCT-1000, Stratus OCT and a research device were used in one study each. In the studies that used the Spectralis, ten different thickness estimates were identified, while thickness estimates of the Cirrus OCT were based on two different scan settings. In the simulation dataset, thickness estimates averaging larger areas showed an excellent repeatability for all retinal layers except the outer plexiform layer (OPL).

Conclusions

Given the good reliability, the thickness estimate of the 6mm-diameter area around the fovea should be favored when OCT is used in clinical research. Assessment of the OPL was weak in general and needs further investigation before OPL thickness can be used as a reliable parameter.     

A multiplex biomarker approach for the diagnosis of transitional cell carcinoma from canine urine

Transitional cell carcinoma (TCC), the most common cancer of the urinary bladder in dogs, is usually diagnosed at an advanced disease stage with limited response to chemotherapy. Commercial screening tests lack specificity and current diagnostic procedures are invasive. A proof of concept pilot project for analyzing the canine urinary proteome as a noninvasive diagnostic tool for TCC identification was conducted. Urine was collected from 12 dogs in three cohorts (healthy, urinary tract infection, TCC) and analyzed using liquid chromatography tandem mass spectrometry. The presence of four proteins (macrophage capping protein, peroxiredoxin 5, heterogeneous nuclear ribonucleoproteins A2/B, and apolipoprotein A1) was confirmed via immunoblot. Of the total 379 proteins identified, 96 were unique to the TCC group. A statistical model, designed to evaluate the accuracy of this multiplex biomarker approach for diagnosis of TCC, predicted the presence of disease with 90% accuracy.     

Sensational placodes: Neurogenesis in the otic and olfactory systems

For both the intricate morphogenetic layout of the sensory cells in the ear and the elegantly radial arrangement of the sensory neurons in the nose, numerous signaling molecules and genetic determinants are required in concert to generate these specialized neuronal populations that help connect us to our environment. In this review, we outline many of the proteins and pathways that play essential roles in the differentiation of otic and olfactory neurons and their integration into their non-neuronal support structures. In both cases, well-known signaling pathways together with region-specific factors transform thickened ectodermal placodes into complex sense organs containing numerous, diverse neuronal subtypes. Olfactory and otic placodes, in combination with migratory neural crest stem cells, generate highly specialized subtypes of neuronal cells that sense sound, position and movement in space, odors and pheromones throughout our lives.     

Trace elements and antioxidant enzymes in extremely low birthweight infants

Oxygen radicals are believed to contribute to typical diseases of prematurity, such as bronchopulmonary dysplasia (BPD), intraventricular haemorrhage (IVH), retinopathy of prematurity (ROP) and necrotising enterocolitis (NEC). Our aim was to investigate whether these disorders are associated with disturbances in antioxidant enzyme activities and with low trace elements, which are co-factors of antioxidant enzymes. 209 infants with birthweight less than 1000 g were enrolled into a European multicentre randomised erythropoietin (rhEPO) trial; 155 developed one or more of the above mentioned diseases. We analysed Zn, Cu, Fe, Se in plasma and red blood cells (RBCs), superoxide dismutase (CuZn-SOD), glutathione peroxidase (GSH-Px), and catalase (CAT) in RBCs on the 3rd and 68th day of life. Zn, Fe, Se in plasma, and Se in RBCs decreased (p<0.01), and Zn in RBC (p<0.001), CuZn-SOD (p<0.01) and CAT increased (p<0.05), whereas GSH-Px remained unchanged. No differences were observed between the rhEPO and control groups. Antioxidant enzyme activities did not correlate with gestational age. In infants with BPD, IVH, ROP, or NEC, CuZn-SOD and CAT (p<0.05) were higher at day 68 than in infants without these diseases. CuZn-SOD and GSH-Px at 3 days and CuZn-SOD at 68 days correlated positively (p<0.05) with the duration of oxygen treatment. In conclusion, in ELBW infants, trace element concentrations decreased over the first 10 weeks of life. Lower trace element concentrations, did not affect the activities of CuZn-SOD, GSH-Px, and CAT. Typical diseases of prematurity were not associated with decreased antioxidant enzyme activities.     

Impact of calcifications on patient-specific wall stress analysis of abdominal aortic aneurysms

As a degenerative and inflammatory desease of elderly patients, about 80% of abdominal aortic aneurysms (AAA) show considerable wall calcification. Effect of calcifications on computational wall stress analyses of AAAs has been rarely treated in literature so far. Calcifications are heterogeneously distributed, non-fibrous, stiff plaques which are most commonly found near the luminal surface in between the intima and the media layer of the vessel wall. In this study, we therefore investigate the influence of calcifications as separate AAA constituents on finite element simulation results. Thus, three AAAs are reconstructed with regard to intraluminal thrombus (ILT), calcifications and vessel wall. Each patient-specific AAA is simulated twice, once including all three AAA constituents and once neglecting calcifications as it is still common in literature. Parameters for constitutive modeling of calcifications are thereby taken from experiments performed by the authors, showing that calcifications exhibit an almost linear stress–strain behavior with a Young’s modulus E ≥ 40 MPa. Simulation results show that calcifications exhibit significant load-bearing effects and reduce stress in adjacent vessel wall. Average stress within the vessel wall is reduced by 9.7 to 59.2%. For two out of three AAAs, peak wall stress decreases when taking calcifications into consideration (8.9 and 28.9%). For one AAA, simulated peak wall stress increases by 5.5% due to stress peaks near calcification borders. However, such stress singularities due to sudden stiffness jumps are physiologically doubtful. It can further be observed that large calcifications are mostly situated in concavely shaped regions of the AAA wall. We deduce that AAA shape is influenced by existent calcifications, thus crucial errors occur if they are neglected in computational wall stress analyses. A general increase in rupture risk for calcified AAAs is doubted.     

Growth of Quailbush in Acidic, Metalliferous Desert Mine Tailings: Effect of Azospirillum brasilense Sp6 on Biomass Production and Rhizosphere Community Structure

Mine tailing deposits in semiarid and arid environments frequently remain devoid of vegetation due to the toxicity of the substrate and the absence of a diverse soil microbial community capable of supporting seed germination and plant growth. The contribution of the plant growth promoting bacterium (PGPB) Azospirillum brasilense Sp6 to the growth of quailbush in compost-amended, moderately acidic, high-metal content mine tailings using an irrigation-based reclamation strategy was examined along with its influence on the rhizosphere bacterial community. Sp6 inoculation resulted in a significant (2.2-fold) increase in plant biomass production. The data suggest that the inoculum successfully colonized the root surface and persisted throughout the 60-day experiment in both the rhizosphere, as demonstrated by excision and sequencing of the appropriate denaturing gradient gel electrophoresis (DGGE) band, and the rhizoplane, as indicated by fluorescent in situ hybridization of root surfaces. Changes in rhizosphere community structure in response to Sp6 inoculation were evaluated after 15, 30, and 60 days using DGGE analysis of 16S rRNA polymerase chain reaction amplicons. A comparison of DGGE profiles using canonical correspondence analysis revealed a significant treatment effect (Sp6-inoculated vs. uninoculated plants vs. unplanted) on bacterial community structure at 15, 30, and 60 days (p?<?0.05). These data indicate that in an extremely stressed environment such as acid mine tailings, an inoculated plant growth promoting bacterium not only can persist and stimulate plant growth but also can directly or indirectly influence rhizobacterial community development.     

Culturable Microbial Diversity and the Impact of Tourism in Kartchner Caverns,Arizona

Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year^–1) and compared to samples taken from areas designated as having medium (30–40 visitors year^–1) and low (2–3 visitors year^–1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.     

Protein targeting into complex diatom plastids: functional characterisation of a specific targeting motif

Plastids of diatoms and related algae evolved by secondary endocytobiosis, the uptake of a eukaryotic alga into a eukaryotic host cell and its subsequent reduction into an organelle. As a result diatom plastids are surrounded by four membranes. Protein targeting of nucleus encoded plastid proteins across these membranes depends on N-terminal bipartite presequences consisting of a signal and a transit peptide-like domain. Diatoms and cryptophytes share a conserved amino acid motif of unknown function at the cleavage site of the signal peptides (ASAFAP), which is particularly important for successful plastid targeting. Screening genomic databases we found that in rare cases the very conserved phenylalanine within the motif may be replaced by tryptophan, tyrosine or leucine. To test such unusual presequences for functionality and to better understand the role of the motif and putative receptor proteins involved in targeting, we constructed presequence:GFP fusion proteins with or without modifications of the “ASAFAP”-motif and expressed them in the diatom Phaeodactylum tricornutum. In this comprehensive mutational analysis we found that only the aromatic amino acids phenylalanine, tryptophan, tyrosine and the bulky amino acid leucine at the +1 position of the predicted signal peptidase cleavage site allow plastid import, as expected from the sequence comparison of native plastid targeting presequences of P. tricornutum and the cryptophyte Guillardia theta. Deletions within the signal peptide domains also impaired plastid import, showing that the presence of F at the N-terminus of the transit peptide together with a cleavable signal peptide is crucial for plastid import. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. A. Gruber and S. Vugrinec contributed equally to this work.     

A "gold cluster-linked immunosorbent assay": optical near-field biosensor chip for the detection of allergenic beta-lactoglobulin in processed milk matrices

A new optical biosensor based on the resonance enhanced absorption (REA) effect is described. REA effects are observed when noble metal nanoclusters are deposited at a nanometric distance from a highly reflective mirror. The aim of our study was to adopt the REA effect for the rapid testing of proteins in a direct immunoassay format on chip and to adjust a conventional enzyme-linked immunosorbent assay (ELISA) to a cluster-linked immunosorbent assay (CLISA) by labelling the read-out antibody with monodisperse colloidal gold clusters. For generation of a strong REA signal 30 min of coating of the target protein was sufficient. To evaluate our approach we used the milk allergen β-lactoglobulin (β-LG) as analyte, and β-LG-isolations of processed milk products to prove the applicability of our method to the analysis of proteins in complex matrices at even the trace level. For validating the specificity of the CLISA biosensor we used the non-functionalised cluster reagent without antibody and a non-immunoreactive milk matrix as controls. As expected, very weak background signals were obtained with the controls, whereas the purified food samples clearly showed that β-LG was present and detectable. In conclusion, we were able to describe the successful development of a new biosensor chip for assaying proteins using the REA effect.