Hexafluoroisopropanol as a Bioconjugation Medium of Ultrafast, Tryptophan-Selective Catalysis.

The past decade has seen a remarkable growth in the number of bioconjugation techniques in chemistry, biology, material science, and biomedical fields. A core design element in bioconjugation technology is a chemical reaction that can form a covalent bond between the protein of interest and the labeling reagent. Achieving chemoselective protein bioconjugation in aqueous media is challenging, especially for generally less reactive amino acid residues, such as tryptophan. We present here the development of tryptophan-selective bioconjugation methods through ultrafast Lewis acid-catalyzed reactions in hexafluoroisopropanol (HFIP). Structure-reactivity relationship studies have revealed a combination of thiophene and ethanol moieties to give a suitable labeling reagent for this bioconjugation process, which enables modification of peptides and proteins in an extremely rapid reaction unencumbered by noticeable side reactions. The capability of the labeling method also facilitated radiofluorination application as well as antibody functionalization. Enhancement of an α-helix by HFIP leads to its compatibility with a certain protein, and this report also demonstrates a further stabilization strategy achieved by the addition of an ionic liquid to the HFIP medium. The nonaqueous bioconjugation approaches allow access to numerous chemical reactions that are unavailable in traditional aqueous processes and will further advance the chemistry of proteins.

Correction: Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids.

[This corrects the article DOI: 10.1039/D1SC05204G.].

Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids.

Development of multiple chemical tools for deoxyribonucleic acid (DNA) labeling has facilitated wide use of their functionalized conjugates, but significant practical and methodological challenges remain to achievement of site-specific chemical modification of the biomacromolecule. As covalent labeling processes are more challenging in aqueous solution, use of nonaqueous, biomolecule-compatible solvents such as an ionic liquid consisting of a salt with organic molecule architecture, could be remarkably helpful in this connection. Herein, we demonstrate site-specific chemical modification of unprotected DNAs through a tetrazene-forming amine-azide coupling reaction using an ionic liquid. This ionic liquid-enhanced reaction process has good functional group tolerance and precise chemoselectivity, and enables incorporation of various useful functionalities such as biotin, cholesterol, and fluorophores. A site-specifically labeled oligonucleotide, or aptamer interacting with a growth factor receptor (Her2) was successfully used in the fluorescence imaging of breast cancer cell lines. The non-traditional medium-promoted labeling strategy described here provides an alternative design paradigm for future development of chemical tools for applications involving DNA functionalization.

Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes.

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free, level-1 network model with any fixed number of reticulation vertices is generically identifiable under the Jukes-Cantor, Kimura 2-parameter, or Kimura 3-parameter constraints.

An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method.

While a diverse set of design strategies have produced various chemical tools for biomolecule labeling in aqueous media, the development of nonaqueous, biomolecule-compatible media for bioconjugation has significantly lagged behind. In this report, we demonstrate that an aprotic ionic liquid serves as a novel reaction solvent for protein bioconjugation without noticeable loss of the biomolecule functions. The ionic liquid bioconjugation approach led to discovery of a novel triphenylphosphine-mediated amine-azide coupling reaction that forges a stable tetrazene linkage on unprotected peptides and proteins. This strategy of using untraditional media would provide untapped opportunities for expanding the scope of chemical approaches for bioconjugation.

Cognitive Processes Unfold in a Social Context: A Review and Extension of Social Baseline Theory.

Psychologists often assume that social and cognitive processes operate independently, an assumption that prompts research into how social context influences cognitive processes. We propose that social and cognitive processes are not necessarily separate, and that social context is innate to resource dependent cognitive processes. We review the research supporting social baseline theory, which argues that our default state in physiological, cognitive, and neural processing is to incorporate the relative costs and benefits of acting in our social environment. The review extends social baseline theory by applying social baseline theory to basic cognitive processes such as vision, memory, and attention, incorporating individual differences into the theory, reviewing environmental influences on social baselines, and exploring the dynamic effects of social interactions. The theoretical and methodological implications of social baseline theory are discussed, and future research endeavors into social cognition should consider that cognitive processes are situated within our social environments.

Joining and decomposing reaction networks.

In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e.g., cross-talk) or decomposing networks (e.g., inhibition or knock-outs) affects three properties that reaction networks may possess-identifiability (recoverability of parameter values from data), steady-state invariants (relationships among species concentrations at steady state, used in model selection), and multistationarity (capacity for multiple steady states, which correspond to multiple cell decisions). Specifically, we prove results that clarify, for a network obtained by joining two smaller networks, how properties of the smaller networks can be inferred from or can imply similar properties of the original network. Our proofs use techniques from computational algebraic geometry, including elimination theory and differential algebra.

IDENTIFYING THE NUMBER OF COMPONENTS IN GAUSSIAN MIXTURE MODELS USING NUMERICAL ALGEBRAIC GEOMETRY.

Using Gaussian mixture models for clustering is a statistically mature method for clustering in data science with numerous successful applications in science and engineering. The parameters for a Gaussian mixture model are typically estimated from training data using the iterative expectation-maximization algorithm, which requires the number of Gaussian components a priori. In this study, we propose two algorithms rooted in numerical algebraic geometry, namely an area-based algorithm and a local maxima algorithm, to identify the optimal number of components. The area-based algorithm transforms several Gaussian mixture models with varying number of components into sets of equivalent polynomial regression splines. Next, it uses homotopy continuation methods for evaluating the resulting splines to identify the number of components that results in the best fit. The local maxima algorithm forms a set of polynomials by fitting a smoothing spline to a kernel density estimate of the data. Next, it uses numerical algebraic geometry to solve the system of the first derivatives for finding the local maxima of the resulting smoothing spline, which estimates the number of mixture components. The local maxima algorithm also identifies the location of the centers of Gaussian components. Using a real-world case study in automotive manufacturing and multiple simulations, we compare the performance of the proposed algorithms with that of Akaike information criterion (AIC) and Bayesian information criterion (BIC), which are popular methods in the literature. We show the proposed algorithms are more robust than AIC and BIC when the Gaussian assumption is violated.

Algebraic signatures of convex and non-convex codes.

A convex code is a binary code generated by the pattern of intersections of a collection of open convex sets in some Euclidean space. Convex codes are relevant to neuroscience as they arise from the activity of neurons that have convex receptive fields. In this paper, we use algebraic methods to determine if a code is convex. Specifically, we use the neural ideal of a code, which is a generalization of the Stanley-Reisner ideal. Using the neural ideal together with its standard generating set, the canonical form, we provide algebraic signatures of certain families of codes that are non-convex. We connect these signatures to the precise conditions on the arrangement of sets that prevent the codes from being convex. Finally, we also provide algebraic signatures for some families of codes that are convex, including the class of intersection-complete codes. These results allow us to detect convexity and non-convexity in a variety of situations, and point to some interesting open questions.

Dimensions of Group-Based Phylogenetic Mixtures.

Mixtures of group-based Markov models of evolution correspond to joins of toric varieties. In this paper, we establish a large number of cases for which these phylogenetic join varieties realize their expected dimension, meaning that they are nondefective. Nondefectiveness is not only interesting from a geometric point-of-view, but has been used to establish combinatorial identifiability for several classes of phylogenetic mixture models. Our focus is on group-based models where the equivalence classes of identified parameters are orbits of a subgroup of the automorphism group of the abelian group defining the model. In particular, we show that for these group-based models, the variety corresponding to the mixture of r trees with n leaves is nondefective when [Formula: see text]. We also give improved bounds for claw trees and give computational evidence that 2-tree and 3-tree mixtures are nondefective for small n.

Numerical algebraic geometry for model selection and its application to the life sciences.

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation and model selection. These are all optimization problems, well known to be challenging due to nonlinearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data are available. Here, we consider polynomial models (e.g. mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometrical structures relating models and data, and we demonstrate its utility on examples from cell signalling, synthetic biology and epidemiology.

Algebraic Systems Biology: A Case Study for the Wnt Pathway.

Steady-state analysis of dynamical systems for biological networks gives rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here, the variety is described by a polynomial system in 19 unknowns and 36 parameters. It has degree 9 over the parameter space. This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view. We employ current methods from computational algebraic geometry, polyhedral geometry, and combinatorics.

Sugarcoated isolation: evidence that social avoidance is linked to higher basal glucose levels and higher consumption of glucose.

OBJECTIVE: The human brain adjusts its level of effort in coping with various life stressors as a partial function of perceived access to social resources. We examined whether people who avoid social ties maintain a higher fasting basal level of glucose in their bloodstream and consume more sugar-rich food, reflecting strategies to draw more on personal resources when threatened. METHODS: In Study 1 (N = 60), we obtained fasting blood glucose and adult attachment orientations data. In Study 2 (N = 285), we collected measures of fasting blood glucose and adult attachment orientations from older adults of mixed gender, using a measure of attachment style different from Study 1. In Study 3 (N = 108), we examined the link between trait-like attachment avoidance, manipulation of an asocial state, and consumption of sugar-rich food. In Study 4 (N = 115), we examined whether manipulating the social network will moderate the effect of attachment avoidance on consumption of sugar-rich food. RESULTS: In Study 1, fasting blood glucose levels corresponded with higher attachment avoidance scores after statistically adjusting for time of assessment and interpersonal anxiety. For Study 2, fasting blood glucose continued to correspond with higher adult attachment avoidance even after statistically adjusting for interpersonal anxiety, stress indices, age, gender, social support and body mass. In Study 3, people high in attachment avoidance consume more sugar-rich food, especially when reminded of asocial tendencies. Study 4 indicated that after facing a stressful task in the presence of others, avoidant people gather more sugar-rich food than more socially oriented people. CONCLUSION: RESULTS are consistent with the suggestion that socially avoidant individuals upwardly adjust their basal glucose levels and consume more glucose-rich food with the expectation of increased personal effort because of limited access to social resources. Further investigation of this link is warranted.

The economy of social resources and its influence on spatial perceptions.

Survival for any organism, including people, is a matter of resource management. To ensure survival, people necessarily budget their resources. Spatial perceptions contribute to resource budgeting by scaling the environment to an individual's available resources. Effective budgeting requires setting a balance of income and expenditures around some baseline value. For social resources, this baseline assumes that the individuals are embedded in their social network. A review of the literature supports the proposal that our visual perceptions vary based on the implicit budgeting of physical and social resources, where social resources, as they fluctuate relative to a baseline, can directly alter our visual perceptions.

Nasal epithelial lesions in F344 rats following a 90-day inhalation exposure to naphthalene.

Naphthalene (NA) was shown to be carcinogenic, causing respiratory epithelial adenoma in the nasal cavity of male F344 rats and olfactory epithelial neuroblastoma in female F344 rats at exposure concentrations of 10-60 ppm in a 2-year inhalation study conducted by the National Toxicology Program. To explore the exposure-response relationship and threshold for nasal epithelial effects in F344 rats, a 90-day (6 h/d, 5 d/wk) inhalation study was conducted at 0, 0.1, 1, 10 and 30 ppm NA vapor. Group size for nasal cavity histopathology was 10/sex with an additional 10/sex evaluated 4 wk post-exposure. NA exposure concentrations were measured by GC/MS, and aerosol testing verified that solid NA particles were not present. There were no NA exposure-related clinical observations and mild decreases in body weight (<10%) and food/water consumption were observed primarily in the 30 ppm rats. Rat heads were cross-sectioned at six levels for microscopic examination. There were no nasal cavity lesions related to NA exposure in rats of the 0.1 ppm group. Minimal hyperplasia was observed in the transitional/respiratory epithelium of rats exposed to 1 ppm. Mild hyperplasia and minimal squamous metaplasia were observed in the respiratory epithelium of rats exposed to 10 or 30 ppm. Lesions in the olfactory epithelium were observed only in rats of the 10 or 30 ppm groups and consisted of degeneration, necrosis, areas of re-epithelialization and basal cell hyperplasia. There was remarkable recovery of effects after 4 weeks, but residual olfactory epithelial degeneration and basal cell hyperplasia were still evident.

The fractions of respiratory tract cells at risk in formaldehyde carcinogenesis.

Clonal growth modeling of carcinogenesis requires data on the number of cells at risk of becoming cancerous. We synthesized literature data to estimate the fraction of respiratory tract epithelial cells that are progenitor cells, and therefore at risk, in formaldehyde carcinogenesis for specific respiratory tract regions. We concluded that the progenitor cells for the transitional and respiratory epithelia of the nose are basal and nonciliated cells and Type II cells in the alveolar region. In the conducting airways, our evaluation indicated that ciliated and basal cells are not in the progenitor pool. Respiratory tract epithelial cell fractions of 0.819 in rats and 0.668 in humans were estimated from the data. The total numbers of epithelial cells in the lower respiratory tract of humans and rats were allocated to individual generations. Cell cycle times were also estimated from literature data, since the reciprocal of cell cycle time is an important variable in clonal growth modeling. Sensitivity analyses of a previously published risk model for formaldehyde carcinogenesis showed that specification of the fraction of cells at risk markedly affects estimates of some parameters of the clonal growth model. When all epithelial cells are considered part of the progenitor pool, additional risks for the non-smoking population was typically over predicted by about 35% for high exposure levels. These results demonstrate the importance of accurately identifying cell populations at risk when applying quantitative models in risk assessments.

p53 codon 271 CGT to CAT mutant fraction does not increase in nasal respiratory and olfactory epithelia of rats exposed to inhaled naphthalene.

A 2-year rat tumor bioassay testing whole body exposure to naphthalene (NA) vapor found a significant increase in nasal respiratory epithelial adenomas in male rats and in olfactory epithelial neuroblastomas in female rats. To obtain mechanistic insight into NA-induced nasal carcinogenesis, NA dose-response was characterized in nasal epithelium using a tumor-relevant endpoint. Specifically, levels of p53 codon 271 CGT to CAT mutation were measured in nasal respiratory and olfactory epithelium of NA-exposed male and female rats by allele-specific competitive blocker-PCR (ACB-PCR). Male and female, 8-9 week-old F344 rats (5 rats/group) were exposed to 0, 0.1, 1.0, 10, and 30ppm NA vapor for 13 weeks (6h/day, 5 days/week). The geometric mean p53 mutant fraction (MF) levels in nasal epithelium of control treatment groups ranged between 2.05 × 10(-5) and 3.05 × 10(-5). No significant dose-related changes in p53 mutant fraction (MF) were observed in the olfactory or respiratory epithelia of female rats. However, statistically significant treatment-related differences were observed in male respiratory and olfactory epithelium, with the p53 MF in the respiratory epithelium of male rats exposed to 30ppm NA significantly lower than that in controls. Further, a significant trend of decreasing p53 MF with increasing dose was observed in the male respiratory epithelium. Of the tissue types analyzed, respiratory epithelium is the most sensitive to the cytotoxic effects of NA, suggesting cytotoxicity may be responsible for the loss of p53 mutation. Because ACB-PCR has been used successfully to detect the effects of known mutagenic carcinogens, the absence of any significant increases in p53 MF associated with NA exposure adds to the weight of evidence that NA does not operate through a directly mutagenic mode of action.

Nasal olfactory epithelial lesions in F344 and SD rats following 1- and 5-day inhalation exposure to naphthalene vapor.

The exposure-response relationship and threshold for nasal epithelial effects of naphthalene (NP) vapor in F344 and SD rats were investigated in 1-day (6 hours) and 5-day (6 h/d) studies at concentration ranges of 0 to 30 ppm. Lesions related to 1-day exposure were predominantly necrosis of the olfactory epithelium (OE). The severity of OE lesions was concentration dependent and ranged from minimal (< or =1 ppm) to marked (10-30 ppm). In the 5-day study, degeneration of OE was observed in both strains, both sexes, with increasing incidence and severity that correlated with concentration. The epithelial degeneration lesion was minimal to moderate in severity. At 0.1 ppm, minimal OE lesions were observed in female SD rats only (20% incidence). Animals exposed to 10 ppm NP followed by 14 days without exposure also had OE lesions, but of lower severity, showing evidence of good recovery. In both studies, differences between sex or strain were not remarkable.

Respiratory tract responses in male rats following subchronic acrolein inhalation.

The goal of this study was to characterize the respiratory tract toxicity of acrolein, including nasal and pulmonary effects, in adult male F344 rats. Animals underwent whole-body exposure to 0, 0.02, 0.06, 0.2, 0.6, or 1.8 ppm acrolein for 6 hr/day, five days/week for up to 65 exposure days (13 exposure weeks). Respiratory tract histopathology was evaluated after 4, 14, 30, and 65 exposure days, as well as 60 days after the end of the 13 week exposure. Acrolein exposure was associated with reduced body weight gain. Rats exposed to > or = 0.06 ppm acrolein had depressed terminal body weights when compared with air-exposed controls. Histologic evaluation of the nasal cavity showed olfactory epithelial inflammation and olfactory neuronal loss (ONL) following exposure to 1.8 ppm acrolein. Moderately severe ONL in the dorsal meatus and ethmoid turbinates occurred within four days while septal involvement developed with ongoing exposure. A rostral-caudal gradient in lesion severity was noted, with the anterior portion of the nasal cavity being more severely affected. Acrolein exposure was associated with inflammation, hyperplasia, and squamous metaplasia of the respiratory epithelium. The lateral wall was amongst the most sensitive locations for these responses and increased respiratory epithelial cell proliferation occurred at this site following 4 to 30 days of exposure to > or = 0.6 ppm acrolein. The NOAEL for nasal pathology seen in this study was 0.2 ppm acrolein.