bluuebunny/crossref_metadata_2025 huggingface dataset:
The assembly history of the nearest S0 galaxy NGC 3115 from its kinematics out to six half-light radii
Authors: Dolfi Arianna , Forbes Duncan A , Couch Warrick J , Ferré-Mateu Anna , Bellstedt Sabine , Bekki Kenji , Diaz Jonathan , Romanowsky Aaron J , Brodie Jean P
Published: April 2020

Using new and archival data, we study the kinematic properties of the nearest field S0 galaxy, NGC 3115, out to ∼6.5 half-light radii (Re) from its stars (integrated starlight), globular clusters (GCs), and planetary nebulae (PNe). We find evidence of three kinematic regions with an inner transition at ∼0.2 Re from a dispersion-dominated bulge (Vrot/σ < 1) to a fast-rotating disc (Vrot/σ > 1), and then an additional transition from the disc to a slowly rotating spheroid at $\sim 2\!-\!2.5\, R_\mathrm{e}$, as traced by the red GCs and PNe (and possibly by the blue GCs beyond $\sim 5\, R_\mathrm{e}$). From comparison with simulations, we propose an assembly history in which the original progenitor spiral galaxy undergoes a gas-rich minor merger that results in the embedded kinematically cold disc that we see today in NGC 3115. At a later stage, dwarf galaxies, in mini mergers (mass ratio < 1:10), were accreted building up the outer slowly rotating spheroid, with the central disc kinematics largely unaltered. Additionally, we report new spectroscopic observations of a sample of ultracompact dwarfs (UCDs) around NGC 3115 with the Keck/KCWI instrument. We find that five UCDs are inconsistent with the general rotation field of the GCs, suggesting an ex situ origin for these objects, i.e. perhaps the remnants of tidally stripped dwarfs. A further seven UCDs follow the GC rotation pattern, suggesting an in situ origin and, possibly a GC-like nature.
Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants
Authors: Shi Tao , Rahmani Razgar Seyed , Gugger Paul F , Wang Muhua , Li Hui , Zhang Yue , Li Zhizhong , Wang Qingfeng , Van de Peer Yves , Marchal Kathleen , Chen Jinming
Published: April 2020

For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
The cell line A-to-I RNA editing catalogue
Authors: Schaffer Amos A , Kopel Eli , Hendel Ayal , Picardi Ernesto , Levanon Erez Y , Eisenberg Eli
Published: April 2020

Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.
Effect of the proton-pump Inhibitor pantoprazole on MycoPhenolic ACid exposure in kidney and liver transplant recipienTs (IMPACT study): a randomized trial
Authors: Sunderland Andrew , Russ Graeme , Sallustio Benedetta , Cervelli Matthew , Joyce David , Ooi Esther , Jeffrey Gary , Boudville Neil , Chakera Aron , Dogra Gursharan , Chan Doris , Wong Germaine , Lim Wai H
Published: April 2020

Background

Mycophenolic acid (MPA) is widely utilized as an immunosuppressant in kidney and liver transplantation, with reports suggesting an independent relationship between MPA concentrations and adverse allograft outcome. Proton-pump inhibitors (PPIs) may have variable effects on the absorption of different MPA formulations leading to differences in MPA exposure.

Methods

A multicentre, randomized, prospective, double-blind placebo-controlled cross-over study was conducted to determine the effect of the PPI pantoprazole on the MPA and its metabolite MPA-glucuronide (MPA-G) area under the curve (AUC) >12 h (MPA-AUC12 h) in recipients maintained on mycophenolate mofetil (MMF) or enteric-coated mycophenolate sodium (EC-MPS). We planned a priori to examine separately recipients maintained on MMF and EC-MPS for each pharmacokinetic parameter. The trial (and protocol) was registered with the Australian New Zealand Clinical Trials Registry on 24 March 2011, with the registration number of ACTRN12611000316909 (‘IMPACT’ study).

Results

Of the 45 recipients screened, 40 (19 MMF and 21 EC-MPS) were randomized. The mean (standard deviation) recipient age was 58 (11) years with a median (interquartile range) time post-transplant of 43 (20–132) months. For recipients on MMF, there was a significant reduction in the MPA-AUC12 h [geometric mean (95% confidence interval) placebo: 53.9 (44.0–65.9) mg*h/L versus pantoprazole: 43.8 (35.6–53.4) mg*h/L; P = 0.004] when pantoprazole was co-administered compared with placebo. In contrast, co-administration with pantoprazole significantly increased MPA-AUC12 h [placebo: 36.1 (26.5–49.2) mg*h/L versus pantoprazole: 45.9 (35.5–59.3) mg*h/L; P = 0.023] in those receiving EC-MPS. Pantoprazole had no effect on the pharmacokinetic profiles of MPA-G for either group.

Conclusions

The co-administration of pantoprazole substantially reduced the bioavailability of MPA in patients maintained on MMF and had the opposite effect in patients maintained on EC-MPS, and therefore, clinicians should be cognizant of this drug interaction when prescribing the different MPA formulations.
We are in This Together: Promoting Health Equity, Diversity, and Inclusion in Tobacco Research for Sexual and Gender Minority Populations
Authors: Dermody Sarah S , Heffner Jaimee L , Hinds Josephine T , McQuoid Julia , Quisenberry Amanda J , Tan Andy S L , Vogel Erin A
Published: April 2020

Introduction

Sexual and gender minority (SGM) individuals have higher tobacco use prevalence and consequently higher burden of tobacco-caused diseases, including cancer and cardiovascular disease compared with their heterosexual or cisgender counterparts. Yet, there is a critical gap in research focused on measuring SGM tobacco-related health disparities and addressing unmet needs of SGM individuals in the context of nicotine and tobacco research.

Aims and Methods

In this commentary, we summarize recommendations discussed during a pre-conference workshop focused on challenges and opportunities in conducting SGM tobacco control research at the 2019 Society for Research on Nicotine and Tobacco Annual Meeting.

Results

Specifically, we recommend defining and measuring SGM identity in all nicotine and tobacco research routinely, using novel methods to engage a demographically diverse sample of the SGM population, and eliciting SGM community voices in tobacco control research.

Conclusions

Addressing these critical research gaps will enable the scientific community to generate the data to fully understand and support SGM individuals in tobacco use prevention and cessation.

Implications

Tobacco use and its consequences have become increasingly concentrated in disadvantaged groups, including sexual and gender minority (SGM) populations. Through concrete recommendations in this commentary, we aimed to promote health equity, diversity, and inclusion in tobacco research for SGM populations by urging the scientific community to consider expanding efforts to monitor and address tobacco-related health disparities of SGM populations within their respective research programs.
Epidural Anesthesia in Liver Surgery—A Propensity Score–Matched Analysis
Authors: Knaak Cornelia , Spies Claudia , Schneider Alice , Jara Maximilian , Vorderwülbecke Gerald , Kuhlmann Anna Dorothea , von Haefen Clarissa , Lachmann Gunnar , Schulte Erika
Published: April 2020

Objective

To assess the effects of epidural anesthesia (EA) on patients who underwent liver resection.

Design

Secondary analysis of a prospective randomized controlled trial.

Setting

This single-center study was conducted at an academic medical center.

Methods

A subset of 110 1:1 propensity score–matched patients who underwent liver resection with and without EA were analyzed. Outcome measures were pain intensity ≥5 on a numeric rating scale (NRS) at rest and during movement on postoperative days 1–5, analyzed with logistic mixed-effects models, and postoperative complications according to the Clavien-Dindo classification, length of hospital stay (LOS), and one-year survival. One-year survival in the matched cohorts was compared using a frailty model.

Results

EA patients were less likely to experience NRS ≥5 at rest (odds ratio = 0.06, 95% confidence interval [CI] = 0.01 to 0.28, P < 0.001). These findings were independent of age, sex, Charlson comorbidity index, baseline NRS, and surgical approach (open vs laparoscopic). The number and severity of postoperative complications and LOS were comparable between groups (P = 0.258, P > 0.999, and P = 0.467, respectively). Reduced mortality rates were seen in the EA group one year after surgery (9.1% vs 30.9%, hazard ratio = 0.32, 95% CI = 0.11 to 0.90, P = 0.031). No EA-related adverse events occurred. Earlier recovery of bowel function was seen in EA patients.

Conclusions

Patients with EA had better postoperative pain control and required fewer systemic opioids. Postoperative complications and LOS did not differ, although one-year survival was significantly improved in patients with EA. EA applied in liver surgery was effective and safe.
EXPERIMENTAL DETERMINATION OF ANISOTROPIC EMISSION OF NEUTRONS FROM 252CF NEUTRON SOURCE WITH THE SPHERICAL PROTECTION CASE
Authors: Kowatari Munehiko , Nishino Sho , Romallosa Kristine Marie D , Yoshitomi Hiroshi , Tanimura Yoshihiko , Ohishi Tetsuya
Published: April 2020

The anisotropic emission of neutrons from a cylindrical X1 252Cf source with the spherical external casing was experimentally determined. The influence of metal materials and shapes of the external casing to the anisotropy factor, FI(θ), was assessed by the Monte Carlo calculation, before performing the measurement. The results of the calculation implied that light- and spherical-shaped external casing decreases the anisotropic emission of neutrons from a cylindrical source and the nature of the material does not affect the anisotropic emission to a large extent. The experimental results obtained when a spherical-shaped aluminum protection case was employed also revealed that the anisotropy factor was close to 1.0 with a wide zenith angle range. Considering the source handling and measures against mechanical impact to the source, we designed an SUS304-made spherical protection case for a renovated source delivering apparatus. With the SUS304-made spherical protection case, the measured anisotropy factor FI(90) was determined to be 1.002 ± 0.002 (k = 1). Results from the experiments also indicated that the measured anisotropy factor has a flat distribution from 55 to 125° with zenith angle.
A novel dark septate fungal endophyte positively affected blueberry growth and changed the expression of plant genes involved in phytohormone and flavonoid biosynthesis
Authors: Wu Fan-Lin , Li Yan , Tian Wei , Sun Yadong , Chen Feiyan , Zhang Yurou , Zhai Yuxuan , Zhang Jing , Su Hongyan , Wang Lei
Published: April 2020

Dark septate endophytes (DSEs) are one of the most studied groups of root fungal endophytes in recent years. However, the effects of DSE on host plant are still under debate, and the molecular mechanisms are poorly understood. In this study, we identified a DSE fungus of the genus Anteaglonium, named T010, from the wild blueberry. When inoculated into Vaccinium corymbosum L. plants, T010 could enhance root growth and promote shoot branching, leading to increased plant growth. By comparative transcriptome analysis, we obtained 1948 regulated differentially expressed genes (DEGs) from the V. corymbosum plants treated by T010. Further functional enrichment analysis identified a series of DEGs enriched in transcriptional regulation, material transport, phytohormone biosynthesis and flavonoid biosynthesis. Moreover, the comparative analysis of liquid chromatography–mass spectrometry verified that T010 treatment induced the changes in the contents of various phytohormones and flavonoids. This is the first report on the isolation of DSE fungi of the genus Anteaglonium from blueberry roots. Moreover, our results suggested that T010 colonization could result in a series of changes in cell metabolism, biosynthesis and signal pathways, thereby promoting plant growth. Particularly, the changes of phytohormone and flavonoid metabolism induced by T010 colonization might contribute to the promotion of blueberry growth. Our results will provide new insights into understanding of the interaction of DSE fungi and host plants, as well as the development and utilization of DSE preparations.
Sex Differences in Youth Elite Swimming
Authors: Clayburn Andrew , Senefeld Jonathon W , Baker Sarah E , Carter Rickey , Johnson Patrick , Joyner Michael J
Published: April 2020

The timing and magnitude of sex differences in athletic performance during early human development, prior to adulthood, is unknown.

Objective

To compare swimming velocity of boys and girls for all Olympic‐length freestyle swimming events to determine the age of divergence in swimming performance.

Methods

We collected the all‐time top 100 U.S. freestyle swimming performance times of boys and girls age 5 to 18 years for the 50m to 1500m events.

Results

Swimming performance improved with increasing age for boys and girls (p<0.001) until reaching a plateau, which initiated at a younger age for girls (15 years) than boys (17 years; sex×age; p<0.001). Prior to age 10, the top 5 swimming records for girls were 3% faster than the top boys (p<0.001). For the 10th–50th places, however, there were no sex‐related differences in swimming performance prior to age 10 (p=0.227). For both the top 5 and 10th–50th places, the sex difference in performance increased from age 10 (top 5, 2.5%; 10th–50th places, 1.0%) until age 17 (top 5, 7.6%; 10th–50th places, 8.0%). For all places, the sex difference in performance at age 18 was larger for sprint events (9.6%; 50–200m) than endurance events (7.1%; 400–1500m; p<0.001). Additionally, the sex‐related difference in performance increased across age and US ranking from 2.4% for 1st place to 4.3% for 100th place (p<0.001), indicating less depth of performance in girls than boys. However, annual participation was ~20% higher in girls than boys for all ages (p<0.001).

Conclusion

The top 5 girls demonstrated faster swimming velocities and the 10th–50th place girls demonstrated similar swimming velocities than boys (until ~10 years). After age 10, however, boys demonstrated increasingly faster swimming velocities than girls until 17 years. Collectively, these data suggest girls are faster, or at least not slower, than boys prior to the performance‐enhancing effects of puberty.

Support or Funding Information

This study was supported by the National Institutes of Health R‐35‐HL139854‐02 (MJJ), HL139854‐02S1 (AJC), 5T32DK007352‐40 (JWS), and the Mayo Foundation.

Elite swimming performance.

Mean swimming velocity from 5 to 18 years of the top 100 fastest US boys (blue circles) and girls (red triangles) for the 50, 100, 200, 400, 800 and 1500m freestyle swimming distances.

Figure 1

Sex differences in performance of the top 5 places.

The primary plot (heat map) displays the sex differences in swimming velocity (% boy’s swimming velocity) of the top 5 US rankings in each freestyle event distance and age, negative values (red) indicate faster performance of girls. The top displays the mean sex difference across age, and the right plot displays the mean sex difference across swimming event distance.

Figure 2
Resveratrol Attenuates Obesity‐ and Aging‐induced Sarcopenia Mitochondrial Dysfunction in Mice Skeletal Muscle.
Authors: Wu Jia-Ping
Published: April 2020

Sarcopenic obesity is a progressive loss of skeletal muscle mass and strength with increases in adiposity. The aim of this study was to investigate the effects of resveratrol on obesity and sarcopenia to potential therapy risk for skeletal muscle decline in physical function. C57BL/6J male mice fed either a high‐fat diet for 4 weeks and resveratrol (low‐, middle‐, and high‐dose) for 8 weeks to express the obesity effect. SAMP8 mice sarcopenic skeletal muscle functional deterioration expressed an age‐associated decline. Resveratrol (150 mg/kgBW) was administered by oral gavage two times a week one month of the experimental period. Exercise training based on adaptations in the muscle is training twice a week for 4 weeks. The skeletal muscles from mice in each group were analyzed by H&E staining, TUNEL and western blot analysis to determine mitochondrial function expression, apoptosis and relative fibrosis signaling. Results of the present study indicate that resveratrol in obesity skeletal muscle is linked to an increase in the expression of mitochondrial function involved in Bcl‐2 and PI3K/AKT. On the other hand, resveratrol attenuates sarcopenic SAMP8 mice, the age‐related loss of skeletal muscle mass and mitochondrial function involved Bad, caspase 3 and IL‐6/ERK1. However, exercise training did not find a significant difference in sarcopenic skeletal muscles SAMP8 mice. Exercise training did not induce sarcopenic skeletal muscle hypertrophy in SAMP8 mice. Therefore, we suggest that resveratrol as a therapeutic potential in the combination of sarcopenia and obesity, the state called sarcopenic obesity.

Support or Funding Information

Funding of this study was provided by the Ministry of science and technology (MOST 104‐2811‐B‐009‐007, MOST 105‐2811‐B‐039‐008, and MOST 106‐2811‐B‐650‐003)

Schematic representation of the inhibition effects of resveratrol on obesity and aging sarcopenia. The mechanisms underlying the pathophysiology of sarcopenic obesity. In obesity skeletal muscle, adipocytes undergo hypertrophy activation resulted in skeletal muscle atrophy due to accumulation of pro‐inflammation as well as mitochondrial dysfunction together with senescent muscle cells. Skeletal muscle inflammation trigger and support sarcopenic obesity development.

Figure 7
LFA‐9, a Selective Inhibitor of Microsomal Prostaglandin Synthase‐1 and 5‐Lipoxygenase: Prevention of Inflammatory and Oncologic Diseases
Authors: Yarla Nagendra Sastry , Pathuri Gopal , Gali Hariprasad , Panneerselvam Janani , Chandrakesan Parthasarathy , Madka Venkateshwar , Rao Chinthalapally V.
Published: April 2020

Cyclooxygenase‐1 (COX‐1), COX‐2 and 5‐lipoxygenase (5‐LOX) as targets for inflammatory diseases and many agents were developed and extensively used in the clinic. Chronic use of drugs that target COX‐1/COX‐2 are associated with unwanted side effects including GI toxicity and cardiovascular risk. Hence, the main aim of this work is to develop mechanistic based safer agents that would target microsomal prostaglandin synthase‐1 (mPGES‐1) (a downstream enzyme of COX‐2) and 5‐LOX, while sparing COX‐1&‐2 activity. LFA‐9 was designed using structure‐based drug discovery and synthesized from licofelone by adding 2‐aminoethanoic acid (Glycine) at its carboxylic end that led to targeting mPGES‐1 and 5‐LOX but not COX‐1&2. In silico, in vitro and ex vivo studies on LFA‐9 were performed using human/mouse/rat mPGES‐1 and 5‐LOX to facilitate pre‐clinical experimentation and clinical translation. In the molecular docking studies, LFA‐9 showed strong binding affinity against 5‐LOX (binding energies range between −199.85 & −215.3 Kcal/mol) and mPGES‐1 (binding energies range between −238.27 & −257.76 Kcal/mol), but not with COX‐1&2. In cell free system studies, LFA‐9 substantially inhibited mPGES‐1 (range of IC50 between 0.52 – 1.40 μM) and 5‐LOX (range of IC50 between 0.89 – 2.75 μM) but not COX‐1&2 (IC50>1mM) when assayed using fluorometric and colorimetric methods. Moreover, LFA‐9 substantially inhibited PGE2 (IC50 range between 0.47 – 0.78 μM) and LTB4 (IC50 range between 0.56 – 1.24 μM) production and spared PGI2 (IC50>1 mM) and TXB2 (IC50>1 mM) production in LPS‐stimulated human/mouse/rat macrophages and whole blood as the cell‐based system using ELISA technique. Further, circular dichroism and isothermal calorimetric based studies demonstrated that LFA‐9 strongly binds and induces changes in secondary structure of human mPGES‐1 and 5‐LOX enzymes, thereby inhibits their activities. In addition, LFA‐9 (cLogP = 4.34) obeys Lipinsky’s rule of 5 for druglikeness and shows better water solubility unlike licofelone (cLogP = 6.15). Furthermore, LFA9 prevented tumor stemness of APC mutant colonic epithelial cells from PIRC rats in vitro and inhibited exogenous PGE2 in tumor like microenvironment. Therefore, LFA9 is a novel mPGES‐1 and 5‐LOX inhibitor and safer drug candidate for inflammatory and oncologic diseases.

Support or Funding Information

Authors acknowledged NIH/NCI R01CA 213987 and NIH/NCI HHSN261201500024I for funding support.

Chemical structures of Licofelone and LFA9

Figure 1
Identification of additive formulations for enhanced shelf‐life and productivity of E. coli cell‐free protein synthesis extracts
Authors: Gregorio Nicole E. , Kao Wesley Y. , Williams Layne C. , Patel Pratish A. , Watts Katharine R. , Oza Javin P.
Published: April 2020

Cell‐Free Protein Synthesis (CFPS) is a platform biotechnology that enables a breadth of applications, from expressing traditionally intractable proteins to metabolic engineering and point‐of‐care diagnostics. However, field applications have remained limited due to the poor shelf stability of aqueous E. coli cell‐free extracts, which contain a complex mixture of cellular machinery. Lyophilization of the E. coli extract improves shelf‐life, but remains insufficient for maintaining extract productivity over extended storage periods at room temperature. For many pure protein‐based biologics, a variety of additives have been identified that help to stabilize the protein for lyophilization, transportation, and storage. However, the advances made for pure proteins cannot be directly applied to the complex cell extract, and current investigations into improving cell extract stability via additives has been limited. Thus, we have addressed the cold chain limitation in cell‐free by mapping the chemical space of ten low‐cost additives with four distinct mechanisms of action in a combinatorial manner to elucidate their capacity to further stabilize lyophilized cell extract. We report three key findings: 1) unique additive formulations that maintain full productivity of the cell extract at 4°C and 23°C; 2) additive formulations that enhance extract productivity up to 195%; 3) a machine learning algorithm that provides predictive capacity for the stabilizing effects of additive formulations that were not tested experimentally. The identified additive formulations provide a simple and low‐cost advance toward making CFPS field‐ready.

Support or Funding Information

Bill and Linda Frost Fund, Center for Applications in Biotechnology’s Chevron Biotechnology Applied Research Endowment Grant, Cal Poly Research, Scholarly, and Creative Activities Grant Program (RSCA 2017), and the National Science Foundation (NSF‐1708919)

Comparison of traditional cellfree extract production and reaction setup with our modified workflow for improved stability and productivity to enable field applications.

Figure 1
A Click Chemistry Approach to Reveal the chromatin‐Dependent Histone H3 K36 Deacetylase Nature of SIRT7
Authors: Liu Wenshe Ray , Wang Wesley Z.
Published: April 2020

Using an engineered pyrrolysyl‐tRNA synthetase mutant together with tRNAPyl, we have genetically encoded Ne‐(7‐azidoheptanoyl)‐L‐lysine (AzHeK) by amber codon in Escherichia coli for recombinant expression of a number of AzHeK‐containing histone H3 proteins. We assembled in vitro acyl‐nucleosomes from these recombinant acyl‐H3 histones. All these acyl‐nucleosomes contained an azide functionality that allowed quick click labeling with a strained alkyne dye for in‐gel fluorescence analysis. Using these acyl‐nucleosomes as substrates and click labeling as a detection method, we systematically investigated chromatin deacylation activities of SIRT7, a class III NAD+‐dependent histone deacylase with roles in aging and cancer biology. Besides confirming the previously reported histone H3K18 deacylation activity, our results revealed that SIRT7 has an astonishingly high activity to catalyze deacylation of H3K36 and is also catalytically active to deacylate H3K37. We further demonstrated that this H3K36 deacylation activity is nucleosome dependent and can be significantly enhanced when appending the acyl‐nucleosome substrate with a short double‐stranded DNA that mimics the bridging DNA between nucleosomes in native chromatin. By overexpressing SIRT7 in human cells, we verified that SIRT7 natively removes acetylation from histone H3K36. Moreover, SIRT7‐deficient cells exhibited H3K36 hyperacetylation in whole cell extracts, at rDNA sequences in nucleoli, and at select SIRT7 target loci, demonstrating the physiologic importance of SIRT7 in determining endogenous H3K36 acetylation levels. H3K36 acetylation has been detected at active gene promoters, but little is understood about its regulation and functions. Our findings establish H3K36 as a physiologic substrate of SIRT7 and implicate this modification in potential SIRT7 pathways in heterochromatin silencing and genomic stability.

Support or Funding Information

NIH GM121584, NIH AG050997, NIH GM086703, Welch A‐1715

Figure 1
A Module Swapping Approach to Engineer Allosterically Regulated Transcriptional Regulators
Authors: Chan Clement T.Y.
Published: April 2020

Allosterically regulated transcriptional regulators are key biological components for genetic response to environmental signals. These proteins bind to DNA to control gene expression, and their interactions with DNA are regulated by molecular signals. Transcriptional regulators in the LacI family are composed of two discrete and sequence modules, in which one senses molecular signals (ligand‐binding module) and the other one interacts with promoters to regulate gene expression (DNA‐binding module). Recently, we demonstrated that these LacI family modules can be interchanged robustly to generate functional regulators. We swapped ligand‐binding modules and DNA‐binding modules among LacI family members. The resulting hybrid regulators possess a new combination of allosteric response and DNA recognition properties that are originated from the ligand‐binding module and DNA‐binding module, respectively. Additionally, we showed that this module swapping approach can also be applied to regulators in the TetR family to create a hybrid protein with desirable functions.

These hybrid regulators enable flexible connections between environmental signals and genetic elements, which were harnessed to implement two genetic circuit designs that were previously infeasible. These genetic circuits include a programmable ‘Passcode’ genetic device, which potentially serves as a biocontainment system to limit the proliferation of engineered cells in a highly specific environment, preventing their spread to natural environments and enhancing biosafety. As another example, we have developed a system of Multiple Toggle Switches with a Master OFF signal, which enable the equipped cells to simultaneously monitor multiple biological and environmental traits.

Overall, we have established a protein design principle for creating genetic regulatory elements that facilitate cell engineering. We demonstrated that these engineered parts are sufficient for generating new cellular behaviors for potential applications in biotechnology and biomedicine.

Support or Funding Information

This research is supported by National Science Foundation [MCB‐1914538], the University of Texas System Rising STARs Program, and the Welch Foundation [# BP‐0037].

Allosterically regulated transcriptional regulators within the same protein family have ligand‐binding modules and DNA‐binding modules that are conserved, discrete, and functional. By combining the module that responds to effector A and the module that recognizes operator B, we can create a regulator enabling the use of effector A to control activities of promoter B, which is a new input‐output connection. These engineered regulators have been used to develop several genetic networks.

Figure 1
Bioorthogonal Chemical Probes of Lysine Acetyltransferases
Authors: Zheng Y. George
Published: April 2020

Acetylation of lysine residues is one of the most important posttranslational modifications that diversify protein functions. Thousands of acetylated lysine residues have been identified, suggesting that the effects of lysine acetyltransferases (KATs) go far beyond the chromatin kingdom. However, there is a missing link connecting the compositions of the cellular acetylome networks to the enzymatic activities of different KAT members. The outstanding challenge is how to dissect the subacetylomes of individual KATs and address their functions on the proteomic scale. We have explored a
bioorthogonal
profiling of
protein
acetylation strategy to label and interrogate substrates of KAT enzymes. In this strategy, a suite of Ac‐CoA analogs containing either alkynyl or azido functional group (e.g. 3AZ‐CoA, 4AZ‐CoA, 4PY‐CoA, 5HY‐CoA, 6HY‐CoA) were synthesized as potential cofactor surrogate for selective labeling of KAT substrates. Meanwhile, the active site of the KATs was engineered in order to expand the cofactor binding capability of the enzymes to accommodate the bulkier synthetic cofactors. The acylated substrates can be selectively linked through the copper‐catalyzed azide‐alkyne cycloaddition (CuAAC) reaction with fluorescent reporter or biotin affinity tag for optical imaging or protein enrichment on streptavidin‐coated resin. We have successfully used this bioorthogonal technology to profile substrates of p300 and GCN5 in the context of complex cellular proteomes. Together with LC‐MS/MS technology, more than four hundred proteins were identified as GCN5 or p300 substrate candidates. These proteins are extensively involved in various biological events including gene expression, cell cycle, and cellular metabolism. Overall, we have invented a bioorthogonal, chemoproteomic technology to investigate KAT biology. This chemical biology strategy provides a powerful enabling technology for activity‐based lysine acylation profiling on proteomic scale. Indeed, our KAT activity profiling demonstrates extensive engagement of KATs in cellular pathways and provides new molecular insights into understanding their functions in epigenetics and other biological processes.

bioorthogonal profiling

Figure 1
Antidepressant Effect of Methanol Root Bark Extract of Acacia seyal: Involvement of Monominergic, Nitric Oxide and Opiodergic Pathways
Authors: Magaji Mohammed Garba , Gambo Amanda Yelmis , Shehu Aishatu Garba , Danjuma Nuhu Mohammed
Published: April 2020

Background

Depression is a common mental disorder which affects more than 300 million people and is a leading cause of disability worldwide (
WHO, 2017). Available antidepressants are only effective in 50% of patients (
Simon, 2002). The treatment resistance has been linked to the multiple pathways involved in the pathology of depression. Acacia seyal root is used traditionally for the management of depression (
Shehu, 2017). However, there is no report of the scientific validation of this ethnomedicinal claim.

Objective

To determine the antidepressant activity of the methanol root bark extract of A. seyal (AS) and its possible mechanism(s) of antidepressant action.

Materials and Methods

Ethical Approval for the use of laboratory animals was sought and obtained from Ahmadu Bello University Committee on Animal Use and Care (ABUCAUC/2018/094). Antidepressant activity of AS was evaluated using tail suspension test (TST) at a dose of 250, 500 and 1000 mg/kg. For the mechanistic studies, mice were pretreated with Sulpiride (50 mg/kg), Prazosin (1 mg/kg), Yohimbine (1 mg/kg), Metergoline (1 mg/kg), Cyproheptadine (3 mg/kg), L‐Arginine (50 mg/kg), L‐NNA (50 mg/kg), atropine (1 mg/kg) and naloxone (2 mg/kg) 15 minutes prior to AS (500 mg/kg) administration, then assessed using TST one hour later.

Results

The extract (at the doses of 250–1000 mg/kg) significantly (p<0.05) decreased the duration of immobility in the TST. Sulpiride (D2 receptor antagonist), Prazosin and Yohimbine (α1 and α2 receptor antagonists respectively), Metergoline, Cyproheptadine (5‐HT1 and 5‐HT2 receptor antagonist respectively), L‐Arginine and L‐NNA (substrate and inhibitor of nitric oxide synthase enzyme respectively) and naloxone (opioid receptor antagonist) significantly (p<0.05) reversed the antidepressant effect of AS

Conclusion

The methanol root bark extract of Acacia seyal possesses antidepressant activity possibly mediated via the dopaminergic, serotonergic, adrenergic, nitric oxide and opioidergic pathways.

Effect of Methanol Root Bark Extract of Acacia seyal on Duration Immobility of Mice in Tail Suspension Test

Animals were acutely treated with AS (250, 500 or 1000 mg kg, po), distilled water (10 ml/kg, po), or Fluoxetine (20 mg/kg, po). Each column represents the mean ± SEM of 8 animals. Data was analyzed using one‐way ANOVA followed by Bonferroni post hoc test, *p≤0.05, **p≤0.001, ***p≤0.0001 significantly different from distilled water treated group.AS=Acacia seyal, DW= 10 ml/kg of Distilled water, FTX= Fluoxetine

Figure 1

Acknowledgement

The technical assistance of staff of the Department of Pharmacology and Therapeutics, Ahmadu Bello University, Zaria‐Nigeria is acknowledged
Staphylococcus aureus Evasion Proteins EapH1 and EapH2: Residue‐Level Investigation of an Alternative Binding Motif for Human Neutrophil Elastase
Authors: Herdendorf Timothy , Geisbrecht Brian
Published: April 2020

The Staphylococcus aureus
Extracellular
Adherence
Protein (Eap) and its homologs, EapH1 and EapH2, are a family of secreted proteins that potently inhibit the neutrophil serine proteases Neutrophil Elastase (hNE), Cathepsin G, and Proteinase 3. Similarly to EapH1, inhibition of hNE by EapH2 is characterized by a rapid association rate (2.9×105 M−1s−1) coupled with a very slow dissociation rate (5.9×10−4 s−1), yielding an apparent inhibition constant of 2.11 nM. Due to this slow off‐rate, inhibition of hNE by EapH2 is time‐dependent. A phenylalanine in EapH2 replaces the leucine in EapH1 that sits over the hNE catalytic serine and creates a potential steric clash. Indeed, the EapH1 L59F mutant is severely decreased in its ability to inhibit hNE (~9,500‐fold). When compared to the EapH1:hNE co‐crystal structure, a model of the EapH2:hNE complex predicts an alternative binding motif comprised of EapH2 residues 120 – 127. These putative interfacing residues were individually mutated and kinetically interrogated. The EapH2 N127A mutant resulted in the largest decrease in hNE inhibition (~200‐fold) and loss of the time‐dependent characteristic. Surprisingly, the time‐dependent characteristic was still abolished in the EapH2 T125A mutant, even though it was less perturbed in hNE inhibition (~25‐fold). T125 forms an intra‐molecular hydrogen bond to the carbonyl oxygen of N127 in the EapH2 crystal structure. Given these observations, we conclude (i) that EapH2 has an altogether distinct hNE binding motif than EapH1, (ii) that N127 is the main functional determinant in EapH2, and (iii) that T125 serves an ancillary role aiding in the optimal orientation of N127.

Support or Funding Information

Funding was provided by a grant from the National Institute of General Medical Sciences (R01‐GM121511) to B.V.G.

Comparison of EapH1 and EapH2 binding motifs.

(A) EapH2 (magenta) binding to hNE, based on the energy minimized model. (B) EapH2 residues involved in the interface with hNE. (C) EapH1(green) binding to hNE (PDB:4nzl). (D) EapH1 residues involved in the interface with hNE.

Figure 1
Threshold Concepts in Medical Physiology
Authors: Derias Nardin , Loftus Stephen , Kamel-ElSayed Suzan
Published: April 2020

INTRODUCTION

Threshold concepts are those ideas that learners often find difficult, but must understand in order to master the discipline. In order for a concept to be defined as a threshold concept, it must meet at least three out of five characteristics: transformative, irreversible, integrative, bounded, and troublesome. In the realm of threshold concepts research, there has been very little conducted in regards to medical school curriculum specifically. Medical physiology has often been a challenging core topic for medical students. The goal of this study is to better understand what students considered to be threshold concepts in physiology so medical school curricula can better address the needs of students and ensure that they have a strong foundation.

METHODS

Volunteers from a medical school were recruited and three focus groups were conducted during the preclinical years. Each focus group consisted of 7–8 students. The focus groups began with a brief introduction of what threshold concepts are followed by the presentation of a brief clinical case. The students were given a case that integrated knowledge that had been taught in organ system courses prior to the focus groups. Students were asked to come up with a differential diagnosis and suggestions for underlying pathophysiology. After this, they were allowed to ask questions to gather a history and explain the underlying physiological concepts that led them to their differential diagnoses. A fourth focus group was conducted in the early weeks of the clinical years and after USMLE Step 1 examination. Following all focus groups, the audio was transcribed and thematic analysis was conducted.

RESULTS

Based on the four focus groups conducted, several potential candidate threshold concepts emerged including secondary messenger pathways, Starling forces, preload and afterload, and cell membrane potentials.

CONCLUSION

This study identified a set of candidate threshold concepts in medical physiology from the students’ perspective. Further characterization of these candidate threshold concepts can be used as a foundation for designing an effective and powerful physiology curriculum.

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How Well Does the Biochemistry Authentic Scientific Inquiry Lab (BASIL) Promote Expert Understanding of Michaelis‐Menten Kinetics by Undergraduate Students?
Authors: Roberts Rebecca , Palaez Nancy , Anderson Trevor
Published: April 2020

BASIL is a course‐based undergraduate research experience (CURE) that focuses on enzyme function prediction. The Protein Data Bank (PDB) contains the structures of over 4000 proteins of unknown function and BASIL provides a basis to assign functions by combining in silico and in vitro analyses. The final BASIL module focuses on a kinetic analysis of the purified protein. In this study we investigate if the BASIL CURE promotes the development of student understanding of Michaelis‐Menten kinetics. Through content analysis of the written BASIL modules and inductive analysis of instructor interview transcripts, we have determined an “expert answer” that has been categorized into three overarching themes: the function of an enzyme is to convert a substrate to a product; the conversion of substrate to product can be tested with experimental assays; and data from assays can be visualized with a graph to characterize the kinetics of enzyme function. These ideal answer subthemes then were aligned with the course‐based undergraduate research abilities (CURAs) identified by Irby et al. (2018). We analyzed student research posters and coded semi‐structured interviews with students who have participated in BASIL at Ursinus College in order to compare them with the “expert answer”. Results suggest that students appear to understand the function of an enzyme and can interpret findings from an activity assay, yet they are lacking in a full understanding of the required data manipulation or underlying meaning of a graphical analysis of kinetics data. In the longer term, this research is aimed at informing improvements in the teaching, learning, and assessment of this area of the BASIL CURE. In particular, the findings will focus on addressing the various identified student difficulties so that the BASIL CURE can come closer to achieving its main goal of developing students as research scientists.

Support or Funding Information

This work was supported by the National Science Foundation under grants #1503811 & 1709805 for the Biochemistry Authentic Scientific Inquiry Lab (BASIL) CURE and #1346567 for the Advancing Competencies in Experimentation ‐ Biology (ACE‐Bio) Network. Any opinions, findings, and conclusions or recommendations expressed in this workshop are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Biochemistry Authentic Scientific Inquiry Lab

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Energetic dependencies dictate folding mechanism in a complex protein
Authors: Kaiser Christian , Chen Xiuqi , Liu Kaixian
Published: April 2020

Large proteins composed of multiple domains are abundant in all proteomes, but their folding and structural dynamics remain poorly understood. Multi‐domain proteins are thought to fold sequentially as they emerge from the ribosome, which minimizes interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. In elongation factor G (EF‐G), a highly conserved protein composed of five domains, the two N‐terminal domains form a stably structured unit co‐translationally. Using single‐molecule optical tweezers, we have defined the steps leading to fully folded EF‐G. We find that the central domain III of EF‐G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N‐terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C‐terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C‐terminal neighbors disrupts co‐translational folding and imposes a post‐translational mechanism on the folding of the C‐terminal part of EF‐G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large‐scale conformational transitions that are part of the EF‐G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF‐G function, complicates the folding of this large multi‐domain protein. EF‐G thus provides an example of how distinct biological ends – robust folding and functionally important flexibility – come into conflict during protein biogenesis.

Support or Funding Information

This work was supported by a grant from the National Institutes of Health (5R01GM121567)

Coupled synthesis and folding of the multi‐domain protein EF‐G. Domain III (green) is highly dynamic in the absence of fully folded domains IV (blue) and V (purple). As a consequence, co‐translational folding is interrupted. Accumulation of unfolded polypeptide results in the formation of misfolded species, sidetracking the molecule into non‐productive states and slowing down folding.

Figure 1
HIV Tat Protein Induces the TGF‐β Signaling Pathway and Suppresses the CFTR Biogenesis and Activity by microRNA‐Regulated Gene‐Silencing Mechanism
Authors: Dutta Rajib Kumar , Chinnapaiyan Srinivasan , Unwalla Hoshang
Published: April 2020

The advent of combination antiretroviral therapy (cART) has led to a dramatic decline in morbidity and mortality from HIV/AIDS. HIV infected subjects are still six times more likely to contract pneumonia compared to non‐infected age matched controls. Mortality, following an episode of bacterial pneumonia was also four times higher in HIV infected subjects compared to non‐infected controls. Thus, pneumonia can also contribute to HIV progression. Understanding the pathophysiological mechanisms that lead to microbial colonization of the airways in HIV infected patients is therefore important to public health. HIV Tat and CS can suppress CFTR function, which is a critical determinant of ASL depth and this can lead to depressed MCC and consequent microbial colonization. Our study showed that HIV‐infected cells in the airway namely alveolar macrophages, other immune cells or bronchial epithelial cells can serve as reservoirs and a source of HIV proteins like Tat which upregulates TGF‐beta mRNA in primary human bronchial epithelial cells with a corresponding decrease in CFTR mRNA. Chromatin immunoprecipitation with RNA Polymerase II demonstrated that transcription from the CFTR promoter is unaffected and blocking the miRNA processing pathway with Aurin Tricarboxylic acid (ATA) restore CFTR inhibition caused by TGF‐ beta. Our data showed that HIV infection suppress CFTR mRNA and function and blocking TGF‐beta signaling rescues this. Together this posits a strong role for (TGF‐beta induced) miRNA in Tat mediated CFTR gene silencing.

Support or Funding Information

Flight Attendant Medical Research Institute (FAMRI)

Hypothesis

Figure 1

HIV Tat suppresses CFTR via common TGF‐beta signaling

Figure 2