Donut dynamics: localized allosteric activation and ligand-binding kinetics in the ring-shaped ligand-responsive regulatory protein TRAP

Mathematical and Physical Sciences: 1st Place (The Ohio State University Edward F. Hayes Graduate Research Forum)The overarching goal of this research is to gain insight into mechanisms of ligand-modulated gene regulation by studying the trp RNA-binding Attenuation Protein (TRAP). TRAP is a biological Trp-sensor endogenous in bacilli: when cellular free Trp concentration is low, TRAP predominates in the inactive apo form and the micro-organism may synthesize additional Trp using a specific molecule of RNA. However, when the Trp concentration rises TRAP may bind this excess Trp and thus become activated to bind that RNA molecule. When TRAP binds the RNA, it disables downstream production of additional Trp. Thus, the micro-organism employs TRAP in this simple feedback mechanism to ensure that it will only synthesize Trp if it is scarce. The goal of the current study is to rigorously and quantitatively examine the details of TRAP activation which occur upon Trp-binding using two distinct approaches: (1) NMR spectroscopy is used to probe the structure and dynamics of TRAP. This study quantifies μs-ms molecular dynamics present in apo TRAP which are hypothetically required for proper function. Upon Trp-binding, there are quantifiable changes in both the structure and dynamics of TRAP. Importantly, the protein appears to rigidify at the μs-ms timescale. (2) Stopped-flow fluorescence spectroscopy is used to investigate the time course of Trp binding upon rapid mixing with apo TRAP. These data reveal not one, but two kinetic steps interpreted as (a) Trp-binding which occurs slower than the diffusion limited rate, followed by (b) conformation exchange of TRAP between two distinct states. These data also indicate formation of bonds, increase in order and compression of TRAP structure upon binding. These investigations help Biologists to understand TRAP at a mechanistic level. They are also of broad interest towards rigorously quantifying the time-dependent behavior of any ligand-responsive protein (many of which are essential for life).A three-year embargo was granted for this item

Review of the Role of the Brain in Chemotherapy-Induced Peripheral Neuropathy

Chemotherapy-induced peripheral neuropathy (CIPN) is a common, debilitating, and dose-limiting side effect of many chemotherapy regimens yet has limited treatments due to incomplete knowledge of its pathophysiology. Research on the pathophysiology of CIPN has focused on peripheral nerves because CIPN symptoms are felt in the hands and feet. However, better understanding the role of the brain in CIPN may accelerate understanding, diagnosing, and treating CIPN. The goals of this review are to (1) investigate the role of the brain in CIPN, and (2) use this knowledge to inform future research and treatment of CIPN. We identified 16 papers using brain interventions in animal models of CIPN and five papers using brain imaging in humans or monkeys with CIPN. These studies suggest that CIPN is partly caused by (1) brain hyperactivity, (2) reduced GABAergic inhibition, (3) neuroinflammation, and (4) overactivation of GPCR/MAPK pathways. These four features were observed in several brain regions including the thalamus, periaqueductal gray, anterior cingulate cortex, somatosensory cortex, and insula. We discuss how to leverage this knowledge for future preclinical research, clinical research, and brain-based treatments for CIPN

Evidence for a Large-Scale Brain System Supporting Allostasis and Interoception in Humans

Large-scale intrinsic brain systems have been identified for exteroceptive senses (e.g., sight, hearing, touch). We introduce an analogous system for representing sensations from within the body, called interoception, and demonstrate its relation to regulating peripheral systems in the body, called allostasis. Employing the recently introduced Embodied Predictive Interoception Coding (EPIC) model, we used tract-tracing studies of macaque monkeys, followed by two intrinsic functional magnetic resonance imaging samples (N = 280 and N = 270) to evaluate the existence of an intrinsic allostatic/interoceptive system in the human brain. Another sample (N = 41) allowed us to evaluate the convergent validity of the hypothesized allostatic/interoceptive system by showing that individuals with stronger connectivity between system hubs performed better on an implicit index of interoceptive ability related to autonomic fluctuations. Implications include insights for the brain’s functional architecture, dissolving the artificial boundary between mind and body, and unifying mental and physical illness

Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells

Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and Ring1B/Eed-containing polycomb repressive complexes in mouse embryonic stem cells. Furthermore, our computational analysis of retrotransposon silencing suggests that multiple silencing mechanisms are independently targeted to retrotransposons in embryonic stem cells, that different genomic copies of the same retrotransposon can be differentially sensitive to these silencing mechanisms, and helps define retrotransposon sequence elements that are targeted by silencing machineries. Thus repeat annotation of gene expression microarray data suggests that a complex interplay between silencing mechanisms represses retrotransposon loci in germ cells and embryonic stem cells

Type and Amount of Lipids Influence the Molecular and Textural Properties of a Soy Soft Pretzel

Altering baked goods by the addition of nutrient-rich ingredients, such as soy and ground almonds, affects the water and lipid distribution of the product and, subsequently, its final quality. Here, we studied how three lipid sources, shortening, canola oil, and ground almonds, affected texture and water distribution in a baked soy pretzel and the molecular mobility in the dough. Pretzel crumb from all formulations exhibited 40–43% moisture with a little more than half present as “freezable” water. Firmness and chewiness decreased with increased shortening and canola oil, whereas firmness and chewiness increased with additional almonds. In contrast, neither springiness nor cohesiveness was affected by the lipid quantity or source. Finally, magnetic resonance imaging of the soy pretzel dough revealed two or three populations of dough components that have distinct molecular mobilities. With increased lipid content, the mobility of each population increased in magnitude and heterogeneity. Interestingly, almonds had the smallest effect on the molecular mobility of the dough but had the largest effect on textural properties. These results provide quantitative insight into the mechanisms by which the lipid source can influence molecular properties that have textural implications for bakery products

Mechanisms, Mediators, and Moderators of the Effects of Exercise on Chemotherapy-Induced Peripheral Neuropathy

Chemotherapy-induced peripheral neuropathy (CIPN) is an adverse effect of neurotoxic antineoplastic agents commonly used to treat cancer. Patients with CIPN experience debilitating signs and symptoms, such as combinations of tingling, numbness, pain, and cramping in the hands and feet that inhibit their daily function. Among the limited prevention and treatment options for CIPN, exercise has emerged as a promising new intervention that has been investigated in approximately two dozen clinical trials to date. As additional studies test and suggest the efficacy of exercise in treating CIPN, it is becoming more critical to develop mechanistic understanding of the effects of exercise in order to tailor it to best treat CIPN symptoms and identify who will benefit most. To address the current lack of clarity around the effect of exercise on CIPN, we reviewed the key potential mechanisms (e.g., neurophysiological and psychosocial factors), mediators (e.g., anti-inflammatory cytokines, self-efficacy, and social support), and moderators (e.g., age, sex, body mass index, physical fitness, exercise dose, exercise adherence, and timing of exercise) that may illuminate the relationship between exercise and CIPN improvement. Our review is based on the studies that tested the use of exercise for patients with CIPN, patients with other types of neuropathies, and healthy adults. The discussion presented herein may be used to (1) guide oncologists in predicting which symptoms are best targeted by specific exercise programs, (2) enable clinicians to tailor exercise prescriptions to patients based on specific characteristics, and (3) inform future research and biomarkers on the relationship between exercise and CIPN

Racial Differences in Information Needs During and After Cancer Treatment: a Nationwide, Longitudinal Survey by the University of Rochester Cancer Center National Cancer Institute Community Oncology Research Program

Before treatment, cancer patients need information about side effects and prognosis, while after treatment they need information to transition to survivorship. Research documenting these needs is limited, especially among racial and ethnic minorities. This study evaluated cancer patients\u27 needs according to race both before and after treatment. We compared white (n = 904) to black (n = 52) patients receiving treatment at 17 National Cancer Institute Community Oncology Research Program (NCORP) sites on their cancer-related concerns and need for information before and after cancer treatment. Two-sample t test and chi-squared analyses were used to assess group differences. Compared to white patients, black patients reported significantly higher concerns about diet (44.3 vs. 25.4 %,) and exercise (40.4 vs. 19.7 %,) during the course of treatment. Compared to whites, blacks also had significantly higher concern about treatment-related issues (white vs. black mean, 25.52 vs. 31.78), self-image issues (7.03 vs. 8.60), family-related issues (10.44 vs. 12.84), and financial concerns (6.42 vs. 8.90, all p \u3c 0.05). Blacks, compared to whites, also had significantly greater post-treatment information needs regarding follow-up tests (8.17 vs. 9.44), stress management (4.12 vs. 4.89), and handling stigma after cancer treatment (4.21 vs. 4.89) [all p \u3c 0.05]. Pre-treatment concerns and post-treatment information needs differed by race, with black patients reporting greater information needs and concerns. In clinical practice, tailored approaches may work particularly well in addressing the needs and concerns of black patients

Conscious awareness is necessary for affective faces to influence social judgments.

A growing body of research claims that stimuli presented outside conscious awareness can influence affect, speech perception, decision-making, eating behavior, and social judgments. However, research has shown that conscious awareness is a continuous phenomenon. Using a continuous flash suppression (CFS) paradigm to suppress awareness of affective faces (smiling and scowling), we demonstrate that some awareness of suppressed stimuli is required for the stimuli to influence social judgments. We discovered this using a rigorous within-participants psychophysics method that allowed us to assess awareness at very low levels, which is difficult using traditional methods. Our findings place boundary conditions on claims (made previously by us and others) that stimuli presented completely outside conscious awareness influence judgments. This work contributes to the literature highlighting the need to study conscious awareness as a continuous phenomenon and provides a framework for researchers to ask and answer questions regarding conscious awareness and its relation to judgment and behavior

Homotropic Cooperativity from the Activation Pathway of the Allosteric Ligand-Responsive Regulatory <i>trp</i> RNA-Binding Attenuation Protein

The <i>trp</i> RNA-binding attenuation protein (TRAP) assembles into an 11-fold symmetric ring that regulates transcription and translation of <i>trp</i>-mRNA in bacilli via heterotropic allosteric activation by the amino acid tryptophan (Trp). Whereas nuclear magnetic resonance studies have revealed that Trp-induced activation coincides with both microsecond to millisecond rigidification and local structural changes in TRAP, the pathway of binding of the 11 Trp ligands to the TRAP ring remains unclear. Moreover, because each of 11 bound Trp molecules is completely surrounded by protein, its release requires flexibility of Trp-bound (holo) TRAP. Here, we used stopped-flow fluorescence to study the kinetics of Trp binding by <i>Bacillus stearothermophilus</i> TRAP over a range of temperatures and observed well-separated kinetic steps. These data were analyzed using nonlinear least-squares fitting of several two- and three-step models. We found that a model with two binding steps best describes the data, although the structural equivalence of the binding sites in TRAP implies a fundamental change in the time-dependent structure of the TRAP rings upon Trp binding. Application of the two-binding step model reveals that Trp binding is much slower than the diffusion limit, suggesting a gating mechanism that depends on the dynamics of apo TRAP. These data also reveal that dissociation of Trp from the second binding mode is much slower than after the first Trp binding mode, revealing insight into the mechanism for positive homotropic allostery, or cooperativity. Temperature-dependent analyses reveal that both binding modes imbue increases in bondedness and order toward a more compressed active state. These results provide insight into mechanisms of cooperative TRAP activation and underscore the importance of protein dynamics for ligand binding, ligand release, protein activation, and allostery

Nutritional Status Predicts Fatty Acid Uptake from Fish and Soybean Oil Supplements for Treatment of Cancer-Related Fatigue: Results from a Phase II Nationwide Study

Cancer-related fatigue is a prevalent and debilitating condition that persists for years into survivorship. Studies evaluating both fish oil supplementation on fatigue and associations between fish oil consumption and fatigue have shown mixed effects; it is unknown what factors contribute to these differential effects. Herein, we investigate whether the nutritional status of cancer survivors was associated with serum omega-3 concentration or change in serum omega-3s throughout a fish oil supplementation study, and then if any of these factors were associated with fatigue. Breast cancer survivors 4&ndash;36 months post-treatment with moderate-severe fatigue were randomized to take 6 g fish oil, 6 g soybean oil, or 3 g of each daily for 6 weeks. Baseline nutritional status was calculated using the Controlling Nutritional Status tool (serum albumin, lymphocytes, cholesterol). At baseline and post-intervention, serum fatty acids were quantified and fatigue was assessed using the Multidimensional Fatigue Symptom Inventory. Participants (n = 85) were 61.2 &plusmn; 9.7 years old with a body mass index of 31.9 &plusmn; 6.7 kg/m2; 69% had a good nutritional score and 31% had light-moderate malnutrition. Those with good nutritional status had greater total serum omega-3s at baseline (p = 0.013) and a greater increase in serum omega-3s with supplementation (p = 0.003). Among those who were supplemented with fish oil, greater increases in serum omega-3s were associated with greater improvements in fatigue. In conclusion, good nutritional status may increase uptake of fatty acid supplements, increasing their ability to improve fatigue