bluuebunny/crossref_metadata_2025 huggingface dataset:
Trees and Liberty
Authors: Marks Susan
Published: February 2020

Trees feature repeatedly in the preceding chapters of this book — whether as metaphors or in the material form of forests, hedges, and wood. As a way of drawing the various strands of the discussion together, this chapter foregrounds that arboreal preoccupation. Among other things, it highlights the trope of the tree of liberty, and finds not one, but three liberty trees in the public discourse of 1790s England, one of which identifies the rights of man promoted by Thomas Paine and others with a ‘false tree of liberty’ that would cause people to rise up and governments to be overthrown but oppression still to remain.
Afterword
Authors: Marks Susan
Published: February 2020

If the ‘Paineite’ approach associates the rights of man with popular sovereignty, together with social welfare and decent wages, the ‘Spencean’ approach insists that political revolution needs to be accompanied by social revolution, and remedial measures by efforts to seek out and transform the roots of injustice. It is, of course, the former that has been most important in shaping the course of history (including the history of human rights), and that is most familiar today. This Afterword gives brief consideration to the question of what it might mean to recover the Spencean alternative in a world of ‘new enclosures’ and ‘new commons’.
Bluegrass Unlimited (1966–1977)
Authors: Lornell Kip
Published: February 2020

Both as a radio program on WAMU-FM and as a specialized magazine, Bluegrass Unlimited informed local fans about “their” music. The impact of the radio show was local, but the magazine soon garnered national attention. The Birchmere, which became the premier spot for bluegrass in the region, was founded by Gary Oelze who still operates this venue. By 1967 all three of these forces were underpinning the local bluegrass community. In the early 1970s the Seldom Scene formed out of the core of the original Country Gentlemen and soon became the most important bluegrass band in DC and, arguably, across the United States. During this period bluegrass became increasingly popular, a trend that only accelerated during the late 1970s and early 1980s.
Not Seldom Heard or Scene (1977–1991)
Authors: Lornell Kip
Published: February 2020

This chapter focuses on the era when bluegrass was most popular in and around Washington, DC. Several dozen venues, ranging from Tiffany Tavern in Old Town Alexandria to Lucketts Bluegrass in Loudon County, offered live bluegrass performances at least once a week and dozens of bands formed to meet this interest. In the early 1980s WAMU-FM offered up to forty hours of bluegrass weekly and much of the station’s income derived from contributions by bluegrass fans. For many months in 1980 the Birchmere booked nothing but bluegrass. Bluegrass reached its height of popularity around the DMV starting in the late 1970s through the early 1980s but by the early 1990s, signs were developing that this halcyon era was coming to an end.
Toward a History of Social Construction
Authors: Seeman Sonia Tamar
Published: February 2020

This chapter discusses the historical origins and experiences of Roma and related groups in Anatolia from Byzantine to the Ottoman Empires. Byzantine and Ottoman philosophical beliefs regarding moral order informed administrative controls on subject populations. In particular, social segregational practices implemented during the Byzantine and Ottoman administrative periods facilitated exploitation of Romani labor, particularly for auxiliary military services, agrarian work, commercial trade, and other marginalized services such as entertainment. Social marginalization was reinforced by government edicts and sanctions, and furthered by physical segregation and marginalization into Romani neighborhoods (mahalle). The experience of place from which Roma expressed their sense of belonging to a community was also shaped by their emplacement in the larger social hierarchy. Because most extant writings regarding the history of Roma were in the hands of those institutions wielding political power over Roma, this chapter also explores alternative interpretations of official government texts and church sanctions.
Exnominating Turk, Hypernominating çingene
Authors: Seeman Sonia Tamar
Published: February 2020

The dramatic political shift from the Ottoman Imperial polity to that of an ethnonational state was implemented by creating the “Turk” as the singular subject citizen of the new Republic. To shore up a new national identity through contrast against non-Turkish others, culture power holders deployed musical discourses that effectively folded in qualities and attributes of “non-Turkish others” into the representations of çingene and negative evaluations of Romani musical labor. This strategy enabled “others” to disappear on the one hand and to hypermark çingene as the epitome of alterity against which Turkish music could be positively valued. This complex set of processes enabled the creation of Turkish folk and classical genres as legitimated categories, which formed the basis of a national musical canon. Against these structural political and cultural transformations, a critical reading of biographies and melancholy reminiscences about Romani artists Nasip Hanım and Tahsin Bey discloses the extraordinary and yet everyday contributions of professional Romani musicians. These artists mediated class and ethnic differences while maintaining musical practices that were undergoing dramatic cultural management.
The Poetics of Singing Roman
Authors: Seeman Sonia Tamar
Published: February 2020

This chapter traces a poetics of emergent meaning in sözlü Roman oyun havası from static iconicity drawn from çingene references in kanto songs through musicians’ creative incorporation of improvised poetic mani and shouted hocali forms. While expressing communal reactions to specifically Roman experiences, the inclusion of patricularistic references from mani and hocali inscribed revised social distinctions along gendered, generational, class, and status lines. Through musical analysis and observations of musicians creating new songs, I demonstrate how musicians drew on keriz-style improvisations to expand melodic repertoires for song settings in response to the increased demand for new and relevant dance tunes. Commercial circulation and copyrighting of these songs also increased tensions between artists themselves and studio heads, thus reshaped community-based practices of borrowing and performing. The chapter ends with narrations of three performance events to illustrate the dynamic relationship between an ongoing metaphoricity of sound to a mimesis of enlarged presence and pluralized identities.
Politicizing Roman and the Folklorization of Ethnicity
Authors: Seeman Sonia Tamar
Published: February 2020

Two fundamental shifts in national policies post-2000 set into motion new forms of Roman expression: Turkey’s responses to European Union accession process; Urban Renewal Law 5366. The first promoted Roman as a model minority through the establishment of Roman cultural associations (dernek-s), thereby opening up political space for Roman ethnic identity. The second mobilized extensive expropriation of Roman neighborhoods under Law 5366. Using pedagogy-by-performance to “make oneself known” (tanıtma), dernek-s began forging an emergent Roman-as-folklore. I trace the uneven process of folkloric canon-formation through three performances: an international festival in Istanbul, in Keşan’s annual festival, and in response to the destruction of Istanbul’s entertainment district, Sulukule. The collision of dernek-inspired political action with land expropriation were encapsulated in discourses surrounding—and enabling—municipal destruction of Sulukule. The chapter reflects on the problem of heightened attention to Sulukule as a form of political iconicization that eclipsed suffering experienced in other sites.
Empirical Asset Pricing via Machine Learning
Authors: Gu Shihao , Kelly Bryan , Xiu Dacheng
Published: February 2020

We perform a comparative analysis of machine learning methods for the canonical problem of empirical asset pricing: measuring asset risk premiums. We demonstrate large economic gains to investors using machine learning forecasts, in some cases doubling the performance of leading regression-based strategies from the literature. We identify the best-performing methods (trees and neural networks) and trace their predictive gains to allowing nonlinear predictor interactions missed by other methods. All methods agree on the same set of dominant predictive signals, a set that includes variations on momentum, liquidity, and volatility.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Weekly alternation of morning and afternoon school start times: implications for sleep and daytime functioning of adolescents
Authors: Koscec Bjelajac Adrijana , Bakotic Marija , Ross Biserka
Published: February 2020

Study objectives

To examine sleep patterns of adolescents attending school on alternating morning schedule (MS) and afternoon schedule (AS) and to explore the contribution of sleep characteristics on the AS to prediction of adolescents’ daytime functioning.

Methods

The Croatian adaptation of the School Sleep Habits Survey for a two-shift school system was completed by 2,033 students (11–18 years old, 54 per cent females) whose school start times alternated weekly between 08:00 am and 14:00 pm.

Results

All age groups of adolescents reported delayed sleep when on the school week with an AS as compared with a MS. The average delay of bedtime was 36 minutes, and delay of wake-up time 121 minutes, which resulted in average sleep durations from 9.80 hours in 11-year olds to 8.39 hours in 18-year olds. Having more delayed wake-up times on the AS predicted more substance use and poorer grades. Having more delayed bedtimes not only predicted poorer grades but also predicted less depressed mood. Obtaining relatively longer sleep on AS predicted lower sleepiness, less depressed mood, and less frequent substance use.

Conclusions

The afternoon school start time enables sleep duration that is in line with adolescent sleep biology and contributes positively to daytime functioning. In many cases, a large delay in wake-up time is observed. At least part of that delay is not associated with adolescents’ circadian biology and contributes negatively to some indices of their daytime functioning. Further research of factors associated with extreme delays of sleep and/or interventions that could limit extreme sleep irregularity is required.
Solomon v McCarthy: unwritten trusts of land
Authors: Atkins Scott
Published: February 2020

Unwritten trusts of land have always been troublesome, given that they prima facie infringe the writing requirement set out in section 53 (1) (b) of the Law of Property Act 1925. Ways around the problem exist, so that an unwritten trust may be recognised, but those ways usually rely on an implied trust (which does not require writing under section 53 (2) of the Law of Property Act 1925) or the court to disapply the writing requirement by invoking the maxim that equity will not permit a statute to be used as an instrument of fraud. The latter principle has been recognised as applying where a settlor claims that he himself is also the beneficiary. Recently, the county court in Bristol considered whether that maxim might be used to support an unwritten trust of land made by a settlor in favour of a third-party beneficiary and, for the first time in a reported case, came to the conclusion that it could not.
Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017
Authors: Pightling Arthur W. , Pettengill James , Luo Yan , Strain Errol , Rand Hugh
Published: February 2020

In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55

Salmonella enterica

that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3’)-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.
Evidence for gastrointestinal infection of SARS-CoV-2
Authors: Xiao Fei , Tang Meiwen , Zheng Xiaobin , Li Chunna , He Jianzhong , Hong Zhongsi , Huang Siwen , Zhang Zhenyi , Lin Xianqi , Fang Zhaoxiong , Lai Renxu , Chen Shoudeng , Liu Jing , Huang Jin , Xia Jinyu , Li Zhonghe , Jiang Guanmin , Liu Ye , Li Xiaofeng , Shan Hong
Published: February 2020

The new coronavirus (SARS-CoV-2) outbreak originating from Wuhan, China, poses a threat to global health. While it’s evident that the virus invades respiratory tract and transmits from human to human through airway, other viral tropisms and transmission routes remain unknown. We tested viral RNA in stool from 73 SARS-CoV-2-infected hospitalized patients using rRT-PCR. 53.42% of the patients tested positive in stool. 23.29% of the patients remained positive in feces even after the viral RNA decreased to undetectable level in respiratory tract. The viral RNA was also detected in gastrointestinal tissues. Furthermore, gastric, duodenal and rectal epithelia showed positive immunofluorescent staining of viral host receptor ACE2 and viral nucleocapsid protein in a case of SARS-CoV-2 infection. Our results provide evidence for gastrointestinal infection of SARS-CoV-2, highlighting its potential fecal-oral transmission route.
Electrical coupling between chromatophore muscle fibers allows for versatile control of chromatophore expansion in squid
Authors: Liu Yen-Chyi , Wang Wei-Chun , Grasse Bret
Published: February 2020

Camouflage color change in cephalopods is generated by the expansion and relaxation of hundreds to thousands of chromatophore pigment organs in the skin. Individual chromatophores display color when the central pigment sac is expanded to several times its original size by a ring of 20-30 radial muscles, which are electrically coupled and are innervated by multiple motoneurons. However, mechanisms for their neuromuscular control are unclear. Here we characterize chromatophore expansion kinematics and perform simultaneous whole-cell recordings on pairs of muscle fibers of a chromatophore in squid hatchlings. We show that activity is highly correlated between muscle fibers of a chromatophore due to a high ratio of electrical coupling between all muscles for slow currents. However, fast currents are filtered and decrease rapidly further away from the muscle receiving the inputs. This low-pass filtering property of electrical coupling allows fast inputs to activate one muscle while persistent inputs spread throughout the chromatophore to synchronously activate all muscles, providing a versatile mode of control for chromatophore expansion.
Visualizing tumour self-homing with magnetic particle imaging
Authors: Parkins Katie M , Melo Kierstin P , Ronald John A , Foster Paula J
Published: February 2020

Due to their innate tumour homing capabilities, in recent years, CTCs have been engineered to express therapeutic genes for targeted treatment of primary and metastatic lesions. Additionally, previous studies have incorporated optical or PET imaging reporter genes to enable noninvasive monitoring of therapeutic CTCs in preclinical tumour models. Here, we demonstrate for the first time, the ability of magnetic particle imaging (MPI) to sensitively detect systemically administered iron-labeled CTCs and to visualize tumour self-homing in a murine model of human breast cancer.
Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study
Authors: Li Jinghua , Wang Yijing , Gilmour Stuart , Wang Mengying , Yoneoka Daisuke , Wang Ying , You Xinyi , Gu Jing , Hao Chun , Peng Liping , Du Zhicheng , Xu Dong Roman , Hao Yuantao
Published: February 2020

Background

The 2019 novel Coronavirus (COVID-19) emerged in Wuhan, China in December 2019 and has been spreading rapidly in China. Decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic.

Methods

We conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (R0) of COVID-19, using data on confirmed cases obtained from the China National Health Commission for the period 10thJanuary – 8thFebruary. We analyzed the data for the period before the closure of Wuhan city (10thJanuary – 23rdJanuary) and the post-closure period (23rdJanuary – 8thFebruary) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of Wuhan city on spread of COVID-19.

Findings

Before the closure of Wuhan city the basic reproduction number of COVID-19 was 4.38 (95% CI: 3.63 – 5.13), dropping to 3.41 (95% CI: 3.16 – 3.65) after the closure of Wuhan city. Over the entire epidemic period COVID-19 had a basic reproduction number of 3.39 (95% CI: 3.09 – 3.70), indicating it has a very high transmissibility.

Interpretation

COVID-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. The closure of Wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of Hubei the virus remained extremely infectious. Emergency planners in other cities should consider this high infectiousness when considering responses to this virus.

Funding

National Natural Science Foundation of China, China Medical Board, National Science and Technology Major Project of China
Is glycaemia associated with poorer brain health and risk of dementia? Cross sectional and follow-up analysis of the UK Biobank
Authors: Garfield Victoria , Farmaki Aliki-Eleni , Eastwood Sophie V. , Mathur Rohini , Rentsch Christopher T. , Bhaskaran Krishnan , Smeeth Liam , Chaturvedi Nish
Published: February 2020

INTRODUCTION

To understand the relationship across the glycaemic spectrum, with brain health.

METHODS

UK Biobank participants. HbA1c and diabetes diagnosis define baseline glycaemic categories. Outcomes: incident vascular dementia (VD), Alzheimer’s dementia (AD), hippocampal volume (HV), white matter hyperintensity (WMH) volume, cognitive function and decline. Reference group: normoglycaemic individuals (HbA1c 35-<42 mmol/mol).

RESULTS

Pre- and known diabetes increased incident VD, (HR 1.54, 95%CI=1.04;2.28 and 2.97, 95%CI=2.26;3.90). Known diabetes increased AD risk (HR 1.84, 95%CI=1.44;2.36). Pre- and known diabetes elevated risks of cognitive decline (OR 1.42, 1.48;2.96 and 1.39, 1.04;1.75). Pre-diabetes, undiagnosed and known diabetes conferred higher WMH volumes (4%, 26%, 5%,) and lower HV (22.4mm3, 15.2mm3, 62.2mm3). Low-normal HbA1c had 2% lower WMH volume and 13.6mm3 greater HV.

DISCUSSION

Pre and known diabetes increase VD risks; known diabetes increases AD risk. Low-normal HbA1c associates with favourable neuroimaging outcomes. Our findings may have implications for cardiovascular medication in hyperglycaemia for brain health.
Dynamic contrast enhanced MRI with clinical hepatospecific MRI contrast agents in pigs: initial experience
Authors: Hix Jeremy M.L. , Mallett Christiane L. , Latourette Matthew , Munoz Kirk A. , Shapiro Erik M.
Published: February 2020

Pigs are an important translational research model for biomedical imaging studies, and especially for modeling diseases of the liver. Dynamic contrast enhanced (DCE)-MRI is experimentally used to measure liver function in humans, but has never been characterized in pig liver. Here we performed DCE-MRI of pig liver following the delivery of two FDA approved hepato-specific MRI contrast agents, Gd-EOB-DTPA (Eovist) and Gd-BOPTA (Multihance), and the non-hepatospecific agent Magnevist, and optimized the anesthesia and animal handling protocol to acquire robust data. A single pig underwent 5 scanning sessions over six weeks, each time injected at clinical dosing either with Eovist (twice), Multihance (twice) or Magnevist (once). DCE-MRI was performed at 1.5T for 60 minutes. DCE-MRI showed rapid hepatic MRI signal enhancement following IV injection of Eovist or Multihance. Efflux of contrast agent from liver exhibited kinetics similar to that in humans, except for one hyperthermic animal where efflux was very fast. As expected, Magnevist was non-enhancing in the liver. The hepatic signal enhancement from Eovist matched that seen in humans and primates, while the hepatic signal enhancement from Multihance was different, similar to rodents and dogs, likely the result of differential hepatic organic anion transport polypeptides. This first experience with these agents in pigs provides valuable information on contrast agent dynamics in normal pig liver. Given the disparity in contrast agent uptake kinetics with humans for Multihance, Eovist should be used in porcine models for biomedical imaging. Proper animal health maintenance, especially temperature, seems essential for accurate and reproducible results.
Plasmon-Coupled Photocapacitor Neuromodulators
Authors: Melikov Rustamzhon , Srivastava Shashi Bhushan , Karatum Onuralp , Dogru Itir Bakis , Jalali Houman Bahmani , Sadeghi Sadra , Dikbas Ugur Meric , Ulgut Burak , Kavakli Ibrahim Halil , Nizamoglu Sedat
Published: February 2020

Efficient transduction of optical energy to bioelectrical stimuli is an important goal for effective communication with biological systems. For that plasmonics has significant potential via boosting the light-matter interactions. However, plasmonics has been primarily used for heat-induced cell stimulation due to membrane capacitance change (i.e., optocapacitance). Instead, here we demonstrate that plasmonic coupling to photocapacitor biointerfaces improves safe and efficacious neuromodulating displacement charges for an average of 185% in the entire visible spectrum while maintaining the Faradaic currents below 1%. Hot-electron injection dominantly leads the enhancement of displacement current at blue spectral window, and nanoantenna effect is mainly responsible for the improvement at red-spectral region. The plasmonic photocapacitor facilitates wireless modulation of single cells at 3-orders of magnitude below the maximum retinal intensity levels corresponding to one of the most sensitive optoelectronic neural interfaces. This study introduces a new way of using plasmonics for safe and effective photostimulation of neurons and paves the way toward ultra-sensitive plasmon-assisted neurostimulation devices.
Altered GABAergic inhibition in CA1 pyramidal neurons modifies despair-like behavior in mice
Authors: Yoon Sang Ho , Chung Geehoon , Song Woo Seok , Oh Sung Pyo , Kim Jeongjin , Kim Sang Jeong , Kim Myoung-Hwan
Published: February 2020

Despair is a common human feeling characterized by the loss of hope and is a core symptom of depressive disorders. However, little is known regarding neural circuits mediating despair and their modulation by antidepressants. Here we show that alterations in inhibitory synaptic transmission in the hippocampus affect behavioral despair in mice. Reduced interneuron density, knockdown of GABAAreceptor gamma 2 subunit gene (Gabrg2) or DREADD-mediated suppression of interneuron activity resulted in disinhibition of CA1 neurons and anti-despair-like behaviors in mice. Similarly, a low dose of pentylenetetrazol, a GABAAR antagonist, induced transient anti-despair-like behaviors, with rapid eukaryotic elongation factor 2 (eEF2) activation in the hippocampus. Conversely, pharmacological and chemogenetic potentiation of GABAergic transmission in CA1 neurons induced despair-like behaviors. The antidepressant ketamine rapidly increased c-Fos expression in CA1 neurons and induced anti-despair-like behaviors. These results suggest that the enhanced hippocampal CA1 neuron activity induces anti-despair-like behaviors and contributes to the antidepressant effects of ketamine.
The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR
Authors: Liu Jinding , Wang Rongshuai , Shi Jie , Cheng Xiaojuan , Hao Ting , Guo Jiangling , Wang Jiaqi , Liu Zidong , Li Wenyan , Fan Haoliang , Yun Keming , Yan Jiangwei , Zhang Gengqian
Published: February 2020

Y-chromosomal short tandem repeat (Y-STR) polymorphisms are useful in forensic identification, population genetics and human structures. However, the current Y-STR systems are limited in discriminating distant relatives in a family with a low discrimination power. Increasing the capacity of detecting Y chromosomal polymorphisms will drastically narrow down the matching number of genealogy populations or pedigrees. In this study, we developed a system containing 17 Y-STRs that are complementary to the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected sizes of 126-400 bp labeled by different fluorescence molecules (DYS715, DYS709, DYS716, DYS713 and DYS607 labeled by FAM; DYS718, DYS723, DYS708 and DYS714 labeled by JOE; DYS712, DYS717, DYS721 and DYS605 labeled by TAMRA; and DYS719, DYS726, DYS598 and DYS722 labeled by ROX). The system was extensively tested for sensitivity, male specificity, species specificity, mixture, population genetics and mutation rates following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The genetic data were obtained from eight populations with a total of 1260 individuals. Our results showed that all the 17 Y-STRs are human- and male-specific and include only one copy of the Y-chromosome. The 17 Y-STR system detects 143 alleles and has a high discrimination power (0.996031746). Mutation rates were different among the 17 Y-STRs, ranging from 0.30% to 3.03%. In conclusion, our study provides a robust, sensitive and cost-effective genotyping method for human identification, which will be beneficial for narrowing the search scope when applied to genealogy searching with the Y-STR DNA databank.
Dynamical persistence in resource-consumer models
Authors: Dalmedigos Itay , Bunin Guy
Published: February 2020

We show how highly-diverse ecological communities may display persistent abundance fluctuations, when interacting through resource competition and subjected to migration from a species pool. This turns out to be closely related to the ratio of realized species diversity to the number of resources. This ratio is set by competition, through the balance between species being pushed out and invading. When this ratio is smaller than one, dynamics will reach stable equilibria. When this ratio is larger than one, fixed-points are either unstable or marginally stable, as expected by the competitive exclusion principle. If they are unstable, the system is repelled from fixed points, and abundances forever fluctuate. While marginally-stable fixed points are in principle allowed and predicted by some models, they become structurally unstable at high diversity. This means that even small changes to the model, such as non-linearities in how resources combine to generate species’ growth, will result in persistent abundance fluctuations.
Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury
Authors: Ettou Sandrine , Jung Youngsook L. , Miyoshi Tomoya , Jain Dhawal , Hiratsuka Ken , Schumacher Valerie , Taglienti Mary E. , Morizane Ryuji , Park Peter J. , Kreidberg Jordan A.
Published: February 2020

In the context of human disease, the mechanisms whereby transcription factors reprogram gene expression in response to injury are not well understood. This is particularly true in kidney podocytes, injury to which is the common and initial event in many processes that lead End Stage Kidney Disease. WT1 is a master regulator of gene expression in podocytes, binding nearly all genes known to be crucial for maintenance of the glomerular filtration barrier. Here, using purified populations of podocytes and glomeruli, we investigated WT1-mediated transcriptional reprogramming during the course of podocyte injury. Using the Adriamycin murine model of Focal Segmental Glomerulosclerosis, we discovered that podocyte injury led to increased intensity of WT1 binding and to the acquisition of new WT1 binding sites, both at previously identified target genes and at newly bound target genes, providing mechanistic insight on the transcriptional response to injury. We also observed a previously unrecognized transient increase in expression of WT1 target genes in both mice and human kidney organoids. Together, these features appear to constitute an attempt to repair the glomerular filtration barrier after podocyte injury. At later stages of injury, when proteinuria became severe, there was greatly decreased WT1 binding to most target genes. Furthermore, WT1 appeared to be required to maintain active chromatin marks at its target genes. These active marks were converted to repressive marks after loss of WT1 or Adriamycin-induced injury. This response to injury suggests that there may be a potential window of opportunity for repairing podocyte injury as a treatment for glomerular disease in humans.
Non-invasive real-time imaging of reactive oxygen species (ROS) using multispectral auto-fluorescence imaging technique: a novel tool for redox biology
Authors: Habibalahi Abbas , Moghari Mahdieh Dashtbani , Campbell Jared M. , Anwer Ayad G. , Mahbub Saabah B. , Gosnell Martin , Saad Sonia , Pollock Carol , Goldys Ewa M.
Published: February 2020

Detecting reactive oxygen species (ROS) that play a critical role as redox modulators and signalling molecules in biological systems currently requires invasive methods such as ROS - specific indicators for imaging and quantification. We developed a non-invasive, real-time, label-free imaging technique for assessing the level of ROS in live cells and thawed cryopreserved tissues that is compatible within-vivoimaging. The technique is based on autofluorescence multispectral imaging (AFMI) carried out in an adapted fluorescence microscope with an expanded number of spectral channels spanning specific excitation (365 nm-495 nm) and emission (420 nm-700 nm) wavelength ranges. We established a strong quantitative correlation between the spectral information obtained from AFMI and the level of ROS obtained from CellROX staining. The results were obtained in several cell types (HeLa, PANC1 and mesenchymal stem cells) and in live kidney tissue. Additioanly, two spectral regimes were considered: with and without UV excitation (wavelengths > 400 nm); the latter being suitable for UV-sensitive systems such as the eye. Data were analyzed by linear regression combined with an optimization method of swarm intelligence. This allowed the calibration of AFMI signals to the level of ROS with excellent correlation (R= 0.84, p=0.00) in the entire spectral range and very good correlation (R= 0.78, p=0.00) in the limited, UV-free spectral range. We also developed a strong classifier which allowed us to distinguish moderate and high levels of ROS in these two regimes (AUC= 0.91 in the entire spectral range and AUC = 0.78 for UV-free imaging). These results indicate that ROS in cells and tissues can be imaged non-invasively, which opens the way to future clinical applications in conditions where reactive oxygen species are known to contribute to progressive disease such as in ophthalmology, diabetes, kidney disease, cancer and neurodegenerative diseases.
Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells
Authors: Weitz Sara H. , Quick-Cleveland Jen , Jacob Jose P. , Barr Ian , Senturia Rachel , Koyano Kikuye , Xiao Xinshu , Weiss Shimon , Guo Feng
Published: February 2020

The essential biological cofactor heme is synthesized in cells in the Fe(II) form. Oxidized Fe(III) heme is specifically required for processing primary transcripts of microRNAs (pri-miRNAs) by the RNA-binding protein DGCR8, a core component of the Microprocessor complex. It is unknown how readily available Fe(III) heme is in the largely reducing environment in human cells and how changes in cellular Fe(III) heme availability alter microRNA (miRNA) expression. Here we address the first question by characterizing DGCR8 mutants with various degrees of deficiency in heme-binding. We observed a strikingly simple correlation between Fe(III) heme affinityin vitroand the Microprocessor activity in HeLa cells, with the heme affinity threshold for activation estimated to be between 0.6-5 pM under typical cell culture conditions. The threshold is strongly influenced by cellular heme synthesis and uptake. We suggest that the threshold reflects a labile Fe(III) heme pool in cells. Based on our understanding of DGCR8 mutants, we reanalyzed recently reported miRNA sequencing data and conclude that heme is generally required for processing canonical pri-miRNAs, that heme modulates the specificity of Microprocessor, and that cellular heme level and differential DGCR8 heme occupancy alter the expression of distinct groups of miRNAs in a hierarchical fashion. Overall, our study provides the first glimpse of a labile Fe(III) heme pool important for a fundamental physiological function and reveal principles governing how Fe(III) heme modulates miRNA maturation at a genomic scale. We also discuss potential states and biological significance of the labile Fe(III) heme pool.
Striatal direct and indirect pathway neurons differentially control the encoding and updating of goal-directed learning
Authors: Peak James , Chieng Billy , Hart Genevra , Balleine Bernard W.
Published: February 2020

The posterior dorsomedial striatum (pDMS) is necessary for goal-directed action, however the role of the direct (dSPN) and indirect (iSPN) spiny projection neurons in the pDMS in such action remains unclear. In this series of experiments, we examined the role of pDMS SPNs in goal-directed action and found that, whereas dSPNs were critical for goal-directed learning and for energizing the learned response, iSPNs were involved in updating that learning to support response flexibility. Instrumental training elevated expression of the plasticity marker Zif268 in dSPNs only, and chemogenetic suppression of dSPN activity during training prevented goal-directed learning. Unilateral optogenetic inhibition of dSPNs induced an ipsilateral response bias in goal-directed action performance. In contrast, although initial goal-directed learning was unaffected by iSPN manipulations, optogenetic inhibition of iSPNs, but not dSPNs, impaired the updating of this learning and attenuated response flexibility after changes in the action-outcome contingency.
Localized activation of ependymal progenitors induces EMT-mediated glial bridging after spinal cord injury
Authors: Zhou Lili , Burris Brooke , Mcadow Ryan , Mokalled Mayssa H.
Published: February 2020

Unlike mammals, adult zebrafish undergo spontaneous recovery after major spinal cord injury. Whereas scarring presents a roadblock for mammalian spinal cord repair, glial cells in zebrafish form a bridge across severed spinal cord tissue to facilitate regeneration. Here, we performed FACS sorting and genome-wide profiling to determine the transcriptional identity of purified bridging glia. We found that Yap-Ctgf signaling activates epithelial to mesenchymal transition (EMT) in localized niches of ependymal cells to promote glial bridging and regeneration. Preferentially activated in early bridging glia, Yap is required for the expression of the glial bridging factor Ctgfa and for functional spinal cord repair. Ctgfa regulation is controlled by an injury responsive enhancer element that drives expression in early bridging glia after injury. Yap-Ctgf signaling activates a mesenchymal transcriptional program that drives glial bridging. This study revealed the molecular signatures of bridging glia and identified an injury responsive gene regulatory network that promotes spinal cord regeneration in zebrafish.
Differential Host Gene Signatures in Response toMycobacterium tuberculosisInfection
Authors: Tazi Loubna , Wang Ping , Fornage Myriam
Published: February 2020

Tuberculosis (TB) represents a global public health threat and is the leading cause of morbidity and mortality worldwide. Effective control of TB is complicated with the emergence of multidrug resistance. Yet, there is still a fundamental gap in understanding the complex and dynamic interactions between differentMycobacterium tuberculosisstrains and the host. In this project, we investigated the host immune response to differentM. tuberculosisstrains, including avirulent or virulent and rifampin-resistant or isoniazid-resistant strains in THP-1 cells. We identified major differences in the gene response profiles in response to infection with these strains. The expression of IDO1 and IL-1β in the infected cells was stronger in all virulentM. tuberculosisstrains. The most striking result was the overexpression of many interferon-stimulated genes (ISGs) in cells infected with the isoniazid-resistant strain, compared to the rifampin-drug resistant strain and the drug-sensitive strain. A transcription regulation analysis of the differentially expressed genes in infected THP-1 cells implicated two major transcription factors, NF-κB and STAT1. The differentially expressed ISGs in response to the isoniazid-resistantM. tuberculosisstrain were associated with STAT1 signaling, while the expression of many cytokines, such IL-1β, was associated with NF-κB signaling. Our data suggest that the isoniazid-resistantM. tuberculosisstrain preferentially activates STAT1 in response to cGAS-STING activation and induces a host immune response signature that is characteristic of isoniazid resistance. This study has a potential to provide important new insights into TB pathogenesis and to characterize host gene signatures specifically involved in isoniazid-resistant TB.
Inositol synthesis gene is required for circadian rhythm ofDrosophila melanogastermating behavior
Authors: Sakata Kazuki , Kawasaki Haruhisa , Ishida Norio
Published: February 2020

Accumulating evidence indicates that the molecular circadian clock underlies the mating behavior ofDrosophila melanogaster.However, information about which gene affects circadian mating behavior is poorly understood in animals. The present study found that feedingMyo-inositol enhanced the close-proximity (CP) rhythm ofD. melanogastermating behavior and lengthened the period of the CP rhythm. Then, to understand a role for inositol synthesis to fly mating behavior, we established theInos(Myo-inositol 1-phosphate synthase)geneknock down fly strains with RNAi. Interestingly, the CP behavior of this three-different driver knock down strains was arrhythmic, but the locomotor rhythm was rhythmic. The data of three-differentInosknock down strains suggests thatInosgene expression of upper LNd, l-LNV, 5ths-LNvin brain is necessary for proper CP rhythm generation inD. melanogaster. The data indicated that theInosgene is involved in the role for the circadian rhythm ofD. melanogastermating behavior.
Bent DNA bows as amplifiers and biosensors for detecting DNA-interacting salts and molecules
Authors: Freeland Jack , Zhang Lihua , Wang Shih-Ting , Ruiz Mason , Wang Yong
Published: February 2020

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important for understanding various fundamental cellular processes in living systems, deciphering the mechanism of many diseases related to DNA damages, and discovering or designing inhibitors and drugs targeting DNA. However, there is still a need for improved sensitivity to detect these interactions, especially in situations where expensive sophisticated equipment is not available. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as monitoring water quality and screening DNA-targeting molecules and drugs.
Differential TM4SF5-mediated SIRT1 modulation and signaling for chronic liver disease
Authors: Ryu Jihye , Kim Eunmi , Kang Min-Kyung , Song Dae-Geun , Shin Eun-Ae , Jung Jae Woo , Nam Seo Hee , Kim Ji Eon , Kim Hye-Jin , Lee Jeong-Hoon , Yoon Jung-Hwan , Son Taekwon , Kim Semi , Kim Hwi Young , Lee Jung Weon
Published: February 2020

Here we show the roles of transmembrane 4 L six family member 5 (TM4SF5) in the progression of nonalcoholic steatosis (or NAFL) to steatohepatitis (NASH). The overexpression of TM4SF5 caused nonalcoholic steatosis and NASH in an age-dependent manner. Initially, TM4SF5-positive hepatocytes and livers exhibited lipid accumulation, decreased SIRT1, increased SREBPs levels, and inactive STAT3 via SOCS1/3 upregulation. In older animals, TM4SF5 under an inflammatory environment increased SIRT1 expression and STAT3 activity with no significant change to SOCSs and SREBPs levels, leading to active STAT3-mediated fibrotic extracellular matrix (ECM) production. Liver tissues from clinical human patients with NAFL or NASH also showed such a TM4SF5-SIRT1-STAT3-ECM relationship correlated with fibrosis score and age. Ligand-independent and TM4SF5-mediated STAT3 activity led to collagen I and laminins/laminin γ2 expression in hepatic stellate cells and hepatocytes, respectively. Laminin γ2 suppression abolished CCl4-mediated liver damage and ECM production and reduced SIRT1 and active-STAT3, but did not alter SREBP1 or SOCSs levels. These findings suggest that TM4SF5, CCL20, SIRT1, and/or laminin γ2 may be promising therapeutic targets against liver disease.
Antimicrobial silver inhibits bacterial movement and stalls flagellar motor
Authors: Russell Benjamin , Rogers Ariel , Kurilich Matthew , Krishnamurthi Venkata Rao , Chen Jingyi , Wang Yong
Published: February 2020

Silver (Ag) has been gaining broad attention due to their antimicrobial activities and the increasing resistance of bacteria to commonly prescribed antibiotics. However, various aspects of the antimicrobial mechanism of Ag have not been understood, including how silver affects the motility of bacteria, a factor that is intimately related to bacterial virulence. Here we report our study on the antibiotic effects of Ag+ions on the motility ofE. colibacteria using swimming and tethering assays. We observed that the bacteria slowed down dramatically when subjected to Ag+ions, providing direct evidence showing that Ag inhibits the motility of bacteria. In addition, through tethering assays, we monitored the rotation of flagellar motors and observed that the tumbling frequency of bacteria increased significantly in the presence of Ag+ions. Furthermore, the rotation of bacteria in the tethering assays were analyzed using hidden Markov model (HMM); and we found that Ag+-treatment led to a significant decrease in the tumbling-to-running transition rate of the bacteria, suggesting that the rotation of bacterial flagellar motors was stalled by Ag+ions. This work provided a new quantitative understanding on the mechanism of Ag-based antimicrobial agents in bacterial motility.
Antifungal symbiotic peptide NCR044.1 exhibits unique structure and multi-faceted mechanisms of action that confer plant protection
Authors: Velivelli Siva L. S. , Czymmek Kirk J. , Li Hui , Shaw Jared B. , Buchko Garry W. , Shah Dilip M.
Published: February 2020

NCR044.1 is a 36-amino acid nodule-specific cysteine-rich antimicrobial peptide expressed in the developing nodules ofMedicago truncatula. Here, we determined its unique NMR structure to be largely disordered, one four-residue α-helix and one three-residue anti-parallel β-sheet stabilized by two disulfide bonds, suggesting it is highly dynamic. NCR044.1 exhibited potent fungicidal activity against multiple plant fungal pathogens. It breached the fungal plasma membrane, bound to multiple phosphoinositides, and induced reactive oxygen species. Time-lapse confocal and super-resolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, and subsequent accumulation in the cytoplasm with elevated levels in nucleoli. Nucleolar localization of NCR044.1 was unique amongst plant antifungal peptides, suggesting its potential interaction with ribosomes and inhibition of translation. Spray-applied NCR044.1 significantly reduced gray mold disease symptoms caused by the fungal pathogenBotrytis cinereain tomato plants and post-harvest products demonstrating its potential as a spray-on peptide-based biofungicide.
Spatiotemporal identification of druggable binding sites using deep learning
Authors: Kozlovskii Igor , Popov Petr
Published: February 2020

Identification of novel protein binding sites expands «druggable genome» and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble to object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, named BiteNet, that considers protein conformations as the 3D-images, binding sites as the objects on these images to detect, and conformational ensembles of proteins as the 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding sites in G protein-coupled receptors. BiteNet outperforms state-of-the-art methods both in terms of accuracy and speed, taking about 1.5 minute to analyze 1000 conformations of a protein with 2000 atoms. BiteNet is available athttps://github.com/i-Molecule/bitenet.