It Takes a Village to Make a Scientist: Reflections of a Faculty Learning Community

Lab components of undergraduate science courses typically have students complete highly directed cookbook-like laboratory activities. These experiences rarely engage students in a meaningful manner and do not accurately convey what the work of science entails. With funding from the Howard Hughes Medical Institute (HHMI), we have created more authentic science research experiences in a variety of undergraduate science courses, including introductory courses. Achieving this among the diversity of freshmen and sophomore science courses—each typically serving hundreds of students on our campus—required careful planning and adaptation. This article describes the many challenges we faced in our effort to create more authentic undergraduate student research experiences and the significant progress we have made in making such experiences more common for our students. Improvements in first-year science, technology, engineering, and mathematics (STEM) retention over the last 2 years suggest that the experiences may be having a positive impact.This article is from Journal of College Science Teaching 44 (2015): 28. Posted with permission.</p

The Circular Dichroism Spectrum and Structure of Unordered Polypeptides and Proteins

The evidence bearing on our revision of the early assignment of the circular dichroism spectrum of the maximally unordered polypeptide chain is reviewed. Our initial, as well as subsequent, studies are believed to support the proposed revision in assignment. This conclusion need not be modified in the light of recent work on water‐soluble, non‐ionizable polymers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/101811/1/197400018_ftp.pd

Computerised interpretation of the fetal heart rate during labour: a randomised controlled trial (INFANT)

Background Continuous electronic fetal monitoring (EFM) in labour is widely used and computerised interpretation has the potential to increase its utility. Objectives This trial aimed to find out whether or not the addition of decision support software to assist in the interpretation of the cardiotocograph (CTG) reduced the number of poor neonatal outcomes, and whether or not it was cost-effective. Design Two-arm individually randomised controlled trial. The allocations were computer generated using stratified block randomisation employing variable block sizes. The trial was not masked. Setting Labour wards in England, Scotland and the Republic of Ireland. Participants Women in labour having EFM, with a singleton or twin pregnancy, at ≥ 35 weeks’ gestation. Interventions Decision support or no decision support. Main outcome measures The primary outcomes were (1) a composite of poor neonatal outcome {intrapartum stillbirth or early neonatal death (excluding lethal congenital anomalies), or neonatal morbidity [defined as neonatal encephalopathy (NNE)], or admission to a neonatal unit within 48 hours for ≥ 48 hours (with evidence of feeding difficulties, respiratory illness or NNE when there was evidence of compromise at birth)}; and (2) developmental assessment at the age of 2 years in a subset of surviving children. Results Between 6 January 2010 and 31 August 2013, 47,062 women were randomised and 46,042 were included in the primary analysis (22,987 in the decision support group and 23,055 in the no decision support group). The short-term primary outcome event rate was higher than anticipated. There was no evidence of a difference in the incidence of poor neonatal outcome between the groups: 0.7% (n = 172) of babies in the decision support group compared with 0.7% (n = 171) of babies in the no decision support group [adjusted risk ratio 1.01, 95% confidence interval (CI) 0.82 to 1.25]. There was no evidence of a difference in the long-term primary outcome of the Parent Report of Children’s Abilities-Revised with a mean score of 98.0 points [standard deviation (SD) 33.8 points] in the decision support group and 97.2 points (SD 33.4 points) in the no decision support group (mean difference 0.63 points, 95% CI –0.98 to 2.25 points). No evidence of a difference was found for health resource use and total costs. There was evidence that decision support did change practice (with increased fetal blood sampling and a lower rate of repeated alerts). Limitations Staff in the control group may learn from exposure to the decision support arm of the trial, resulting in improved outcomes in the control arm. This was identified in the planning stage and felt to be unlikely to have a significant effect on the results. As this was a pragmatic trial, the response to CTG alerts was left to the attending clinicians. Conclusions This trial does not support the hypothesis that the use of computerised interpretation of the CTG in women who have EFM in labour improves the clinical outcomes for mothers or babies

The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau

Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease. To decipher the mechanism underlying the formation of tau aggregates, we developed a novel approach for constructing models of natively unfolded proteins. The method, energy-minima mapping and weighting (EMW), samples local energy minima of subsequences within a natively unfolded protein and then constructs ensembles from these energetically favorable conformations that are consistent with a given set of experimental data. A unique feature of the method is that it does not strive to generate a single ensemble that represents the unfolded state. Instead we construct a number of candidate ensembles, each of which agrees with a given set of experimental constraints, and focus our analysis on local structural features that are present in all of the independently generated ensembles. Using EMW we generated ensembles that are consistent with chemical shift measurements obtained on tau constructs. Thirty models were constructed for the second microtubule binding repeat (MTBR2) in wild-type (WT) tau and a ΔK280 mutant, which is found in some forms of frontotemporal dementia. By focusing on structural features that are preserved across all ensembles, we find that the aggregation-initiating sequence, PHF6*, prefers an extended conformation in both the WT and ΔK280 sequences. In addition, we find that residue K280 can adopt a loop/turn conformation in WT MTBR2 and that deletion of this residue, which can adopt nonextended states, leads to an increase in locally extended conformations near the C-terminus of PHF6*. As an increased preference for extended states near the C-terminus of PHF6* may facilitate the propagation of β-structure downstream from PHF6*, these results explain how a deletion at position 280 can promote the formation of tau aggregates

A Genetic Animal Model of Alcoholism for Screening Medications to Treat Addiction

The purpose of this review is to present up-to-date pharmacological, genetic, and behavioral findings from the alcohol-preferring P rat and summarize similar past work. Behaviorally, the focus will be on how the P rat meets criteria put forth for a valid animal model of alcoholism with a highlight on its use as an animal model of polysubstance abuse, including alcohol, nicotine, and psychostimulants. Pharmacologically and genetically, the focus will be on the neurotransmitter and neuropeptide systems that have received the most attention: cholinergic, dopaminergic, GABAergic, glutamatergic, serotonergic, noradrenergic, corticotrophin releasing hormone, opioid, and neuropeptide Y. Herein, we sought to place the P rat's behavioral and neurochemical phenotypes, and to some extent its genotype, in the context of the clinical literature. After reviewing the findings thus far, this chapter discusses future directions for expanding the use of this genetic animal model of alcoholism to identify molecular targets for treating drug addiction in general

Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information

Funding Information: This work was supported by the National Institute of Mental Health / U.S. Army Medical Research and Development Command (Grant No. R01MH106595 [to CMN, IL, MBS, KJRe, and KCK], National Institutes of Health (Grant No. 5U01MH109539 to the Psychiatric Genomics Consortium ), and Brain & Behavior Research Foundation (Young Investigator Grant [to KWC]). Genotyping of samples was provided in part through the Stanley Center for Psychiatric Genetics at the Broad Institute supported by Cohen Veterans Bioscience . Statistical analyses were carried out on the LISA/Genetic Cluster Computer ( https://userinfo.surfsara.nl/systems/lisa ) hosted by SURFsara. This research has been conducted using the UK Biobank resource (Application No. 41209). This work would have not been possible without the financial support provided by Cohen Veterans Bioscience, the Stanley Center for Psychiatric Genetics at the Broad Institute, and One Mind. Funding Information: MBS has in the past 3 years received consulting income from Actelion, Acadia Pharmaceuticals, Aptinyx, Bionomics, BioXcel Therapeutics, Clexio, EmpowerPharm, GW Pharmaceuticals, Janssen, Jazz Pharmaceuticals, and Roche/Genentech and has stock options in Oxeia Biopharmaceuticals and Epivario. In the past 3 years, NPD has held a part-time paid position at Cohen Veterans Bioscience, has been a consultant for Sunovion Pharmaceuticals, and is on the scientific advisory board for Sentio Solutions for unrelated work. In the past 3 years, KJRe has been a consultant for Datastat, Inc., RallyPoint Networks, Inc., Sage Pharmaceuticals, and Takeda. JLM-K has received funding and a speaking fee from COMPASS Pathways. MU has been a consultant for System Analytic. HRK is a member of the Dicerna scientific advisory board and a member of the American Society of Clinical Psychopharmacology Alcohol Clinical Trials Initiative, which during the past 3 years was supported by Alkermes, Amygdala Neurosciences, Arbor Pharmaceuticals, Dicerna, Ethypharm, Indivior, Lundbeck, Mitsubishi, and Otsuka. HRK and JG are named as inventors on Patent Cooperative Treaty patent application number 15/878,640, entitled “Genotype-guided dosing of opioid agonists,” filed January 24, 2018. RP and JG are paid for their editorial work on the journal Complex Psychiatry. OAA is a consultant to HealthLytix. All other authors report no biomedical financial interests or potential conflicts of interest. Funding Information: This work was supported by the National Institute of Mental Health/ U.S. Army Medical Research and Development Command (Grant No. R01MH106595 [to CMN, IL, MBS, KJRe, and KCK], National Institutes of Health (Grant No. 5U01MH109539 to the Psychiatric Genomics Consortium), and Brain & Behavior Research Foundation (Young Investigator Grant [to KWC]). Genotyping of samples was provided in part through the Stanley Center for Psychiatric Genetics at the Broad Institute supported by Cohen Veterans Bioscience. Statistical analyses were carried out on the LISA/Genetic Cluster Computer (https://userinfo.surfsara.nl/systems/lisa) hosted by SURFsara. This research has been conducted using the UK Biobank resource (Application No. 41209). This work would have not been possible without the financial support provided by Cohen Veterans Bioscience, the Stanley Center for Psychiatric Genetics at the Broad Institute, and One Mind. This material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting true views of the U.S. Department of the Army or the Department of Defense. We thank the investigators who comprise the PGC-PTSD working group and especially the more than 206,000 research participants worldwide who shared their life experiences and biological samples with PGC-PTSD investigators. We thank Mark Zervas for his critical input. Full acknowledgments are in Supplement 1. MBS has in the past 3 years received consulting income from Actelion, Acadia Pharmaceuticals, Aptinyx, Bionomics, BioXcel Therapeutics, Clexio, EmpowerPharm, GW Pharmaceuticals, Janssen, Jazz Pharmaceuticals, and Roche/Genentech and has stock options in Oxeia Biopharmaceuticals and Epivario. In the past 3 years, NPD has held a part-time paid position at Cohen Veterans Bioscience, has been a consultant for Sunovion Pharmaceuticals, and is on the scientific advisory board for Sentio Solutions for unrelated work. In the past 3 years, KJRe has been a consultant for Datastat, Inc. RallyPoint Networks, Inc. Sage Pharmaceuticals, and Takeda. JLM-K has received funding and a speaking fee from COMPASS Pathways. MU has been a consultant for System Analytic. HRK is a member of the Dicerna scientific advisory board and a member of the American Society of Clinical Psychopharmacology Alcohol Clinical Trials Initiative, which during the past 3 years was supported by Alkermes, Amygdala Neurosciences, Arbor Pharmaceuticals, Dicerna, Ethypharm, Indivior, Lundbeck, Mitsubishi, and Otsuka. HRK and JG are named as inventors on Patent Cooperative Treaty patent application number 15/878,640, entitled ?Genotype-guided dosing of opioid agonists,? filed January 24, 2018. RP and JG are paid for their editorial work on the journal Complex Psychiatry. OAA is a consultant to HealthLytix. All other authors report no biomedical financial interests or potential conflicts of interest. Publisher Copyright: © 2021 Society of Biological PsychiatryBackground: Posttraumatic stress disorder (PTSD) is heritable and a potential consequence of exposure to traumatic stress. Evidence suggests that a quantitative approach to PTSD phenotype measurement and incorporation of lifetime trauma exposure (LTE) information could enhance the discovery power of PTSD genome-wide association studies (GWASs). Methods: A GWAS on PTSD symptoms was performed in 51 cohorts followed by a fixed-effects meta-analysis (N = 182,199 European ancestry participants). A GWAS of LTE burden was performed in the UK Biobank cohort (N = 132,988). Genetic correlations were evaluated with linkage disequilibrium score regression. Multivariate analysis was performed using Multi-Trait Analysis of GWAS. Functional mapping and annotation of leading loci was performed with FUMA. Replication was evaluated using the Million Veteran Program GWAS of PTSD total symptoms. Results: GWASs of PTSD symptoms and LTE burden identified 5 and 6 independent genome-wide significant loci, respectively. There was a 72% genetic correlation between PTSD and LTE. PTSD and LTE showed largely similar patterns of genetic correlation with other traits, albeit with some distinctions. Adjusting PTSD for LTE reduced PTSD heritability by 31%. Multivariate analysis of PTSD and LTE increased the effective sample size of the PTSD GWAS by 20% and identified 4 additional loci. Four of these 9 PTSD loci were independently replicated in the Million Veteran Program. Conclusions: Through using a quantitative trait measure of PTSD, we identified novel risk loci not previously identified using prior case-control analyses. PTSD and LTE have a high genetic overlap that can be leveraged to increase discovery power through multivariate methods.publishersversionpublishe

Fire and the invasive annual grass \u3ci\u3eMicrostegium vimineum\u3c/i\u3e in eastern deciduous forests

Non-native plant invasions have the potential to change natural and prescribed fire regimes by increasing fuel loads, continuity of fuels, and fuel composition, which may alter fire intensity, damage native species, and promote further invasions. In this project we sought to evaluate the interaction between fire and the invasive annual grass Microstegium vimineum in eastern deciduous forests. Our goal was to determine if invasions enhance fire intensity, including fire temperatures, flame heights, and fire duration, and negatively affect tree regeneration, and stimulate further invasions. We also sought to determine how prescribed fires and the timing of fires affect the density and demography of Microstegium and we tested the pre and post-fire management options for controlling the post-fire spread of Microstegium invasions. At Big Oaks National Wildlife Refuge in southeastern Indiana, we conducted large-scale prescribed fires to evaluate fire intensity in invaded and uninvaded areas and the response of experimental and naturally regenerating trees. In small-scale plots we manipulated the timing and frequency of fires and applied herbicide treatments to evaluate demographic responses of Microstegium. Our results show that maximum fire temperatures were on average 57% greater in Microstegium-invaded than uninvaded control areas. In addition, fires burned at temperatures over 300 °C for nearly twice as long and flame heights were 98% higher in invaded compared to uninvaded habitats. Microstegium invasion reduced survival of experimental trees by 37% in areas exposed to prescribed fire compared to uninvaded areas and tree survival in invaded, burned plots was 53% lower than invaded, unburned plots. Exposure to prescribed fire increased natural tree regeneration overall but there were 60% and 57% fewer tree seedlings in burned and unburned invaded plots, respectively, compared to control plots with the same treatments. Prescribed fire increased Microstegium biomass by five-fold the following growing season. Experimental spring fires significantly reduced Microstegium seedling numbers by ~75% immediately after the burn, but this did not result in reduced seed production at the end of season or seedling numbers the year following a burn. Burning for two springs in a row similarly reduced seedling numbers during each of the years when the burns were conducted, but this effect did not carry over to reduce Microstegium seedling numbers the following year. Similarly, fall fire reduced seedling numbers by ~50% the following spring, but this reduction also did not result in reduced seed production at the end of that season. The significant effects on seedling numbers but lack of effect on Microstegium seed production was likely due to growth compensation by the surviving plants. Grassspecific, post-emergent herbicide applied without fire was very effective at reducing population numbers, almost eradicating Microstegium populations, but fire reduced herbicide effectiveness. The results of this research demonstrate significant effects of a non-native grass invasion on fire intensity, tree regeneration, and subsequent invasions in eastern deciduous forests, an ecosystem where this phenomenon has not previously been observed. Fire was not useful as a management strategy for Microstegium invasions and interfered with an otherwise effective post-emergent herbicide. To avoid the damaging effects of intense fires in invaded areas, we recommend land managers use herbicides or other treatments to remove invasions prior to the application of prescribed fires

Invasive shrub distribution varies with distance to roads and stand age in eastern deciduous forests in Indiana, USA. Plant Ecology 184: 131–141. doi: 10.1007/ s11258-005-9057-4 Forman RTT

Abstract We documented the relationship between densities of invasive exotic shrubs, distance to road, and successional age of the forest in 14 forested sites throughout central and southern Indiana. Roadways are increasingly abundant, human-made features that can be conduits for the spread of invasive exotic plants in a number of ecosystems. Little is known, however, about the role of roads in eastern deciduous forest ecosystems where road density is high. Further, it is not known whether the distribution of exotic plants along roads depends on the successional age of the forest. In this study, densities of four of seven exotic shrub species declined with increasing distance to the nearest road across all successional ages. Greater densities of exotic shrubs were found in young and mid-successional forests than mature forests. However, there was no interaction between distance to road and forest age, suggesting that the role of roads in the invasion process does not change across forest successional ages. We outline several potential mechanisms that may drive patterns of shrub distribution along roadside edges as a guide for future research