bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycoengineering bioconjugate vaccines, therapeutics, and diagnostics in E. coli
Authors: Harding Christian M , Feldman Mario F
Published: April 2019

The first, general glycosylation pathway in bacteria, the N-linked glycosylation system of Campylobacter jejuni, was discovered two decades ago. Since then, many diverse prokaryotic glycosylation systems have been characterized, including O-linked glycosylation systems that have no homologous counterparts in eukaryotic organisms. Shortly after these discoveries, glycosylation pathways were recombinantly introduced into E. coli creating the field of bacterial glycoengineering. Bacterial glycoengineering is an emerging biotechnological tool that harnesses prokaryotic glycosylation systems for the generation of recombinantly glycosylated proteins using E. coli as a host. Over the last decade, as our understanding of prokaryotic glycosylation systems has advanced, so too has the glycoengineering toolbox. Currently, glycoengineering utilizes two broad approaches to recombinantly glycosylate proteins, both of which can generate N- or O-linkages: oligosaccharyltransferase (OTase)-dependent and OTase-independent. This review discusses the applications of these bacterial glycoengineering techniques as they relate to the development of glycoconjugate vaccines, therapeutic proteins, and diagnostics.
At what cost is performance-based financing implemented? Novel evidence from Malawi
Authors: De Allegri Manuela , Makwero Chris , Torbica Aleksandra
Published: April 2019

Our study estimated the full economic cost of implementing performance-based financing [PBF, the Support for Service Delivery Integration Performance-Based Incentives (SSDI-PBI) programme], as a means of first introducing strategic purchasing in a low-income setting, Malawi. Our analysis distinguished design from implementation costs and traces costs across personnel and non-personnel cost categories over the 2012–15 period. The full cost of the SSDI-PBI programme amounted to USD 3 402 187, equivalent to USD 6.46 per targeted beneficiary. The design phase accounted for about one-third (USD 1 161 332) of the total costs, while the incentives (USD 1 140 436) represented about one-third of the total cost of the intervention and about half the cost of the implementation phase. With a cost of USD 1 605 178, personnel costs represented the dominant cost category. Our study indicated that the introduction of PBF entailed consumption of a substantial amount of resources, hence representing an important opportunity cost for the health system.
Measuring Catastrophic Health Expenditures and its Inequality: Evidence from Iran’s Health Transformation Program
Authors: Yazdi-Feyzabadi Vahid , Mehrolhassani Mohammad Hossein , Darvishi Ali
Published: April 2019

One of the important goals of Iran’s health transformation programme (HTP) is to improve financial protection for households against health expenditure. This study aimed to investigate the occurrence, intensity and inequality in distribution of catastrophic health expenditure (CHE) using the WHO and the World Bank (WB) methodologies with different thresholds in the years before and after HTP. We used data from seven annual national repeated cross-sectional surveys on households’ income and expenditures from 2011 to 2017. The intensity to CHE was calculated using overshoot and mean positive overshoot (MPO) indices. Finally, the inequality in distribution of exposure to CHE was calculated using the concentration index (CI), and the dominance test of concentration curves was used to inference about the significant changes in inequality of the years before and after HTP. The exposure rate to CHE in the total population and at 40% threshold of the WHO methodology changed from 1.99% in 2011 to 3.46% in 2017. Additionally, at 20% threshold of the WB methodology, it was changed from 5.14% to 8.68%. Overshoot and MPO indices increased on average based on two methodologies in urban and rural areas during seven years. The CIs for all the years show a negative value in both methodologies, indicating that CHE occurrence is higher among the poor households. In 2017, at 40% threshold of the WHO, the numerical values of the CIs were −0.15 and −0.14 in urban and rural populations, respectively. These values were −0.07 and −0.05 for the 20% threshold of WB, respectively. Results of dominance test showed no significant change in inequality for the years after than before HTP with two exceptions for total and rural populations based on the WB methodology. Generally, HTP had no considerable success in financial protection, requiring a review in actions to support pro-poor adaptation strategies.
The protective variant rs7173049 at LOXL1 locus impacts on retinoic acid signaling pathway in pseudoexfoliation syndrome
Authors: Berner Daniel , Hoja Ursula , Zenkel Matthias , Ross James Julian , Uebe Steffen , Paoli Daniela , Frezzotti Paolo , Rautenbach Robyn M , Ziskind Ari , Williams Susan E , Carmichael Trevor R , Ramsay Michele , Topouzis Fotis , Chatzikyriakidou Anthi , Lambropoulos Alexandros , Sundaresan Periasamy , Ayub Humaira , Akhtar Farah , Qamar Raheel , Zenteno Juan C , Cruz-Aguilar Marisa , Astakhov Yury S , Dubina Michael , Wiggs Janey , Ozaki Mineo , Kruse Friedrich E , Aung Tin , Reis André , Khor Chiea Chuen , Pasutto Francesca , Schlötzer-Schrehardt Ursula
Published: April 2019

LOXL1 (lysyl oxidase-like 1) has been identified as the major effect locus in pseudoexfoliation (PEX) syndrome, a fibrotic disorder of the extracellular matrix and frequent cause of chronic open-angle glaucoma. However, all known PEX-associated common variants show allele effect reversal in populations of different ancestry, casting doubt on their biological significance. Based on extensive LOXL1 deep sequencing, we report here the identification of a common non-coding sequence variant, rs7173049A>G, located downstream of LOXL1, consistently associated with a decrease in PEX risk (odds ratio, OR = 0.63; P = 6.33 × 10−31) in nine different ethnic populations. We provide experimental evidence for a functional enhancer-like regulatory activity of the genomic region surrounding rs7173049 influencing expression levels of ISLR2 (immunoglobulin superfamily containing leucine-rich repeat protein 2) and STRA6 [stimulated by retinoic acid (RA) receptor 6], apparently mediated by allele-specific binding of the transcription factor thyroid hormone receptor beta. We further show that the protective rs7173049-G allele correlates with increased tissue expression levels of ISLR2 and STRA6 and that both genes are significantly downregulated in tissues of PEX patients together with other key components of the STRA6 receptor-driven RA signaling pathway. siRNA-mediated downregulation of RA signaling induces upregulation of LOXL1 and PEX-associated matrix genes in PEX-relevant cell types. These data indicate that dysregulation of STRA6 and impaired retinoid metabolism are involved in the pathophysiology of PEX syndrome and that the variant rs7173049-G, which represents the first common variant at the broad LOXL1 locus without allele effect reversal, mediates a protective effect through upregulation of STRA6 in ocular tissues.
Multiplicative Dependence Among Iterated Values of Rational Functions Modulo Finitely Generated Groups
Authors: Bérczes Attila , Ostafe Alina , Shparlinski Igor E , Silverman Joseph H
Published: April 2019

We study multiplicative dependence between elements in orbits of algebraic dynamical systems over number fields modulo a finitely generated multiplicative subgroup of the field. We obtain a series of results, many of which may be viewed as a blend of Northcott’s theorem on boundedness of preperiodic points and Siegel’s theorem on finiteness of solutions to $S$-unit equations.
Contagious Environmental Lawmaking
Authors: Affolder Natasha
Published: April 2019

It is rare to find an environmental law development or ‘innovation’ announced or celebrated without some discussion of its transferability. Discourses of diffusion are becoming increasingly central to the way that we develop, communicate and frame environmental law ideas. And yet, this significant dimension of environmental law practice seems to have outgrown existing conceptual scaffolding and scholarly vocabularies. The concept, and intentionally unfamiliar terminology, of ‘contagious lawmaking’ creates a space for both fleshing out, and problematizing, the phenomenon of the dynamic and multi-directional transfer of environmental law ideas. This article sets the stage for further study of the global diffusion of environmental law. It does so by identifying the phenomenon of contagious lawmaking and by making explicit some of the terminological and methodological challenges implicated in its study. The article draws on narratives of the ‘global’ diffusion of environmental impact assessment, cited as ‘the most widely adopted environmental management tool in the world’.
A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation
Authors: Esselstyn Jacob A , Achmadi Anang S , Handika Heru , Giarla Thomas C , Rowe Kevin C
Published: April 2019

We describe a new species of Crocidura (Soricidae) from Sulawesi Island, Indonesia, documenting its novelty with both genetic and morphological characters. The new species is widespread on the island, with vouchered records from nine general localities distributed among five of the island’s areas of endemism. Morphologically, the new species is readily distinguished from all other described Sulawesi Crocidura by its intermediate body size, gray pelage, and long, hairy tail. The new species was mainly captured in pitfalls placed in the ground, but we also obtained evidence that it readily climbs trees and may be scansorial in its locomotor habits. Populations of the new species sampled from across the island are closely related, separated by < 0.02 uncorrected mitochondrial p-distances. The new species is one member of an endemic radiation of shrews on Sulawesi now known to contain six valid species and several undescribed species, all within the genus Crocidura. Resolution of species limits and phylogenetic relationships in this radiation is hindered by habitat loss at type localities, historical designation of new species using very small sample sizes, and a lack of genetic data from type specimens.

Kami mendeskripsikan spesies baru Crocidura (Soricidae) dari Pulau Sulawesi, Indonesia, sekaligus mendokumentasikan keunikan karakter secara genetik maupun morfologi dari spesies tersebut. Spesies baru ini tersebar luas di Pulau Sulawesi, diketahui berdasarkan spesimen yang berasal dari sembilan lokasi umum yang tersebar di lima kawasan endemik di pulau tersebut. Secara morfologi, spesies baru ini dapat dibedakan dari spesies Crocidura lainnya dari Sulawesi berdasarkan ukuran tubuh yang sedang, rambut tubuh berwarna abu-abu, dan ekor yang panjang dan berambut. Spesies baru ini sebagian besar diperoleh dari perangkap sumuran yang ditanam didalam tanah, selain itu kami juga mendapatkan bukti bahwa spesies ini mampu memanjat pohon dan kemungkinan memiliki perilaku sebagai pemanjat. Beberapa populasi spesies yang dikoleksi dari Sulawesi ini mempunyai kekerabatan yang dekat, hanya dipisahkan oleh jarak proporsi DNA mitokondria (tidak terkoreksi) sebesar < 0.02. Spesies baru ini merupakan salah satu anggota dari suatu kelompok radiasi endemik cecurut di Sulawesi yang sampai saat ini diketahui terdiri atas enam spesies yang valid, dan beberapa spesies yang belum dideskripsikan, semuanya termasuk didalam genus Crocidura. Kepastian dalam menetapkan batasan jarak antar spesies dan hubungan kekerabatan genetik dari radiasi kelompok cecurut di Sulawesi terkendala oleh kerusakan habitat pada lokasi spesimen tipe, sejarah penamaan spesies yang hanya berdasarkan sampel yang sedikit, dan keterbatasan data molekuler dari spesimen tipe.
Clinical experience of craniospinal intensity-modulated spot-scanning proton therapy using large fields for central nervous system medulloblastomas and germ cell tumors in children, adolescents, and young adults
Authors: Hashimoto Takayuki , Shimizu Shinichi , Takao Seishin , Terasaka Shunsuke , Iguchi Akihiro , Kobayashi Hiroyuki , Mori Takashi , Yoshimura Takaaki , Matsuo Yuto , Tamura Masaya , Matsuura Taeko , Ito Yoichi M , Onimaru Rikiya , Shirato Hiroki
Published: April 2019

The outcomes of intensity-modulated proton craniospinal irradiation (ipCSI) are unclear. We evaluated the clinical benefit of our newly developed ipCSI system that incorporates two gantry-mounted orthogonal online X-ray imagers with a robotic six-degrees-of-freedom patient table. Nine patients (7–19 years old) were treated with ipCSI. The prescribed dose for CSI ranged from 23.4 to 36.0 Gy (relative biological effectiveness) in 13–20 fractions. Four adolescent and young adult (AYA) patients (15 years or older) were treated with vertebral-body-sparing ipCSI (VBSipCSI). Myelosuppression following VBSipCSI was compared with that of eight AYA patients treated with photon CSI at the same institution previously. The mean homogeneity index (HI) in the nine patients was 0.056 (95% confidence interval: 0.044–0.068). The mean time from the start to the end of all beam delivery was 37 min 39 s ± 2 min 24 s (minimum to maximum: 22 min 49 s – 42 min 51 s). The nadir white blood cell, hemoglobin, and platelet levels during the 4 weeks following the end of the CSI were significantly higher in the VBSipCSI group than in the photon CSI group (P = 0.0071, 0.0453, 0.0024, respectively). The levels at 4 weeks after the end of CSI were significantly higher in the VBSipCSI group than in the photon CSI group (P = 0.0023, 0.0414, 0.0061). Image-guided ipCSI was deliverable in a reasonable time with sufficient HI. Using VBSipCSI, AYA patients experienced a lower incidence of serious acute hematological toxicity than AYA patients treated with photon CSI.
Affective Politics of Structural Adjustment: “Cruel Optimism” and Turhan Selçuk’s Cartoons in Turkey, 1983–1986
Authors: Zencirci Gizem
Published: April 2019

This article contributes to the social history of neoliberalism by analyzing the emotions, feelings, and sentiments through which Turkish people experienced the structural adjustment program of the 1980s. I argue that market reforms were experienced through a paradoxical entanglement of desire and disillusionment—an affective politics that Lauren Berlant defines as “cruel optimism.” This concept captures the ways in which neoliberalism generates a series of aspirations, longings, and yearnings that can never be fully achieved or satisfied but nevertheless pulls subjects toward an imagined future. I examine these collective feelings through a visual analysis of Kemalist intellectual Turhan Selçuk’s editorial cartoons that were published in the center-left newspaper Milliyet between 1983 and 1986. These editorial cartoons function in complex ways, providing relief through satire but also narrating the ways in which a sense of optimism encircled sentiments of anxiety, despair, and precarity. I identify three distinctive instances of cruel optimism in his work: first, the will to retain control over economic affairs despite the dominance of international organizations, second, the hope that trade liberalization shall bring prosperity amidst mounting class inequality, and third, the allure of consumption even when most of the population was unable to afford export commodities. Rather than demonstrating a clear temporal gap between the promise and demise of market reforms, the article reveals the coproduction of two oppositional affective registers and suggests that the fluctuation between willingness and reluctance is a constitutive element of neoliberal subjectivity.
Investigating the origin of the Fe emission lines of the Seyfert 1 galaxy Mrk 205
Authors: Laha Sibasish , Ghosh Ritesh , Tripathi Shruti , Guainazzi Matteo
Published: April 2019

We have investigated the nature and origin of the Fe K emission lines in Mrk 205 using observations with Suzaku and XMM–Newton, aiming to resolve the ambiguity between a broad emission line and multiple unresolved lines of higher ionization. We detect the presence of a narrow Fe K α emission line along with a broad-band Compton reflection hump at energies $E\gt 10\rm \, \, {\rm keV}$. These are consistent with reflected emission of hard X-ray photons off a Compton-thick material of $N_{\rm H}\ge 2.15\times 10^{24}\rm \, \, {\rm cm^{-2}}$. In addition we detect a partially covering ionized absorption with ionization parameter $\log (\xi /\rm \, erg\, cm\, s^{-1})=1.9_{-0.5}^{+0.1}$, column density $N_{\rm H}=(5.6_{-1.9}^{+2.0})\times 10^{22}\rm \, \, {\rm cm^{-2}}$, and a covering factor of $0.22_{-0.06}^{+0.09}$. We detect the presence of emission arising out of ionized disc reflection contributing in the soft and hard X-rays consistently in all the observations. We however, could not definitely ascertain the presence of a relativistically broadened Fe line in the X-ray spectra. Using relativistic reflection models, we found that the data are unable to statistically distinguish between the scenarios when the supermassive black hole is non-rotating and when it is maximally spinning. Using the disc reflection model we also find that the accretion disc of the active galactic nucleus may be truncated at a distance 6RG < R < 12RG, which may suggest why there may not be any broad Fe line. The Eddington rate of the source is low (λEdd = 0.03), which points to an inefficient accretion, possibly due to a truncated disc.
Impacts of Nicotine and Flavoring on the Sensory Perception of E-Cigarette Aerosol
Authors: Pullicin Alexa J , Kim Hyoshin , Brinkman Marielle C , Buehler Stephanie S , Clark Pamela I , Lim Juyun
Published: April 2019

Introduction

To examine the interaction between an added flavoring (cherry) and nicotine on the perception of electronic cigarette (e-cigarette) aerosol and how this impacts the appeal of flavored liquids for e-cigarette (e-liquids).

Methods

A total of 19 subjects (13 male, 6 female) vaped six commercially available e-liquids with varying contents of nicotine (0, 6, 12 mg/mL) and cherry flavor (4.7% or 9.3% vol/vol). For each e-liquid, subjects first rated overall liking/disliking of the aerosol using the Labeled Hedonic Scale, followed by perceived intensities of sweetness, bitterness, harshness (irritation), and cherry flavor of the aerosol using the general version of Labeled Magnitude Scale.

Results

The main findings were that (1) added nicotine increased perceived irritation and bitterness, and decreased the perceived sweetness of the e-cigarette aerosol; (2) cherry flavoring added a characteristic “cherry flavor” and an increase in the flavoring concentration from 4.7% to 9.3% tended to increase perceived intensities of sweetness, harshness, and bitterness; and (3) hedonic ratings of the e-cigarette aerosol decreased as nicotine level increased, but were not affected by flavor level.

Conclusions

Our findings indicate that the appeal of the e-cigarette aerosol decreases as nicotine concentration increases. Conversely, perceived sweetness improved liking. An increase in the concentration of cherry flavoring did not appear to impact any of the measured attributes to a significant degree.

Implications

This work demonstrates that the perception of specific sensory attributes of e-cigarettes and their overall appeal are affected by the e-liquid constituents. Most significantly, the results suggest that nicotine decreases the sensory appeal of e-cigarettes by contributing to the perceived irritation and bitterness of the aerosol. These data have implications for the role that nicotine plays in the sensory perception and appeal of e-cigarettes aerosol and further how these sensory factors can be modulated by sweet flavoring.
Host Determinants of Infectiousness in Smear-Positive Patients With Pulmonary Tuberculosis
Authors: Acuña-Villaorduña Carlos , Ayakaka Irene , Schmidt-Castellani Luiz Guilherme , Mumbowa Francis , Marques-Rodrigues Patricia , Gaeddert Mary , White Laura F , Palaci Moises , Ellner Jerrold J , Dietze Reynaldo , Joloba Moses , Fennelly Kevin P , Jones-López Edward C
Published: April 2019

Background

Epidemiologic data suggests that only a minority of tuberculosis (TB) patients are infectious. Cough aerosol sampling is a novel quantitative method to measure TB infectiousness.

Methods

We analyzed data from three studies conducted in Uganda and Brazil over a 13-year period. We included sputum acid fast bacilli (AFB) and culture positive pulmonary TB patients and used a cough aerosol sampling system (CASS) to measure the number of colony-forming units (CFU) of Mycobacterium tuberculosis in cough-generated aerosols as a measure for infectiousness. Aerosol data was categorized as: aerosol negative (CFU = 0) and aerosol positive (CFU > 0). Logistic regression models were built to identify factors associated with aerosol positivity.

Results

M. tuberculosis was isolated by culture from cough aerosols in 100/233 (43%) TB patients. In an unadjusted analysis, aerosol positivity was associated with fewer days of antituberculous therapy before CASS sampling (p = .0001), higher sputum AFB smear grade (p = .01), shorter days to positivity in liquid culture media (p = .02), and larger sputum volume (p = .03). In an adjusted analysis, only fewer days of TB treatment (OR 1.47 per 1 day of therapy, 95% CI 1.16-1.89; p = .001) was associated with aerosol positivity.

Conclusion

Cough generated aerosols containing viable M. tuberculosis, the infectious moiety in TB, are detected in a minority of TB patients and rapidly become non-culturable after initiation of antituberculous treatment. Mechanistic studies are needed to further elucidate these findings.
Communication of Recommendations for the Disposal of Unused Prescription Opioid Medications by Stakeholders in the News Media
Authors: Petrik Megan L , McNamara Patrick J , Moeschler Susan M , Blair Benjamin D
Published: April 2019

Objective

The opioid epidemic is a national public health emergency that requires a comprehensive approach to reduce opioid-related deaths. Proper and timely disposal of unused prescription opioids is one method to deter improper use of these medications and prevent overdose. The objective of this study was to understand how recommendations for disposing of unused prescription opioids, including both take-back programs and toilet disposal, are communicated to the public.

Methods

Two hundred sixty-three US newspaper articles published between January 1, 2014, and June 30, 2017, containing information on opioids and take-back programs were found using LexisNexis. Using content analysis, articles were coded for the presentation of and recommendation for opioid disposal practices, beliefs about environmental harm from toilet disposal, and additional strategies to reduce opioid supply. The entity responsible for the statement was also captured.

Results

Take-back programs were presented as a recommended disposal strategy for unused prescription opioids in 88.6% of coded articles. Toilet disposal was presented as a recommended disposal strategy for unused prescription opioids in 3.4% of articles and as harmful to the environment in 16.0% of articles. Individuals from health care, government, and law enforcement were primarily involved in discussing opioid disposal practices.

Conclusions

Although toilet disposal is recommended by the US Food and Drug Administration (FDA) for disposal of unused prescription opioids when a take-back program is not readily available, it was infrequently presented or recommended in news media articles. These results highlight the importance of improving communication of FDA guidelines for opioid disposal in the media, particularly by health care providers, government employees, and law enforcement officials.
Law Enforcement and Social Media Usage: An Analysis of Engagement
Authors: Jeanis Michelle N , Muniz Caitlyn N , Molbert Courtney L
Published: April 2019

Social media use by law enforcement agencies has been on the rise in recent years. Given that engaging with the community online has shown significant impact for businesses, there is reason to believe that law enforcement agencies will also benefit from this type of media use. However, success with social media is contingent upon user engagement. Research on law enforcement agencies’ social media use is limited, and examinations of community engagement with law enforcement via social networking sites such as Facebook are non-existent. This study adds to the literature by examining user engagement with social media posts from a law enforcement agency in a large metropolis in Louisiana. Findings indicate that there are significant differences in engagement by the type, time, and content of the posts. Based on these findings, implications for practitioners and law enforcement agencies are discussed.
Borrowed Time and Solidarity: The Multi-Scalar Politics of Time and Gendered Care Work
Authors: Baines Donna , Daly Tamara
Published: April 2019

Exploring long-term residential care (Ontario, Canada), we argue that within the context of late neoliberalism, care time is political, contested, and multi-scalar. Multi-scalar time captures the way that time commodifies, disciplines, and delimits workers’ experience of care, and fractures human relations and solidarities. Drawing on data from nonprofit nursing homes in Canada, the article explores how the larger policy context of care work shapes and hinders workers’ abilities to spend time caring and building relationships with residents, how workers negotiate care provision in austere environments, and how workers use borrowed time to de-commodify care and find spaces for solidarity.
An evidence-based network approach to recommending targeted cancer therapies
Authors: Kancherla Jayaram , Rao Shruti , Bhuvaneshwar Krithika , Riggins Rebecca B. , Beckman Robert A. , Madhavan Subha , Bravo Héctor Corrada , Boca Simina M.
Published: April 2019

In this work, we introduce CDGnet, an evidence-based network approach for recommending targeted cancer therapies, available as a user-friendly informatics tool. Our approach can be used to expand the range of options of targeted therapies for cancer patients who undergo molecular profiling. It considers biological pathway information specifically by looking at downstream targets of oncogenes and is personalized for individual patients via the user-inputted molecular alterations and cancer type. CDGnet integrates disparate sources of knowledge and provides results in a number of easily-accessible and usable forms, while separating targeted cancer therapies into categories in an evidence-based manner.
De novo transcriptome sequencing ofSerangium japonicum(Coleoptera: Coccinellidae) and application of two assembled unigenes
Authors: Hu Ya Hui , Liu Yong , Wei Lin , Chen Hao Tao
Published: April 2019

The ladybird beetleSerangium japonicumis an important predator of whiteflies. Although some ecological and biological characteristics of this predator have been studied, the only molecular data for the ladybird beetle at the NCBI website has been submitted by us. To yield gene sequences of the ladybird beetle, paired-end sequencing was used to sequence its transcriptome. Real-time PCR was used to validate differences in the quantity of RNA expressed by theKrueppel homolog 1(Kr-h1) gene in summer versus winter samples. To find the effective molecular barcode, the annotated cytochrome c oxidase subunit I(COX1) gene fragments were amplified from several ladybird beetle populations. Analysis yielded 191,246 assembled unigenes, of which 127,016 (66.4%) were annotated. The differential expression ofKr-h1in summer versus winter suggests thatS. japonicumcan successfully overwinter because the adults enter diapause. The annotatedCOX1gene can be used to distinguishS. japonicumfrom other ladybird species. These gene sequences are currently available in the National Center for Biotechnology Information (NCBI), and will facilitate the study of molecular mechanism inS. japonicum.
Imaging toxin-induced neuroinflammation in mice using hyperpolarized13C magnetic resonance spectroscopy
Authors: Le Page Lydia M , Guglielmetti Caroline , Najac Chloé , Tiret Brice , Chaumeil Myriam M
Published: April 2019

Lipopolysaccharide (LPS) is a commonly used agent for induction of neuroinflammation in preclinical studies. Upon injection, LPS causes activation of microglia and astrocytes, whose metabolism alters to favor glycolysis. Assessingin vivoneuroinflammation and its modulation following therapy remains challenging, and new non-invasive methods allowing for longitudinal monitoring would be greatly valuable. Hyperpolarized (HP)13C magnetic resonance spectroscopy (MRS) is a promising technique for assessingin vivometabolism. In addition to applications in oncology, the most commonly used probe of [1-13C] pyruvate has shown potential in assessing neuroinflammation-linked metabolism in mouse models of multiple sclerosis and traumatic brain injury. Here, we wished to investigate LPS-induced neuroinflammatory changes using HP [1-13C] pyruvate and HP13C urea.

2D chemical shift imaging following simultaneous intravenous injection of HP [1-13C] pyruvate and HP13C urea was performed at baseline (day 0), day 3 and day 7 post intracranial injection of LPS (n=6) or saline (n=5). Immunofluorescence (IF) analyses were performed for Iba1 (resting and activated microglia/macrophages), GFAP (resting and reactive astrocytes) and CD68 (activated microglia/macrophages).

A significant increase in HP [1-13C] lactate production was observed in the injected (ipsilateral) side at 3 and 7 days of the LPS-treated mouse brain, but not in either the contralateral side or saline-injected animals. HP13C lactate/pyruvate ratio, without and with normalization to urea, was also significantly increased in the ipsilateral LPS-injected brain at 7 days compared to baseline. IF analyses showed a significant increase in CD68 and GFAP at 3 days, followed by increased numbers of Iba1 and GFAP positive cells at 7 days post-LPS injection.

In conclusion, we can detect LPS-induced changes in the mouse brain using HP13C MRS, in alignment with increased numbers of microglia/macrophages and astrocytes. This study demonstrates that HP13C spectroscopy holds much potential for providing non-invasive information on neuroinflammation.
Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers
Authors: Santillan E. , Phua W. X. , Constancias F. , Wuertz S.
Published: April 2019

Sustained disturbances are relevant for environmental biotechnology as they can lead to alternative stable states in a system that may not be reversible. Here, we tested the effect of a sustained organic loading alteration (food-to-biomass ratio, F:M, and carbon-to-nitrogen ratio, C:N) on activated sludge bioreactors, focusing on the stability of nitrification and nitrifiers. Two sets of replicate 5-liter sequencing batch reactors were operated at different, low and high, F:M (0.19-0.36 mgCOD/mgTSS/d) and C:N (3.5-6.3 mgCOD/mgTKN) conditions for a period of 74 days, following 53 days of sludge acclimation. Recovery and resilience were tested during the last 14 days by operating all reactors at low F:M and C:N (henceforth termed F:M-C:N). Stable nitrite accumulation (77%) was achieved through high F:M-C:N loading with a concurrent reduction in the abundance of Nitrospira. Subsequently, only two of the three reactors experiencing a switch back from high to low F:M-C:N recovered the nitrite oxidation function, with an increase in Nitrobacter as the predominant NOB, without a recovery of Nitrospira. The AOB community was more diverse, resistant and resilient than the NOB community. We showed that functional recovery and resilience can vary across replicate reactors, and that nitrification recovery need not coincide with a return to the initial nitrifying community structure.
A fence function for adherens junctions in epithelial cell polarity
Authors: Aguilar-Aragon Mario , Tournier Alex , Thompson Barry J
Published: April 2019

Adherens junctions are a defining feature of all epithelial cells, providing cell-cell adhesion and being essential for cell and tissue morphology. InDrosophila, adherens junctions are concentrated between the apical and basolateral plasma membrane domains, but whether they contribute to apical-basal polarisation itself has been unclear. Here we show that, in the absence of adherens junctions, apical-basal polarity determinants can still segregate into complementary domains, but control of apical versus basolateral domain size is lost. Manipulation of the level of apical or basal polarity determinants in experiments and in computer simulations suggests that junctions provide a moveable diffusion barrier, or fence, that restricts the diffusion of polarity determinants to enable precise domain size control. Movement of adherens junctions in response to mechanical forces during morphogenetic change thus enables spontaneous adjustment of apical versus basolateral domain size as an emergent property of the polarising system.
Topological analysis of the type 3 secretion system translocon pore protein IpaC following its native delivery to the plasma membrane during infection
Authors: Russo Brian C. , Duncan Jeffrey K. , Goldberg Marcia B.
Published: April 2019

Many Gram-negative bacterial pathogens require a type 3 secretion system (T3SS) to deliver effector proteins into eukaryotic cells. Contact of the tip complex of the T3SS with a target eukaryotic cell initiates the secretion of the two bacterial proteins that assemble into the translocon pore in the plasma membrane. The translocon pore functions to regulate effector protein secretion and is the conduit for effector protein translocation across the plasma membrane. To generate insights into how the translocon pore regulates effector protein secretion, we defined the topology of theShigellatranslocon pore protein IpaC in the plasma membrane following its native delivery by the T3SS. Using single-cysteine substitution mutagenesis and site-directed labeling with a membrane-impermeant chemical probe, we mapped residues accessible from the extracellular surface of the cell. Our data support a model in which the N-terminus of IpaC is extracellular and the C-terminus of IpaC is intracellular. These findings resolve previously conflicting data on IpaC topology that were based on non-native delivery of IpaC to membranes.Salmonella entericaserovar Typhimurium also requires the T3SS for effector protein delivery into eukaryotic cells. Although the sequence of IpaC is closely related to theSalmonellatranslocon pore protein SipC, the two proteins have unique functional attributes during infection. We showed a similar overall topology for SipC and IpaC and identified subtle topological differences between their transmembrane α-helixes and C-terminal regions. Together, our data suggest that topological differences among distinct translocon pore proteins may dictate organism-specific functional differences of the T3SSs during infection.

Importance

The type 3 secretion system (T3SS) is a nanomachine required for virulence of many bacterial pathogens that infect humans. The system delivers bacterial virulence proteins into the cytosol of human cells, where the virulence proteins promote bacterial infection. The T3SS forms a translocon pore in the membrane of target cells. This pore is the portal through which bacterial virulence proteins are delivered by the T3SS into the eukaryotic cytosol. The pore also regulates the secretion of these virulence proteins. Our work defines the topology of translocon pore proteins in their native context during infection, resolves previously conflicting reports about the topology of theShigellatranslocon pore protein IpaC, and provides new insights into how interactions of the pore with the T3SS likely produce signals that activate secretion of virulence proteins.
Loss of spatacsin impairs cholesterol trafficking and calcium homeostasis
Authors: Boutry Maxime , Pierga Alexandre , Matusiak Raphaël , Branchu Julien , Houllegatte Marc , Ibrahim Yoan , Balse Elise , El Hachimi Khalid-Hamid , Brice Alexis , Stevanin Giovanni , Darios Frédéric
Published: April 2019

Mutations in SPG11, leading to loss of spatacsin function, impair the formation of membrane tubules in lysosomes and cause the accumulation of lipids in lysosome compartment. However, the full nature of lipids accumulating in lysosomes and the physiological consequences of such accumulation are not known. Here we show that loss of spatacsin, but also downregulation of clathrin, inhibited the formation of tubules on late endosomes/lysosomes and prevented the clearance of cholesterol from this subcellular compartment. Using spatacsin-deficient cells, we evaluated the consequences of impaired cholesterol clearance from late endosomes/lysosomes. The accumulation of cholesterol in late endosomes/lysosomes led to lower cholesterol levels in the plasma membrane, enhancing the entry of extracellular calcium by store-operated calcium entry and increasing resting cytosolic calcium levels. Higher cytosolic calcium levels promoted the nuclear translocation of the master regulator of lysosomes TFEB. Downregulation of TFEB or decrease in resting calcium levels in absence of spatacsin partially corrected the formation of tubules and the accumulation of cholesterol in lysosomes, suggesting that spatacsin could be indirectly implicated in the formation of tubules. Our work reveals a homeostatic balance between cholesterol trafficking and cytosolic calcium levels and shows that loss of spatacsin impairs this homeostatic equilibrium.
Experimentally-induced and real-world acute anxiety have no effect on goal-directed behaviour
Authors: Gillan CM , Vaghi MM , Hezemans FH , van Ghesel Grothe S , Dafflon J , Brühl AB , Savulich G , Robbins TW
Published: April 2019

Compulsivity is associated with failures in goal-directed control, an important cognitive faculty that protects against developing habits. But might this effect be explained by co-occurring anxiety? Previous studies have found goal-directed deficits in other anxiety disorders, and to some extent when healthy individuals are stressed, suggesting this is plausible. We carried out a causal test of this hypothesis in two experiments (between-subject N=88; within-subject N=50) that used the inhalation of hypercapnic gas (7.5% CO2) to induce an acute state of anxiety in healthy volunteers. In both experiments, we successfully induced anxiety, assessed physiologically and psychologically, but this did not affect goal-directed performance. In a third experiment (N=1413), we used a correlational design to test if real-life anxiety-provoking events (panic attacks, stressful events) impair goal-directed control. While small effects were observed, none survived controlling for individual differences in compulsivity. These data suggest that anxiety has no meaningful impact on goal-directed control.
Polygenic risk score based on weight gain trajectories is predictive of childhood obesity
Authors: Craig Sarah J. C. , Kenney Ana M. , Lin Junli , Paul Ian M. , Birch Leann L. , Savage Jennifer S. , Marini Michele E. , Chiaromonte Francesca , Reimherr Matthew L. , Makova Kateryna D.
Published: April 2019

Obesity is highly heritable, yet only a small fraction of its heritability has been attributed to specific genetic variants. These variants are traditionally ascertained from genome-wide association studies (GWAS), which utilize samples with tens or hundreds of thousands of individuals for whom a single summary measurement (e.g., BMI) is collected. An alternative approach is to focus on a smaller, more deeply characterized sample in conjunction with advanced statistical models that leverage detailed phenotypes. Here we use novel functional data analysis (FDA) techniques to capitalize on longitudinal growth information and construct a polygenic risk score (PRS) for obesity in children followed from birth to three years of age. This score, comprised of 24 single nucleotide polymorphisms (SNPs), is significantly higher in children with (vs. without) rapid infant weight gain—a predictor of obesity later in life. Using two independent cohorts, we show that genetic variants identified in early childhood are also informative in older children and in adults, consistent with early childhood obesity being predictive of obesity later in life. In contrast, PRSs based on SNPs identified by adult obesity GWAS are not predictive of weight gain in our cohort of children. Our research provides an example of a successful application of FDA to GWAS. We demonstrate that a deep, statistically sophisticated characterization of a longitudinal phenotype can provide increased statistical power to studies with relatively small sample sizes. This study shows how FDA approaches can be used as an alternative to the traditional GWAS.

Author Summary

Finding genetic variants that confer an increased risk of developing a particular disease has long been a focus of modern genetics. Genome wide association studies (GWAS) have catalogued single nucleotide polymorphisms (SNPs) associated with a variety of complex diseases in humans, including obesity, but by and large have done so using increasingly large samples-- tens or even hundreds of thousands of individuals, whose phenotypes are thus often only superficially characterized. This, in turn, may hide the intricacies of the genetic influence on disease. GWAS findings are also usually study-population dependent. We found that genetic risk scores based on SNPs from large adult obesity studies are not predictive of the propensity to gain weight in very young children. However, using a small cohort of a few hundred children deeply characterized with growth trajectories between birth and two years, and leveraging such trajectories through novel functional data analysis (FDA) techniques, we were able to produce a strong childhood obesity genetic risk score.
Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase
Authors: Cromer Laurence , Jolivet Sylvie , Singh Dipesh Kumar , Berthier Floriane , De Winne Nancy , De Jaeger Geert , Komaki Shinichiro , Prusicki Maria Ada , Schnittger Arp , Guérois Raphael , Mercier Raphael
Published: April 2019

Chromosome distribution at anaphase of mitosis and meiosis is triggered by separase, an evolutionarily conserved protease. Separase must be tightly regulated to prevent the untimely release of chromatid cohesion and disastrous chromosome distribution defects. Securin is the key inhibitor of separase in animals and fungi, but has not been identified in other eukaryotic lineages. Here, we identified PATRONUS1 and PATRONUS2 (PANS1 and PANS2) as the Arabidopsis homologues of securin. Disruption of PANS1 is known to lead to the premature separation of chromosomes at meiosis, and the simultaneous disruption of PANS1 and PANS2 is lethal. Here, we show that PANS1 targeting by the anaphase-promoting-complex is required to trigger chromosome separation, mirroring the regulation of securin. We showed that PANS1 acts independently from Shugosins. In a genetic screen for pans1 suppressors, we identified SEPARASE mutants, showing that PANS1 and SEPARASE have antagonistic functions in vivo. Finally, we showed that the PANS1 and PANS2 proteins interact directly with SEPARASE. Altogether, our results show that PANS1 and PANS2 act as a plant securin. Remote sequence similarity was identified between the plant patronus family and animal securins, suggesting that they indeed derive from a common ancestor. Identification of patronus as the elusive plant securin illustrates the extreme sequence divergence of this central regulator of mitosis and meiosis.
The Virulence Index: A Metric for Quantitative Analysis of Phage Virulence
Authors: Storms Zachary , Teel Matthew R. , Mercurio Kevin , Sauvageau Dominic
Published: April 2019

Background

One of the main challenges in developing phage therapy and manufacturing phage products is the reliable evaluation of their efficacy, performance and quality. Since phage virulence is intrinsically difficult to fully capture, researchers have turned to rapid but partially inadequate methods for its evaluation.

Materials and Methods

The present study demonstrates a standardized, quantitative method to assess phage virulence based on three parameters: the Virulence Index (VP) – quantifying the virulence of a phage against a host, the local virulence (vi) – assessing killing potential at given MOIs, and MV50 – the MOI at which the phage achieves 50% of its maximum theoretical virulence. This was shown through comparative analysis of the virulence of phages T4, T5 and T7.

Results

Under the conditions tested, phage T7 displayed the highest virulence, followed by phage T4 and, finally, phage T5. The impact of parameters such as temperature and medium composition on virulence was shown for each phage. The use of the method to evaluate the virulence of combinations of phages – e.g. for cocktail formulation – is also shown with phages T5 and T7.

Conclusions

The method presented provides a platform for high-throughput quantitative assessment of phage virulence and quality control of phage products. It can also be applied to phage screening, evaluation of phage strains, phage mutants, infection conditions and/or the susceptibility of host strains, and the formulation of phage cocktails.
Endothelial sphingosine 1-phosphate receptors promote vascular normalization to influence tumor growth and metastasis
Authors: Cartier Andreane , Leigh Tani , Liu Catherine H. , Hla Timothy
Published: April 2019

Sphingosine 1-phosphate receptor-1 (S1PR1) is essential for embryonic vascular development and maturation. In the adult, it is a key regulator of vascular barrier function and inflammatory processes. Its roles in tumor angiogenesis, tumor growth and metastasis are not well understood. In this report, we show that S1PR1 is expressed and active in tumor vessels. Tumor vessels that lack S1PR1 (S1pr1 ECKO) show excessive vascular sprouting and branching, decreased barrier function, and poor perfusion accompanied by loose attachment of pericytes. Compound knockout of S1pr1, 2 and 3 genes further exacerbated these phenotypes, suggesting compensatory function of endothelial S1PR2 and 3 in the absence of S1PR1. On the other hand, tumor vessels with high expression of S1PR1 (S1pr1 ECTG) show less branching, tortuosity and enhanced pericyte coverage. Larger tumors and enhanced lung metastasis were seen in S1pr1 ECKO whereas S1pr1 ECTG showed smaller tumors and reduced metastasis. Furthermore, anti-tumor activity of doxorubicin was more effective in S1pr1 ECTG than the wild-type counterparts. These data suggest that tumor endothelial S1PR1 induces vascular normalization and influences tumor growth, evolution and spread. Strategies to enhance S1PR1 signaling in tumor vessels may be an important adjunct to standard cancer therapy.

Significance

Endothelial sphingosine 1-phosphate receptors modulate tumor angiogenesis by inducing vascular normalization, which allows better blood circulation and enhanced anti-tumor therapeutic efficacy.