Vaccine-induced antibodies to contemporary strains of dengue virus type 4 show a mechanistic correlate of protective immunity.

The four dengue virus serotypes (DENV1-4) are mosquito-borne flaviviruses of humans. Several live-attenuated tetravalent DENV vaccines are at different stages of clinical development and approval. In children with no baseline immunity to DENVs, a leading vaccine (Dengvaxia) is efficacious against vaccine-matched DENV4 genotype II (GII) strains but not vaccine-mismatched DENV4 GI viruses. We use a panel of recombinant DENV4 viruses displaying GI or GII envelope (E) proteins to map Dengvaxia-induced neutralizing antibodies (NAbs) linked to protection. The vaccine stimulated antibodies that neutralize the DENV4 GII virus better than the GI virus. The neutralization differences map to 5 variable amino acids on the E protein located within a region targeted by DENV4 NAbs, supporting a mechanistic role for these epitope-specific NAbs in protection. In children with no baseline immunity to DENVs, levels of DENV4 serotype- and genotype-specific NAbs induced by vaccination are predictive of vaccine efficacy.

MRI Evaluation of Complete and Near-Complete Response after Neoadjuvant Therapy in Patients with Locally Advanced Rectal Cancer.

Purpose To evaluate MRI performance in restaging locally advanced rectal cancers (LARC) after neoadjuvant chemoradiotherapy (nCRT) and interobserver agreement in identifying complete response (CR) and near-complete response (nCR). Methods 40 patients with CR and nCR on restaging MRI, surgery and/or endoscopy were enrolled. Two radiologists independently scored the restaging MRI and reported the presence of split scar sign (SSS) and MRI tumor regression grade (mrTRG). Diagnostic accuracy and ROC curves were calculated for single and combined sequences, with inter-reader agreement. Results Diagnostic performance was good for detecting CR and weaker for nCR. T2WI had the highest AUCs among individual sequences. There was a significant positive correlation between SSS and CR, with high Sp (89.5%/73.7%) and PPV (90%/79.2%) for both Readers. Similar accuracy rates were observed for the combination of sequences, with AUCs of 0.828-0.847 for CR and 0.690-0.762 for nCR. Interobserver agreement was strong for SSS, moderate for T2WI, weak for the combination of sequences. Conclusions Restaging MRI had good diagnostic performance in identifying CR and nCR. SSS had high Sp and PPV in diagnosing CR, with a strong level of interobserver agreement. T2WI with DWI was the optimal combination of sequences for selecting good responders.

Dengue vaccine breakthrough infections reveal properties of neutralizing antibodies linked to protection.

The 4 serotypes of dengue virus (DENV1-4) are mosquito-borne flaviviruses that infect humans. Live attenuated tetravalent DENV vaccines are at different phases of clinical testing. DENV vaccine developers have relied on neutralizing antibodies (NAbs) as a correlate of protection. A leading tetravalent vaccine (Dengvaxia) stimulated NAbs to the 4 DENV serotypes, yet overall vaccine efficacy was low in children who were DENV seronegative at baseline before vaccination. We compared the properties of (a) NAbs induced by WT DENV1 or DENV3 infections, which are strongly correlated with protection from repeat infections, and (b) NAbs induced by Dengvaxia in individuals who subsequently experienced DENV1 or DENV3 breakthrough infections. WT infections induced NAbs that recognized epitopes unique (type specific) to each serotype, whereas the vaccine stimulated qualitatively different NAbs that recognized epitopes conserved (crossreactive) between serotypes. Our results indicate that, among children who were DENV-seronegative at baseline, unbalanced replication of the DENV type 4 vaccine component in the tetravalent vaccine stimulates Abs capable of crossneutralizing DENV1 and DENV3 in vitro, but not protecting in vivo. In DENV-seronegative individuals who are vaccinated, we propose that type-specific NAbs are a better correlate of protection than total levels of NAbs.

Deciphering human ribonucleoprotein regulatory networks.

RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules represented functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.

SSMART: sequence-structure motif identification for RNA-binding proteins.

Motivation: RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized. Results: We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3'UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP. Availability and implementation: SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/. Supplementary information: Supplementary data are available at Bioinformatics online.

IL-9 is a key component of memory TH cell peanut-specific responses from children with peanut allergy.

BACKGROUND: Differentiation between patients with peanut allergy (PA) and those with peanut sensitization (PS) who tolerate peanut but have peanut-specific IgE, positive skin prick test responses, or both represents a significant diagnostic difficulty. Previously, gene expression microarrays were successfully used to identify biomarkers and explore immune responses during PA immunotherapy. OBJECTIVE: We aimed to characterize peanut-specific responses from patients with PA, subjects with PS, and atopic children without peanut allergy (NA children). METHODS: A preliminary exploratory microarray investigation of gene expression in peanut-activated memory TH subsets from 3 children with PA and 3 NA children identified potential PA diagnostic biomarkers. Microarray findings were confirmed by using real-time quantitative PCR in 30 subjects (12 children with PA, 12 children with PS, and 6 NA children). Flow cytometry was used to identify the TH subsets involved. RESULTS: Among 12,257 differentially expressed genes, IL9 showed the greatest difference between children with PA and NA children (45.59-fold change, P < .001), followed by IL5 and then IL13. Notably, IL9 allowed the most accurate classification of children with PA and NA children by using a machine-learning approach with recursive feature elimination and the random forest algorithm. Skin- and gut-homing TH cells from donors with PA expressed similar TH2- and TH9-associated genes. Real-time quantitative PCR confirmed that IL9 was the highest differentially expressed gene between children with PA and NA children (23.3-fold change, P < .01) and children with PS (18.5-fold change, P < .05). Intracellular cytokine staining showed that IL-9 and the TH2-specific cytokine IL-5 are produced by distinct TH populations. CONCLUSION: In this study IL9 best differentiated between children with PA and children with PS (and atopic NA children). Mutually exclusive production of IL-9 and the TH2-specific cytokine IL-5 suggests that the IL-9-producing cells belong to the recently described TH9 subset.

COUGER--co-factors associated with uniquely-bound genomic regions.

Most transcription factors (TFs) belong to protein families that share a common DNA binding domain and have very similar DNA binding preferences. However, many paralogous TFs (i.e. members of the same TF family) perform different regulatory functions and interact with different genomic regions in the cell. A potential mechanism for achieving this differential in vivo specificity is through interactions with protein co-factors. Computational tools for studying the genomic binding profiles of paralogous TFs and identifying their putative co-factors are currently lacking. Here, we present an interactive web implementation of COUGER, a classification-based framework for identifying protein co-factors that might provide specificity to paralogous TFs. COUGER takes as input two sets of genomic regions bound by paralogous TFs, and it identifies a small set of putative co-factors that best distinguish the two sets of sequences. To achieve this task, COUGER uses a classification approach, with features that reflect the DNA-binding specificities of the putative co-factors. The identified co-factors are presented in a user-friendly output page, together with information that allows the user to understand and to explore the contributions of individual co-factor features. COUGER can be run as a stand-alone tool or through a web interface: http://couger.oit.duke.edu.

Mapping receptor density on live cells by using fluorescence correlation spectroscopy.

Study of the density, spatial distribution, and molecular interactions of receptors on the cell membrane provides the knowledge required to understand cellular behavior and biological functions, as well as to discover, design, and screen novel therapeutic agents. However, the mapping of receptor distribution and the monitoring of ligand-receptor interactions on live cells in a spatially and temporally ordered manner are challenging tasks. In this paper, we apply fluorescence correlation spectroscopy (FCS) to map receptor densities on live cell membranes by introducing fluorescently marked aptamer molecules, which specifically bind to certain cell-surface receptors. The femtoliter-sized (0.4 fL) observation volume created by FCS allows fluorescent-aptamer detection down to 2 molecules and appears to be an ideal and highly sensitive biophysical tool for studying molecular interactions on live cells. Fluorophore-labeled aptamers were chosen for receptor recognition because of their high binding affinity and specificity. Aptamer sgc8, generated for specific cell recognition by a process called cell systematic evolution of ligands by exponential enrichment, was determined by FCS to have a binding affinity in the picomolar range (dissociation constant K(d)=790+/-150 pM) with its target membrane receptor, human protein tyrosine kinase-7 (PTK7), a potential cancer biomarker. We then constructed a cellular model and applied this aptamer-receptor interaction to estimate receptor densities and distributions on the cell surface. Specifically, different expression levels of PTK7 were studied by using human leukemia CCRF-CEM cells (1300+/-190 receptors microm(-2)) and HeLa cervical cancer cells (550+/-90 receptors microm(-2)). Competition studies with excess nonlabeled aptamers and proteinase treatment studies proved the validity of the density-estimation approach. With its intrinsic advantages of direct measurement, high sensitivity, fast analysis, and single-cell measurement, this FCS density-estimation approach holds potential for future applications in molecular-interaction studies and density estimations for subcellular structures and membrane receptors.

Using bioconjugated nanoparticles to monitor E. coli in a flow channel.

A simple and portable flow channel optical detection system combined with bioconjugated luminescent nanoparticles allows the rapid detection of single bacterial cells without sample enrichment. The optical system is designed to have single-molecule-detection capability in a microcapillary flow channel by decreasing the laser excitation probe volume to a few picoliters, which consequently results in a low background. Specific monoclonal antibodies were immobilized on nanoparticles to form nanoparticle-antibody conjugates. The bioconjugated nanoparticles bind to the target bacteria when they recognize the antigen on the bacterium surface, thus providing a bright luminescent signal for the detection of individual bacteria cells. The high sensitivity provided by the luminescent and photostable silica nanoparticles eliminates the need for further enrichment of bacteria samples and signal amplification. This flow channel detection system is convenient and allows the detection of single bacterial cells within a few minutes.

Molecular beacons for bioanalytical applications.

Molecular beacons (MBs) are hairpin-shaped oligonucleotides that contain both fluorophore and quencher moieties. They act like switches and are normally in a closed state, when the fluorophore and the quencher are brought together to turn "off" the fluorescence. When prompted to undergo conformational changes that open the hairpin structure, the fluorophore and the quencher are separated, and fluorescence is turned "on." This Education will outline the principles of MBs and discuss recent bioanalytical applications of these probes for in vitro RNA and DNA monitoring, biosensors and biochips, real-time monitoring of genes and gene expression in living systems, as well as the next generation of MBs for studies on proteins, the MB aptamers. These important applications have shown that MBs hold great potential in genomics and proteomics where real-time molecular recognition with high sensitivity and excellent specificity is critical.

[Orbito-ocular dermoid cysts--incidence and particular cases]. / Chisturi dermoide oculo-orbitare incidenta si cazuri particulare.

This paper is concerned about a retrospective study on the casuistry of the Ophthalmologic Clinic of Craiova concerning those cases hospitalized and operated for different dermoidal cystic localization. A period of 20 years is under observation. The group of patients is analyzed taking into account the apparent debut age of the tumors, sex and different localization incidence. Both those tumor particular forms are exemplified by the clinic own casuistry and the association to other lesion types and profound localization in the orbit with particular clinic symptomatology. All the cases have been checked up and anatomopathologically confirmed.

[Optic nerve lesions in diabetes mellitus]. / Leziuni ale nervului optic în diabet.

The present paper is a retrospective study revealing some optic nerve lesions on a group of 1.700 diabetic patients which belonged to the common casuistry of the Ophthalmologic Clinic and Diabetic and Nutrition Diseases Clinic in Craiova. A reduced frequency of optic neuropathy in diabetic persons was established such as: 27 patients (1.58%). Affected optic nerve may present various clinical aspects among which ischemic optic neuropathy is predominant (59.20%) followed by secondary optic atrophy, ischemic optic post neuropathy (33.40%) and juxtabulbar optic neuritis (7.40%).