Evaluating the effects of single, multiple, and delayed systemic rapamycin injections to contextual fear reconsolidation: Implications for the neurobiology of memory and the treatment of PTSD-like re-experiencing.

The mechanistic target of rapamycin (mTOR) kinase is known to mediate the formation and persistence of aversive memories. Rapamycin, an mTOR inhibitor, administered around the time of reactivation blocks retrieval-induced mTOR activity and de novo protein synthesis in the brains of rodents, while correspondingly diminishing subsequent fear memory. The goal of the current experiments was to further explore rapamycin's effects on fear memory persistence. First, we examined whether mTOR blockade at different time-points after reactivation attenuates subsequent contextual fear memory. We show that rapamycin treatment 3 or 12 h post-reactivation disrupts memory persistence. Second, we examined whether consecutive days of reactivation paired with rapamycin had additive effects over a single pairing at disrupting a contextual fear memory. We show that additional reactivation-rapamycin pairings exacerbates the reconsolidation impairment. Finally, we examined if impaired reconsolidation of a contextual fear memory from rapamycin treatment had any after-effects on learning and recalling a new fear association. We show that rapamycin-impaired reconsolidation does not affect new learning or recall and protects against fear generalization. Our findings improve our understanding of mTOR- dependent fear memory processes, as well as provide insight into potentially novel treatment options for stress-related psychopathologies such as posttraumatic stress disorder.

The utility of the abdominal series in the emergency setting: a retrospective review.

PURPOSE: The abdominal series (AXR) remains a frequently ordered test in the emergency department (ED), despite existing literature questioning its utility. The aim of this study was to characterize the use of the AXR in the ED by quantifying how often it is ordered and the frequency of subsequent imaging. Additionally, a time estimate in ED associated with the AXR was quantified. We hypothesized that there would be a low clinical utility of the AXR, and long associated time period spent in the ED. METHODS: A retrospective audit of AXRs performed in the ED from January to December 2019 was performed. The local picture archiving and communication system (PACS) and electronic medical record were used to collect the variables. RESULTS: Of 701 AXRs, 438 (62.4%) were reported normal, and 263 (37.6%) were abnormal. A Chi Squared test showed that the two variables (abdominal series result and follow up imaging completion) were significantly related, with p < 0.001. However, the effect size was small (Nagelkerke R square = 0.022). The average time spent in the ED for these patients was 7.27 h, and the average time between the AXR being ordered and interpreted was 1.31 h. CONCLUSION: The majority of AXRs were reported as normal. Our results showed that AXR had a statistically significant, but low clinically significant predictive ability on subsequent imaging ordering. This supports our hypothesis that the AXR is of low clinical utility with respect to the rate of ordering follow up imaging. The AXR also translated to a quantifiable time interval during the patient's stay in ED. Minimizing overuse of the AXR may result in a decrease in patient duration in the ED.

Brain PET Imaging: Frontotemporal Dementia.

Brain PET adds value in diagnosing neurodegenerative disorders, especially frontotemporal dementia (FTD) due to its syndromic presentation that overlaps with a variety of other neurodegenerative and psychiatric disorders. 18F-FDG-PET has improved sensitivity and specificity compared with structural MR imaging, with optimal diagnostic results achieved when both techniques are utilized. PET demonstrates superior sensitivity compared with SPECT for FTD diagnosis that is primarily a supplement to other imaging and clinical evaluations. Tau-PET and amyloid-PET primary use in FTD diagnosis is differentiation from Alzheimer disease, although these methods are limited mainly to research settings.

Synthesis of mono-nitroxides and of bis-nitroxides with varying electronic through-bond communication.

Nitroxides are a unique class of persistent radicals finding a wide range of applications, from spin probes to polarizing agents, and recently bis-nitroxides have been used as proof-of-concept molecules for quantum information processing. Here we present the syntheses of pyrroline-based nitroxide (NO) radicals and give a comparision of two possible synthetic routes to form two key intermediates, namely 2,2,5,5-tetramethylpyrroline-1-oxyl-3-acetylene (TPA) and 1-oxyl-2,2,5,5-tetramethylpyrroline-3-carboxylic acid (TPC). TPC and TPA were then used as precursors for the synthesis of three model compounds featuring two distant NO groups with a variable degree of conjugation and thus electronic communication between them. Using relatively facile synthetic routes, we produced a number of mono- and bis-nitroxides with the structures of multiple compounds unambiguously characterized by X-ray crystallography, while Continuous Wave Electron Paramagnetic Resonance (CW-EPR) allowed us to quantify the electronic communication in the bis-nitroxides. Our study expands the repertoire of mono- and bis-nitroxides with possibilities of exploiting them for studying quantum coherence effects and as polarizing agents.

Racial and Ethnic Differences in the Prevalence of Do-Not-Resuscitate Orders among Older Adults with Severe Traumatic Brain Injury.

BACKGROUND: Older adults suffering from traumatic brain injury (TBI) are subject to higher injury burden and mortality. Do Not Resuscitate (DNR) orders are used to provide care aligned with patient wishes, but they may not be equitably distributed across racial/ethnic groups. We examined racial/ethnic differences in the prevalence of DNR orders at hospital admission in older patients with severe TBI. METHODS: We conducted a retrospective cohort study using the National Trauma Databank (NTDB) between 2007 to 2016. We examined patients ≥ 65 years with severe TBI. For our primary aim, the exposure was race/ethnicity and outcome was the presence of a documented DNR at hospital admission. We conducted an exploratory analysis of hospital outcomes including hospital mortality, discharge to hospice, and healthcare utilization (intracranial pressure monitor placement, hospital LOS, and duration of mechanical ventilation). RESULTS: Compared to White patients, Black patients (OR 0.48, 95% CI 0.35-0.64), Hispanic patients (OR 0.54, 95% CI 0.40-0.70), and Asian patients (OR 0.63, 95% CI 0.44-0.90) had decreased odds of having a DNR order at hospital admission. Patients with DNRs had increased odds of hospital mortality (OR 2.16, 95% CI 1.94-2.42), discharge to hospice (OR 2.08, 95% CI 1.75-2.46), shorter hospital LOS (-2.07 days, 95% CI -3.07 to -1.08) and duration of mechanical ventilation (-1.09 days, 95% CI -1.52 to -0.67). There was no significant difference in the utilization of ICP monitoring (OR 0.94, 95% CI 0.78-1.12). CONCLUSIONS: We found significant racial and ethnic differences in the utilization of DNR orders among older patients with severe TBI. Additionally. DNR orders at hospital admission were associated with increased in-hospital mortality, increased hospice utilization, and decreased healthcare utilization. Future studies should examine mechanisms underlying race-based differences in DNR utilization.

Similar acute physiological responses from effort and duration matched leg press and recumbent cycling tasks.

The present study examined the effects of exercise utilising traditional resistance training (leg press) or 'cardio' exercise (recumbent cycle ergometry) modalities upon acute physiological responses. Nine healthy males underwent a within session randomised crossover design where they completed both the leg press and recumbent cycle ergometer conditions. Conditions were approximately matched for effort and duration (leg press: 4 × 12RM using a 2 s concentric and 3 s eccentric repetition duration controlled with a metronome, thus each set lasted  60 s; recumbent cycle ergometer: 4 × 60 s bouts using a resistance level permitting 80-100 rpm but culminating with being unable to sustain the minimum cadence for the final 5-10 s). Measurements included VO2, respiratory exchange ratio (RER), blood lactate, energy expenditure, muscle swelling, and electromyography. Perceived effort was similar between conditions and thus both were well matched with respect to effort. There were no significant effects by 'condition' in any of the physiological responses examined (all p > 0.05). The present study shows that, when both effort and duration are matched, resistance training (leg press) and 'cardio' exercise (recumbent cycle ergometry) may produce largely similar responses in VO2, RER, blood lactate, energy expenditure, muscle swelling, and electromyography. It therefore seems reasonable to suggest that both may offer a similar stimulus to produce chronic physiological adaptations in outcomes such as cardiorespiratory fitness, strength, and hypertrophy. Future work should look to both replicate the study conducted here with respect to the same, and additional physiological measures, and rigorously test the comparative efficacy of effort and duration matched exercise of differing modalities with respect to chronic improvements in physiological fitness.

Bridged Epipolythiodiketopiperazines from Penicillium raciborskii, an Endophytic Fungus of Rhododendron tomentosum Harmaja.

Three new epithiodiketopiperazine natural products [outovirin A (1), outovirin B (2), and outovirin C (3)] resembling the antifungal natural product gliovirin have been identified in extracts of Penicillium raciborskii, an endophytic fungus isolated from Rhododendron tomentosum. The compounds are unusual for their class in that they possess sulfide bridges between α- and ß-carbons rather than the typical α-α bridging. To our knowledge, outovirin A represents the first reported naturally produced epimonothiodiketopiperazine, and antifungal outovirin C is the first reported trisulfide gliovirin-like compound. This report describes the identification and structural elucidation of the compounds by LC-MS/MS and NMR.

Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method.

The potential for reliably predicting relative binding enthalpies, ΔΔE, from a direct method utilizing molecular dynamics is examined for a system of three phosphotyrosyl peptides binding to a protein receptor, the Src SH2 domain. The binding enthalpies were calculated from the potential energy differences between the bound and the unbound end-states of each peptide from equilibrium simulations in explicit water. The statistical uncertainties in the ensemble-mean energy values from multiple, independent simulations were obtained using a bootstrap method. Simulations were initiated with different starting coordinates as well as different velocities. Statistical uncertainties in ΔΔE are 2 to 3 kcal/mol based on calculations from 40, 10 ns trajectories for each system (three SH2-peptide complexes or unbound peptides). Uncertainties in relative component energies, comprising solute-solute, solute-solvent and solvent-solvent interactions, are considerably larger. Energy values were estimated from an unweighted ensemble averaging of multiple trajectories with the a priori assumption that all trajectories are equally likely. Distributions in energy-rmsd space indicate that the trajectories sample the same basin and the difference in mean energy values between trajectories is due to sampling of alternative local regions of this superbasin. The direct estimate of relative binding enthalpies is concluded to be a reasonable approach for well-ordered systems with ΔΔE values greater than ∼3 kcal/mol, although the approach would benefit from future work to determine properly distributed starting points that would enable efficient sampling of conformational space using multiple trajectories.

Twinning and survivorship of captive common marmosets (Callithrix jacchus) and cotton-top tamarins (Saguinus oedipus).

Here we present the results of a demographic analysis of 25 y (1985 to 2010) of common marmoset (Callithrix jacchus) and cotton-top tamarin (Saguinus oedipus) records from the New England Primate Research Center. Summaries of longevity and survivorship are analyzed by birth-type category (including singletons, twins, triplets, and quadruplets) and sex. In addition, a brief evolutionary review is presented. Surrogates of hematopoietic chimerism, twinning, and reproductive output are explored in a large number of animals to help decipher the potential effects of chimerism on life history in marmosets and tamarins. In addition to exploring chimerism through demographic data, multiple-birth frequency and survivorship are compared between species. New World primates can make ideal translational models for disease and behavioral research across multiple disciplines. A better understanding of their reproductive success and survivorship in captivity helps develop these nonhuman primate models, their role in aging research, and understanding of their behavioral ecology. This mission is likely to only increase in its importance to biomedical research due to both the sequencing of the marmoset genome and the growing demand for alternatives to Old World primate models.

Large-scale polymorphism discovery in macaque G-protein coupled receptors.

BACKGROUND: G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis). RESULTS: Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals. CONCLUSIONS: In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.

Children's daily exposure to polychlorinated biphenyls from dietary supplements containing fish oils.

In children, omega-3 polyunsaturated fatty acids (PUFAs) may elicit a suite of health benefits including enhancement of cognitive development. Subsequently, dietary supplements containing omega-3 PUFAs have become increasingly popular. Often, the largest source of beneficial PUFAs in these supplements is fish oil, which may contain significant levels of contaminants such as polychlorinated biphenyls (PCBs). The objectives of this study were to evaluate congener-specific PCB concentrations in 13 over-the-counter children's dietary supplements containing fish oils/powders and assess potential PCB exposures through ingestion of these products on a daily basis. Every supplement analysed contained PCBs, with a mean concentration of 9 ± 8 ng PCBs/g supplement. When following serving size suggestions, mean daily exposure values ranged from 2.5 to 50.3 ng PCBs/day. Daily exposures for children's supplements were significantly lower than those previously reported for adult supplements and may be explained, in part, by the variability in the amount of fish oil (and PUFA content) in a serving size. Based on this study, factors such as fish oil purification methods (e.g., molecular distillation) and the trophic level of the fish species used to make the fish oil cannot be used as indicators of PCB levels within children's supplements. Fish supplements may decrease or increase daily PCB exposure compared with ingestion of fresh fish. However, eating fish high in omega-3 PUFAs and low in PCBs may reduce PCB exposure compared with daily supplementation with fish oils for some products studied.

The resurgence and genetic implications of New World primates in biomedical research.

There has been a recent resurgence of interest in New World monkeys within the biomedical research community, driven by both the sequencing of the common marmoset (Callithrix jacchus) genome and a growing demand for alternatives to Old World primates. New World monkeys offer attractive advantages over Old World species, including cheaper and simpler husbandry, while still maintaining a greater evolutionary proximity to humans compared with other animal models. Although numerous commonalities across primate species exist, there are also important genetic and reproductive differences that can and should play a critical role in selecting appropriate animal models. Common marmosets in particular have significantly reduced diversity at the major histocompatibility complex (MHC) loci and are born as hematopoietic chimeras. New World primates can make ideal translational models for research, but scientists must necessarily incorporate complete understandings of their genetic and phenotypic differences from humans and other model organisms.

Very large residual dipolar couplings from deuterated ubiquitin.

Main-chain (1)H(N)-(15)N residual dipolar couplings (RDCs) ranging from approximately -200 to 200 Hz have been measured for ubiquitin under strong alignment conditions in Pf1 phage. This represents a ten-fold increase in the degree of alignment over the typical weakly aligned samples. The measurements are made possible by extensive proton-dilution of the sample, achieved by deuteration of the protein with partial back-substitution of labile protons from 25 % H(2)O / 75 % D(2)O buffer. The spectral quality is further improved by application of deuterium decoupling. Since standard experiments using fixed-delay INEPT elements cannot accommodate a broad range of couplings, the measurements were conducted using J-resolved and J-modulated versions of the HSQC and TROSY sequences. Due to unusually large variations in dipolar couplings, the trosy (sharp) and anti-trosy (broad) signals are often found to be interchanged in the TROSY spectra. To distinguish between the two, we have relied on their respective (15)N linewidths. This strategy ultimately allowed us to determine the signs of RDCs. The fitting of the measured RDC values to the crystallographic coordinates of ubiquitin yields the quality factor Q = 0.16, which confirms the perturbation-free character of the Pf1 alignment. Our results demonstrate that RDC data can be successfully acquired not only in dilute liquid crystals, but also in more concentrated ones. As a general rule, the increase in liquid crystal concentration improves the stability of alignment media and makes them more tolerant to variations in sample conditions. The technical ability to measure RDCs under moderately strong alignment conditions may open the door for development of alternative alignment media, including new types of media that mimic biologically relevant systems.

Naturally occurring, physiologically normal, primate chimeras.

Callitrichids, South American primates including marmosets and tamarins, have evolved a unique physiology. Twins share a placenta during gestation and exchange stem cells, resulting in naturally occurring chimeric adults. Our study used a quantitative PCR-based assay to address whether this chimerism was restricted to blood and other cells of the hematopoietic lineage or whether it extended to other somatic tissues. These studies help to characterize species that have adapted evolutionarily to pervasive chimerism, with every individual healthy and unperturbed. This experiment of evolution offers insight into transplantation and histocompatibility, reproductive biology and behavior, and innate and adaptive immunity.

Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data.

With the advent of ultra-long MD simulations it becomes possible to model microsecond time-scale protein dynamics and, in particular, the exchange broadening effects (R(ex)) as probed by NMR relaxation dispersion measurements. This new approach allows one to identify the exchanging species, including the elusive "excited states". It further helps to map out the exchange network, which is potentially far more complex than the commonly assumed 2- or 3-site schemes. Under fast exchange conditions, this method can be useful for separating the populations of exchanging species from their respective chemical shift differences, thus paving the way for structural analyses. In this study, recent millisecond-long MD trajectory of protein BPTI (Shaw et al. Science 2010, 330, 341) is employed to simulate the time variation of amide (15)N chemical shifts. The results are used to predict the exchange broadening of (15)N lines and, more generally, the outcome of the relaxation dispersion measurements using Carr-Purcell-Meiboom-Gill sequence. The simulated R(ex) effect stems from the fast (~10-100 µs) isomerization of the C14-C38 disulfide bond, in agreement with the prior experimental findings (Grey et al. J. Am. Chem. Soc. 2003, 125, 14324).

Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding.

NMR spectroscopy and molecular dynamics (MD) simulations were used to probe the structure and dynamics of complexes of three phosphotyrosine-derived peptides with the Src SH2 domain in an effort to uncover a structural explanation for enthalpy-entropy compensation observed in the binding thermodynamics. The series of phosphotyrosine peptide derivatives comprises the natural pYEEI Src SH2 ligand, a constrained mimic, in which the phosphotyrosine (pY) residue is preorganized in the bound conformation for the purpose of gaining an entropic advantage to binding, and a flexible analogue of the constrained mimic. The expected gain in binding entropy of the constrained mimic was realized; however, a balancing loss in binding enthalpy was also observed that could not be rationalized from the crystallographic structures. We examined protein dynamics to evaluate whether the observed enthalpic penalty might be the result of effects arising from altered motions in the complex. (15)N-relaxation studies and positional fluctuations from molecular dynamics indicate that the main-chain dynamics of the protein show little variation among the three complexes. Root mean squared (rms) coordinate deviations vary by less than 1.5 A for all non-hydrogen atoms for the crystal structures and in the ensemble average structures calculated from the simulations. In contrast to this striking similarity in the structures and dynamics, there are a number of large chemical shift differences from residues across the binding interface, but particularly from key Src SH2 residues that interact with pY, the "hot spot" residue, which contributes about one-half of the binding free energy. Rank-order correlations between chemical shifts and ligand binding enthalpy for several pY-binding residues, coupled with available mutagenesis and calorimetric data, suggest that subtle structural perturbations (<1 A) from the conformational constraint of the pY residue sufficiently alter the geometry of enthalpically critical interactions in the binding pocket to cause the loss of binding enthalpy, leading to the observed enthalpy-entropy compensation. We find no evidence to support the premise that enthalpy-entropy compensation is an inherent property and conclude that preorganization of Src SH2 ligand residues involved in binding hot spots may eventuate in suboptimal interactions with the domain. We propose that introducing constraints elsewhere in the ligand could minimize enthalpy-entropy compensation effects. The results illustrate the utility of the NMR chemical shift to highlight small, but energetically significant, perturbations in structure that might otherwise go unnoticed in an apparently rigid protein.

Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in self-consistent normal mode analysis.

Self-consistent normal mode analysis (SCNMA) is applied to heme c type cytochrome f to study temperature-dependent protein motion. Classical normal mode analysis assumes harmonic behavior and the protein mean-square displacement has a linear dependence on temperature. This is only consistent with low-temperature experimental results. To connect the protein vibrational motions between low and physiological temperatures, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, quantum harmonic-oscillator theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests that it may be the cause of the non-Gaussian behavior of the protein motions probed by elastic incoherent neutron scattering. The combined theory displays a dynamical transition caused by the softening of few "torsional" modes in the low-frequency regime ( <50 cm(-1) or <6 meV or >0.6 ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.