bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissatisfaction with family members’ medical care: the relationship with trust in personal physicians and physicians generally in Japan
Authors: Oguro Nao , Suzuki Ryo , Yajima Nobuyuki , Sakurai Kosuke , Wakita Takafumi , Hall Mark A. , Kurita Noriaki
Published: April 2021

Negative experiences with medical care have long-term effects on family members’ attitudes and emotions. However, the impact of family members’ experiences on patients’ trust in their physicians and in physicians generally is poorly understood. We aimed to quantify these associations. Our cross-sectional online survey, conducted in Japan during April 2020, involved adults with non-communicable diseases (cardiac disease, diabetes, cancer, depression, and rheumatic disease). The main exposure variable was dissatisfaction with the medical care that family members had received. The main outcomes were patients’ (N=661) trust in their personal physicians and in physicians generally. The study adopted the Japanese version of the Abbreviated Wake Forest Physician Trust Scales. We translated and validated both 5-item scales (general and individual physician trust) for the study. The results showed a lower rating for trust in physicians generally compared to trust in the respondent’s personal physician. Furthermore, dissatisfaction with a family member’s medical care was associated with lower trust in physicians generally. Interestingly, dissatisfaction with a family member’s care was also associated with lower trust in the respondent’s personal physician, but the magnitude of this association was weaker. The lower trust in personal physicians may be mediated by reduced trust in physicians generally. We suggest that physicians enquire about past patients’ negative experiences, including dissatisfaction with family members’ medical care, to repair hidden loss of trust, when they sense that patients doubt them or physicians generally.
Prevalence of Metabolic Syndrome in the United States National Health and Nutrition Examination Survey (NHANES) 2011-2018
Authors: Liang Xiaopeng , Or Benjamin , Tsoi Man Fung , Cheung Ching Lung , Cheung Bernard MY
Published: April 2021

Importance

Metabolic syndrome (MetS) is a cluster of risk factors presaging the development of cardiovascular diseases and diabetes. It is a risk factor for severe coronavirus disease 2019 (COVID-19).

Objective

To estimate the prevalence of MetS in the US National Health and Nutrition Examination Survey (NHANES) 2011-2018.

Design, Setting, and Participants

This cohort study included 22370 eligible participants aged ≥20 years from the NHANES 2011-2018.

Main Outcome and Measure

MetS was defined as the presence of at least three of these components: central obesity, reduced high-density lipoprotein, elevated triglycerides, elevated blood pressure and elevated fasting blood glucose. The prevalence of MetS was estimated taking into account the complex sampling. The time trend was evaluated using logistic regression. Annual percentage changes (APC) were used to measure the trends in MetS prevalence.

Results

The prevalence of MetS was 36.2% (95% CI, 32.3-40.3), 34.8% (95% CI, 32.3-37.4), 39.9% (95% CI, 36.6-43.2) and 38.3% (95% CI, 35.3-41.3) in 2011-2, 2013-4, 2015-6, 2017-8, respectively (P for trend =.08). Among the MetS components, the prevalence of elevated glucose increased from 48.7% (95% CI, 45.9-51.5) in 2011-2 to 64.3% (95% CI, 61.0-67.4) in 2017-8 [P for trend <.001; APC=11.7, (95% CI, 3.5-21.0)]. The prevalence of MetS in non-Hispanic Asian increased from 21.8% (95% CI, 16.7-28.0) in 2011-2 to 31.2% (95% CI, 27.4-35.3) in 2017-8 [P for trend <.001; APC=14.6, (95% CI, 2.5-34.8)].

Conclusion and Relevance

The prevalence of MetS remained stable from 2011 to 2018, but increased among non-Hispanic Asians. Lifestyle modification is needed to prevent metabolic syndrome and the associated risks of diabetes and cardiovascular disease.
Emotional symptoms, mental fatigue and behavioral adherence after 72 continuous days of strict lockdown during the COVID-19 pandemic in Argentina
Authors: Torrente F , Yoris A , Low DM , Lopez PL , Bekinschtein P , Vázquez G , Manes F , Cetkovich M
Published: April 2021

Background

An early, total, and prolonged lockdown was adopted in Argentina during the first wave of COVID-19 as the main sanitary strategy to reduce the spread of the virus in the population. The aim of this study was to explore emotional symptoms, mental fatigue, and behavioral adherence associated with the COVID-19 pandemic after an average of 72 days of continuous lockdown in Argentina. Specifically, we intended to know: 1) if the prolongation of the lockdown was associated with elevated emotional symptoms; 2) if the prolonged lockdown affected adherence, a phenomenon called “behavioral fatigue”; and 3) how financial concerns in a developing country affected adherence to the lockdown and emotional status of the population.

Method

A survey was designed to evaluate the psychological impact of the pandemic and lockdown. The survey included standardized questionnaires to assess the severity of depressive (PHQ-9) and anxious (GAD-7) symptoms, a questionnaire to evaluate mental fatigue, and several additional instruments to assess other variables of interest: risk perception, lockdown adherence, financial concerns, daily stress, loneliness, intolerance to uncertainty, negative repetitive thinking, and cognitive problems. Three LASSO regression analyses were carried to evaluate the predictive role of the different variables over depression, anxiety, and lockdown adherence

Results

The survey was responded by 3617 individuals over the age of 18 (85.2% female) from all the provinces of Argentina. Using the Oxford stringency index, Argentina had one of the most stringent and prolonged lockdowns when the sample was collected with 63 to 77 continuous days with a stringency index of more than 85/100. 45.6% of the sample met the cut-off for depression and 27% for anxiety. Previous mental health treatment, low income, being younger, and being female were associated with higher levels of emotional symptoms. Mental fatigue, cognitive failures, and financial concerns were also associated with emotional and subjective complaints, but not with adherence to the lockdown. In the regression models, mental fatigue, cognitive failures, and loneliness were the most important variables to predict depression, meanwhile intolerance to uncertainty and lockdown difficulty were the most important in the case of anxiety. Perceived threat was the most important variable predicting lockdown adherence.

Conclusions

Emotional symptoms persisted and even increased during the extended lockdown, but we found no evidence of behavioral fatigue. Instead, mental fatigue, cognitive difficulties, and financial concerns were expressions of the emotional side of the pandemic and the restrictive measures.
Addressing racial/ethnic disparities in the COVID-19 vaccination campaign
Authors: Reitsma Marissa B. , Goldhaber-Fiebert Jeremy D. , Salomon Joshua A.
Published: April 2021

Background

As of April 19, all adults aged 16 years and older are eligible for COVID-19 vaccination. Unequal vaccination rates across racial/ethnic groups may compound existing disparities in cases, hospitalizations, and deaths among Black, Indigenous, and Hispanic communities.

Methods

From state websites, we extracted shares of people receiving ≥1 vaccine dose, stratified by age and separately by race/ethnicity, through March 31, 2021. Combining these data with demographic data from the American Community Survey, we estimated relative uptake rates by race/ethnicity within each state as the observed share of vaccinations for a racial/ethnic group, divided by the expected share if uptake across racial/ethnic groups within each age group were proportional to population size, an approach that allowed us to control for historical age-based eligibility. We modeled vaccination scale-up within each census tract in a state under three scenarios: 1) a scenario in which unequal uptake rates persist, 2) a scenario in which uptake rates are equalized across race/ethnicity groups over six weeks, and 3) a scenario in which uptake is equalized and states employ place-based allocation strategies that prioritizes disadvantaged census tracts.

Results

White adults received a disproportionate share of vaccinations compared to Black and Hispanic adults through March 31, 2021. Across states, relative uptake rates, adjusted for eligible population size, were a median 1.3 (IQR, 1.2-1.4) times higher for White compared to Black adults, and a median 1.4 (IQR, 1.2-1.8) times higher for White compared to Hispanic adults. Projecting vaccination coverage under persistence of current disparities in uptake, we found that Black and Hispanic populations would reach 75% coverage among adults almost one month later than White populations. In alternative scenarios, we found that interventions to equalize uptake rates across racial/ethnic groups could narrow but not erase these gaps, and that geographic targeting of vaccine doses to disadvantaged communities may be needed to produce a more equitable convergence of coverage by July.

Discussion

Interventions are urgently needed to eliminate disparities in COVID-19 vaccination rates. Eliminating access barriers and increasing vaccine confidence among marginalized populations can narrow gaps in coverage. Combining these interventions with place-based allocation strategies can accelerate vaccination in disadvantaged communities, who have borne a disproportionate burden from COVID-19.
Associations of SARS-CoV-2 serum IgG with occupation and demographics of military personnel
Authors: Zell Joseph , Klein Jon , Lucas Carolina , Slade Martin , Liu Jian , Iwasaki Akiko , Wisnewski Adam V , Redlich Carrie A
Published: April 2021

Background

Countries across the globe have mobilized their armed forces in response to COVID-19, placing them at increased risk for viral exposure. Humoral responses to SARS-CoV-2 among military personnel serve as biomarkers of infection and provide a basis for disease surveillance and recognition of work-related risk factors.

Methods

Enzyme-linked immunosorbent assays (ELISA) were used to measure SARS-CoV-2 spike antigen-specific IgG in serum obtained from N=995 US National Guard soldiers between April-June 2020. Occupational information, e.g. military operating specialty (MOS) codes, and demographic data were obtained via questionnaire. Plaque assays with live SARS-CoV-2 were used to assess serum neutralizing capacity for limited subjects (N=12).

Results

The SARS-CoV-2 IgG seropositivity rate among the study population was 10.3% and significantly associated with occupation and demographics. Odds ratios were highest for those working in MOS 2T-Transportation (3.6; 95% CI 0.7-18) and 92F-Fuel specialist/ground and aircraft (6.8; 95% CI 1.5-30), as well as black race (2.2; 95% CI 1.2-4.1), household size ≥6 (2.5; 95% CI 1.3-4.6) and known COVID-19 exposure (2.0; 95% CI 1.2-3.3). Seropositivity tracked along major interstate highways and clustered near the international airport and the New York City border. SARS-CoV-2 spike IgG+ serum exhibited low to moderate SARS-CoV-2 neutralizing capacity with IC50s ranging from 1:15 to 1:280. In limited follow-up testing SARS-CoV-2 serum IgG levels remained elevated up to 7 months.

Conclusions

The data highlight increased SARS-CoV-2 seroprevalence among National Guard vs. the local civilian population in association with transportation-related occupations and specific demographics.
Abnormalities in migration of neural precursor cells in familial bipolar disorder
Authors: Sukumaran Salil K. , Paul Pradip , Guttal Vishwesha , Holla Bharath , Vemula Alekhya , Bhatt Harsimar , Bisht Piyush , Mathew Kezia , Nadella Ravi K , Varghese Anu Mary , Vijayalakshmi K , Purushottam Meera , Jain Sanjeev ,   ADBS Consortium, Sud Reeteka , Viswanath Biju
Published: April 2021

Cellular migration is a ubiquitous feature that brings brain cells into appropriate spatial relationships over time; and it helps in the formation of a functional brain. We studied the migration patterns of induced pluripotent stem cell (IPSC)-derived neural precursor cells (NPCs) from individuals with familial bipolar disorder (BD), in comparison with healthy controls. The BD patients also had morphological brain abnormalities in magnetic resonance imaging. Time-lapse analysis of migrating cells was conducted, through which we were able to identify several parameters to be abnormal in cellular migration, including the speed and directionality of NPCs. We also performed transcriptomic analysis to probe the mechanisms behind aberrant cellular phenotype identified. Our analysis showed downregulation of a network of genes, centering on EGF/ERBB proteins. Present findings indicate that collective, systemic dysregulation may produce the aberrant cellular phenotype; which could contribute to the functional and structural changes in the brain, reported in bipolar disorder.

SUMMARY STATEMENT

We report abnormal cell migration patterns in neural precursors derived from bipolar disorder patients, which could contribute to already known structural changes in the brain.
Mutation-specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation
Authors: Wang Huanyu , Jean Sophonie , Eltringham Richard , Madison John , Snyder Pamela , Tu Huolin , Jones Daniel M. , Leber Amy L.
Published: April 2021

The emergence of more transmissible and/or more virulent SARS-CoV-2 variants of concern (VOCs) has triggered intensive genomic surveillance, which is costly and difficult to sustain operationally over the long-term. To address this problem, we developed a set of four multiplex mutation-specific PCR-based assays with same-day reporting that can detect five VOCs and three variants of interest (VOIs), as defined in the March 2021 guidelines from the United States (US) Centers for Disease Control and Prevention. The screening results were compared to the whole genome sequencing (WGS) and showed 100% concordance for strain typing for B.1.1.7 (25) and P.1 (5) variants using Spike (S) mutations N501Y, E484K and H69_V70del assays. The S L450R assay, designed to detect the B.1.427/429 VOCs, also identified multiple isolates of a newly emerging multiply-mutated B.1.526.1 variant that is now rapidly increasing in the Eastern US. PCR approaches can be easily adopted in clinical laboratories, provide rapid screening methods to allow early detection of newly emergent variants and to efficiently triage cases for full genomic sequencing.
The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom
Authors: Wei Jia , Stoesser Nicole , Matthews Philippa C. , Studley Ruth , Bell Iain , Bell John I , Newton John N , Farrar Jeremy , Diamond Ian , Rourke Emma , Howarth Alison , Marsden Brian D. , Hoosdally Sarah , Jones E Yvonne , Stuart David I , W .Crook Derrick , Peto Tim E. A. , Pouwels Koen B. , Eyre David W. , Walker A. Sarah ,   COVID-19 Infection Survey team
Published: April 2021

Real-world data on antibody response post-vaccination in the general population are limited. 45,965 adults in the UK’s national COVID-19 Infection Survey receiving Pfizer-BioNTech or Oxford-AstraZeneca vaccines had 111,360 anti-spike IgG measurements. Without prior infection, seroconversion rates and quantitative antibody levels post single dose were lower in older individuals, especially >60y. Two doses achieved high responses across all ages, particularly increasing seroconversion in older people, to similar levels to those achieved after prior infection followed by a single dose. Antibody levels rose more slowly and to lower levels with Oxford-AstraZeneca vs Pfizer-BioNTech, but waned following a single Pfizer-BioNTech dose. Latent class models identified four responder phenotypes: older people, males, and those having long-term health conditions were more commonly ‘low responders’. Where supplies are limited, vaccines should be prioritised for those not previously infected, and second doses to individuals >60y. Further data on the relationship between vaccine-mediated protection and antibody responses are needed.
To what extent is the altitude at which we live associated with 10-year cardiovascular risk?
Authors: Guerrero Andrea Cevallos , Fernández Heidi Angela , León-Cáceres Ángela , Armijos-Acurio Luciana , Erazo Carlos , Jimbo-Sotomayor Ruth , Pereira-Olmos Hugo , Pineda-Abarca Henry , Quishpe-Narváez Erika , Sánchez Xavier , Sevilla Carmenza , Tello Betzabé , Torres-Castillo Ana , Villacrés Tatiana , Dueñas-Espín Iván
Published: April 2021

Introduction

There is evidence that demonstrates lower incidence rates of cardiometabolic factors at the highlands. There are no studies which correlate the altitude with formally calculated cardiovascular risk by a meter-by-meter approach. Under the hypothesis that cardiovascular risk is inversely associated with altitude, this study was aimed to assess such association.

Materials and methods

Cross sectional study using data from the Ecuadorian National Health Survey of 2012. We analyzed available information of adults of ≥ 40 to 60 years old who have sociodemographic, anthropometric, cardiovascular risk factors, and laboratory biomarkers that were included in the survey. We assessed the independent association between altitude of the housing in which survey participants lived at, on a meter-by-meter approach, and cardiovascular health risk at ten years, formally calculated by Framingham equations.

Results

Linear regression model showed that participants had 0.0005 % less probability of developing cardiovascular disease at 10 years per each increase in a meter in the altitude that participants live at (p<0.001), adjusted for sex, age, ethnicity, educational level, availability of social security, immigrants in family, area, income quintile, overcrowding (≥ 7 inhabitants in the house), any alcohol consumption, history of hypertension, body mass index, hematocrit, and triglycerides.

Conclusion

From a public health perspective, altitude at which individuals live is an important health determinant of cardiovascular risk. Specifically, per each increase of 1000 m in the altitude that people live at, there is a reduction of almost half a percentual point in the cardiovascular risk at 10 years.
Of Rats and Men, a Translational Model to Understand Vancomycin Pharmacokinetic/Toxicodynamic relationships
Authors: Scheetz Marc H. , Pais Gwendolyn , Lodise Thomas P. , Tong Steven Y.C. , Davis Joshua S. , O’Donnell J. Nicholas , Liu Jiajun , Neely Michael , Prozialeck Walter C. , Lamar Peter C. , Rhodes N.Jim , Holland Thomas , Avedissian Sean N.
Published: April 2021

Background

Vancomycin is a first line antibiotic for many common infectious diseases and is the most commonly prescribed antibiotic in the United States hospital setting. Vancomycin is also well known to cause kidney injury; two recent prospective studies have identified that increasing vancomycin area under the concentration curve predicts vancomycin induced kidney injury (VIKI). However, outside of clinical trials, it is unclear if pre-clinical data can quantitatively describe VIKI in patients.

Methods

Data were simultaneously analyzed from a pre-clinical rat model and two prospective clinical studies. Logged vancomycin area under the concentration curve (AUC) data for rats (n=48) and patients from PROVIDE (n=263) and CAMERA2 (n=291) were included. VIKI was defined as urinary KIM-1 concentrations ≥9.42 ng/mL in the rat and according to KDIGO stage 1 kidney injury for all human patients. Multiple generalized linear models were explored, and the order of magnitude was calculated between the probability of acute kidney injury (AKI) from the average obtained in the clinical studies (i.e. CAMERA2 and PROVIDE) and the rat for 0.1 increments in Log10AUC bounded common concentrations obtained in the therapeutic range (i.e. ~200 −800 mg*24h/L).

Results

A logit link model best fit the data. When calculating the multiplicative factors between the studies therapeutic range AUCs, the rat was an average 2.7 to 4.2 times more sensitive to AKI between AUCs of 199.5 (i.e. log 10 AUC=2.3) and 794.3 mg*h/L (i.e. log 10 AUC=2.9), respectively.

Conclusions

A pre-clinical rat model was quantitatively linked to toxicity data from two large human studies. The rat is an attractive pre-clinical model to explore exposure toxicity relationships with vancomycin. External validation is required.
Dynamics of a hepatocyte-cholangiocyte decision-making gene regulatory network during liver development and regeneration
Authors: Sahoo Sarthak , Mishra Ashutosh , Diehl Anna Mae , Jolly Mohit Kumar
Published: April 2021

Liver is one of the few organs with immense regenerative potential even at adulthood in mammals. It is composed of primarily two cell types: hepatocytes and cholangiocytes, that can trans-differentiate to one another either directly or through intermediate progenitor states, contributing to remarkable regenerative potential of the liver. However, the dynamical features of decision-making between these cell-fates during liver development and regeneration remains elusive. Here, we identify a core gene regulatory network comprising c/EBPα, TGFBR2 and SOX9 that underlies liver development and injury-induced reprogramming. Dynamic simulations for this network reveal its multistable nature, enabling three distinct cell states – hepatocytes, cholangiocytes and liver progenitor cells (hepatoblasts/oval cells) – and stochastic switching among them. Predicted expression signature for these three states are validated through multiple bulk and single-cell transcriptomic datasets collected across developmental stages and injury-induced liver repair. This network can also explain the experimentally observed spatial organisation of phenotypes in liver parenchyma and predict strategies for efficient cellular reprogramming among these cell-fates. Our analysis elucidates how the emergent multistable dynamics of underlying gene regulatory networks drive diverse cell-state decisions in liver development and regeneration.
Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy Body diseases
Authors: Feleke Rahel , Reynolds Regina H. , Smith Amy , Tilley Bension , Gagliano Taliun Sarah A. , Hardy John , Matthews Paul M. , Gentleman Steve , Owen David , Johnson Michael R. , Srivastava Prashant , Ryten Mina
Published: April 2021

Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular “window” of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.
Platelet HMGB1 in Platelet-Rich Plasma Promotes Tendon Wound Healing
Authors: Zhang Jianying , Li Feng , Augi Tyler , Williamson Kelly M. , Onishi Kentaro , Hogan MaCalus V. , Neal Matthew D. , Wang James H-C.
Published: April 2021

Platelet-rich plasma (PRP) is a widely used autologous treatment for tendon injuries in clinics, but clinical trials often produce conflicting results. Platelets (PLTs) are a major source of high mobility group box1 (HMGB1) that is gaining attention as a chemoattractant that can recruit stem cells to the wound area to enhance healing; however, the contribution of PLT HMGB1 in wounded tendon healing remains unexplored. This study investigated the effect of PLT HMGB1 within PRP to enhance healing in an acute patellar tendon injury model in PLT HMGB1 knockout (KO) mice and GFP mice. A window defect was created in the patellar tendons of both groups of mice, and wounds were treated with either saline, PRP isolated from PLT HMGB1 KO mice, or PRP isolated from GFP mice. Seven days post-treatment, animals were sacrificed and analyzed by gross inspection, histology, and immunostaining for characteristic signs of tendon healing and repair. Our results showed that in comparison to mice treated with PRP from PLT HMGB1-KO mice, wounds treated with PRP from GFP mice healed faster and exhibited a better organization in tendon structure. Mice treated with PRP from PLT HMGB1-KO mice produced tendon tissue with large premature wound areas and low cell densities. However, wounds of PLT HMGB1 KO mice showed better healing with PRP from HMGB1 KO mice compared to saline treatment. Moreover, wounds treated with PRP from GFP mice had increased extracellular HMGB1, decreased CD68, increased stem cell markers CD146 and CD73, and increased collagen III protein expression levels compared to those treated with PRP from PLT HMGB1 KO mice. Thus, PLT HMGB1 within PRP plays an important role in the healing of wounded tendon. Our findings also suggest that the efficacy of PRP treatment for tendon injuries in clinics may be affected by PLT HMGB1 within PRP preparations.
Identification of heat responsive genes in pea stipules and anthers through transcriptional profiling
Authors: Huang Shaoming , Kishore Krishna K. , Lachagari Reddy V.B. , Chakravartty Navajeet , Bueckert Rosalind A. , Tar’an Bunyamin , Warkentin Thomas D.
Published: April 2021

Field pea (Pisum sativumL.), a cool-season legume crop, is known for poor heat tolerance. Our previous work identified PR11-2 and PR11-90 as heat tolerant and susceptible lines in a recombinant inbred population. CDC Amarillo, a Canadian elite pea variety, was considered as another heat tolerant variety based on its similar field performance as PR11-2. This study aimed to characterize the differential transcription. Plants of these three varieties were stressed for 3h at 38°C prior to self-pollination, and RNAs from heat stressed anthers and stipules on the same flowering node were extracted and sequenced via the Illumina NovaSeq platform for the characterization of heat responsive genes.In silicoresults were further validated by qPCR assay. Differentially expressed genes (DEGs) were identified at log2 fold change, the three varieties shared 588 DEGs which were up-regulated and 220 genes which were down-regulated in anthers when subjected to heat treatment. In stipules, 879 DEGs (463/416 upregulation/downregulation) were consistent among varieties. The above heat-induced genes of the two plant organs were related to several biological processes i.e., response to heat, protein folding and DNA templated transcription. Ten gene ontology (GO) terms were over-represented in the consistently down-regulated DEGs of the two organs, and these terms were mainly related to cell wall macromolecule metabolism, lipid transport, lipid localization, and lipid metabolic processes. GO enrichment analysis on distinct DEGs of individual pea varieties suggested that heat affected biological processes were dynamic, and variety distinct responses provide insight into molecular mechanisms of heat-tolerance response. Several biological processes, e.g., cellular response to DNA damage stimulus in stipule, electron transport chain in anther that were only observed in heat induced PR11-2 and CDC Amarillo, and their relevance to field pea heat tolerance is worth further validation.
Nonlinear control of transcription through enhancer-promoter interactions
Authors: Zuin Jessica , Roth Gregory , Zhan Yinxiu , Cramard Julie , Redolfi Josef , Piskadlo Ewa , Mach Pia , Kryzhanovska Mariya , Tihanyi Gergely , Kohler Hubertus , Meister Peter , Smallwood Sebastien , Giorgetti Luca
Published: April 2021

Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs)1–4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. To address this question we use a novel assay to position an enhancer at a large number of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. Quantitative analysis of hundreds of cell lines reveal that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a non-linear relationship. Mathematical modeling and validation against experimental data further provide evidence that nonlinearity arises from transient enhancer-promoter interactions being memorized into longer-lived promoter states in individual cells, thus uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism for how enhancers control transcription across large genomic distances despite rarely meeting their target promoters, and for how TAD boundaries can block distal enhancers. We finally show that enhancer strength additionally determines not only absolute transcription levels, but also the sensitivity of a promoter to CTCF-mediated functional insulation. Our unbiased, systematic and quantitative measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.
Grandmaternal smoking during pregnancy is associated with differential DNA methylation in their grandchildren
Authors: Watkins Sarah Holmes , Iles-Caven Yasmin , Pembrey Marcus , Golding Jean , Suderman Matthew
Published: April 2021

The idea that information can be transmitted to subsequent generation(s) by epigenetic means has been studied for decades but remains controversial in humans. Epidemiological studies have established that grandparental exposures are associated with health outcomes in their grandchildren, often with sex-specific effects; however the mechanism of transmission is still unclear. We conducted Epigenome Wide Association Studies (EWAS) to test whether grandmaternal smoking during pregnancy is associated with altered DNA methylation (DNAm) in their adolescent grandchildren. We used data from a birth cohort, with discovery and replication datasets of 1225 and 708 individuals (respectively), aged 15-17 years, and tested replication in the same individuals at birth and 7 years. We show for the first time that DNAm at a small number of loci is associated with grandmaternal smoking in humans, and their locations in the genome suggest hypotheses of transmission. We observe and replicate sex-specific associations at two sites on the X chromosome, one located in an imprinting control region and both within transcription factor binding sites (TFBSs). In fact, we observe enrichment for TFBSs among the CpG sites with the strongest associations, suggesting that TFBSs may be a mechanism by which grandmaternal exposures influence offspring DNA methylation. There is limited evidence that these associations appear at earlier timepoints, so effects are not static throughout development. The implication of this work is that effects of smoking during pregnancy may induce DNAm changes in later generations and that these changes are often sex-specific, in line with observational associations.
Immune cell networks uncover candidate biomarkers of cancer immunotherapy response
Authors: Vo Duong H.T. , McGleave Gerard , Overton Ian M.
Published: April 2021

Therapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types, and application to interrogate control of nivolumab response in advanced melanoma cohorts. Results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, ‘immune hot’ status, including T cell proliferation, confers good response to first line ICI therapy. Genes regulated in NK, dendritic and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights B cell genes as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.
Developmental Alcohol Exposure in Drosophila: Effects on Adult Phenotypes and Gene Expression in the Brain
Authors: Mokashi Sneha S. , Shankar Vijay , MacPherson Rebecca A. , Hannah Rachel C. , Mackay Trudy F. C. , Anholt Robert R. H.
Published: April 2021

Fetal alcohol exposure can lead to developmental abnormalities, intellectual disability, and behavioral changes, collectively termed fetal alcohol spectrum disorder (FASD). In 2015, the Centers for Disease Control found that 1 in 10 pregnant women report alcohol use and more than 3 million women in the USA are at risk of exposing their developing baby to alcohol.Drosophila melanogasteris an excellent genetic model to study developmental effects of alcohol exposure because many individuals of the same genotype can be reared rapidly and economically under controlled environmental conditions. Flies exposed to alcohol undergo physiological and behavioral changes that resemble human alcohol-related phenotypes. Here, we show that adult flies that developed on ethanol-supplemented medium have decreased viability, reduced sensitivity to ethanol, and disrupted sleep and activity patterns. To assess the effects of exposure to alcohol during development on brain gene expression, we performed single cell RNA sequencing and resolved cell clusters with differentially expressed genes which represent distinct neuronal and glial populations. Differential gene expression showed extensive sexual dimorphism with little overlap between males and females. Gene expression differences following developmental alcohol exposure were similar to previously reported differential gene expression following cocaine consumption, suggesting that common neural substrates respond to both drugs. Genes associated with glutathione metabolism, lipid transport, glutamate and GABA metabolism, and vision feature in sexually dimorphic global multi-cluster interaction networks. Our results provide a blueprint for translational studies on alcohol-induced effects on gene expression in the brain that may contribute to or result from FASD in human populations.
RNA beacons for detecting the human testis-determining factor
Authors: Joseph Diego F. , Nakamoto Jose Alberto , Milón Pohl
Published: April 2021

The testis-determining factor (TDF) is an essential transcriptional protein for male differentiation in mammals, expressed along spermatids to early zygotes and, to some extent, in diverse cellular lines. In this study, we developed fluorescent biosensors capable of indicating the presence of TDF. We usedin vitroevolution techniques to produce RNA aptamers that bind the recombinantly expressed HMG-box, the DNA binding domain of TDF. Bioinformatic analysis alongin vitroevolution setup suggested two predominant aptamer clusters with distinctive motifs. The top ranked aptamer from each cluster, M1 and M2, showed specific binding to TDF. Aptamers were fluorescently modified as molecular beacons. Pre-steady-state kinetics indicated the beacons bind rapidly, within 50 seconds, yet M1 showed better signal to noise ratios than M2. Structural predictions of the aptamer interaction indicated that M1 is composed by three stem loops and likely interact with the HMG-box of TDF through the pocket formed by the three loops. Molecular modelling of M1 beacon shows that binding to TDF entails a conformational change of the sensor resulting in the measured fluorescence changes. To our knowledge, this is the first work describing an RNA beacon for detecting the essential TDF. Potential applications and advantages over alternative methods are provided and discussed.
The trade-off between pulse duration and power in optical excitation of midbrain dopamine neurons approximates Bloch’s law
Authors: Pallikaras Vasilios , Carter Francis , Martínez David Natanael Velázquez , Arvanitogiannis Andreas , Shizgal Peter
Published: April 2021

Background

Optogenetic experiments reveal functional roles of specific neurons. However, such inferences have been restricted by widespread adoption of a fixed set of stimulation parameters. Broader exploration of the parameter space can deepen insight into the mapping between selective neural activity and behavior. In this way, characteristics of the activated neurons, such as temporal integration, can be inferred.

Objective

To determine whether an equal-energy principle accounts for the interaction of pulse duration and optical power in optogenetic excitation.

Methods

Six male TH::Cre rats worked for optogenetic (ChannelRhodopsin-2) stimulation of Ventral Tegmental Area dopamine neurons. We used a within-subject design to describe the trade-off between pulse duration and optical power in determining reward seeking. Parameters were customized for each subject on the basis of behavioral effectiveness.

Results

Within a useful range of powers (~12.6-31.6 mW) the product of optical power and pulse duration required to produce a given level of reward seeking was roughly constant. Such reciprocity is consistent with Bloch’s law, which posits an equal-energy principle of temporal summation over short durations in human vision. The trade-off between pulse duration and power broke down at higher powers.

Conclusions

Optical power can be substituted for pulse duration to scale the region of neuronal excitation in behavioral optogenetic experiments. Power and duration can be adjusted reciprocally for brief durations and lower powers. The findings demonstrate the utility of within-subject and trade-off designs in optogenetics and of parameter adjustment based on functional endpoints instead of physical properties of the stimulation.

Highlights

We provide behaviorally derived intensity-duration curves for ChannelRhodopsin-2.

Duration trades off almost perfectly with power within useful ranges.

This trade-off breaks down at high optical powers.

Pulse duration and optical power scale the area of neuronal excitation equivalently.

Behaviorally derived trade-offs can reveal optogenetic excitation mechanisms.
Actin polymerization and crosslinking drive left-right asymmetry in single cell and cell collectives
Authors: Tee Y. H. , Goh W. J. , Yong X. , Ong H. T. , Hu J. , Tay I. Y. Y. , Shi S. , Jalal S. , Barnett S. F. H. , Kanchanawong P. , Huang W. , Yan J. , Thiagarajan V. , Bershadsky A. D.
Published: April 2021

Deviations from mirror symmetry in the development of bilateral organisms are highly stereotypic and genetically predetermined, but their mechanisms are not sufficiently understood. At the cellular level, self-organization of the actin cytoskeleton results in chiral actin swirling, and cells in groups confined to micropatterns demonstrate chiral cell alignment. The relationship between individual and collective cell chirality is unclear, and molecular players involved remain essentially unidentified. Here, by screening major actin-associated proteins and deep-learning-based morphometric analysis of actin patterns, we found that knockdowns of specific actin polymerization regulators, such as mDia1, ARPC2, and cofilins 1&2, abolished chiral actin swirling, while depletion of profilin 1 and CapZβ, reversed its direction in an actin crosslinker α-actinin1-dependent manner. Analysis of these and other knockdowns and pharmacological treatments revealed a robust correlation between their effects on the chirality of individual cells and confined cell groups. Thus, actin-driven cell chirality may underlie tissue and organ asymmetry.

One Sentence Summary

Cell chirality determined by specific regulators of actin polymerization drives left-right asymmetry emergence in cell groups
Associations between MHC class II variation and phenotypic traits in a free-living sheep population
Authors: Huang Wei , Dicks Kara L , Ballingall Keith T , Johnston Susan E , Sparks Alexandra M , Watt Kathryn , Pilkington Jill G. , Pemberton Josephine M
Published: April 2021

Pathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC diversity and phenotypic traits which include direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five representative phenotypic traits measured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasiteTeladorsagia circumcinctain a free-living population of Soay sheep. We found no association between MHC class II variation and August weight or strongyle faecal egg count. We did however find associations between MHC class II variation and immunoglobulin levels which varied with age, isotype and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as body weight and highlight a useful role of MHC-antibody associations in examining selection on MHC genes.
Chronic Presence of Blood Circulating Anti-NMDAR1 Autoantibodies Impairs Cognitive Function in Mice
Authors: Yue William , Caldwell Sorana , Risbrough Victoria , Powell Susan , Zhou Xianjin
Published: April 2021

High titers of anti-NMDAR1 autoantibodies in brain cause anti-NMDAR1 encephalitis that displays psychiatric symptoms of schizophrenia and/or other psychiatric disorders in addition to neurological symptoms. Low titers of anti-NMDAR1 autoantibodies are reported in the blood of a subset of the general human population and psychiatric patients. Since ∼0.1-0.2% of blood circulating antibodies cross the blood-brain barriers and antibodies can persist for months and years in human blood, it is important to investigate whether chronic presence of these blood circulating anti- NMDAR1 autoantibodies may impair human cognitive functions and contribute to the development of psychiatric symptoms. Here, we generated mice carrying low titers of anti-NMDAR1 autoantibodies in blood against a single antigenic epitope of mouse NMDAR1. Mice carrying the anti-NMDAR1 autoantibodies are healthy and display no differences in locomotion, sensorimotor gating, and contextual memory compared to controls. Chronic presence of the blood circulating anti-NMDAR1 autoantibodies, however, is sufficient to specifically impair T-maze spontaneous alternation in the integrity of blood-brain barriers across all 3 independent mouse cohorts, indicating a robust cognitive deficit in spatial working memory and/or novelty detection. Our studies implicate that chronic presence of low titers of blood circulating anti-NMDAR1 autoantibodies may impair cognitive functions in both the general healthy human population and psychiatric patients.
Expression of fatty acyl-CoA ligase drives one-pot de novo synthesis of membrane-bound vesicles in a cell free transcription-translation system
Authors: Bhattacharya Ahanjit , Cho Christy J. , Brea Roberto J. , Devaraj Neal K.
Published: April 2021

Despite the central importance of lipid membranes in cellular organization, it is challenging to reconstitute their de novo formation from minimal chemical and biological elements. Here we describe a chemoenzymatic route to membrane-forming non-canonical phospholipids in which cysteine-modified lysolipids undergo spontaneous coupling with fatty acyl-CoA thioesters generated enzymatically by a fatty acyl-CoA ligase. Due to the high efficiency of the reaction, we were able to optimize phospholipid membrane formation in a cell-free transcription-translation (TX-TL) system. Combining DNA encoding for the fatty acyl-CoA ligase with suitable lipid precursors, enabled spontaneous one-pot de novo synthesis of membrane-bound vesicles. Non-canonical sphingolipid synthesis was also possible by using a cysteine-modified lysosphingomyelin as a precursor. When the sphingomyelin-interacting protein lysenin is co-expressed alongside the acyl CoA ligase, the in situ assembled membranes were spontaneously modified with protein. Our strategy of coupling gene expression with membrane lipid synthesis in a one-pot fashion could facilitate the generation of proteoliposomes and brings us closer to the bottom-up generation of synthetic cells using recombinant synthetic biology platforms.
Directed Evolution of Enzymes based on in vitro Programmable Self-Replication
Authors: Dramé-Maigné Adèle , Espada Rocío , McCallum Giselle , Sieskind Rémi , Rondelez Yannick
Published: April 2021

High-throughput directed evolution, implemented in well-controlled in vitro conditions, provides a powerful route for enzyme engineering. Most existing technologies are based on activity screening and require the sequential observation and sorting of each individual variant. By contrast, approaches based on autonomous feedback loops, linking phenotype to genotype replication, enable autonomous selection without screening. However, these approaches are only possible in vivo, or applicable to very specific activities, such as polymerases or ligases. Here, we leverage synthetic molecular networks to create a programmable in vitro feedback loop linking a target enzymatic activity to gene amplification. After encapsulation and lysis of up to 107 transformed variants, the genes present in each droplet are amplified according to the activity of the encoded enzyme, resulting in the autonomous enrichment of interesting sequences. Applied to a nicking enzyme with thermal or kinetic selection pressures, this method reveals detailed mutational landscapes and provides improved variants.