The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant ...calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies.
Adaptation to human‐induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where ...anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton‐feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt‐cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD‐seq‐enabled genome scan to identify loci with significant allele frequency changes over the 15‐year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.
Daily physical activity remains an effective strategy to prevent obesity and type 2 diabetes. However, the metabolic response to exercise training is variable, and the precise clinical and molecular ...determinants that mark the metabolic improvements remain unknown. We tested the hypothesis that clinical improvements in glucose control after low-intensity exercise in individuals with impaired glucose tolerance (IGT) are coupled to alterations in skeletal muscle gene expression.
We investigated 14 overweight individuals with IGT before and after a 4-month low-intensity unsupervised walking exercise intervention. Clinical and anthropometric measurements and glucose tolerance were determined before and after the intervention. Skeletal muscle biopsy specimens were obtained for mRNA expression analysis.
Waist circumference and work capacity during cycle ergometry were improved in individuals who achieved normal glucose tolerance (NGT) after exercise training (IGT-NGT; n = 9) but in not individuals who remained IGT (IGT-IGT; n = 5). Pretraining glycemic control was better in IGT-NGT compared with IGT-IGT. mRNA expression of mitochondrial markers and transcription factors was increased in IGT-NGT after exercise intervention and normalized to levels measured in a separate cohort of nonexercised individuals with NGT. Conversely, these markers were unaltered after exercise intervention in IGT-IGT.
Normalization of metabolic control can be achieved after low-intensity exercise in individuals with IGT. This can be tracked with increased mRNA expression of mitochondrial and metabolic genes in skeletal muscle. However, for individuals presenting with a greater derangement in glycemia, the potential for clinical and metabolic improvements after this low-intensity unsupervised exercise protocol appears to be limited.
Abstract The delicate homeostatic balance between glucose and fatty acid metabolism in relation to whole-body energy regulation is influenced by mitochondrial function. We determined expression and ...regulation of mitochondrial enzymes including pyruvate dehydrogenase kinase (PDK) 4, PDK2, carnitine palmitoyltransferase 1b, and malonyl–coenzyme A decarboxylase in skeletal muscle from people with normal glucose tolerance (NGT) or type 2 diabetes mellitus (T2DM). Vastus lateralis biopsies were obtained from NGT (n = 79) or T2DM (n = 33) men and women matched for age and body mass index. A subset of participants participated in a 4-month lifestyle intervention program consisting of an unsupervised walking exercise. Muscle biopsies were analyzed for expression and DNA methylation status. Primary myotubes were derived from biopsies obtained from NGT individuals for metabolic studies. Cultured skeletal muscle was exposed to agents mimicking exercise activation for messenger RNA (mRNA) expression analysis. The mRNA expression of PDK4, PDK2, and malonyl–coenzyme A decarboxylase was increased in skeletal muscle from T2DM patients. Methylation of the PDK4 promoter was reduced in T2DM and inversely correlated with PDK4 expression. Moreover, PDK4 expression was positively correlated with body mass index, blood glucose, insulin, C peptide, and hemoglobin A1c . A lifestyle intervention program resulted in increased PDK4 mRNA expression in NGT individuals, but not in those with T2DM. Exposure to caffeine or palmitate increased PDK4 mRNA in a cultured skeletal muscle system. Our findings reveal that skeletal muscle expression of PDK4 and related genes regulating mitochondrial function reflects alterations in substrate utilization and clinical features associated with T2DM. Furthermore, hypomethylation of the PDK4 promoter in T2DM coincided with an impaired response of PDK4 mRNA after exercise.
Background
COVID-positive outpatients may benefit from remote monitoring, but such a program often relies on smartphone apps. This may introduce racial and socio-economic barriers to participation. ...Offering multiple methods for participation may address these barriers.
Objectives
(1) To examine associations of race and neighborhood disadvantage with patient retention in a monitoring program offering two participation methods. (2) To measure the association of the program with emergency department visits and hospital admissions.
Design
Retrospective propensity-matched cohort study.
Participants
COVID-positive outpatients at a single university-affiliated healthcare system and propensity-matched controls.
Interventions
A home monitoring program providing daily symptom tracking via patient portal app or telephone calls.
Main Measures
Among program enrollees, retention (until 14 days, symptom resolution, or hospital admission) by race and neighborhood disadvantage, with stratification by program arm. In enrollees versus matched controls, emergency department utilization and hospital admission within 30 days.
Key Results
There were 7592 enrolled patients and 9710 matched controls. Black enrollees chose the telephone arm more frequently than White enrollees (68% versus 44%,
p
= 0.009), as did those from more versus less disadvantaged neighborhoods (59% versus 43%,
p
= 0.02). Retention was similar in Black enrollees and White enrollees (63% versus 62%,
p
= 0.76) and in more versus less disadvantaged neighborhoods (63% versus 62%,
p
= 0.44). When stratified by program arm, Black enrollees had lower retention than White enrollees in the app arm (49% versus 55%,
p
= 0.01), but not in the telephone arm (69% versus 71%,
p
= 0.12). Compared to controls, enrollees more frequently visited the emergency department (HR 1.71 95% CI 1.56–1.87) and were admitted to the hospital (HR 1.16 95% CI 1.02–1.31).
Conclusions
In a COVID-19 remote patient monitoring program, Black enrollees preferentially selected, and had higher retention in, telephone- over app-based monitoring. As a result, overall retention was similar between races. Remote monitoring programs with multiple modes may reduce barriers to participation.
Musculoskeletal conditions are common and cause high levels of disability and costs. Physical therapy is recommended for many musculoskeletal conditions. Past research suggests that referral rates ...appear to have increased over time, but the rate of accessing a physical therapist appears unchanged.
Our retrospective cohort study describes the rate of physical therapy use after referral for a variety of musculoskeletal diagnoses while comparing users and non-users of physical therapy services after referral.
The study sample included patients in the University of Utah Health system who received care from a medical provider for a musculoskeletal condition. We included a comprehensive set of variables available in the electronic data warehouse possibly associated with attending physical therapy. Our primary analysis compared differences in patient factors between physical therapy users and non-users using Poisson regression.
15 877 (16%) patients had a referral to physical therapy, and 3812 (24%) of these patients accessed physical therapy after referral. Most of the factors included in the model were associated with physical therapy use except for sex and number of comorbidities. The receiver operating characteristic curve was 0.63 suggesting poor predictability of the model but it is likely related to the heterogeneity of the sample.
We found that obesity, ethnicity, public insurance and urgent care referrals were associated with poor adherence to physical therapy referral. However, the limited predictive power of our model suggests a need for a deeper examination into factors that influence patients access to a physical therapist.
The purpose of this study was to evaluate whether physical therapy use influenced subsequent use of musculoskeletal-related surgeries, injections, magnetic resonance imaging (MRI), and other imaging.
...We conducted a retrospective cohort study of patients aged 18 to 64 years who had an ambulatory care visit at the University of Utah system, after implementation of the 10th revision of the International Statistical Classification of Diseases and Related Health Problems with adequate data collection in the system at the time of the data pull, between October 1, 2015, and September 30, 2018. We identified patients (n = 85 186) who received care for a musculoskeletal condition (lower back pain, cervical, knee, shoulder, hip, elbow, ankle, wrist/hand, thoracic, and arthritis diagnoses). Regression analyses were used to evaluate the association between physical therapy use and medical care use while controlling for relevant factors.
In patients referred to physical therapy (n = 15 870), physical therapy use (n = 3812) was associated with increased MRI use (incidence rate ratio, 1.24; 95% confidence interval, 1.15-1.33; P < .001) and surgery use (incidence rate ratio, 1.11; 95% confidence interval, 1.00-1.23; P < .001). Several other factors were also associated with increased health care use, including being referred by an orthopedic provider, obesity, non–lower back pain diagnoses, and having 1 or more comorbidities.
Outpatient physical therapy use for musculoskeletal conditions in adult patients younger than 65 years at the University of Utah system, a mountain west United States academic health care system, was associated with increased rates of MRI and surgery. This finding is contrary to prior research suggesting that physical therapy improves outcomes in some diagnosis groups. A referral from an orthopedic provider, non–lower back pain diagnoses, and obesity were also associated with increased medical care utilization.
The role of Mu opioid receptor (MOR)‐mediated regulation of GABA transmission in opioid reward is well established. Much less is known about MOR‐mediated regulation of glutamate transmission in the ...brain and how this relates to drug reward. We previously found that MORs inhibit glutamate transmission at synapses that express the Type 2 vesicular glutamate transporter (vGluT2). We created a transgenic mouse that lacks MORs in vGluT2‐expressing neurons (MORflox‐vGluT2cre) to demonstrate that MORs on the vGluT2 neurons themselves mediate this synaptic inhibition. We then explored the role of MORs in vGluT2‐expressing neurons in opioid‐related behaviors. In tests of conditioned place preference, MORflox‐vGluT2cre mice did not acquire place preference for a low dose of the opioid, oxycodone, but displayed conditioned place aversion at a higher dose, whereas control mice displayed preference for both doses. In an oral consumption assessment, these mice consumed less oxycodone and had reduced preference for oxycodone compared with controls. MORflox‐vGluT2cre mice also failed to show oxycodone‐induced locomotor stimulation. These mice displayed baseline withdrawal‐like responses following the development of oxycodone dependence that were not seen in littermate controls. In addition, withdrawal‐like responses in these mice did not increase following treatment with the opioid antagonist, naloxone. However, other MOR‐mediated behaviors were unaffected, including oxycodone‐induced analgesia. These data reveal that MOR‐mediated regulation of glutamate transmission is a critical component of opioid reward.
In this study, the authors created a transgenic mouse line that lacked expression of Mu opioid receptors only in a subtype of glutamate neurons that express the Type 2 vesicular glutamate transporter. These mice had disrupted behaviors related to opioid reward but not ethanol or natural reward and had intact opioid analgesic responses. These findings indicate that Mu opioid receptors in glutamate neurons are major contributors to opioid reward related behaviors.
‘Cell Painting’ is an imaging-based high-throughput phenotypic profiling (HTPP) method in which cultured cells are fluorescently labeled to visualize subcellular structures (i.e., nucleus, nucleoli, ...endoplasmic reticulum, cytoskeleton, Golgi apparatus / plasma membrane and mitochondria) and to quantify morphological changes in response to chemicals or other perturbagens. HTPP is a high-throughput and cost-effective bioactivity screening method that detects effects associated with many different molecular mechanisms in an untargeted manner, enabling rapid in vitro hazard assessment for thousands of chemicals. Here, 1201 chemicals from the ToxCast library were screened in concentration-response up to ∼100 μM in human U-2 OS cells using HTPP. A phenotype altering concentration (PAC) was estimated for chemicals active in the tested range. PACs tended to be higher than lower bound potency values estimated from a broad collection of targeted high-throughput assays, but lower than the threshold for cytotoxicity. In vitro to in vivo extrapolation (IVIVE) was used to estimate administered equivalent doses (AEDs) based on PACs for comparison to human exposure predictions. AEDs for 18/412 chemicals overlapped with predicted human exposures. Phenotypic profile information was also leveraged to identify putative mechanisms of action and group chemicals. Of 58 known nuclear receptor modulators, only glucocorticoids and retinoids produced characteristic profiles; and both receptor types are expressed in U-2 OS cells. Thirteen chemicals with profile similarity to glucocorticoids were tested in a secondary screen and one chemical, pyrene, was confirmed by an orthogonal gene expression assay as a novel putative GR modulating chemical. Most active chemicals demonstrated profiles not associated with a known mechanism-of-action. However, many structurally related chemicals produced similar profiles, with exceptions such as diniconazole, whose profile differed from other active conazoles. Overall, the present study demonstrates how HTPP can be applied in screening-level chemical assessments through a series of examples and brief case studies.
•The percentage of ToxCast chemicals active in Cell Painting was 49.3%.•Pharmaceuticals and pesticides were more active than food additives and inerts.•4.4% of chemicals were bioactive at predicted human exposure concentrations.•Pyrene produced a profile similar to known glucocorticoid receptor agonists.•Diniconazole bioactivity differed from other conazoles and structurally related chemicals.
Abstract
Background
The Defense Health Agency has prioritized system-level pain management initiatives within the Military Health System (MHS), with low back pain as one of the key focus areas. A ...stepped care model focused on nonpharmacologic treatment to promote self-management is recommended. Implementation of stepped care is complicated by lack of information on the most effective nonpharmacologic strategies and how to sequence and tailor the various available options. The Sequential Multiple-Assignment Randomization Trial for Low Back Pain (SMART LBP) is a multisite pragmatic trial using a SMART design to assess the effectiveness of nonpharmacologic treatments for chronic low back pain.
Design
This SMART trial has two treatment phases. Participants from three military treatment facilities are randomized to 6 weeks of phase I treatment, receiving either physical therapy (PT) or Army Medicine’s holistic Move2Health (M2H) program in a package specific to low back pain. Nonresponders to treatment in phase I are again randomized to phase II treatment of combined M2H + PT or mindfulness-based treatment using the Mindfulness-Oriented Recovery Enhancement (MORE) program. The primary outcome is the Patient-Reported Outcomes Measurement Information System pain interference computer-adapted test score.
Summary
This trial is part of an initiative funded by the National Institutes of Health, Veterans Affairs, and the Department of Defense to establish a national infrastructure for effective system-level management of chronic pain with a focus on nonpharmacologic treatments. The results of this study will provide important information on nonpharmacologic care for chronic LBP in the MHS embedded within a stepped care framework.
PDF
