Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization.

T cells recognize antigen using a large and diverse set of antigen-specific receptors created by a complex process of imprecise somatic cell gene rearrangements. In response to antigen-/receptor-binding-specific T cells then divide to form memory and effector populations. We apply high-throughput sequencing to investigate the global changes in T cell receptor sequences following immunization with ovalbumin (OVA) and adjuvant, to understand how adaptive immunity achieves specificity. Each immunized mouse contained a predominantly private but related set of expanded CDR3β sequences. We used machine learning to identify common patterns which distinguished repertoires from mice immunized with adjuvant with and without OVA. The CDR3β sequences were deconstructed into sets of overlapping contiguous amino acid triplets. The frequencies of these motifs were used to train the linear programming boosting (LPBoost) algorithm LPBoost to classify between TCR repertoires. LPBoost could distinguish between the two classes of repertoire with accuracies above 80%, using a small subset of triplet sequences present at defined positions along the CDR3. The results suggest a model in which such motifs confer degenerate antigen specificity in the context of a highly diverse and largely private set of T cell receptors

Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.

The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different T-cell receptors (TcR) in CD4 + T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis, using high throughput parallel sequencing of the TcRβ chain. Our initial hypothesis that immunization would induce repertoire convergence proved to be incorrect, and therefore an alternative approach was developed that allows accurate stratification of TcR repertoires and provides novel insights into the nature of CD4 + T-cell receptor recognition

Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires.

MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone. RESULTS: The CDR3β sequences were deconstructed into short stretches of overlapping contiguous amino acids. The motifs were ranked according to a one-dimensional Bayesian classifier score comparing their frequency in the repertoires of the two immunization classes. The top ranking motifs were selected and used to create feature vectors which were used to train a support vector machine. The support vector machine achieved high classification scores in a leave-one-out validation test reaching  : >90% in some cases. SUMMARY: The study describes a novel two-stage classification strategy combining a one-dimensional Bayesian classifier with a support vector machine. Using this approach we demonstrate that the frequency of a small number of linear motifs three amino acids in length can accurately identify a CD4 T cell response to ovalbumin against a background response to the complex mixture of antigens which characterize Complete Freund's Adjuvant. AVAILABILITY AND IMPLEMENTATION: The sequence data is available at www.ncbi.nlm.nih.gov/sra/?term¼SRP075893 The Decombinator package is available at github.com/innate2adaptive/Decombinator The R package e1071 is available at the CRAN repository https://cran.r-project.org/web/packages/e1071/index.html CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online

Evaluation of mechanical and interfacial properties of bio-composites based on poly(lactic acid) with natural cellulose fibers

The circular economy policy and the interest for sustainable material are inducing a constant expansion of the bio-composites market. The opportunity of using natural fibers in bio-based and biodegradable polymeric matrices, derived from industrial and/or agricultural waste, represents a stimulating challenge in the replacement of traditional composites based on fossil sources. The coupling of bioplastics with natural fibers in order to lower costs and promote degradability is one of the primary objectives of research, above all in the packaging and agricultural sectors where large amounts of non-recyclable plastics are generated, inducing a serious problem for plastic disposal and potential accumulation in the environment. Among biopolymers, poly(lactic acid) (PLA) is one of the most used compostable, bio-based polymeric matrices, since it exhibits process ability and mechanical properties compatible with a wide range of applications. In this study, two types of cellulosic fibers were processed with PLA in order to obtain bio-composites with different percentages of microfibers (5%, 10%, 20%). The mechanical properties were evaluated (tensile and impact test), and analytical models were applied in order to estimate the adhesion between matrix and fibers and to predict the material's stiffness. Understanding these properties is of particular importance in order to be able to tune and project the final characteristics of bio-composites

Descriptors of Posidonia oceanica meadows: Use and application

The conservation of the coastal marine environment requires the possession of information that enables the global quality of the environment to be evaluated reliably and relatively quickly. The use of biological indicators is often an appropriate method. Seagrasses in general, and Posidonia oceanica meadows in particular, are considered to be appropriate for biomonitoring because of their wide distribution, reasonable size, sedentary habit, easy collection and abundance and sensitivity to modifications of littoral zone. Reasoned management, on the scale of the whole Mediterranean basin, requires standardized methods of study, to be applied by both researchers and administrators, enabling comparable results to be obtained. This paper synthesises the existing methods applied to monitor P. oceanica meadows, identifies the most suitable techniques and suggests future research directions. From the results of a questionnaire, distributed to all the identified laboratories working on this topic, a list of the most commonly used descriptors was drawn up, together with the related research techniques (e.g. standardization, interest and limits, valuation of the results). It seems that the techniques used to study meadows are rather similar, but rarely identical, even though the various teams often refer to previously published works. This paper shows the interest of a practical guide that describes, in a standardized way, the most useful techniques enabling P. oceanica meadows to be used as an environmental descriptor. Indeed, it constitutes the first stage in the process. (c) 2005 Elsevier Ltd. All rights reserved.Peer reviewe

GABAergic and glycinergic inputs modulate rhythmogenic mechanisms in the lamprey respiratory network

We have previously shown that GABA and glycine modulate respiratory activity in the in vitro brainstem preparations of the lamprey and that blockade of GABA(A) and glycine receptors restores the respiratory rhythm during apnoea caused by blockade of ionotropic glutamate receptors. However, the neural substrates involved in these effects are unknown. To address this issue, the role of GABA(A), GABA(B) and glycine receptors within the paratrigeminal respiratory group (pTRG), the proposed respiratory central pattern generator, and the vagal motoneuron region was investigated both during apnoea induced by blockade of glutamatergic transmission and under basal conditions through microinjections of specific antagonists. The removal of GABAergic, but not glycinergic transmission within the pTRG, causes the resumption of rhythmic respiratory activity during apnoea, and reveals the presence of a modulatory control of the pTRG under basal conditions. A blockade of GABA(A) and glycine receptors within the vagal region strongly increases the respiratory frequency through disinhibition of neurons projecting to the pTRG from the vagal region. These neurons were retrogradely labelled (neurobiotin) from the pTRG. Intense GABA immunoreactivity is observed both within the pTRG and the vagal area, which corroborates present findings. The results confirm the pTRG as a primary site of respiratory rhythm generation, and suggest that inhibition modulates the activity of rhythm-generating neurons, without any direct role in burst formation and termination mechanisms

Inhibition of Interferon-Gamma-Stimulated Melanoma Progression by Targeting Neuronal Nitric Oxide Synthase (nNOS)

Interferon-gamma (IFN-γ) is shown to stimulate melanoma development and progression. However, the underlying mechanism has not been completely defined. Our study aimed to determine the role of neuronal nitric oxide synthase (nNOS)-mediated signaling in IFN-γ-stimulated melanoma progression and the anti-melanoma effects of novel nNOS inhibitors. Our study shows that IFN-γ markedly induced the expression levels of nNOS in melanoma cells associated with increased intracellular nitric oxide (NO) levels. Co-treatment with novel nNOS inhibitors effectively alleviated IFN-γ-activated STAT1/3. Further, reverse phase protein array (RPPA) analysis demonstrated that IFN-γ induced the expression of HIF1α, c-Myc, and programmed death-ligand 1 (PD-L1), in contrast to IFN-α. Blocking the nNOS-mediated signaling pathway using nNOS-selective inhibitors was shown to effectively diminish IFN-γ-induced PD-L1 expression in melanoma cells. Using a human melanoma xenograft mouse model, the in vivo studies revealed that IFN-γ increased tumor growth compared to control, which was inhibited by the co-administration of nNOS inhibitor MAC-3-190. Another nNOS inhibitor, HH044, was shown to effectively inhibit in vivo tumor growth and was associated with reduced PD-L1 expression levels in melanoma xenografts. Our study demonstrates the important role of nNOS-mediated NO signaling in IFN-γ-stimulated melanoma progression. Targeting nNOS using highly selective small molecular inhibitors is a unique and effective strategy to improve melanoma treatment

Electrosprayed shrimp and mushroom nanochitins on cellulose tissue for skin contact application

Cosmetics has recently focused on biobased skin-compatible materials. Materials from natural sources can be used to produce more sustainable skin contact products with enhanced bioactivity. Surface functionalization using natural-based nano/microparticles is thus a subject of study, aimed at better understanding the skin compatibility of many biopolymers also deriving from biowaste. This research investigated electrospray as a method for surface modification of cellulose tissues with chitin nanofibrils (CNs) using two different sources—namely, vegetable (i.e., from fungi), and animal (from crustaceans)—and different solvent systems to obtain a biobased and skin-compatible product. The surface of cellulose tissues was uniformly decorated with electrosprayed CNs. Biological analysis revealed that all treated samples were suitable for skin applications since human dermal keratinocytes (i.e., HaCaT cells) successfully adhered to the processed tissues and were viable after being in contact with released substances in culture media. These results indicate that the use of solvents did not affect the final cytocompatibility due to their effective evaporation during the electrospray process. Such treatments did not also affect the characteristics of cellulose; in addition, they showed promising anti-inflammatory and indirect antimicrobial activity toward dermal keratinocytes in vitro. Specifically, cellulosic substrates decorated with nanochitins from shrimp showed strong immunomodulatory activity by first upregulating then downregulating the pro-inflammatory cytokines, whereas nanochitins from mushrooms displayed an overall anti-inflammatory activity via a slight decrement of the pro-inflammatory cytokines and increment of the anti-inflammatory marker. Electrospray could represent a green method for surface modification of sustainable and biofunctional skincare products

A controlled study comparing salivary osmolality, caries experience and caries risk in patients with cerebral palsy

Cerebral palsy (CP) is a permanent neurological disorder accompanied by secondary musculoskeletal masticatory disorder, with repercussion on chewing and deglutition functions. In these conditions, the liquids ingestion is compromised resulting in salivary osmolality alteration. The objective of this study was to compare salivary osmolality, caries experience and caries risk between normoreactive individuals and patients with CP. The participants were 4-20 years old: 52 patients with CP treated at a reference rehabilitation centre (study group, SG), and 52 normoreactive individuals (control group, CG). Saliva was collected for five minutes using cotton rolls. Following centrifugation, salivary osmolality was determined by freezing point depression osmometry. Evaluations included caries experience (DMFT index), and caries risk based on a caries-risk assessment tool (CAT). Descriptive and inferential statistics (Chi square and Student t tests) were used to compare the groups. Receiver operating characteristic (ROC) analyses were performed and the area under the ROC curve (Az) was calculated. The level of significance was set at 5%. The groups were homogeneous for sex (p=0.843) and age (p=0.128). In the SG, spastic type CP was the most prevalent (80.8%), and patients showed significantly higher salivary osmolality values compared with the CG (p74 for the SG and >54 for the CG in the presence of dental caries. A significant correlation was verified between salivary osmolality and the DMFT index for the SG (p?0.05). Although patients with CP showed higher salivary osmolality values, higher caries experience and caries risk were not observed compared with normoreactive individuals