207 research outputs found
Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells
Glycosylation is a highly complex process to produce a diverse repertoire of
cellular glycans that are attached to proteins and lipids. Glycans are involved
in fundamental biological processes, including protein folding and clearance,
cell proliferation and apoptosis, development, immune responses, and
pathogenesis. One of the major types of glycans, N-linked glycans, is formed by
sequential attachments of monosaccharides to proteins by a limited number of
enzymes. Many of these enzymes can accept multiple N-linked glycans as
substrates, thereby generating a large number of glycan intermediates and their
intermingled pathways. Motivated by the quantitative methods developed in
complex network research, we investigated the large-scale organization of such
N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation
pathways are extremely modular, and are composed of cohesive topological
modules that directly branch from a common upstream pathway of glycan
synthesis. This unique structural property allows the glycan production between
modules to be controlled by the upstream region. Although the enzymes act on
multiple glycan substrates, indicating cross-talk between modules, the impact
of the cross-talk on the module-specific enhancement of glycan synthesis may be
confined within a moderate range by transcription-level control. The findings
of the present study provide experimentally-testable predictions for
glycosylation processes, and may be applicable to therapeutic glycoprotein
engineering
Intrinsic gain modulation and adaptive neural coding
In many cases, the computation of a neural system can be reduced to a
receptive field, or a set of linear filters, and a thresholding function, or
gain curve, which determines the firing probability; this is known as a
linear/nonlinear model. In some forms of sensory adaptation, these linear
filters and gain curve adjust very rapidly to changes in the variance of a
randomly varying driving input. An apparently similar but previously unrelated
issue is the observation of gain control by background noise in cortical
neurons: the slope of the firing rate vs current (f-I) curve changes with the
variance of background random input. Here, we show a direct correspondence
between these two observations by relating variance-dependent changes in the
gain of f-I curves to characteristics of the changing empirical
linear/nonlinear model obtained by sampling. In the case that the underlying
system is fixed, we derive relationships relating the change of the gain with
respect to both mean and variance with the receptive fields derived from
reverse correlation on a white noise stimulus. Using two conductance-based
model neurons that display distinct gain modulation properties through a simple
change in parameters, we show that coding properties of both these models
quantitatively satisfy the predicted relationships. Our results describe how
both variance-dependent gain modulation and adaptive neural computation result
from intrinsic nonlinearity.Comment: 24 pages, 4 figures, 1 supporting informatio
Placebo Adherence and Its Association with Morbidity and Mortality in the Studies of Left Ventricular Dysfunction
A provocative finding from several double-blind clinical trials has been the association between greater adherence to placebo study medication and better health outcomes. We used data from the Studies of Left Ventricular Dysfunction (SOLVD) Treatment Trial (SOLVD-TT) and the SOLVD Prevention Trial (SOLVD-PT) to examine whether such associations could be validated and to examine several sources of bias and potential confounding.
Survival analytic methods were used to estimate the association between placebo adherence and several health outcomes, employing a number of modeling techniques to test for the existence of alternative explanations for the association. Higher adherence was defined as having taken ≥75% of prescribed study medication.
Higher placebo adherence was associated with improved overall survival in both SOLVD-TT and SOLVD-PT [hazard ratio (HR) = 0.52, 95% confidence interval (CI): 0.35 to 0.79 and HR = 0.52, 95%CI: 0.38 to 0.71, respectively]. Associations were similar for fatal or non-fatal cardiovascular or coronary heart disease events. Adjustment for both modifiable and non-modifiable cardiac risk factors (including age, gender, diabetes, blood pressure, smoking, weight, alcohol use, and levels of education) had minimal effect on the strength of the association. Little evidence of bias was found as an explanation for this relationship.
In these two trials, better adherence to placebo was associated with markedly superior health outcomes, including total in-study mortality and incident cardiovascular events. No important confounders were identified. These data suggest there may exist strong but unrecognized determinants of health outcomes for which placebo adherence is a marker
Fundamental movement skills are more than run, throw and catch: The role of stability skills.
Introduction In motor development literature fundamental movement skills are divided into three constructs: locomotive, object control and stability skills. Most fundamental movement skills research has focused on children's competency in locomotor and object control skills. The first aim of this study was to validate a test battery to assess the construct of stability skills, in children aged 6 to 10 (M age = 8.2, SD = 1.2). Secondly we assessed how the stability skills construct fitted into a model of fundamental movement skill. Method The Delphi method was used to select the stability skill battery. Confirmatory factor analysis (CFA) was used to assess if the skills loaded onto the same construct and a new model of FMS was developed using structural equation modelling. Results Three postural control tasks were selected (the log roll, rock and back support) because they had good face and content validity. These skills also demonstrated good predictive validity with gymnasts scoring significantly better than children without gymnastic training and children from a high SES school performing better than those from a mid and low SES schools and the mid SES children scored better than the low SES children (all p < .05). Inter rater reliability tests were excellent for all three skills (ICC = 0.81, 0.87, 0.87) as was test retest reliability (ICC 0.87-0.95). CFA provided good construct validity, and structural equation modelling revealed stability skills to be an independent factor in an overall FMS model which included locomotor (r = .88), object control (r = .76) and stability skills (r = .81). Discussion This study provides a rationale for the inclusion of stability skills in FMS assessment. The stability skills could be used alongside other FMS assessment tools to provide a holistic assessment of children's fundamental movement skills. Copyright
Early Priming Minimizes the Age-Related Immune Compromise of CD8+ T Cell Diversity and Function
The elderly are particularly susceptible to influenza A virus infections, with increased occurrence, disease severity and reduced vaccine efficacy attributed to declining immunity. Experimentally, the age-dependent decline in influenza-specific CD8+ T cell responsiveness reflects both functional compromise and the emergence of ‘repertoire holes’ arising from the loss of low frequency clonotypes. In this study, we asked whether early priming limits the time-related attrition of immune competence. Though primary responses in aged mice were compromised, animals vaccinated at 6 weeks then challenged >20 months later had T-cell responses that were normal in magnitude. Both functional quality and the persistence of ‘preferred’ TCR clonotypes that expand in a characteristic immunodominance hierarchy were maintained following early priming. Similar to the early priming, vaccination at 22 months followed by challenge retained a response magnitude equivalent to young mice. However, late priming resulted in reduced TCRβ diversity in comparison with vaccination earlier in life. Thus, early priming was critical to maintaining individual and population-wide TCRβ diversity. In summary, early exposure leads to the long-term maintenance of memory T cells and thus preserves optimal, influenza-specific CD8+ T-cell responsiveness and protects against the age-related attrition of naïve T-cell precursors. Our study supports development of vaccines that prime CD8+ T-cells early in life to elicit the broadest possible spectrum of CD8+ T-cell memory and preserve the magnitude, functionality and TCR usage of responding populations. In addition, our study provides the most comprehensive analysis of the aged (primary, secondary primed-early and secondary primed-late) TCR repertoires published to date
Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate
Many natural product-derived lectins such as the red algal lectin griffithsin (GRFT) have potent in vitro activity against viruses that display dense clusters of oligomannose N-linked glycans (NLG) on their surface envelope glycoproteins. However, since oligomannose NLG are also found on some host proteins it is possible that treatment with antiviral lectins may trigger undesirable side effects. For other antiviral lectins such as concanavalin A, banana lectin and cyanovirin-N (CV-N), interactions between the lectin and as yet undescribed cellular moieties have been reported to induce undesirable side effects including secretion of inflammatory cytokines and activation of host T-cells. We show that GRFT, unlike CV-N, binds the surface of human epithelial and peripheral blood mononuclear cells (PBMC) through an exclusively oligosaccharide-dependent interaction. In contrast to several other antiviral lectins however, GRFT treatment induces only minimal changes in secretion of inflammatory cytokines and chemokines by epithelial cells or human PBMC, has no measureable effect on cell viability and does not significantly upregulate markers of T-cell activation. In addition, GRFT appears to retain antiviral activity once bound to the surface of PBMC. Finally, RNA microarray studies show that, while CV-N and ConA regulate expression of a multitude of cellular genes, GRFT treatment effects only minimal alterations in the gene expression profile of a human ectocervical cell line. These studies indicate that GRFT has an outstanding safety profile with little evidence of induced toxicity, T-cell activation or deleterious immunological consequence, unique attributes for a natural product-derived lectin
Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units Contribute Substantially to Divergence Between Human and Chimpanzee Y Chromosomes
Comparison of human and chimpanzee genomes has received much attention,
because of paramount role for understanding evolutionary step distinguishing us
from our closest living relative. In order to contribute to insight into Y
chromosome evolutionary history, we study and compare tandems, higher order
repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y
chromosome contigs, using robust Global Repeat Map algorithm. We find a new
type of long-range acceleration, human-accelerated HOR regions. In peripheral
domains of 35mer human alphoid HORs, we find riddled features with ten
additional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. We
construct alphoid HOR schemes showing significant human-chimpanzee difference,
revealing rapid evolution after human-chimpanzee separation. We identify and
analyze over 20 large repeat units, most of them reported here for the first
time as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and
~23.5 kb tertiary repeat unit (~0.55 kb primary repeat unit, PRU); human 10848,
15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (~2.4 kb PRU); 715mer
and 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; and
chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial
human-chimpanzee differences are concentrated in large repeat structures, at
the level of as much as ~70% divergence, sizably exceeding previous numerical
estimates for some selected noncoding sequences. Smeared over the whole
sequenced assembly (25 Mb) this gives ~14% human--chimpanzee divergence. This
is significantly higher estimate of divergence between human and chimpanzee
than previous estimates.Comment: 22 pages, 7 figures, 12 tables. Published in Journal of Molecular
Evolutio
Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals
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