Computational approaches to investigate fluoride binding, selectivity and transport across the membrane.

The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.

Allosteric Modulation of the YAP/TAZ-TEAD Interaction by Palmitoylation and Small-Molecule Inhibitors.

The Hippo signaling pathway is a highly conserved signaling network that plays a central role in regulating cellular growth, proliferation, and organ size. This pathway consists of a kinase cascade that integrates various upstream signals to control the activation or inactivation of YAP/TAZ proteins. Phosphorylated YAP/TAZ is sequestered in the cytoplasm; however, when the Hippo pathway is deactivated, it translocates into the nucleus, where it associates with TEAD transcription factors. This partnership is instrumental in regulating the transcription of progrowth and antiapoptotic genes. Thus, in many cancers, aberrantly hyperactivated YAP/TAZ promotes oncogenesis by contributing to cancer cell proliferation, metastasis, and therapy resistance. Because YAP and TAZ exert their oncogenic effects by binding with TEAD, it is critical to understand this key interaction to develop cancer therapeutics. Previous research has indicated that TEAD undergoes autopalmitoylation at a conserved cysteine, and small molecules that inhibit TEAD palmitoylation disrupt effective YAP/TAZ binding. However, how exactly palmitoylation contributes to YAP/TAZ-TEAD interactions and how the TEAD palmitoylation inhibitors disrupt this interaction remains unknown. Utilizing molecular dynamics simulations, our investigation not only provides detailed atomistic insight into the YAP/TAZ-TEAD dynamics but also unveils that the inhibitor studied influences the binding of YAP and TAZ to TEAD in distinct manners. This discovery has significant implications for the design and deployment of future molecular interventions targeting this interaction.

Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter.

Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLCF F-/H+ antiporter protein, a member of the CLC superfamily of anion-transport proteins. Though previous studies have examined this F- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLCF, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first studies of the CLCF F-/H+ antiporter and is the first computational investigation to model the full transport process, proposing a mechanism which couples the F- export with the H+ import.

Inverse potential scaling in co-electrocatalytic activity for CO2 reduction through redox mediator tuning and catalyst design.

Electrocatalytic CO2 reduction is an attractive strategy to mitigate the continuous rise in atmospheric CO2 concentrations and generate value-added chemical products. A possible strategy to increase the activity of molecular systems for these reactions is the co-catalytic use of redox mediators (RMs), which direct reducing equivalents from the electrode surface to the active site. Recently, we demonstrated that a sulfone-based RM could trigger co-electrocatalytic CO2 reduction via an inner-sphere mechanism under aprotic conditions. Here, we provide support for inner-sphere cooperativity under protic conditions by synthetically modulating the mediator to increase activity at lower overpotentials (inverse potential scaling). Furthermore, we show that both the intrinsic and co-catalytic performance of the Cr-centered catalyst can be enhanced by ligand design. By tuning both the Cr-centered catalyst and RM appropriately, an optimized co-electrocatalytic system with quantitative selectivity for CO at an overpotential (η) of 280 mV and turnover frequency (TOF) of 194 s-1 is obtained, representing a three-fold increase in co-catalytic activity at 130 mV lower overpotential than our original report. Importantly, this work lays the foundation of a powerful tool for developing co-catalytic systems for homogeneous electrochemical reactions.

Application of somatic embryogenesis for development of emerald ash borer-resistant white ash and green ash varietals.

Emerald ash borer (Agrilus planipennis; EAB) has devastated populations of ash (Fraxinus spp.) trees in dozens of U.S. states and Canada over the past few decades. The continued survival of scattered ash trees known as "lingering ash" in heavily infested natural stands, however, offers evidence of genetic resistance or tolerance to EAB. These surviving or "lingering" ash individuals may form the basis for reforestation programs in EAB-impacted areas, and clonal mass-propagation of these genotypes can help accelerate these efforts. Between 2013 and 2018, we initiated embryogenic cultures by culturing immature zygotic embryos from open-pollinated (OP) seeds collected from several surviving white ash and green ash trees in Michigan and Pennsylvania. In addition, in 2018, we initiated cultures from crosses made between lingering green ash parents from the USDA Forest Service ash breeding program in Ohio. Somatic embryos were produced by growing cultures in liquid suspension, followed by fractionation and plating on semisolid medium to produce developmentally synchronous populations of somatic embryos. Somatic embryo germination and conversion were enhanced by a combination of pre-germination cold treatment and inclusion of activated charcoal and gibberellic acid in the germination medium. Ash somatic seedlings derived from OP explants grew rapidly following transfer to potting mix and somatic seedlings representing nine ash clones were acclimatized, grown in the greenhouse and planted in a preliminary field test, along with EAB-resistant Manchurian ash (F. mandshurica) and EAB-susceptible control seedlings. Somatic seedlings have now been produced from cultures that originated from seeds derived from the progeny of lingering green ash parents and an ex vitro germination protocol has shown some promise for accelerating early somatic seedling growth. Results of this research could provide the basis for scaled-up production of EAB-resistant ash varieties for seed orchard production for forest restoration and cultivar development for urban tree restoration.

An activity-based fluorescent sensor for the detection of the phenol sulfotransferase SULT1A1 in living cells.

Human phenol sulfotransferases mediate the transfer of a sulfuryl moiety from the activated sulfate donor PAPS to hydroxy-containing substrates, altering substrate solubility and charge to affect phase II metabolism and cell signaling. Here, we present the development, computational modeling, in vitro enzymology, and biological application of STS-3, an activity-based fluorescent sensor for the SULT1A1 isoform.

Spatially varying correlation between environmental conditions and human leptospirosis in Sarawak, Malaysia.

The spatial distribution of environmental conditions may influence the dynamics of vectorborne diseases like leptospirosis. This study aims to investigate the global and localised relationships between leptospirosis with selected environmental variables. The association between environmental variables and the spatial density of geocoded leptospirosis cases was determined using global Poisson regression (GPR) and geographically weighted Poisson regression (GWPR). A higher prevalence of leptospirosis was detected in areas with higher water vapour pressure (exp(â): 1.12; 95% CI: 1.02 - 1.25) and annual precipitation (exp(â): 1.15; 95% CI: 1.02 - 1.31), with lower precipitation in the driest month (exp(â): 0.85; 95% CI: 0.75 - 0.96) and the wettest quarter (exp(â): 0.88; 95% CI: 0.77 - 1.00). Water vapor pressure (WVP) varied the most in the hotspot regions with a standard deviation of 0.62 (LQ: 0.15; UQ; 0.99) while the least variation was observed in annual precipitation (ANNP) with a standard deviation of 0.14 (LQ: 0.11; UQ; 0.30). The reduction in AICc value from 519.73 to 443.49 indicates that the GWPR model is able to identify the spatially varying correlation between leptospirosis and selected environmental variables. The results of the localised relationships in this study could be used to formulate spatially targeted interventions. This would be particularly useful in localities with a strong environmental or socio-demographical determinants for the transmission of leptospirosis.

Spatially varying correlation between environmental conditions and human leptospirosis in Sarawak, Malaysia

@#The spatial distribution of environmental conditions may influence the dynamics of vectorborne diseases like leptospirosis. This study aims to investigate the global and localised relationships between leptospirosis with selected environmental variables. The association between environmental variables and the spatial density of geocoded leptospirosis cases was determined using global Poisson regression (GPR) and geographically weighted Poisson regression (GWPR). A higher prevalence of leptospirosis was detected in areas with higher water vapour pressure (exp(â): 1.12; 95% CI: 1.02 - 1.25) and annual precipitation (exp(â): 1.15; 95% CI: 1.02 - 1.31), with lower precipitation in the driest month (exp(â): 0.85; 95% CI: 0.75 – 0.96) and the wettest quarter (exp(â): 0.88; 95% CI: 0.77 – 1.00). Water vapor pressure (WVP) varied the most in the hotspot regions with a standard deviation of 0.62 (LQ: 0.15; UQ; 0.99) while the least variation was observed in annual precipitation (ANNP) with a standard deviation of 0.14 (LQ: 0.11; UQ; 0.30). The reduction in AICc value from 519.73 to 443.49 indicates that the GWPR model is able to identify the spatially varying correlation between leptospirosis and selected environmental variables. The results of the localised relationships in this study could be used to formulate spatially targeted interventions. This would be particularly useful in localities with a strong environmental or socio-demographical determinants for the transmission of leptospirosis.

Taste as a marker for behavioral energy regulation:Replication and extension of meal pattern evidence from selectively bred rats.

A key feature of energy regulation among species that eat discrete meals is meal patterning - meal frequency, size, and duration. Such animals can adjust to internal states and external circumstances with changes in one or more of those meal parameters, with or without altering total food intake. Relatively little is known about individual differences in meal patterning. We previously reported meal patterning differences between rat lines selectively bred for differential saccharin solution intake, lines that also differ in sensitivity to metabolic challenges: Relative to high-saccharin-consuming counterparts (HiS), male low-saccharin-consuming rats (LoS) ate smaller, more frequent meals. Those findings provided evidence of an association between taste and short term satiety. Twenty generations later, we describe systematic replication of the line difference in meal patterns in males and females using two different kinds of reinforcer pellet. The previous study was further extended by examining meal parameters (1) with bi- and multivariate analyses and (2) after acute food restriction and a moderate stressor. Results are discussed within a behavior-systems framework incorporating taste as a marker for behavioral energy regulation.

A nationwide survey of pediatric acquired demyelinating syndromes in Japan.

OBJECTIVE: To investigate the clinical and epidemiologic features of pediatric acquired demyelinating syndromes (ADS) of the CNS in Japan. METHODS: We conducted a nationwide survey and collected clinical data on children with ADS aged 15 years or younger, who visited hospitals between 2005 and 2007. RESULTS: Among 977 hospitals enrolled, 723 (74.0%) responded to our inquiries and reported a total of 439 patients as follows: 244 with acute disseminated encephalomyelitis (ADEM), 117 with multiple sclerosis (MS), 14 with neuromyelitis optica (NMO), and 64 with other ADS. We collected and analyzed detailed data from 204 cases, including those with ADEM (66), MS (58), and NMO (10). We observed the following: (1) the estimated annual incidence rate of pediatric ADEM in Japan was 0.40 per 100,000 children (95% confidence interval [CI], 0.34-0.46), with the lowest prevalence in the north; (2) the estimated prevalence rate of MS was 0.69 per 100,000 children (95% CI, 0.58-0.80), with the lowest prevalence in the south; (3) NMO in Japan was rare, with an estimated prevalence of 0.06 per 100,000 children (95% CI, 0.04-0.08); and (4) the sex ratio and mean age at onset varied by ADS type, and (5) male/female ratios correlated with ages at onset in each ADS group. CONCLUSIONS: Our results clarify the characteristic clinical features of pediatric ADS in the Japanese population.

Better rested, but more stressed? Evidence of the effects of resident work hour restrictions.

OBJECTIVE: After the publication of the 2009 Institute of Medicine report addressing resident sleep, the Accreditation Council for Graduate Medical Education implemented new work hour restrictions in 2011. We explored the effects of a resident schedule compliant with 2011 limits on resident sleep, fatigue, education, and aspects of professionalism. METHODS: Partially randomized cohort study of residents and hospitalist attendings on general pediatric inpatient teams at a large children's hospital. Five intervention group interns worked a shift-based schedule compliant with 2011 restrictions with a 12 hour maximum shift. Six control group interns maintained the existing every fourth night, 30-hour call schedule. Interns kept daily work and sleep logs. Interns and attendings were surveyed regarding perceptions of education, professionalism, and overall well-being. RESULTS: The average amount of intern sleep per 24 hours did not differ between intervention and control groups (7.5 vs 7.3 hours; P = .63). However, intervention interns had a lower proportion of duty hours without any sleep in the preceding 24 hours compared to interns in the control group (1% vs 15%; P < .001). Twenty-one of 22 survey items on perceptions of education and professionalism were rated lower in the intervention group with absolute differences ranging from 18% to 86% between the control and intervention groups, but only 5 items were statistically significant. CONCLUSION: Implementation of new duty hour restrictions should produce more rested interns at work. However, resident and faculty perceptions of education and professionalism may be adversely affected. The unexpected finding of increased work load compression may contribute to these outcomes.

Importance of MUC1 and spontaneous mouse tumor models for understanding the immunobiology of human adenocarcinomas.

Many important aspects of cancer biology, such as cancer initiation, progression, and metastasis, have been studied in animal models, mostly mice. As long as cancer was considered primarily a genetic disease, the study of transplantable mouse tumors, or even human tumor xenografts in immunocompromised mice, appeared to suffice. Many important genetic events that lead to transformation and in vivo tumor growth were elucidated. However, many even more important factors that determine whether or not the genetic potential of a tumor cell will be realized, such as the host response to the tumor and the tumor microenvironment that influences this response over a long period of time of tumor development, remained untested and unappreciated. This is slowly changing with the advent of molecular techniques that have spurred efforts to engineer better mouse models of human tumors. In this review, we show results of our efforts to combine a genetic mouse model of spontaneous human adenocarcinomas based on a Kras mutation, with an important human molecule MUC1 that is abnormally expressed on human adenocarcinomas, promoting oncogenesis, proinflammatory tumor microenvironment, and immunosurveillance.

The Clinical Efficacy and Safety of Glucagon-Like Peptide-1 (GLP-1) Agonists in Adults with Type 2 Diabetes Mellitus.

OBJECTIVE: To review the efficacy and safety of glucagon-like peptide-1 (GLP-1) agonists to determine their role in type 2 diabetes mellitus (T2DM). DATA SOURCES: A Medline search was conducted using the keywords exenatide, liraglutide, glucagon-like peptide-1, type 2 diabetes mellitus, hyperglycemia, pharmacokinetics, pharmacology and safety. STUDY SELECTION: All identified articles written in English were evaluated with priority given to controlled, randomized trials including human data. References of identified published trials were reviewed for additional trials to be included in the review. DATA SYNTHESIS: Exenatide and liraglutide are GLP-1 agonists approved for the treatment of T2DM. Several randomized, active and placebo controlled trials examining the efficacy and safety of exenatide and liraglutide both as monotherapy and in combination therapy have been conducted. Both agents have demonstrated improved glycemic control in addition to weight loss and increased beta-cell function. The most common adverse effects are gastrointestinal in nature and appear to be transient. CONCLUSION: It appears exenatide and liraglutide are safe and effective in the treatment of T2DM and may exhibit effects that make them preferred over other anti-diabetic medications.

Class effect of erythropoietin therapy on hemoglobin A(1c) in a patient with diabetes mellitus and chronic kidney disease not undergoing hemodialysis.

In patients with diabetes mellitus, hemoglobin A(1c) (A1C) is commonly interpreted as a measure of long-term glycemic control, reflecting a mean glucose level over the previous 2-3 months. Although some reports suggest that treatment with recombinant erythropoietin may affect A1C values in patients undergoing hemodialysis, we know of no evidence to support this interaction in patients with chronic renal insufficiency who are not undergoing hemodialysis. In addition, we know of no evidence specific to the treatment effect of epoetin alfa and/or darbepoetin alfa on A1C. We describe a 64-year-old man with diabetes, chronic kidney disease, and anemia who was treated consecutively with epoetin alfa and darbepoetin alfa and experienced a temporal reduction in A1C level to a nadir of 4.4%. Throughout approximately 3 years of treatment with these erythropoietin analogs, the patient's total daily dose of insulin was reduced in response to his decreasing A1C values, despite elevated blood glucose levels and the absence of patient-reported hypoglycemic events. Five months after the patient's erythropoietin therapy was discontinued, his A1C value increased to 8.8%, leading us to conclude that management of the insulin dose may have been different without the falsely lowered A1C levels. Use of the Naranjo adverse drug reaction probability scale indicated a probable association between this patient's reduced A1C levels and erythropoietin therapy. This case demonstrates that both epoetin alfa and darbepoetin alfa may artificially lower A1C levels in a patient with diabetes who is not undergoing dialysis, and therefore this finding can be interpreted as a class effect. Clinicians should be aware of factors that affect A1C values, specifically erythrocyte life span. In patients receiving erythropoietin, therapeutic decisions should be based on A1C and glucose levels, as well as patient symptoms suggestive of hypo- or hyperglycemia, to avoid therapy changes that could complicate disease management.

Failure to thrive: pediatric residents weigh in on feasibility trial of the proposed 2008 institute of medicine work hour restrictions.

BACKGROUND: In December 2008 the Institute of Medicine (IOM) released a report recommending limits on resident hours that are considerably more restrictive than the current Accreditation Council for Graduate Medical Education duty hour standards. INTERVENTION: In March 2009, a large pediatric residency program implemented a 1-month trial of a schedule and team structure fully congruent with the IOM recommendations to study the implications of such a schedule. METHODS: Comparison of the interns' experience in the trialed intervention schedule was made to interns working a traditional schedule with every fourth night call. RESULTS: The residents on the intervention schedule averaged 7.8 hours of sleep per 24-hour period compared to 7.6 hours for interns in a traditional schedule. Participation in bedside rounds and formal didactic conferences was decreased in the intervention schedule. Several factors contributed to increased perceived work intensity for interns in the intervention schedule. Redistribution of work during busy shifts altered the role of senior residents and attending physicians which may have a negative effect on senior residents' ability to develop skills as supervisors and educators. CONCLUSIONS: The trial implementation suggests it is possible to implement the proposed duty hour limits in a pediatric residency, but it would require a significant increase in the resident workforce (at least 25% and possibly 50%) to care for the same number of patients. Furthermore, the education model would need to undergo significant changes. Further trials of the IOM recommendations are needed prior to widespread implementation in order to learn what works best and causes the least harm, disruption, and unnecessary cost to the system.

Physician-industry cooperation in the medical device industry.

Anecdotal evidence suggests that innovative medical devices often arise from physicians' inventive activity, but no studies have documented the extent of such physician-engaged innovation. This paper uses patent data and the American Medical Association Physician Masterfile to provide evidence that physicians contribute to medical device innovation, accounting for almost 20 percent of approximately 26,000 medical device patents filed in the United States during 1990-1996. Moreover, two measures indicate that physician patents had more influence on subsequent inventive activity than nonphysician patents. This finding supports the maintenance of an open environment for physician-industry collaboration in the medical device discovery process.

Tumor antigen-based immunotherapy and immunoprevention of cancer.

Any approach to the treatment and prevention of cancer must face the daunting reality that each cancer may be as individual as the patient in whom it has evolved. The challenge is also to develop a therapy that would eradicate that which is abnormal while preserving what is normal. For many years, therapies have been sought that could target a specific abnormal cancerous processes, such as rapid division or increased vascular flow, but with only limited success. Unfortunately, these successes have also been accompanied by varying degrees of toxicity and there is currently no standard therapy that can eradicate clinical disease and prevent recurrence while leaving normal tissue unharmed. However, approaches directed towards manipulating tumor-specific immunity hold promise for effective treatment and lasting cure. These approaches are based on the exceptional specificity of the immune system, the potential for long-term protective memory, and the accumulated evidence that affected individuals have spontaneous immune responses against their own tumors.

Analysis of MxA, IL-4, and IRF-1 genes in Filipino patients with subacute sclerosing panencephalitis.

BACKGROUND: Subacute sclerosing panencephalitis (SSPE) is a chronic and debilitating disease of the central nervous system caused by a latent measles virus infection. Three candidate genes, MxA, IL-4, and IRF-1 genes were shown to be associated with SSPE in Japanese patients. These genes have been suggested to play a role in the establishment of persistent viral infection in the central nervous system. SUBJECTS AND METHODS: Sixty Filipino SSPE patients and 120 healthy control subjects were included in the study. Single nucleotide polymorphisms at promoter regions ( IL-4-590C/T and MXA-88G/T) were screened using PCR-RFLP method. Genotyping was done for GT repeat polymorphism within intron 7 of IRF-1. RESULTS: The TT genotype of MXA, as well as the CT genotype of IL-4, were seen a little more frequently among the SSPE patients as compared to the control subjects. The values though, did not reach statistical significance. IRF-1 analysis did not differ between the two groups. CONCLUSION: Our study failed to demonstrate a significant association between IL-4, MXA, or IRF-1, and SSPE in the Filipino population. Our results might be explained by a greater contribution of environmental factors such as the socio-economic and nutritional factors in the susceptibility of Filipinos to SSPE other than genetic factors.