Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.

Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.

Combinatorial and statistical prediction of gene expression from haplotype sequence.

MOTIVATION: Genome-wide association studies (GWAS) have discovered thousands of significant genetic effects on disease phenotypes. By considering gene expression as the intermediary between genotype and disease phenotype, expression quantitative trait loci studies have interpreted many of these variants by their regulatory effects on gene expression. However, there remains a considerable gap between genotype-to-gene expression association and genotype-to-gene expression prediction. Accurate prediction of gene expression enables gene-based association studies to be performed post hoc for existing GWAS, reduces multiple testing burden, and can prioritize genes for subsequent experimental investigation. RESULTS: In this work, we develop gene expression prediction methods that relax the independence and additivity assumptions between genetic markers. First, we consider gene expression prediction from a regression perspective and develop the HAPLEXR algorithm which combines haplotype clusterings with allelic dosages. Second, we introduce the new gene expression classification problem, which focuses on identifying expression groups rather than continuous measurements; we formalize the selection of an appropriate number of expression groups using the principle of maximum entropy. Third, we develop the HAPLEXD algorithm that models haplotype sharing with a modified suffix tree data structure and computes expression groups by spectral clustering. In both models, we penalize model complexity by prioritizing genetic clusters that indicate significant effects on expression. We compare HAPLEXR and HAPLEXD with three state-of-the-art expression prediction methods and two novel logistic regression approaches across five GTEx v8 tissues. HAPLEXD exhibits significantly higher classification accuracy overall; HAPLEXR shows higher prediction accuracy on approximately half of the genes tested and the largest number of best predicted genes (r2>0.1) among all methods. We show that variant and haplotype features selected by HAPLEXR are smaller in size than competing methods (and thus more interpretable) and are significantly enriched in functional annotations related to gene regulation. These results demonstrate the importance of explicitly modeling non-dosage dependent and intragenic epistatic effects when predicting expression. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available at https://github.com/rapturous/HAPLEX. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Suppression of myocardial glucose metabolism in FDG PET/CT: impact of dose variation in heparin bolus pre-administration.

INTRODUCTION: Adequate suppression of physiologic myocardial glucose uptake is important to ensure the interpretability and diagnostic reliability of [18F]fluorodeoxyglucose (FDG) PET/CT studies performed in the context of cardiac inflammation and infection. This study describes our experience with 4 preparatory protocols used in our institution. METHODS: FDG PET/CT scans were performed according to 4 preparatory protocols (716 scans total), i.e. 6-h fast (group 1), low-carbohydrate diet plus 12-h fast (group 2), low-carbohydrate diet plus 12-h fast plus intravenous heparin pre-administration (15 IU/kg) (group 3), and low-carbohydrate diet plus 12-h fast plus intravenous heparin pre-administration (50 IU/kg) (group 4). Consecutive scans were retrospectively included from time frames during which the particular protocol was used. FDG uptake in normal myocardium was scored on a scale ranging from 0 (uptake less than that in the left ventricular blood pool) to 4 (diffuse uptake greater than that in the liver). Complete suppression was defined as uptake less than or equal to the blood pool (scores 0-1). RESULTS: Complete suppression was accomplished in 27% in group 1, 68% in group 2, 69% in group 3 and 81% in group 4. Complete suppression was significantly lower in group 1 compared with all other groups (P < 0.0001 for all comparisons) and significantly higher in group 4 compared with group 2 (P = 0.005) and group 3 (P = 0.007). Groups 2 and 3 did not differ significantly (P = 0.92). CONCLUSION: A total of 50 IU/kg single-dose heparin administration before FDG PET/CT in addition to a low-carbohydrate diet and prolonged fast significantly outperformed protocols with no or lower dose (15 IU/kg) heparin in completely suppressing myocardial glucose metabolism.

Protocol of a randomized open label multicentre trial comparing continuous intrajejunal levodopa infusion with deep brain stimulation in Parkinson's disease - the INfusion VErsus STimulation (INVEST) study.

BACKGROUND: Both Deep Brain Stimulation (DBS) and Continuous intrajejunal Levodopa Infusion (CLI) are effective therapies for the treatment of Parkinson's disease (PD). To our knowledge, no direct head-to-head comparison of DBS and CLI has been performed, whilst the costs probably differ significantly. In the INfusion VErsus STimulation (INVEST) study, costs and effectiveness of DBS and CLI are compared in a randomized controlled trial (RCT) in patients with PD, to study whether higher costs of one of the therapies are justified by superiority of that treatment. METHODS: A prospective open label multicentre RCT is being performed, with ancillary patient preference observational arms. Patients with PD who, despite optimal pharmacological treatment, have severe response fluctuations, bradykinesia, dyskinesias, or painful dystonia are eligible for inclusion. A total of 66 patients will be randomized. There is no minimal inclusion in the patient preference arms. The primary health economic outcomes are costs per unit on the Parkinson's Disease Questionnaire-39 (PDQ-39) and costs per unit Quality-Adjusted Life Year (QALY) at 12 months. The main clinical outcome is patient-reported quality of life measured with the PDQ-39 at 12 months. Patients will additionally be followed during 36 months after initiation of the study treatment. DISCUSSION: The INVEST trial directly compares the costs and effectiveness of the advanced therapies DBS and CLI. TRIAL REGISTRATION: Dutch Trial Register identifier 4753, registered November 3rd, 2014; EudraCT number 2014-001501-32, Clinicaltrials.gov: NCT02480803.

Effects of two commercial diets and technical feed treatment on stomach lesions and immune system of fattening pigs.

The impact of technical feed treatment and diet on stomach lesions and traits of the local and systemic immune system were investigated in fattening pigs. Feeding groups differed in technical feed treatment (standard ground meal vs. finely ground and pelleted feed) and diet (soya bean meal vs. rapeseed meal/DDGS/soya beans). Pigs were fattened approximately 10 weeks by ad libitum feeding and slaughtered subsequently. Gastric alterations were assessed by a macroscopic scoring system [macroscopic stomach score (MSC) 0 =  normal to 4 =  severe lesions]. For immunological investigations, lymphocytes from blood and jejunal tissues were isolated. T-cell phenotyping was carried out by staining intestinal lymphocytes with monoclonal antibodies for CD4 and CD8 and flow cytometric measurements. MSC was higher in animals fed finely ground and pelleted feed compared with their counterparts. Significant interactions between diet and feed treatment considering the MSC were observed (p = 0.027). There was no effect of diet or technical feed treatment on T cells of blood, Lymphonodi gastrici or lamina propria (LP) and intraepithelial cells. However, technical feed treatment significantly affected subsets of CD4+ , CD8+ , CD8low , CD4/CD8 double-positive T cells, the mean fluorescence intensity of CD4+ T cells and the ratio of CD8low /CD8high T cells in Peyer's patches (PP). All named parameters were reduced in PP of animals fed finely ground and pelleted feed compared with animals fed standard ground meal. Furthermore, significant differences between T cells of lymph nodes and LP were observed between animals with middle MSC (MSC = 1-2.5) and animals with high MSC (MSC = 3-4). Significant alterations in T cells of PP were observed between animals of low (MSC = 0-0.5) and high MSC. The observed effects provide the evidence that the impact of technical feed treatment is not limited on the stomach lesions. Possible stimuli and consequences of the immune system should be studied in more detail.

Comparison of calculated and experimentally determined SID of CP and AA in complex diets differing in AA contents for grower finisher pigs.

In practice, the content of standardized ileal digestible AA in complex feeds for pigs is calculated on the basis of tabulated values for individual feedstuffs. It comes into question, however, whether this truly reflects an accurate content based upon the estimate made for the individual feedstuffs. The objective of this study was to compare standardized ileal digestibility (SID) of crude protein (CP) and selected AA in complex feeds for grower and finisher pigs either calculated or experimentally determined. Six diets with increasing AA levels were prepared for grower (BW from 30 to 70 kg) and finisher (BW from 70 to 120 kg) feed. Crystalline L-lys, DL-met and L-thr were added to both diets, L-trp and L-val only to the grower feed. SID of both CP and AA was calculated from feed tables and experimentally determined in six adult minipigs (MINILEWE) with ileorectal anastomosis. With increasing AA levels, experimentally determined SID of supplemented AA increased (p < 0.05), but SID of CP (p ≥ 0.05) was not affected. In both grower and finisher feed, calculated and experimentally determined SID of CP, Met, Cys, Trp, Ile and Tyr differed by more than 2% units, but those of Lys and His only in the finisher feed. Yet this effect was not directly consistent. The margin of error following estimation of SID of AA via tabulated values for individual feedstuffs, however, seems to be acceptable for practical use.

Effects of selection stringency on the outcomes of directed evolution.

Directed evolution makes mutant lineages compete in climbing complicated sequence-function landscapes. Given this underlying complexity it is unclear how selection stringency, a ubiquitous parameter of directed evolution, impacts the outcome. Here we approach this question in terms of the fitnesses of the candidate variants at each round and the heterogeneity of their distributions of fitness effects. We show that even if the fittest mutant is most likely to yield the fittest mutants in the next round of selection, diversification can improve outcomes by sampling a larger variety of fitness effects. We find that heterogeneity in fitness effects between variants, larger population sizes, and evolution over a greater number of rounds all encourage diversification.

Comparison of TP53 Mutations in Myelodysplasia and Acute Leukemia Suggests Divergent Roles in Initiation and Progression.

TP53 mutation predicts adverse prognosis in many cancers, including myeloid neoplasms, but the mechanisms by which specific mutations impact disease biology, and whether they differ between disease categories, remain unknown. We analyzed TP53 mutations in four myeloid neoplasm subtypes (MDS, AML, AML with myelodysplasia-related changes (AML-MRC), and therapy-related acute myeloid leukemia (tAML)), and identified differences in mutation types, spectrum, and hotspots between disease categories and compared to solid tumors. Missense mutations in the DNA-binding domain were most common across all categories, whereas inactivating mutations and mutations outside the DNA binding domain were more common in AML-MRC compared to MDS. TP53 mutations in MDS were more likely to retain transcriptional activity, and co-mutation profiles were distinct between disease categories and mutation types. Our findings suggest that mutated TP53 contributes to initiation and progression of neoplasia via distinct mechanisms, and support the utility of specific identification of TP53 mutations in myeloid malignancies.

Evaluating molecular fingerprint-based models of drug side effects against a statistical control.

There are many machine learning models that use molecular fingerprints of drugs to predict side effects. Characterizing their skill is necessary for understanding their usefulness in pharmaceutical development. Here, we analyze a statistical control of side effect prediction skill, develop a pipeline for benchmarking models, and evaluate how well existing models predict side effects identified in pharmaceutical documentation. We demonstrate that molecular fingerprints are useful for ranking drugs by their likelihood to cause a given side effect. However, the predictions for one or more drugs overall benefit only marginally from molecular fingerprints when ranking the likelihoods of many possible side effects, and display at most modest overall skill at identifying the side effects that do and do not occur.

Review: Bioavailability of trace elements in farm animals: definition and practical considerations for improved assessment of efficacy and safety.

Currently, the authorisation procedure of trace elements as feed additives in the European Union according to Regulation (EC) No. 1831/2003 does not consider the bioavailability of trace element sources. This manuscript provides framework conditions for in vivo experiments that aim to estimate differences in the relative bioavailability between supplements of essential trace elements. Framework conditions encompass necessary technical information on the test substance, the experimental design and diet composition as well as the suitability of status parameters that allow for relative comparisons of regression variables. This manuscript evolves recommendations for researchers to conduct solid and reliable experiments on the matter as well as decision makers to interpret the value of studies submitted with authorisation applications regarding a certain trace element supplement.

Activation of RNA polymerase II transcription.

Multiple alternative interactions between activators and co-activators stimulate transcription by RNA polymerase II. In the past two years, multiprotein co-activator complexes have been characterized and their subunits defined. TATA-box binding protein associated factor (TAF) subunits of yeast TFIID were found to be generally required for transcription in vivo. Mammalian multisubunit coactivator complexes with homologs of the yeast SRB/Mediator subunits have been characterized. Structures of nuclear receptor-coactivator complexes have been determined.

Delivery of an EBV episome by a self-circularizing helper-dependent adenovirus: long-term transgene expression in immunocompetent mice.

Epstein-Barr virus (EBV) evolved an episomal system for maintaining life-long, latent infection of human B lymphocytes. Circular episomes engineered from EBV components required for this latent form of infection have the capacity to persist in most types of replicating mammalian cells without DNA integration and the pitfalls of insertional mutagenesis. EBV episomes are typically transduced using low-efficiency methods. Here we present a method for efficient delivery of EBV episomes to nuclei of hepatocytes in living mice using a helper-dependent adenoviral vector and Cre-mediated recombination in vivo to generate circular EBV episomes following infection. Cre is transiently expressed from a hepatocyte-specific promoter so that vector generation and transgene expression are tissue specific. We show long-term persistence of the circularized vector DNA and expression of a reporter gene in hepatocytes of immunocompetent mice.

Detoxifying deoxynivalenol (DON)-contaminated feedstuff: consequences of sodium sulphite (SoS) treatment on performance and blood parameters in fattening pigs.

A 10-week feeding experiment was carried out examining the effects of deoxynivalenol (DON)-contaminated maize treated with different sodium sulphite (SoS) concentrations on performance, health and DON-plasma concentrations in fattening pigs. Two maize batches were used: background-contaminated (CON, 0.73 mg/kg maize) and Fusarium-toxin contaminated (DON, 44.45 mg/kg maize) maize. Both were wet preserved at 20% moisture content, with one of three (0.0, 2.5, 5.0 g/kg maize) sodium sulphite concentrations and propionic acid (15%). Each maize batch was then mixed into a barley-wheat-based diet at a proportion of 10%, resulting in the following 6 feeding groups: CON- (CON + 0.0 g SoS/kg maize), CON2.5 (CON + 2.5 g SoS/kg maize), CON5.0 (CON + 5.0 g SoS/kg maize), DON- (DON + 0.0 g SoS/kg maize), DON2.5 (DON + 2.5 g SoS/kg maize) and DON5.0 (DON + 5.0 g SoS/kg maize). Dietary DON concentration was reduced by ~ 36% in group DON2.5 and ~ 63% in group DON5.0. There was no impact on ZEN concentration in the diets due to SoS treatment. Pigs receiving diet DON- showed markedly lower feed intake (FI) compared to those fed the control diets. With SoS-treatment of maize, FI of pigs fed the DON diet (DON5.0: 3.35 kg/d) were comparable to that control (CON-: 3.30 kg/day), and these effects were also reflected in live weight gain. There were some effects of SoS, DON or their interaction on serum urea, cholesterol and albumin, but always within the physiological range and thus likely negligible. SoS wet preservation of Fusarium-toxin contaminated maize successfully detoxified DON to its innocuous sulfonates, thus restoring impaired performance in fatteners.

Transcription of class III genes activated by viral immediate early proteins.

The adenovirus EIA and pseudorabies virus immediate early (IE) proteins induce transcription from transfected viral and nonviral genes transcribed by RNA polymerase II (class II genes). These proteins have now been shown also to activate transcription of transfected genes transcribed by RNA polymerase III (class III genes). As previously observed for class II genes, this stimulation of class III gene transcription was much greater for transfected genes than for the major endogenous cellular class III genes. Extracts made from cell lines stably expressing a transfected pseudorabies virus IE gene were 10 to 20 times more active in the in vitro transcription of exogenously added class III genes than extracts of the parental cell line. These results indicate that the E1A and IE proteins stimulate the expression of class III genes by a mechanism similar to the mechanism for stimulation of class II gene transcription by these proteins.

Cloning of a transcriptionally active human TATA binding factor.

Transcription factor IID (TFIID) binds to the TATA box promoter element and regulates the expression of most eukaryotic genes transcribed by RNA polymerase II. Complementary DNA (cDNA) encoding a human TFIID protein has been cloned. The human TFIID polypeptide has 339 amino acids and a molecular size of 37,745 daltons. The carboxyl-terminal 181 amino acids of the human TFIID protein shares 80% identity with the TFIID protein from Saccharomyces cerevisiae. The amino terminus contains an unusual repeat of 38 consecutive glutamine residues and an X-Thr-Pro repeat. Expression of DNA in reticulocyte lysates or in Escherichia coli yielded a protein that was competent for both DNA binding and transcription activation.

Evaluation of maternal attachment, self-efficacy, levels of depression, and anxiety in mothers who have babies diagnosed with retinopathy of prematurity.

PURPOSE: The aim of this study is to evaluate the emotional stress and its effects on parental self-efficacy and mother-infant attachment in mothers whose babies were diagnosed with retinopathy of prematurity (ROP). METHODS: Study sample was consisted of voluntarily participating 82 mothers whose babies were first diagnosed with ROP, 83 mothers of preterm babies without ROP, and 85 mothers of term babies admitting for their routine visits. Sociodemographic data form maternal attachment scale, state-trait anxiety inventory, Edinburgh postnatal depression scale, and parental self-efficacy scale were applied to study participants, and the overall results of three groups were statistically compared. RESULTS: The sociodemographic features of three study groups were similar. Statistical significant differences were found in depression and state anxiety levels among study groups, while maternal attachment scale and trait anxiety level scores and parental self-efficacy scale total score were similar in study groups. Maternal depression and state-anxiety levels were tend to be higher in mother of children diagnosed with ROP and prematurity; however, there were no statistically significant differences between levels of mothers' of premature children with or without ROP. CONCLUSION: This is the first study in literature assessing the additional effect of ROP on the anxiety and depression levels of recent mothers, as well as mother-infant attachment and parental self-efficacy. Supporting of mothers having an infant with diagnosed ROP is crucial because of feeling themselves inefficient and responsible for all interventions applied to their babies.

Ordering promoter binding of class III transcription factors TFIIIC1 and TFIIIC2.

The separation of the mammalian class III transcription factor TFIIIC into two functional components, termed TFIIIC1 and TFIIIC2, enabled an analysis of their functions in transcription initiation. Template competition assays were used to define the order with which these factors interact in vitro to form stable preinitiation complexes on the adenovirus VAI and Drosophila melanogaster tRNA(Arg) genes. The interaction between these genes and TFIIIC2, the factor that binds with high affinity to the B block, was both necessary and sufficient for template commitment. When either the VAI or tRNA(Arg) gene was preincubated with TFIIIC2 alone, transcription of a second gene added subsequently was excluded, indicating that TFIIIC2 bound stably to the first template. Furthermore, the interaction between TFIIIC2 and these genes must occur prior to that of TFIIIC1 or TFIIIB. Once TFIIIC2 was bound, TFIIIC1 could bind to the tRNA(Arg) and VAI genes, although its interaction with the VAI gene was less stable than that with the tRNA(Arg) gene. TFIIIB activity bound stably to the complex of both genes with TFIIIC2. These results demonstrate that TFIIIC2 is the first transcription factor to bind to these genes and that TFIIIB and TFIIIC1 can then interact in either order to form a preinitiation complex.

Factors responsible for the higher transcriptional activity of extracts of adenovirus-infected cells fractionate with the TATA box transcription factor.

Extracts of adenovirus-infected HeLa cells have 5- to 10-fold-higher activity for transcription from the major late promoter in vitro than do extracts of mock-infected or E1A mutant-infected cells (K. Leong and A. J. Berk, Proc. Natl. Acad. Sci. USA 83:5844-5848, 1986). In this study, we analyzed extracts from mock-infected cells and from cells infected with an E1A mutant, pm975, which expresses principally the large E1A protein responsible for the stimulation of transcription. These extracts were fractionated by phosphocellulose chromatography, a procedure which separates factors required for transcription from this promoter (J. D. Dignam, B. S. Shastry, and R. G. Roeder, Methods Enzymol. 101:582-589, 1983), allowing the quantitative assay of individual factors (M. Samuels, A. Fire, and P. A. Sharp, J. Biol. Chem. 257:14419-14427, 1982). Fractions eluted with 0.04, 0.35, and 0.6 M KCl, which contained RNA polymerase II, the upstream factor MLTF, and three general polymerase II transcription factors, had similar activities when prepared from virus-infected or from mock-infected cells. The sequence-specific DNA-binding activity of MLTF was also similar in the virus-infected- and mock-infected-cell extracts. In contrast, the 1.0 M KCl fraction prepared from virus-infected cells consistently exhibited activity severalfold higher than that of the equivalent fraction prepared in parallel from mock-infected cells. E1A protein eluted principally (greater than 80%) in the 0.35 M KCl fraction. Results of others (M. Sawadogo and R. G. Roeder, Cell 43:165-175, 1985) have shown that the 1.0 M KCl fraction, containing 2 to 5% of the unfractionated protein extract, contains a factor which binds specifically to the major late promoter TATA box. These results, together with a recent genetic analysis of the E1B promoter which demonstrated that the TATA box was required for its efficient transcriptional activation (transactivation) by E1A (L. Wu, D. S. E. Rosser, M. Schmidt, and A. J. Berk, Nature (London) 326:512-515, 1987), are consistent with the model that E1A protein indirectly activates the TATA box transcription factor. Consistent with this model was the finding that mutants of the major late promoter containing only the TATA box and cap site region were transcribed at higher rates with extracts from virus-infected cells than with extracts from mock-infected cells. Other models consistent with the results are also discussed.

Concentration dependence of transcriptional transactivation in inducible E1A-containing human cells.

The adenovirus E1A proteins are essential for the normal temporal activation of transcription from every other adenoviral early promoter. High-level E1A expression in the absence of viral infection would facilitate biochemical studies of E1A-mediated transactivation. Toward this end, we introduced the adenovirus type 2 E1A gene under the control of the murine mammary tumor virus promoter into HeLa cells. Uninduced cells expressed little or no detectable E1A mRNA. Upon induction, mRNA levels accumulated to about 50% of the level observed in 293 cells. The level of E1A expression in these cells could be controlled by varying the concentration of the inducing glucocorticoid. Under these conditions of varying E1A concentrations, it was observed that activation of the E2, E3, and E4 promoters of H5dl312 initiated at the same E1A concentration and that transcription from each promoter increased as the E1A concentration increased. These results indicate that E1A-mediated transactivation is proportional to the concentration of E1A protein. E1A-dependent transcriptional stimulation of the E4 promoter was reproduced in an in vitro transcription system, demonstrating that expression of only the E1A proteins was sufficient to increase the transcriptional activity of nuclear extracts.

Reversal of in vitro p53 squelching by both TFIIB and TFIID.

p53, the protein encoded by one of the most significant human tumor suppressor genes, is a sequence-specific transcriptional activator. When activated by a double-stranded DNA break, p53 function arrests cells in G1 and can induce apoptosis. Transcriptional activation function is critical for p53 tumor suppression, although transcriptional repressing and nontranscriptional functions of p53 may contribute. p53 activation requires that it bind to TFIID through interactions with TATA box-binding protein (TBP)-associated factors and potentially with TBP. Here, we studied the mechanism of p53 activation using in vitro transcription and a sufficiently high p53 concentration to squelch activated transcription. Squelching is thought to result when target molecules that interact with activation domains are titrated by binding to excess activator. Addition of either excess TFIIB or TFIID but not other proteins required for p53-activated transcription reversed squelching by high p53 concentrations, whereas neither stimulated transcription in reactions without excess p53. These results reveal that both TFIIB and TFIID are inhibited by high concentrations of p53 and suggest that p53 activation may work through direct or indirect interactions with both TFIIB and TFIID.