bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional Water Dynamics in Rhodopsin Using Solid‐State Deuterium NMR Spectroscopy
Authors: Weerasinghe Nipuna , Perera Suchithranga M.D.C. , Molugu Trivikram R. , Brown Michael F.
Published: February 2021

G‐protein‐coupled receptors (GPCRs) are the largest family of cell membrane‐bound proteins that detect extracellular stimuli and transduce signals to activate intracellular functions. Drugs that target GPCRs also account for about 27% of the global market share of therapeutic drugs, with aggregated sales for 2011–2015 of ca. US $890 billion [1]. Hydration is essential for protein tertiary folding and activity, and therefore knowledge of hydration water dynamics is vital for understanding the GPCR activation mechanism [2]. We studied rhodopsin hydration as a prototype for GPCRs, where the role of water in the rhodopsin activation mechanism has been recently explored using quasi‐elastic neutron scattering (QENS) methods [3]. We developed methods for generating powdered samples, notable for exceptionally high protein content while retaining photochemical functionality. The powdered GPCR samples are suitable for biophysical experiments to study the dynamic process of rhodopsin activation [4], where the protein is hydrated using vapor phase absorption in a controlled manner. We propose that the internal protein dynamics (β‐fluctuations) are coupled to the solvent shell, while large‐scale protein domain motions (α‐fluctuations) are coupled to the bulk solvent. To test our hypothesis of functional water interactions, we studied rhodopsin hydration shell dynamics using solid‐state 2H NMR spectroscopy at various hydration levels and temperatures [5]. From the spectral features at 200 K, we identified two dynamically distinguishable protein hydration regions. The broad quadrupolar splitting at approximately 180 kHz is due to bulk water; however, the anisotropic narrow component is a result of water molecules dynamically perturbed by rhodopsin. Additional solid‐state 2H NMR relaxation investigations of molecular dynamics of the rhodopsin‐bound water shell are in progress. Our future focus is on a comparative study of water dynamics in the light activated state and the dark state of the visual photoreceptor.

Support or Funding Information

This work was supported by the NIH (EY026041 and EY012049) and the NSF (MCB 1817862).

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Improving Surgical Informed Consent
Authors: Raper Steven E. , Clapp Justin T. , Fleisher Lee A.
Published: February 2021

Objective:

This study reviews randomized clinical trials that have attempted to improve the process of informed consent. Consent should be guided by the ethical imperatives of autonomy, beneficence, and social justice.

Summary Background:

Informed consent is constantly evolving. Yet our review of the randomized trials done to improve the surgical informed consent process raises a number of questions: How does one define surgical informed consent? What interventions have been tried to measure and improve informed consent? Have the interventions in informed consent actually led to improvements? What efforts have been made to improve informed consent? And what steps can be taken to improve the process further?

Methods:

A literature search for randomized controlled trials (RCTs)on informed consent identified 70 trials. Demographics, interventions, assessments, and a semi-quantitative summary of the findings were tabulated. The assessments done in the RCTs, show the surrogate for patient autonomy was comprehension; for beneficence, satisfaction and mental state (anxiety or depression); and, for social justice, language, literacy, learning needs, and cost.

Results:

There were 4 basic categories of interventions: printed matter; non-interactive audiovisual tools; interactive multimedia; and a smaller group defying easy description. Improvement was documented in 46 of the 65 trials that studied comprehension. Thirteen of 33 trials showed improved satisfaction. Three of 30 studies showed an increase in anxiety. Few studies tried to assess primary language or literacy, and none looked at learning needs or cost.

Conclusions:

No single study improved all 3 principles of informed consent. Validated interventions and assessments were associated with greater impact on outcomes. All 3 ethical principles should be assessed; autonomy (as comprehension), beneficence (as satisfaction, anxiety), and social justice. Not enough consideration has been given to social justice; appropriate language translation, standardized reading levels, assessment of learning needs, and cost to the individual are all important elements worthy of future study.
Clinical Impact of Stump Closure Reinforced With Hemopatch on the Prevention of Clinically Relevant Pancreatic Fistula After Distal Pancreatectomy: A Multicenter Randomized Trial
Authors: Uranues Selman , Fingerhut Abraham , Belyaev Orlin , Zerbi Alessandro , Boggi Ugo , Hoffmann Matthias W. , Reim Daniel , Esposito Alessandro , Primavesi Florian , Kornprat Peter , Coppola Roberto , Fragulidis Georgio P. , Serradilla-Martin Mario , Alimoglu Orhan , Peri Andrea , Diaconescu Bogdan
Published: February 2021

Introduction:

Postoperative pancreatic fistula (POPF) is the most dreaded complication after distal pancreatectomy (DP). This multicenter randomized trial evaluated the efficacy, safety, and tolerance of Hemopatch in preventing clinically relevant (grades B/C according to the ISGPS classification) POPF after DP.

Material and methods:

After stump closure, patients were randomized to affix Hemopatch to the stump or not. Statistical significance was set at 0.025. Clinical significance was defined as the number of patients needed to treat (NNT) to avoid 1 B/C POPF.

Results:

Of 631 eligible patients, 360 were randomized and 315 analyzed per protocol (155 in the standard closure group; 160 in the Hemopatch group). The rates of B/C POPF (the primary endpoint) were 23.2% and 16.3% (P = 0.120), while the number of patients with 1 or more complications (including patients with B/C POPF) was 34.8% and 24.4% (P = 0.049) in the standard and Hemopatch groups, respectively. In patients with hand-sewn stump and main duct closure, the rates were 26.2% versus 10.0% (P = 0.014) and 23.3% versus 7.7% (P = 0.015) in the standard and Hemopatch groups, respectively. The NNT in these 2 subgroups was 6 and 6.4, respectively.

Conclusion:

The results of the first randomized trial evaluating Hemopatch-reinforced pancreatic stump after DP to prevent type B/C POPF do not allow us to conclude that the risk of B/C POPF was lower. Based on the NNT, however, routine use of Hemopatch after DP may result in fewer complications (including POPF) overall, especially in cases with hand-sewn closure of the pancreatic stump or main pancreatic duct.
Gaps in Emergency General Surgery Coverage in the United States
Authors: Ingraham Angela M. , Chaffee Scott M. , Ayturk M. Didem , Heh Victor K. , Kiefe Catarina I. , Santry Heena P.
Published: February 2021

Introduction:

Despite 3 million adults in the United States being admitted annually for emergency general surgery (EGS) conditions, which disproportionately affect vulnerable populations, we lack an understanding of the barriers to round-the-clock EGS care. Our objective was to measure gaps in round-the-clock EGS care.

Methods:

From August 2015 to December 2015, we surveyed all US-based adult acute care general hospitals that have an emergency room and ≥1 operating room and provided EGS care, utilizing paper and electronic methods. Surgeons or chief medical officers were queried regarding EGS practices.

Results:

Of 2811 hospitals, 1634 (58.1%) responded; 279 (17.1%) were unable to always provide round-the-clock EGS care. Rural location, smaller bed size, and nonteaching status were associated with lack of round-the-clock care. Inconsistent surgeon coverage was the primary reason for lacking round-the-clock EGS care (n = 162; 58.1%). However, lack of a tiered system for booking emergency cases, no anesthesia availability overnight, and no stipend for EGS call were also associated with the inability to provide round-the-clock EGS care.

Discussion:

We found significant gaps in access to EGS care, often attributable to workforce deficiencies.
d-dimer and Death in Critically Ill Patients With Coronavirus Disease 2019
Authors: Short Samuel A. P. , Gupta Shruti , Brenner Samantha K. , Hayek Salim S. , Srivastava Anand , Shaefi Shahzad , Singh Harkarandeep , Wu Benjamin , Bagchi Aranya , Al-Samkari Hanny , Dy Rajany , Wilkinson Katherine , Zakai Neil A. , Leaf David E.
Published: February 2021

OBJECTIVES:

Hypercoagulability may be a key mechanism for acute organ injury and death in patients with severe coronavirus disease 2019, but the relationship between elevated plasma levels of d-dimer, a biomarker of coagulation activation, and mortality has not been rigorously studied. We examined the independent association between d-dimer and death in critically ill patients with coronavirus disease 2019.

DESIGN:

Multicenter cohort study.

SETTING:

ICUs at 68 hospitals across the United States.

PATIENTS:

Critically ill adults with coronavirus disease 2019 admitted to ICUs between March 4, 2020, and May 25, 2020, with a measured d-dimer concentration on ICU day 1 or 2.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

The primary exposure was the highest normalized d-dimer level (assessed in four categories: < 2×, 2–3.9×, 4–7.9×, and ≥ 8× the upper limit of normal) on ICU day 1 or 2. The primary endpoint was 28-day mortality. Multivariable logistic regression was used to adjust for confounders. Among 3,418 patients (63.1% male; median age 62 yr [interquartile range, 52–71 yr]), 3,352 (93.6%) had a d-dimer concentration above the upper limit of normal. A total of 1,180 patients (34.5%) died within 28 days. Patients in the highest compared with lowest d-dimer category had a 3.11-fold higher odds of death (95% CI, 2.56–3.77) in univariate analyses, decreasing to a 1.81-fold increased odds of death (95% CI, 1.43–2.28) after multivariable adjustment for demographics, comorbidities, and illness severity. Further adjustment for therapeutic anticoagulation did not meaningfully attenuate this relationship (odds ratio, 1.73; 95% CI, 1.36–2.19).

CONCLUSIONS:

In a large multicenter cohort study of critically ill patients with coronavirus disease 2019, higher d-dimer levels were independently associated with a greater risk of death.
Exposure to metal mixtures in relation to blood pressure among children 5–7 years old
Authors: Shih Yu-Hsuan , Howe Caitlin G. , Scannell Bryan Molly , Shahriar Mohammad , Kibriya Muhammad G. , Jasmine Farzana , Sarwar Golam , Graziano Joseph H. , Persky Victoria W. , Jackson Brian , Ahsan Habibul , Farzan Shohreh F. , Argos Maria
Published: February 2021

Background:

Hypertension in later life, a significant risk factor for cardiovascular disease, has been linked to elevated blood pressure in early life. Exposure to metals may influence childhood blood pressure; however, previous research is limited and has mainly focused on evaluating the toxicity of single metal exposures. This study evaluates the associations between exposure to metal mixtures and blood pressure among Bangladeshi children age 5–7 years.

Methods:

We investigated the associations of 17 toenail metal concentrations with blood pressure using linear regression models. Principal component analysis (PCA), weighted quantile sum (WQS) regression, and Bayesian kernel machine regression (BKMR) were conducted as secondary analyses.

Results:

Associations were observed for selenium with diastolic blood pressure (per doubling of exposure β = 2.91, 95% confidence interval [CI] = 1.08, 4.75), molybdenum with systolic (β = 0.33, 95% CI = 0.05, 0.61) and diastolic blood pressure (β = 0.39, 95% CI = 0.12, 0.66), tin with systolic blood pressure (β = –0.33, 95% CI = –0.60, –0.06), and mercury with systolic (β = –0.83, 95% CI = –1.49, –0.17) and diastolic blood pressure (β = –0.89, 95% CI = –1.53, –0.26). Chromium was associated with diastolic blood pressure among boys only (β = 1.10, 95% CI = 0.28, 1.92, P for interaction = 0.02), and copper was associated with diastolic blood pressure among girls only (β = –1.97, 95% CI = –3.63, –0.32, P for interaction = 0.01). These findings were largely robust to the secondary analyses that utilized mixture modeling approaches (PCA, WQS, and BKMR).

Conclusions:

Future prospective studies are needed to investigate further the impact of early life exposure to metal mixtures on children’s blood pressure trajectories and cardiovascular disease risk later in life.
Nutritional Status at Diagnosis and Pre-transplant Weight Loss Impact Outcomes of Acute Myeloid Leukemia Patients Following Allogeneic Stem Cell Transplantation
Authors: Brauer Dominic , Backhaus Donata , Pointner Rosmarie , Vucinic Vladan , Niederwieser Dietger , Platzbecker Uwe , Schwind Sebastian , Jentzsch Madlen
Published: February 2021

The nutritional status at diagnosis, as well as weight loss during chemotherapy, are important factors for morbidity and mortality in cancer patients. They might also influence outcomes in patients with acute myeloid leukemia (AML) receiving allogeneic hematopoietic stem cell transplantation (HSCT). We evaluated the body mass index (BMI) at diagnosis, prior to HSCT, and the BMI difference (ΔBMI = BMIHSCT–BMIdiagnosis) in 662 AML patients undergoing allogeneic HSCT. Patients being obese at AML diagnosis had significantly higher nonrelapse mortality (NRM) and shorter overall survival (OS) after HSCT, but no distinct cumulative incidence of relapse than nonobese patients. Weight loss during chemotherapy (ΔBMI > –2) was a strong predictor for higher NRM and shorter OS in univariate and multivariate analyses. These results were observed across all European LeukemiaNet (ELN) 2017 risk groups but especially in patients with favorable or intermediate ELN2017 risk and patients transplanted in morphologic complete remission. Only in patients being obese at AML diagnosis, weight loss did not result in adverse outcomes. ΔBMI > –2 represents a strong, independent, and modifiable risk factor for AML patients treated with HSCT. Nutritional monitoring and supplementation during disease course might improve patients’ outcomes.
Cost and social distancing dynamics in a mathematical model of COVID-19 with application to Ontario, Canada
Authors: Moyles I. R. , Heffernan J. M. , Kong J. D.
Published: February 2021

A mathematical model of COVID-19 is presented where the decision to increase or decrease social distancing is modelled dynamically as a function of the measured active and total cases as well as the perceived cost of isolating. Along with the cost of isolation, we define an overburden healthcare cost and a total cost. We explore these costs by adjusting parameters that could change with policy decisions. We observe that two disease prevention practices, namely increasing isolation activity and increasing incentive to isolate do not always lead to optimal health outcomes. We demonstrate that this is due to the fatigue and cost of isolation. We further demonstrate that an increase in the number of lock-downs, each of shorter duration can lead to minimal costs. Our results are compared with case data in Ontario, Canada from March to August 2020 and details of expanding the results to other regions are presented.
An experimental investigation to model wheezing in lungs
Authors: Gregory A. L. , Agarwal A. , Lasenby J.
Published: February 2021

A quarter of the world's population experience wheezing. These sounds have been used for diagnosis since the time of the Ebers Papyrus (
ca
1500 BC). We know that wheezing is a result of the oscillations of the airways that make up the lung. However, the physical mechanisms for the onset of wheezing remain poorly understood, and we do not have a quantitative model to predict when wheezing occurs. We address these issues in this paper. We model the airways of the lungs by a modified Starling resistor in which airflow is driven through thin, stretched elastic tubes. By completing systematic experiments, we find a generalized ‘tube law’ that describes how the cross-sectional area of the tubes change in response to the transmural pressure difference across them. We find the necessary conditions for the onset of oscillations that represent wheezing and propose a flutter-like instability model for it about a heavily deformed state of the tube. Our findings allow for a predictive tool for wheezing in lungs, which could lead to better diagnosis and treatment of lung diseases.
In vitro growth-inhibitory effects of Portulaca oleracea L. formulation on intestinal pathogens
Authors: Okuda Sae , Wajima Takeaki , Yamada Tetsuya , Nakaminami Hidemasa , Ikoshi Hideaki , Noguchi Norihisa
Published: February 2021

Introduction. Empirical evidence suggests that Portulaca oleracea L. treats enteric infections, including dysentery, cholera, and acute infectious gastroenteritis.

Aim. The aim of this study is to clarify the growth-inhibitory effects of Portulaca oleracea L. extract against 56 strains of intestinal pathogens.

Methodology. ‘Gogyo-so-cha (GSC)’ was used as the P. oleracea L. formulation. A growth curve analysis was used to measure the growth-inhibitory effects of GSC, and Shiga toxin induction was measured using the latex agglutination test.

Results. GSC demonstrated strong bactericidal effects against

Shigella dysenteriae

and

Vibrio cholerae

strains from various isolates. GSC demonstrated weak or no bactericidal effects against intestinal commensal bacteria, including

Enterococcus

spp. and

Escherichia coli

. GSC did not induce

Shigella

toxins.

Conclusion. GSC significantly inhibited the growth of intestinal pathogens, including

S. dysenteriae

and

V. cholerae

, without adversely affecting the intestinal flora, supporting the usage of GSC in traditional Chinese medicine. Taken together, GSC would be of immense value in the developing world, where diarrhoeal infectious diseases continue to pose a major health risk.
Rapid SARS-CoV-2 variants spread detected in France using specific RT-PCR testing
Authors: Haim-Boukobza Stéphanie , Roquebert Benedicte , Trombert-Paolantoni Sabine , Lecorche Emmanuel , Verdurme Laura , Foulongne Vincent , Selinger Christian , Michalakis Yannis , Sofonea Mircea T. , Alizon Samuel
Published: February 2021

SARS-CoV-2 variants raise major concerns regarding the control of COVID-19 epidemics. We analyse 40,000 specific RT-PCR tests performed on SARS-CoV-2-positive samples collected between Jan 26 and Feb 16, 2021. We find a high transmission advantage of variants and show that their spread in the country is more advanced than anticipated.
Associations Between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States
Authors: Abbas Mostafa , Morland Thomas B. , Hall Eric S. , EL-Manzalawy Yasser
Published: February 2021

We utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19 related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.
Lactic Acid Production byClostridium acetobutylicumandClostridium beijerinckiiUnder Anaerobic Conditions Using a Complex Substrate
Authors: L. Mattiello-Franisco , F.M. Vieira , G. Peixoto , G. Mockaitis
Published: February 2021

SUMMARY/ ABSTRACT

High societies consumption, elevated residues generation and environmental awareness strengthen alternatives solutions for bioprocess’ residues. This study investigated the production of volatile acids from a complex substrate, which intends to be replaceable in the future by vinasse of sugar cane, in anaerobic reactors operated in triplicates at 35 °C. Two different inoculum were studied:Clostridium acetobutylicumATCC 824 andClostridium beijerinckiiATCC 25752. The nutrient medium had as carbon source a complex substrate containing sucrose without addition of vitamins, buffer solution and micronutrients. The experiment was conducted in the variation of F/M-ratio (food-to-microorganisms) by increasing substrate concentration.

The concentration of sucrose in the complex substrate were 5.2 g·L-1(conditions of 10,000 mg O2· L-1in terms of COD) and 10.5 g· L-1(conditions of 20,000 mg O2·L-1in terms of COD), keeping the initial concentration of inoculum in 500 mg SVT·L-1. CulturesC. acetobutylicumandC. beijerinckiiresulted in high lactic acid production. Concentrations of COD of 10,000 mg O2· L-1produced optimum lactic acid of 3,331 mg·L-1and 5,709 mg·L-1with respectively C.acetobutylicumandC. beijerinckii.Moreover, cultures C.acetobutylicumandC. beijerinckiiwith 20,000 mg O2· L-1concentrations in terms of COD produced optimum lactic acid of 6,417 mg· L-1and 7.136 mg·L-1respectively. There was repeatability in the reactors when considering level of significance of 0.05, independent of the concentration and inoculum used.
Genomics-based deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid AHR signaling dynamics
Authors: Gupta Arnav , Sasse Sarah K , Gruca Margaret A. , Sanford Lynn , Dowell Robin D. , Gerber Anthony N.
Published: February 2021

Heterogeneity of respirable particulates and compounds complicates understanding transcriptional responses to air pollution. Here, we address this problem through applying precision nuclear run-on sequencing (PRO-seq) to measure nascent transcription and the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to airway epithelial cells after wood smoke particle (WSP) exposure. We used transcription factor enrichment analysis to agnostically identify temporally distinct roles for the TCF/SRF family, the aryl hydrocarbon receptor (AHR), and NFkB in regulating transcriptional changes induced by WSP. Transcription of canonical targets of the AHR, such asCYP1A1andAHRR, was robustly increased after just 30 minutes of WSP exposure, and we discovered novel AHR-regulated pathways and targets including the DNA methyltransferase,DNMT3L. Transcription of these genes and associated enhancers rapidly returned to near baseline by 120 minutes. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining NFkB responses through 120 minutes of exposure. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression. This work also defines an integrated genomics-based strategy for deconvoluting multiplexed transcriptional responses to heterogeneous environmental exposures.
Emergence of variation between groups through time in fish shoal collective motion
Authors: MacGregor Hannah E. A. , Ioannou Christos C.
Published: February 2021

Despite extensive interest in the dynamic interactions between individuals that drive collective motion in animal groups, the dynamics of collective motion over longer time frames are understudied. Using three-spined sticklebacks,Gasterosteus aculateus, randomly assigned to twelve shoals of eight fish, we tested how six key traits of collective motion changed over shorter (within trials) and longer (between days) timescales under controlled laboratory conditions. Over both timescales, groups became less social with reduced cohesion, polarisation, group speed and information transfer. There was consistent inter-group variation (i.e. collective personality variation) for all collective motion parameters, but groups also differed in how their collective motion changed over days in their cohesion, polarisation, group speed and information transfer. This magnified differences between groups, suggesting that over time the ‘typical’ collective motion cannot be easily characterised. The minimal sample size of independent groups and their divergence over time need to be considered in future studies.
Comprehensive evaluation ofACE2expression in female ovary by single-cell RNA-seq analysis
Authors: Kong Siming , Yan Zhiqiang , Yuan Peng , Liu Xixi , Chen Yidong , Yang Ming , Chen Wei , Song Shi , Yan Jie , Yan Liying , Qiao Jie
Published: February 2021

Pneumonia induced by severe acute respiratory coronavirus 2 (SARS-CoV-2) via ACE2 receptor may affect many organ systems like lung, heart and kidney. An autopsy report revealed positive SARS-Cov-2 detection results in ovary, however, the developmental-stage-specific and cell-type-specific risk in fetal primordial germ cells (PGCs) and adult women ovary remained unclear. In this study, we used single-cell RNA-sequencing (scRNA-seq) datasets spanning several developmental stages of ovary including PGCs and cumulus-oocyte complex (COC) to investigate the potential risk of SARS-CoV-2 infection. We found that PGCs and COC exhibited highACE2expression. More importantly, the ratio ofACE2-positive cells was sharply up-regulated in primary stage andACE2was expressed in all oocytes and cumulus cells in preovulatory stage, suggesting the possible risk of SARS-CoV-2 infection in follicular development. CatB/L, not TMPRSS2, was identified to prime for SARS-CoV-2 entry in follicle. Our findings provided insights into the potential risk of SARS-CoV-2 infection during folliculogenesis in adulthood and the possible risk in fetal PGCs.
IFNγ and iNOS-mediated alterations in the bone marrow and thymus and its impact onMycobacterium avium-induced thymic atrophy
Authors: Barreira-Silva Palmira , Melo-Miranda Rita , Nobrega Claudia , Roque Susana , Serre-Miranda Cláudia , Borges Margarida , de Sá Calçada Daniela , Behar Samuel M. , Appelberg Rui , Correia-Neves Margarida
Published: February 2021

Disseminated infection with the high virulence strain ofMycobacterium avium25291 lead to progressive thymic atrophy. We previously uncovered thatM. avium-induced thymic atrophy is due to increased levels of glucocorticoids synergizing with nitric oxide (NO) produced by interferon gamma (IFNγ) activated macrophages. Where and how these mediators are playing, was yet to be understood. We hypothesized that IFNγ and NO might be affecting bone marrow (BM) T cell precursors and/or T cell differentiation in the thymus. We show thatM. aviuminfection causes a reduction on the percentage of lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP). Additionally, BM precursors from infected mice are unable to reconstitute thymi of RAGKO mice in an IFNγ-dependent way. Thymi from infected mice presents a NO-dependent inflammation. When transplanted under the kidney capsule of non-infected mice, thymic stroma from infected mice is unable to sustain T cell differentiation. Finally, we observed increased thymocyte death via apoptosis after infection, independent of both IFNγ and iNOS, and a decrease on activated caspase-3 positive thymocytes, that was not observed in the absence of iNOS expression. Together our data suggests thatM. avium-induced thymic atrophy results from a combination of impairments, mediated by IFNγ and NO, affecting different steps of T cell differentiation from T cell precursor cells in the BM to the thymic stroma and thymocytes.
Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremulaL.)
Authors: Rendón-Anaya Martha , Wilson Jonathan , Sveinsson Sæmundur , Fedorkov Aleksey , Cottrell Joan , Bailey Mark E.S. , Ruņģis Dainis , Lexer Christian , Jansson Stefan , Robinson Kathryn M. , Street Nathaniel R. , Ingvarsson Pär K.
Published: February 2021

Understanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.
A framework for selectively breeding corals for assisted evolution
Authors: Humanes Adriana , Bythell John , Beauchamp Elizabeth , Carl Mitch , Craggs Jamie , Edwards Alasdair , Golbuu Yimnang , Lachs Liam , Randle Janna Leigh , Martinez Helios , Palmowski Pawel , Paysinger Faith , van der Steeg Eveline , Sweet Michael , Treumann Achim , Guest James
Published: February 2021

Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches, such as selective breeding for adaptive traits combined with large-scale sexual propagation, are being developed with the aim of pre-adapting reefs to increased ocean warming. However, there are still major gaps in our understanding of the technical and methodological constraints to producing corals for such restoration interventions. Here we propose a framework for selectively breeding corals and rearing them from eggs to 2.5-year old colonies using the coralAcropora digitiferaas a model species. We present methods for choosing colonies for selective crossing, enhancing early survivorship inex situandin situnurseries, and outplanting and monitoring colonies on natal reefs. We used a short-term (7-day) temperature stress assay to select parental colonies based on heat tolerance of excised branches. From six parental colonies, we produced 12 distinct crosses, and compared survivorship and growth of colonies transferred toin situnurseries or outplanted to the reef at different ages. We demonstrate that selectively breeding and rearing coral colonies is technically feasible at small scales and could be upscaled as part of restorative assisted evolution initiatives. Nonetheless, there are still challenges to overcome before selective breeding can be implemented as a viable conservation tool, especially at the post-settlement and outplanting phases. Although interdisciplinary approaches will be needed to overcome many of the challenges identified in this study, selective breeding has the potential to be a viable tool within reef managers’ toolbox to support the persistence of selected reefs in the face of climate change.
Longitudinal preclinical imaging characterization of drug delivery potential after radiotherapy in the healthy and leukemic bone marrow vascular microenvironment
Authors: Brooks Jamison , Zuro Darren , Song Joo Y. , Sargur Madabushi Srideshikan , Sanchez James F , Kortylewski Marcin , Chen Bihong T. , Gupta Kalpna , Storme Guy , Froelich Jerry , Hui Susanta K
Published: February 2021

Objectives

Radiotherapy improves blood perfusion and cellular chemotherapy uptake in mice with acute lymphoblastic leukemia (ALL). However, its ability to influence drug delivery and permeation through the bone marrow vasculature (BMV) is unknown, due in part to a lack of methodology. This study developed longitudinal quantitative multiphoton (L-QMPM) imaging and used it to characterize drug delivery potential and the BMV before and after radiotherapy in mice bearing leukemia.

Methods

We developed a longitudinal window implant for L-QMPM imaging of the calvarium BMV before, 2 days after, and 5 days after radiotherapy. Live time-lapsed images of a fluorescent drug surrogate were used to obtain measurements including tissue wash-in slope (WIStissue) to measure drug delivery potential. We performed L-QMPM imaging using 2 Gy and 10 Gy total body irradiation (TBI) on C57/B6 (WT) mice, mice bearing ALL, and acute myeloid leukemia (AML).

Results

Implants had no effects on calvarium dose, and parameters for WT untreated mice were stable during imaging. We observed increased angiogenesis, decreased single-vessel blood flow, and decreased WIStissuewith the onset of AML and ALL. 2Gy and 10Gy TBI increased WIStissue2 days after radiotherapy in all 3 groups of mice and increased single-vessel blood flow in mice bearing ALL and AML. Significant increases in WIStissuewere observed 2 days after 2Gy TBI compared to 5 days. Morphological and functional alterations in the BMV were sustained for a significantly longer time period after 10Gy TBI (5 days post-treatment) compared to 2Gy TBI (2 days post-treatment).

Conclusion

L-QMPM provides stable functional assessments of the BMV. TBI increases the drug delivery potential of the leukemic BMV 2-5 days post-treatment, likely through improved blood perfusion and drug exchange from the BMV to the extravascular tissue. Our data show that neo-adjuvant 2Gy and 10Gy TBI condition the BMV for increased drug delivery.
Potassium isomerized linoleate satisfies EPA MB-35-00 for surface disinfection ofCandida auris(AR-0381)
Authors: Changaris David , Carenbauer Anne
Published: February 2021

Four distinct lots of Potassium Isomerized Linoleate, 442 mM or 141 mg/ml (within the cosmetic-cleanser and commercial-soap acceptable concentration ranges but much greater than physiologic conditions), showed greater than 5 log kill rates (total) forCandida auris(AR-0381) for all carriers during 5 separate procedural runs of EPA MB-35-00. After exposing the inoculated stainless-steel carriers to the plant-oil soap for 1, 2, or 10 minute(s), we recovered noCandida aurison these tested carriers. Control carriers with phosphate-buffered saline applied, recovered 5.0-6.8 Log of colony-forming units per carrier.
Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?
Authors: Looney Brian , Miyauchi Shingo , Morin Emmanuelle , Drula Elodie , Courty Pierre Emmanuel , Kohler Annegret , Kuo Alan , LaButti Kurt , Pangilinan Jasmyn , Lipzen Anna , Riley Robert , Andreopoulos William , He Guifen , Johnson Jenifer , Nolan Matt , Tritt Andrew , Barry Kerrie W. , Grigoriev Igor V. , Nagy László G. , Hibbett David , Henrissat Bernard , Matheny P. Brandon , Labbé Jessy , Martin Francis M.
Published: February 2021

The ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the most diverse lineages of ectomycorrhizal fungi. We present comparative analyses of the pangenome and gene repertoires of 21 species across the order Russulales, including a closely related saprotrophic member of Russulaceae. The ectomycorrhizal Russulaceae is inferred to have originated around the Cretaceous-Paleogene extinction event (73.6-60.1 million years ago (MY)). The genomes of the ectomycorrhizal Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of genes coding for certain secreted proteins with TE “nests”. The saprotrophic sister group of the ectomycorrhizal Russulaceae,Gloeopeniophorella convolvens, possesses some of these aspects (e.g., loss of some PCWDE and protease orthologs, TE expansion, reduction in secondary metabolism clusters), resulting from an accelerated rate of gene evolution in the shared ancestor of Russulaceae that predates the evolution of the ectomycorrhizal habit. Genomes of Russulaceae possess a high degree of synteny, including a conserved set of terpene secondary metabolite gene clusters. We hypothesize that the evolution of the ectomycorrhizal habit requires premodification of the genome for plant root association followed by an accelerated rate of gene evolution within the secretome for host-defense circumvention and symbiosis establishment.
Generation and validation of a CRF1:Cre transgenic rat: The role of central amygdala CRF1in nociception and anxiety-like behavior
Authors: Weera Marcus M. , Agoglia Abigail E. , Douglass Eliza , Jiang Zhiying , Rajamanickam Shivakumar , Shackett Rosetta S. , Herman Melissa A. , Justice Nicholas J. , Gilpin Nicholas W.
Published: February 2021

Corticotropin-releasing factor type-1 (CRF1) receptors are critical to stress responses because they allow neurons to respond to CRF released in response to stress. Our understanding of the precise role of CRF1-expressing neuronal populations in CRF-mediated behaviors has been largely limited to mouse experiments due to the lack of genetic tools available to selectively visualize and manipulate CRF1+cells in rats. Here, we describe the generation and validation of a transgenic CRF1:Cre-tdTomato rat, which expresses a bicistroniciCre-2A-tdTomatotransgene directed by 200kb of promoter and enhacer sequence surrounding theCrhr1cDNA present within a BAC clone, that has been transgenically inserted into the rat genome. We report thatCrhr1andCremRNA expression are highly colocalized in CRF1:Cre-tdTomato rats within both the central amygdala (CeA), composed of mostly GABAergic neurons, and in the basolateral amygdala (BLA), composed of mostly glutamatergic neurons. In the CeA, membrane properties, inhibitory synaptic transmission, and responses to CRF bath application intdTomato+neurons are similar to those previously reported in GFP+cells in CRFR1-GFP mice. We show that stimulatory DREADD receptors can be selectively targeted to CeA CRF1+cells via virally delivered Cre-dependent transgenes, that transfected Cre/tdTomato+cells are activated by clozapine-n-oxidein vitroandin vivo, and that activation of these cellsin vivoincreases anxiety-like behavior and nocifensive responses. Given the accuracy of expression in the CRF1:Cre rat, modern genetic techniques used to investigate the anatomy, physiology, and behavioral function of CRF1+neurons and circuits can now be performed in assays that require the use of rats as the model organism.

Impact Statement

A novel transgenic rat for studying the role of specific corticotropin-releasing factor type-1 receptor-expressing cell populations in physiology and behavior.
MetaPro: A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities
Authors: Taj Billy , Adeolu Mobolaji , Xiong Xuejian , Ang Jordan , Nursimulu Nirvana , Parkinson John
Published: February 2021

Background

Whole microbiome RNASeq (metatranscriptomics) has emerged as a powerful technology to functionally interrogate microbial communities. A key challenge is how best to process, analyze and interpret these complex datasets. In a typical application, a single metatranscriptomic dataset may comprise from tens to hundreds of millions of sequence reads. These reads must first be processed and filtered for low quality and potential contaminants, before being annotated with taxonomic and functional labels and subsequently collated to generate global bacterial gene expression profiles.

Results

Here we present MetaPro, a flexible, massively scalable metatranscriptomic data analysis pipeline that is cross-platform compatible through its implementation within a Docker framework. MetaPro starts with raw sequence read input (single end or paired end reads) and processes them through a tiered series of filtering, assembly and annotation steps. In addition to yielding a final list of bacterial genes and their relative expression, MetaPro delivers a taxonomic breakdown based on the consensus of complementary prediction algorithms, together with a focused breakdown of enzymes, readily visualized through the Cytoscape network visualization tool. We benchmark the performance of MetaPro against two current state of the art pipelines and demonstrate improved performance and functionality.

Conclusion

MetaPro represents an effective integrated solution for the processing and analysis of metatranscriptomic datasets. Its modular architecture allows new algorithms to be deployed as they are developed, ensuring its longevity. To aid user uptake of the pipeline, MetaPro, together with an established tutorial that has been developed for educational purposes is made freely available athttps://github.com/ParkinsonLab/MetaPro. The software is freely available under the GNU general public license v3.
Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber
Authors: Noby Nehad , Johnson Rachel L. , Tyzack Jonathan D. , Embaby Amira M. , Saeed Hesham , Hussein Ahmed , Khattab Sherine N. , Rizkallah Pierre J. , Jones D. Dafydd
Published: February 2021

Cold active esterases represent an important class of enzymes capable of undertaking useful chemical transformations at low temperatures. EstN7 fromBacillus cohniirepresents a true psychrophilic esterase with a temperature optimum below 20°C. We have recently determined the structure of EstN7 and have used this knowledge to understand substrate specificity and expands its substrate range through protein engineering. Substrate range is determined by a plug at the end of acyl binding pocket that blocks access to a buried water filled cavity, so limiting EstN7 to turnover of C2 and C4 substrates. Data mining revealed a potentially important commercial reaction, conversion of triacetin to only the 1,2-glyceryl diacetate isomer, which the EstN7 could achieve. Residues M187, N211 and W206 were identified as plug residues. M187 was identified as the key plug residue but mutation to alanine destabilised the structure as whole. Another plug mutation, N211A had a stabilising effect on EstN7 and suppressed the destabilising M187A mutation. The M187A-N211A variant had the broadest substrate range, capable of hydrolysing a C8 substrate. Thus, the structure of EstN7 together with focused engineering has provided new insights into the structural stability and substrate specificity that allowed expansion of substrate range.
Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses
Authors: Nambulli Sham , Xiang Yufei , Tilston-Lunel Natasha L. , Rennick Linda J. , Sang Zhe , Klimstra William B. , Reed Douglas S. , Crossland Nicholas A. , Shi Yi , Duprex W. Paul
Published: February 2021

Globally there is an urgency to develop effective, low-cost therapeutic interventions for coronavirus disease 2019 (COVID-19). We previously generated the stable and ultrapotent homotrimeric Pittsburgh inhalable Nanobody 21 (PiN-21). Using Syrian hamsters that model moderate to severe COVID-19 disease, we demonstrate the high efficacy of PiN-21 to prevent and treat SARS-CoV-2 infection. Intranasal delivery of PiN-21 at 0.6 mg/kg protects infected animals from weight loss and substantially reduces viral burdens in both lower and upper airways compared to control. Aerosol delivery of PiN-21 facilitates deposition throughout the respiratory tract and dose minimization to 0.2 mg/kg. Inhalation treatment quickly reverses animals’ weight loss post-infection and decreases lung viral titers by 6 logs leading to drastically mitigated lung pathology and prevents viral pneumonia. Combined with the marked stability and low production cost, this novel therapy may provide a convenient and cost-effective option to mitigate the ongoing pandemic.
Glia-neuron signaling mediated by two different BMP ligands impacts synaptic growth
Authors: Bartoletti Mathieu , Knight Tracy , Held Aaron , Rand Laura M. , Wharton Kristi A.
Published: February 2021

The nervous system is a complex network of cells whose interactions provide circuitry necessary for an organism to perceive and move through its environment. Revealing the molecular basis of how neurons and non-neuronal glia communicate is essential for understanding neural development, behavior, and abnormalities of the nervous system. BMP signaling in motor neurons, activated in part by retrograde signals from muscle expressed Gbb (BMP5/6/7) has been implicated in synaptic growth, function and plasticity inDrosophila melanogaster. Through loss-of-function studies, we establish Gbb as a critical mediator of glia to neuron signaling important for proper synaptic growth. Furthermore, the BMP2/4 ortholog, Dpp, expressed in a subset of motor neurons, acts by autocrine signaling to also facilitate neuromuscular junction (NMJ) growth at specific muscle innervation sites. In addition to signaling from glia to motor neurons, autocrine Gbb induces signaling in larval VNC glia which strongly express the BMP type II receptor, Wit. In addition to Dpp’s autocrine motor neuron signaling, Dpp also engages in paracrine signaling to adjacent glia but not to neighboring motor neurons. In one type of dorsal midline motor neuron, RP2,dpptranscription is under tight regulation, as its expression is under autoregulatory control in RP2 but not aCC neurons. Taken together our findings indicate that bi-directional BMP signaling, mediated by two different ligands, facilitates communication between glia and neurons. Gbb, prominently expressed in glia, and Dpp acting from a discrete set of neurons induce active Smad-dependent BMP signaling to influence bouton number during neuromuscular junction growth.