Increasing the antioxidant capacity of ceria nanoparticles with catechol-grafted poly(ethylene glycol).

Ceria nanoparticles are remarkable antioxidants due to their large cerium(III) content and the possibility of recovering cerium(III) from cerium(IV) after reaction. Here we increase the cerium(III) content of colloidally stable nanoparticles (e.g., nanocrystals) using a reactive polymeric surface coating. Catechol-grafted poly(ethylene glycols) (PEG) polymers of varying lengths and architectures yield materials that are non-aggregating in a variety of aqueous media. Cerium(IV) on the ceria surface both binds and oxidizes the catechol functionality, generating a dark-red colour emblematic of surface-oxidized catechols with a concomitant increase in cerium(III) revealed by X-ray photoemission spectroscopy (XPS). The extent of ceria reduction depends sensitively on the architecture of the coating polymer; small and compact polymer chains pack with high density at the nanoparticle surface yielding the most cerium(III). Nanoparticles with increased surface reduction, quantified by the intensity of their optical absorption and thermogravimetric measures of polymer grafting densities, were more potent antioxidants as measured by a standard TEAC antioxidant assay. For the same core composition nanoparticle antioxidant capacities could be increased over an order of magnitude by tailoring the length and architecture of the reactive surface coatings.

Perspectives of Parents/Legal Guardians of Children With Down Syndrome Requiring Anesthesia: Concerns and Sources of Information.

This descriptive exploratory study sought to gain insight about where caregivers of children with Down syndrome find information regarding anesthesia and the experiences of these caregivers when their child had to receive an anesthetic. We hypothesized that the Internet and social media were major sources of information. We recruited parents/caregivers via Down syndrome organizational websites and social media. A total of 515 participants completed a 24-question survey. Descriptive analysis and content analysis were used to analyze the data. Nearly all participants (96%) indicated their child had received an anesthetic. Reportedly, 41.2% had never searched the Internet about anesthesia. Responses indicated that caregivers obtained information mostly from Facebook groups and local websites and groups. Respondents believed the information was helpful (88.2%) but considered it to be only somewhat trustworthy (73.3%). Most (82%) indicated they would prefer a face-to-face conversation with the anesthesia provider. Among participants, 45% reported having a positive experience with anesthesia, 25% reported a negative experience, and 30% responded neither. Negative experiences involved children who had symptoms of emergence delirium and regression or when the caregiver perceived there were unexpected complications. These results are intended to be used to develop a checklist for caregivers when speaking to anesthesia providers.

Machine learning for metabolic engineering: A review.

Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.

Evaluation of the Cunningham Panel™ in pediatric autoimmune neuropsychiatric disorder associated with streptococcal infection (PANDAS) and pediatric acute-onset neuropsychiatric syndrome (PANS): Changes in antineuronal antibody titers parallel changes in patient symptoms.

OBJECTIVE: This retrospective study examined whether changes in patient pre- and post-treatment symptoms correlated with changes in anti-neuronal autoantibody titers and the neuronal cell stimulation assay in the Cunningham Panel in patients with Pediatric Autoimmune Neuropsychiatric Disorder Associated with Streptococcal Infection (PANDAS), and Pediatric Acute-onset Neuropsychiatric Syndrome (PANS). METHODS: In an analysis of all tests consecutively performed in Moleculera Labs' clinical laboratory from April 22, 2013 to December 31, 2016, we identified 206 patients who were prescribed at least one panel prior to and following treatment, and who met the PANDAS/PANS diagnostic criteria. Patient follow-up was performed to collect symptoms and treatment or medical intervention. Of the 206 patients, 58 met the inclusion criteria of providing informed consent/assent and documented pre- and post-treatment symptoms. Clinician and parent-reported symptoms after treatment or medical intervention were categorized as "Improved/Resolved" (n = 34) or "Not-Improved/Worsened" (n = 24). These were analyzed for any association between changes in clinical status and changes in Cunningham panel test results. Clinical assay performance was also evaluated for reproducibility and reliability. RESULTS: Comparison of pre- and post-treatment status revealed that the Cunningham Panel results correlated with changes in patient's neuropsychiatric symptoms. Based upon the change in the number of positive tests, the overall accuracy was 86%, the sensitivity and specificity were 88% and 83% respectively, and the Area Under the Curve (AUC) was 93.4%. When evaluated by changes in autoantibody levels, we observed an overall accuracy of 90%, a sensitivity of 88%, a specificity of 92% and an AUC of 95.7%. Assay reproducibility for the calcium/calmodulin-dependent protein kinase II (CaMKII) revealed a correlation coefficient of 0.90 (p < 1.67 × 10-6) and the ELISA assays demonstrated test-retest reproducibility comparable with other ELISA assays. CONCLUSION: This study revealed a strong positive association between changes in neuropsychiatric symptoms and changes in the level of anti-neuronal antibodies and antibody-mediated CaMKII human neuronal cell activation. These results suggest there may be clinical utility in monitoring autoantibody levels and stimulatory activity against these five neuronal antigen targets as an aid in the diagnosis and treatment of infection-triggered autoimmune neuropsychiatric disorders. Future prospective studies should examine the feasibility of predicting antimicrobial and immunotherapy responses with the Cunningham Panel.

ACCESS Open Minds at the University of Alberta: Transforming student mental health services in a large Canadian post-secondary educational institution.

AIM: Demands for mental health services in post-secondary institutions are increasing. This paper describes key features of a response to these needs: ACCESS Open Minds University of Alberta (ACCESS OM UA) is focused on improving mental health services for first-year students, as youth transition to university and adulthood. METHODS: The core transformation activities at ACCESS OM UA are described, including early case identification, rapid access, appropriate and timely connections to follow-up care and engagement of students and families/carers. In addition, we depict local experiences of transforming existing services around these objectives. RESULTS: The ACCESS OM UA Network has brought together staff with diverse backgrounds in order to address the unique needs of students. Together with the addition of ACCESS Clinicians these elements represent a systematic effort to support not just mental health, but the student as a whole. Key learnings include the importance of community mapping to developing networks and partnerships, and engaging stakeholders from design through to implementation for transformation to be sustainable. CONCLUSIONS: Service transformation grounded in principles of community-based research allows for incorporation of local knowledge, expertise and opportunities. This approach requires ample time to consult, develop rapport between staff and stakeholders across diverse units and develop processes in keeping with local opportunities and constraints. Ongoing efforts will continue to monitor changing student needs and to evaluate and adapt the transformations outlined in this paper to reflect those needs.

Translation from unconventional 5' start sites drives tumour initiation.

We are just beginning to understand how translational control affects tumour initiation and malignancy. Here we use an epidermis-specific, in vivo ribosome profiling strategy to investigate the translational landscape during the transition from normal homeostasis to malignancy. Using a mouse model of inducible SOX2, which is broadly expressed in oncogenic RAS-associated cancers, we show that despite widespread reductions in translation and protein synthesis, certain oncogenic mRNAs are spared. During tumour initiation, the translational apparatus is redirected towards unconventional upstream initiation sites, enhancing the translational efficiency of oncogenic mRNAs. An in vivo RNA interference screen of translational regulators revealed that depletion of conventional eIF2 complexes has adverse effects on normal but not oncogenic growth. Conversely, the alternative initiation factor eIF2A is essential for cancer progression, during which it mediates initiation at these upstream sites, differentially skewing translation and protein expression. Our findings unveil a role for the translation of 5' untranslated regions in cancer, and expose new targets for therapeutic intervention.

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.

BACKGROUND: Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. RESULTS: Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid's data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. CONCLUSIONS: Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays. Examples, tutorials, and extensive documentation can be found at https://plastid.readthedocs.io .

Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity.

Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and microgravity-grown crystals had a slightly improved mosaicity (decreased by 0.03°) and diffraction resolution (decreased by 0.2 Å) compared with control crystals grown on Earth. However, the highest resolution and lowest mosaicity crystals were formed on Earth, and the highest-quality crystal overall was formed on Earth after return from microgravity.

Presenting Symptoms and Dysphagia Screen Predict Outcome in Mild and Rapidly Improving Acute Ischemic Stroke Patients.

OBJECTIVE: There are limited data on which patients not treated with intravenous (IV) tissue-type plasminogen activator (tPA) due to mild and rapidly improving stroke symptoms (MaRISS) have unfavorable outcomes. MATERIALS AND METHODS: Acute ischemic stroke (AIS) patients not treated with IV tPA due to MaRISS from January 1, 2009 to December 31, 2013 were identified as part of the Georgia Coverdell Acute Stroke Registry. Multivariable regression analysis was used to identify factors associated with a lower likelihood of favorable outcome, defined as discharge to home. RESULTS: There were 1614 AIS patients who did not receive IV tPA due to MaRISS (median National Institutes of Health stroke scale [NIHSS] 1], of which 305 (19%) did not have a favorable outcome. Factors associated with lower likelihood of favorable outcome included Medicare insurance status (odds ratio [OR]: .53, 95% confidence interval [CI]: .34-.84), arrival by emergency medical services (OR: .46, 95% CI: .29-.73), increasing NIHSS score (per unit OR: .89, 95% CI: .84-.93), weakness as the presenting symptom (OR: .50, 95% CI: .30-.84), and a failed dysphagia screen (OR: .43, 95% CI: .23-.80). During the study period, <1% of patients presenting to participating hospitals with MaRISS within the eligible time window received IV tPA. CONCLUSIONS: Baseline characteristics, presenting symptoms, and response to dysphagia screen identify a subgroup of patients who are more likely to have an unfavorable outcome. Whether IV tPA treatment can improve the outcome in this subgroup of patients needs to be evaluated in a randomized placebo-controlled trial.

Characterization of the ß-barrel assembly machine accessory lipoproteins from Borrelia burgdorferi.

BACKGROUND: Like all diderm bacteria studied to date, Borrelia burgdorferi possesses a ß-barrel assembly machine (BAM) complex. The bacterial BAM complexes characterized thus far consist of an essential integral outer membrane protein designated BamA and one or more accessory proteins. The accessory proteins are typically lipid-modified proteins anchored to the inner leaflet of the outer membrane through their lipid moieties. We previously identified and characterized the B. burgdorferi BamA protein in detail and more recently identified two lipoproteins encoded by open reading frames bb0324 and bb0028 that associate with the borrelial BamA protein. The role(s) of the BAM accessory lipoproteins in B. burgdorferi is currently unknown. RESULTS: Structural modeling of B. burgdorferi BB0028 revealed a distinct ß-propeller fold similar to the known structure for the E. coli BAM accessory lipoprotein BamB. Additionally, the structural model for BB0324 was highly similar to the known structure of BamD, which is consistent with the prior finding that BB0324 contains tetratricopeptide repeat regions similar to other BamD orthologs. Consistent with BB0028 and BB0324 being BAM accessory lipoproteins, mutants lacking expression of each protein were found to exhibit altered membrane permeability and enhanced sensitivity to various antimicrobials. Additionally, BB0028 mutants also exhibited significantly impaired in vitro growth. Finally, immunoprecipitation experiments revealed that BB0028 and BB0324 each interact specifically and independently with BamA to form the BAM complex in B. burgdorferi. CONCLUSIONS: Combined structural studies, functional assays, and co-immunoprecipitation experiments confirmed that BB0028 and BB0324 are the respective BamB and BamD orthologs in B. burgdorferi, and are important in membrane integrity and/or outer membrane protein localization. The borrelial BamB and BamD proteins both interact specifically and independently with BamA to form a tripartite BAM complex in B. burgdorferi. A working model has been developed to further analyze outer membrane biogenesis and outer membrane protein transport in this pathogenic spirochete.

The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.

Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1--with conserved functions in cell division and morphogenesis from plants to humans-as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system.

Structural modeling and physicochemical characterization provide evidence that P66 forms a ß-barrel in the Borrelia burgdorferi outer membrane.

The Borrelia burgdorferi outer membrane (OM) contains numerous surface-exposed lipoproteins but a relatively low density of integral OM proteins (OMPs). Few membrane-spanning OMPs of B. burgdorferi have been definitively identified, and none are well characterized structurally. Here, we provide evidence that the borrelial OMP P66, a known adhesin with pore-forming activity, forms a ß-barrel in the B. burgdorferi OM. Multiple computer-based algorithms predict that P66 forms a ß-barrel with either 22 or 24 transmembrane domains. According to our predicted P66 topology, a lysine residue (K487) known to be sensitive to trypsin cleavage is located within a surface-exposed loop. When we aligned the mature P66 amino acid sequences from B. burgdorferi and B. garinii, we found that K487 was present only in the B. burgdorferi P66 protein sequence. When intact cells from each strain were treated with trypsin, only B. burgdorferi P66 was trypsin sensitive, indicating that K487 is surface exposed, as predicted. Consistent with this observation, when we inserted a c-Myc tag adjacent to K487 and utilized surface localization immunofluorescence, we detected the loop containing K487 on the surface of B. burgdorferi. P66 was examined by both Triton X-114 phase partitioning and circular dichroism, confirming that the protein is amphiphilic and contains extensive (48%) ß-sheets, respectively. Moreover, P66 also was able to incorporate into liposomes and form channels in large unilamellar vesicles. Finally, blue native PAGE (BN-PAGE) revealed that under nondenaturing conditions, P66 is found in large complexes of ∼400 kDa and ∼600 kDa. Outer surface lipoprotein A (OspA) and OspB both coimmunoprecipitate with P66, demonstrating that P66 associates with OspA and OspB in B. burgdorferi. The combined computer-based structural analyses and supporting physicochemical properties of P66 provide a working model to further examine the porin and integrin-binding activities of this OMP as they relate to B. burgdorferi physiology and Lyme disease pathogenesis.

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.

Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. DOI: http://dx.doi.org/10.7554/eLife.01179.001.

A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress.

The conserved transcriptional regulator heat shock factor 1 (Hsf1) is a key sensor of proteotoxic and other stress in the eukaryotic cytosol. We surveyed Hsf1 activity in a genome-wide loss-of-function library in Saccaromyces cerevisiae as well as ~78,000 double mutants and found Hsf1 activity to be modulated by highly diverse stresses. These included disruption of a ribosome-bound complex we named the Ribosome Quality Control Complex (RQC) comprising the Ltn1 E3 ubiquitin ligase, two highly conserved but poorly characterized proteins (Tae2 and Rqc1), and Cdc48 and its cofactors. Electron microscopy and biochemical analyses revealed that the RQC forms a stable complex with 60S ribosomal subunits containing stalled polypeptides and triggers their degradation. A negative feedback loop regulates the RQC, and Hsf1 senses an RQC-mediated translation-stress signal distinctly from other stresses. Our work reveals the range of stresses Hsf1 monitors and elucidates a conserved cotranslational protein quality control mechanism.

Genome-wide genetic analysis of polyploidy in yeast.

Polyploidy, increased sets of chromosomes, occurs during development, cellular stress, disease and evolution. Despite its prevalence, little is known about the physiological alterations that accompany polyploidy. We previously described 'ploidy-specific lethality', where a gene deletion that is not lethal in haploid or diploid budding yeast causes lethality in triploids or tetraploids. Here we report a genome-wide screen to identify ploidy-specific lethal functions. Only 39 out of 3,740 mutations screened exhibited ploidy-specific lethality. Almost all of these mutations affect genomic stability by impairing homologous recombination, sister chromatid cohesion, or mitotic spindle function. We uncovered defects in wild-type tetraploids predicted by the screen, and identified mechanisms by which tetraploidization affects genomic stability. We show that tetraploids have a high incidence of syntelic/monopolar kinetochore attachments to the spindle pole. We suggest that this defect can be explained by mismatches in the ability to scale the size of the spindle pole body, spindle and kinetochores. Thus, geometric constraints may have profound effects on genome stability; the phenomenon described here may be relevant in a variety of biological contexts, including disease states such as cancer.

Bathing. Pleasure or pain?

Bathing creates some of the highest levels of discomfort in the lives of individuals diagnosed with dementia. The present study measured the frequency of 14 agitated behaviors during bathing in 15 elderly residents with dementia residing in a continuing care center. Each resident was observed for four sessions of two different bathing methods, the conventional tub bath and a modification of the bed bath, known as the Thermal bath. The summed frequencies of all agitated behaviors was significantly less for the Thermal bath than the tub bath. This overall effect was greater in men than women and in one particular behavior, shivering. The results suggest that for individuals with dementia the Thermal bath offers a viable alternative to the conventional tub method. Further research may clarify other parameters, such as cost effectiveness and long-term effects of the use of non-rinse cleansers for elderly individuals.