bluuebunny/crossref_metadata_2025 huggingface dataset:
Anoxia-induced mitophagy in the yeastKluyveromyces marxianus
Authors: Hoshida Hisashi , Kagawa Shota , Ogami Kentaro , Akada Rinji
Published: October 2020

Kluyveromyces marxianus is a thermotolerant, ethanol-producing yeast that requires oxygen for efficient ethanol fermentation. Under anaerobic conditions, glucose consumption and ethanol production are retarded, suggesting that oxygen affects the metabolic state of K. marxianus. Mitochondria require oxygen to function, and their forms and number vary according to environmental conditions. In this study, the effect of anoxia on mitochondrial behavior in K. marxianus was examined. Under aerobic growth conditions, mitochondria-targeted GFP exhibited a tubular and dotted localization, representing a typical mitochondrial morphology, but under anaerobic conditions, GFP localized in vacuoles, suggesting that mitophagy occurs under anaerobic conditions. To confirm mitophagy induction, the ATG32, ATG8, ATG11 and ATG19 genes were disrupted. Vacuolar localization of mitochondria-targeted GFP under anaerobic conditions was interrupted in the Δatg32 and Δatg8 strains but not the Δatg11 and Δatg19 strains. Electron microscopy revealed mitochondria-like membrane components in the vacuoles of wild-type cells grown under anaerobic conditions. Quantitative analyses using mitochondria-targeted Pho8 demonstrated that mitophagy was induced in K. marxianus by anoxia but not nitrogen starvation. To the best of our knowledge, this is the first demonstration of anoxia-induced mitophagy in yeasts.
Horticultural Therapy Reduces Biomarkers of Immunosenescence and Inflammaging in Community-Dwelling Older Adults: A Feasibility Pilot Randomized Controlled Trial
Authors: Wong Glenn Choon Lim , Ng Ted Kheng Siang , Lee Jia Le , Lim Pei Yi , Chua Sean Kai Jie , Tan Crystal , Chua Michelle , Tan Janice , Lee Samantha , Sia Angelia , Ng Maxel K W , Mahendran Rathi , Kua Ee Heok , Ho Roger C M , Larbi Anis
Published: October 2020

Background

With the challenges that aging populations pose to health care, interventions that facilitate alleviation of age-related morbidities are imperative. A prominent risk factor for developing age-related morbidities is immunosenescence, characterized by increased chronic low-grade inflammation, resulting in T-cell exhaustion and senescence. Contact with nature and associated physical activities have been shown to boost immunity in older adults and may be promoted in the form of horticultural therapy (HT). We aimed to examine the effects of HT on immunosenescence.

Method

We conducted a randomized controlled trial with 59 older adults assigned to either the HT intervention or waitlist control group. Older adults in the HT intervention group underwent HT intervention program over 6 months. Venous blood was drawn at baseline and at the third and sixth month from the commencement of this study. For participants who attended all 3 blood collection time points (HT: n = 22; waitlist: n = 24), flow cytometry analysis was performed on whole blood samples to evaluate the kinetics of lymphocyte subsets over the intervention period, revealing the composition of CD4+ and CD8+ subsets expressing exhaustion markers—CD57, CTLA4, and KLRG1. Enzyme-linked immunosorbent assays were employed to measure changes in plasma IL-6 levels.

Results

HT is associated with increased numbers of naive CD8+ T cells and fewer CTLA4-expressing terminally differentiated effector CD4+ and CD8+ memory T cells re-expressing CD45RA (TEMRA). Furthermore, IL-6 levels were reduced during HT, and the frequencies of naive and TEMRA CD8+ T cells were found to be associated with IL-6 levels.

Conclusion

HT is associated with a reduction in the levels of biomarkers that measure the extent of T-cell exhaustion and inflammaging in older adults. The positive effects of HT on T-cell exhaustion were associated with the reduction of IL-6 levels.
Ageism Linked to Culture, Not Demographics: Evidence From an 8-Billion-Word Corpus Across 20 Countries
Authors: Ng Reuben , Lim-Soh Jeremy W
Published: October 2020

Objectives

Ageism has increased over 200 years and costs the U.S. health care system $63 billion a year. While scholars agree on the consequences of ageism, there are disagreements on whether it is related to the demographics of aging, or society’s cultural values. We test both hypotheses across 20 countries.

Method

To circumvent the sampling limitations of survey studies, we used an 8-billion-word corpus, identified 3 synonyms with the highest prevalence—aged, elderly, old people—and compiled the top 300 words (collocates) that were used most frequently with these synonyms for each of the 20 countries. The resulting 6,000 collocates were rated on an ageism scale by 2 raters to create an ageism score per country. Cultural dimension scores—Power Distance, Individualism, Masculinity, Uncertainty Avoidance, and Long-term Orientation—were taken from Hofstede, and demographics—size and speed of population aging—came from the World Development Indicators.

Results

Of the 20 countries, UK topped the ageism table, while Sri Lanka had the lowest ageism score. Multiple regression models showed that higher levels of masculinity and long-term orientation are associated with ageism, controlling for other cultural dimensions, demographics (size and speed of aging), and economics (GDP-per-capita).

Discussion

Our findings blunt the deterministic nature of ageism at the societal level. Demographics is only one side of the ageism coin, and the cultural side is equally, if not more important. This study lays the groundwork to tackle societal ageism—one of our generation’s most pernicious threats.
“It’s Pure Panic”: The Portrayal of Residential Care in American Newspapers During COVID-19
Authors: Allen Laura D , Ayalon Liat
Published: October 2020

Background and Objectives

This study examines the discursive construction of residential care during the coronavirus disease 2019 (COVID-19) pandemic in 3 leading American newspapers: The New York Times, USA Today, and The New York Post.

Research Design and Methods

A total of 54 news articles between January 21 and May 8, 2020 were identified from the LexisNexis academic database for analysis. The articles were analyzed using both a critical discourse analysis approach and a thematic analytical framework.

Results

Findings indicate that residents’ voices are excluded and superseded by others, namely their family members. Literary elements were used to portray residential care as shockingly dangerous, deceptive, and problematic. Blame was often assigned to an individual or group according to the political tendency of the newspaper.

Discussion and Implications

A cultural model of panic and dishonesty begins to take shape through the COVID-19 pandemic. Fearmongering and the portrayal of residential care as lacking transparency will likely create future mistrust of the industry. The depiction of vulnerability and the illusion of resident inclusion in the news coverage enable paternalistic decision-making and care practices in the name of supposed protection.
Economic development in times of population decline—a century of European eel fishing on the Swedish west coast
Authors: Magnusson A K , Dekker W
Published: October 2020

The European eel stock is in a multi-decadal decline. When fishing yield diminished throughout Europe, the small-scaled fyke-net fishery for eel on the west coast of Sweden gradually increased. This contrary trend lasted from the early-1900s, until the 1990s when fishing restrictions eventually limited the catch. We identified the processes driving this aberrant historical development. Using data on the fisheries from 1914 to 2006, we analysed the relation of total landed quantities to stock abundance indices, weather conditions, technical development, and market indicators. No relation between landed volumes and abundance indices was found, but market price (inflation-adjusted) was clearly correlated. Weather and technical development had a minor influence on landed volumes. This indicates that the commercial eel fishery on the west coast developed due to increasing demand and increasing eel prices. We found no evidence that the local stock has been fully exploited, though the increasing catch must have gradually reduced the contribution to the international spawning stock. These results stress the importance of considering economic processes when interpreting historical catch data as a source of information on population size in stock assessments, and ultimately, understanding the collapse of the eel stock.
Maternal melatonin implants improve twin Merino lamb survival
Authors: Flinn Tom , Gunn Jessica R , Kind Karen L , Swinbourne Alyce M , Weaver Alice C , Kelly Jennifer M , Walker Simon K , Gatford Kathryn L , van Wettere William H E J , Kleemann David O
Published: October 2020

High preweaning mortality rates cost the Australian sheep industry an estimated $540 million annually in lost production, with losses significantly greater in twin (≥30%) compared with singleton lambs (≥10%). Previous intensive studies demonstrated that supplementing pregnant ewes with melatonin reduces adverse effects of fetal growth restriction and perinatal hypoxia on the neonatal brain via increased umbilical blood flow, placental efficiency, and antioxidant actions. The current study examined the effects of supplementing ewes with melatonin on the survival of twin Merino lambs under extensive grazing conditions. Pregnant mixed age ewes were implanted with 1 (M1, n = 50) or 2 (M2, n = 53) slow-release melatonin implants (18 mg, Regulin) at gestational days 70 to 90. Control ewes received no supplementation (CTL, n = 54). Ewes were monitored twice daily throughout the lambing period. Lamb survival, weight, and rectal temperature were recorded on the day of birth. Lamb blood samples were taken the following day for serum immunoglobulin G (IgG) analysis. Lamb survival and weight were recorded again at marking (30.6 ± 0.6 d postpartum) and weaning (70.7 ± 0.6 d postpartum). Lamb survival was increased in both melatonin treatments to 3 d postpartum (M1 = 98.0%; M2 = 95.3%; CTL = 83.3%; each P < 0.01), and this improvement was maintained to weaning (M1 = 94.0%; M2 = 92.5%; CTL = 79.6%; each P < 0.01). Melatonin did not affect lamb birthweight, rectal temperature, or growth rate. However, the rates of parturition-related death (dystocia, stillbirth, and birth injury) were greater in CTL lambs than M1 (P = 0.009) and M2 (P = 0.035). This suggests that improved survival is primarily due to melatonin-induced neuroprotection, although further studies are required to clarify the underlying mechanisms. These data provide evidence that supplementing pregnant twin-bearing Merino ewes with melatonin may be a practical strategy to reduce neonatal mortality and improve weaning rates in extensively managed sheep flocks. Although the present data are promising, this study is limited by small sample size and requires further replication.
Potential of High-Resolution Mass Spectrometry for the Detection of Drugs and Metabolites in Hair: Methoxetamine in a Real Forensic Case
Authors: Matey J M , López-Fernández Adrián , García-Ruiz Carmen , Montalvo Gemma , Moreno M D , Martínez M A
Published: October 2020

The analysis of drugs of abuse in hair and other biological matrices of forensic interest requires great selectivity and sensitivity. This is done traditionally through target analysis, with one or more analytical methods, or with different and specific preanalytical phases, and complex procedures performed by the toxicological laboratories, and there is no exception with ketamine-like compounds, such as methoxetamine, a new psychoactive substance whose use has increased in the last decades, and continues to grow quickly year by year. More validated methods of analysis are needed to detect these substances in low concentrations selectively. Reanalyzing the samples of a former case of a polydrug consumer accused of a crime against public health in Spain, five metabolites of methoxetamine (normethoxetamine, O-desmethylmethoxetamine, dehydromethoxetamine, dihydronormethoxetamine and hydroxynormethoxetamine) were tentatively detected using a high-resolution technique, that is, liquid chromatography coupled to high-resolution mass spectrometry (LC–HR-MS-MS). The highest analytical selectivity of LC–HR-MS-MS method together a universal and simpler pretreatment stages has demonstrated to allow faster analysis and more sensitivity than the one performed traditionally at the INTCF laboratories, which was gas chromatography coupled to mass spectrometry.
CircRNA_0092516 regulates chondrocyte proliferation and apoptosis in osteoarthritis through the miR-337-3p/PTEN axis
Authors: Huang Zhihui , Ma Wenming , Xiao Jinhuai , Dai Xiaoyu , Ling Weiqi
Published: October 2020

The dysregulation of circular RNAs (circRNAs) has been identified in various human diseases. Here, we probed into the potential mechanism of circRNA_0092516 in osteoarthritis (OA). The expression of circRNA_0092516 was tested by quantitative real-time PCR. MTT, flow cytometry and western blot were applied to confirm the functions of circRNA_0092516 in vitro. Besides, RNA pull-down and dual-luciferase reporter gene experiments were applied to probe into the mechanism. circRNA_0092516 was raised in the tissues of OA patients and chondrocytes stimulated by IL-1β. The potential mechanism analysis expounded that circRNA_0092516 bound to miR-337-3p, and the interference with circRNA_0092516 boosted chondrocyte proliferation and restrained cell apoptosis through the miR-337-3p/phosphatase and tensin homolog (PTEN) axis, thereby improving OA. In-vivo experiments expounded that circRNA_0092516 regulated cartilage production through miR-337-3p. Overall, our data expounded that the interference with circRNA_0092516 boosted chondrocyte proliferation and restrained cell apoptosis through the miR-337-3p/PTEN axis, eventually slowed down the progress of OA.
Vertical Distribution of Insect Pests Using Insect Towers Placed Near Potato Fields in the Lower Columbia Basin
Authors: Shrestha Govinda , Thompson Ira D , Rondon Silvia I
Published: October 2020

This study was conducted at the Oregon State University Hermiston Agricultural Research and Extension Center, Hermiston, Umatilla County, OR, during the 2016 and 2017 potato, Solanum tuberosum L. (Solanales: Solanaceae), growing seasons. The objective was to determine the vertical distribution of hemipteran (Bactericera cockerelli Šulc, Circulifer tenellus Baker, Myzus persicae Sulzer, Macrosiphum euphorbiae Thomas, and Lygus spp.) and thysanopteran (Frankliniella occidentalis Pergande and Thrips tabaci Lindeman) potato pests using insect towers placed near potato fields. Towers were 8 m tall and secured to the ground with metal cables. In each tower, yellow sticky cards were mounted at 1.5 m intervals up to 7.6 m aboveground. Data were collected at 7-d intervals from mid-April until mid or end of August. This study showed that B. cockerelli, C. tenellus, M. persicae, Lygus spp., and both species of thrips were captured on sticky cards placed closest to the ground; in both years, as sticky card height increased, abundances decreased. In contrast, trapped M. euphorbiae numbers were not affected by sticky card height. To our knowledge, this is the first study in the lower Columbia Basin of Oregon that evaluated the vertical distribution of major potato pests.
Sweet Corn Sentinel Monitoring for Lepidopteran Field-Evolved Resistance to Bt Toxins
Authors: Dively G P , Kuhar T P , Taylor S , Doughty H B , Holmstrom K , Gilrein D , Nault B A , Ingerson-Mahar J , Whalen J , Reisig D , Frank Daniel L , Fleischer S J , Owens David , Welty C , Reay-Jones F P F , Porter P , Smith J L , Saguez J , Murray S , Wallingford A , Byker H , Jensen B , Burkness E , Hutchison W D , Hamby K A
Published: October 2020

As part of an insect resistance management plan to preserve Bt transgenic technology, annual monitoring of target pests is mandated to detect susceptibility changes to Bt toxins. Currently Helicoverpa zea (Boddie) monitoring involves investigating unexpected injury in Bt crop fields and collecting larvae from non-Bt host plants for laboratory diet bioassays to determine mortality responses to diagnostic concentrations of Bt toxins. To date, this monitoring approach has not detected any significant change from the known range of baseline susceptibility to Bt toxins, yet practical field-evolved resistance in H. zea populations and numerous occurrences of unexpected injury occur in Bt crops. In this study, we implemented a network of 73 sentinel sweet corn trials, spanning 16 U.S. states and 4 Canadian provinces, for monitoring changes in H. zea susceptibility to Cry and Vip3A toxins by measuring differences in ear damage and larval infestations between isogenic pairs of non-Bt and Bt hybrids over three years. This approach can monitor susceptibility changes and regional differences in other ear-feeding lepidopteran pests. Temporal changes in the field efficacy of each toxin were evidenced by comparing our current results with earlier published studies, including baseline data for each Bt trait when first commercialized. Changes in amount of ear damage showed significant increases in H. zea resistance to Cry toxins and possibly lower susceptibility to Vip3a. Our findings demonstrate that the sentinel plot approach as an in-field screen can effectively monitor phenotypic resistance and document field-evolved resistance in target pest populations, improving resistance monitoring for Bt crops.
Functional Characterization of Chemosensory Protein AmalCSP5 From Apple Buprestid Beetle, Agrilus mali (Coleoptera: Buprestidae)
Authors: Li Chunbo , Sun Keke , Li Dexian , Liu Deguang
Published: October 2020

In the sensitive and complex chemo-sensation system of insects, chemosensory proteins (CSPs) can facilitate the transfer of chemical information and play important roles for variable behaviors of insects. We cloned the chemosensory protein AmalCSP5 from antennae of the apple buprestid beetle (Agrilus mali Matsumura), a serious invasive pest of wild apple trees. Expression profiling showed that AmalCSP5 was expressed in various tissues, suggesting its significance in multiple physiological activities and behaviors of A. mali. AmalCSP5 was preferentially expressed in female antennae and male abdomens. AmalCSP5 was able to bind a variety of test volatiles, especially alcohols and esters. AmalCSP5 exhibited good binding affinity for all five test secondary compounds (i.e., procyanidin, phlorizin, kaemferol, chlorogenic acid, and rutin), suggesting its preferential binding abilities to nonvolatile host plant secondary metabolites and critical roles in gustatory perception of nonvolatiles. Tyr27 and Ser69 of AmalCSP5 could form hydrogen bonds with hexyl benzoate and hexyl hexanoate, respectively. Procyanidin, the best ligand among all test compounds, could form hydrogen bonds with three amino acid residues (i.e., Arg7, Leu8, and Lys41) of AmalCSP5. Thus, high ligand binding affinity for AmalCSP5 seemed to be dependent mainly on the formation of hydrogen bonds. The putative key amino acid residues of AmalCSP5 can be used as molecular targets for designing and screening new attractants and repellents for A. mali. Our results provide insights into binding interactions of AmalCSP5 with volatile and nonvolatile ligands, and a firm basis for developing eco-friendly management strategies of A. mali.
‘British Values Are Also Values All Around the World’: Teaching Fundamental British Values through a Human Rights Lens
Authors: Struthers Alison E.C. , Mansuy Julie
Published: October 2020

Since 2014, the promotion of Fundamental British Values (FBV) has been a requirement across formal schooling in England. The agenda has, however, faced criticism from various stakeholders. Much of this denunciation has been directed at the opaque nature of FBV, but the agenda is problematic for more concerning reasons. It is arguable that, in light of the current threat from ethno-nationalism, frameworks such as FBV that focus on a particular definition and formulation of national values run the risk of being interpreted in a manner that is exclusionary and liable to ‘other’ different ethnic groups in the classroom. The FBV framework furthermore overlooks the fact that the UK isalready subject to numerous international human rights obligations, including many that mandate the provision of holistic and effective human rights education at all levels of formal education. This article therefore draws upon the findings of a pilot study conducted with Year 5 learners in four primary schools in the West Midlands showing that teaching about human rights through the FBV agenda is possible, by linking discussion of values at the national level to broader human rights principles. Such an approach satisfies the government’s desire for children to learn about FBV, whilst highlighting that these values also exist in a global context. This, in turn, is likely to be a more effective way of encouraging learners to be global citizens who will contribute to the building of a broader culture that is respectful of human rights.
Nations and Markets
Authors: Cohen Harlan Grant
Published: October 2020

Economics and security seem increasingly intertwined. Citing national security, states subject foreign investments to new scrutiny, even unwinding mergers. The provision of 5G has become a diplomatic battleground—Huawei at its center. Meanwhile, states invoke national security to excuse trade wars. The USA invoked the General Agreement on Tariffs and Trade national security exception to impose steel and aluminum tariffs, threatening more on automotive parts. Russia invoked that provision to justify its blockade of Ukraine, as did Saudi Arabia and the United Arab Emirates to excuse theirs of Qatar. And with the spread of COVID-19, states are invoking national security to scrutinize supply lines. Multiplying daily, such stories have led some observers to dub the era one of geoeconomics. Nonetheless, these developments remain difficult to judge, and the relationship between economics and national security remains confused and slippery. The essay seeks clarity in the deeper logic of these labels, revealing a fundamental choice between the logics of markets and the logics of state. Whether invoked to ‘secure’ borders, privacy, health, the environment, or jobs, ‘national security’ is a claim about the proper location of policymaking. Appeals to economics, with their emphasis on global welfare and global person-to-person relationships, are such claims as well. Resolving disputes, this essay argues, requires recognizing these root choices.
State Variation in Low-Dose Computed Tomography Scanning for Lung Cancer Screening in the United States
Authors: Fedewa Stacey A , Kazerooni Ella A , Studts Jamie L , Smith Robert A , Bandi Priti , Sauer Ann Goding , Cotter Megan , Sineshaw Helmneh M , Jemal Ahmedin , Silvestri Gerard A
Published: October 2020

Background

Annual lung cancer screening (LCS) with low-dose chest computed tomography in older current and former smokers (ie, eligible adults) has been recommended since 2013. Uptake has been slow and variable across the United States. We estimated the LCS rate and growth at the national and state level between 2016 and 2018.

Methods

The American College of Radiology’s Lung Cancer Screening Registry was used to capture screening events. Population-based surveys, the US Census, and cancer registry data were used to estimate the number of eligible adults and lung cancer mortality (ie, burden). Lung cancer screening rates (SRs) in eligible adults and screening rate ratios with 95% confidence intervals (CI) were used to measure changes by state and year.

Results

Nationally, the SR was steady between 2016 (3.3%, 95% CI = 3.3% to 3.7%) and 2017 (3.4%, 95% CI = 3.4% to 3.9%), increasing to 5.0% (95% CI = 5.0% to 5.7%) in 2018 (2018 vs 2016 SR ratio = 1.52, 95% CI = 1.51 to 1.62). In 2018, several southern states with a high lung-cancer burden (eg, Mississippi, West Virginia, and Arkansas) had relatively low SRs (<4%) among eligible adults, whereas several northeastern states with lower lung cancer burden (eg, Massachusetts, Vermont, and New Hampshire) had the highest SRs (12.8%-15.2%). The exception was Kentucky, which had the nation’s highest lung cancer mortality rate and one of the highest SRs (13.7%).

Conclusions

Fewer than 1 in 20 eligible adults received LCS nationally, and uptake varied widely across states. LCS rates were not aligned with lung cancer burden across states, except for Kentucky, which has supported comprehensive efforts to implement LCS.
Regulation of mucosal lectins in the oyster Crassostrea virginica in response to food availability and environmental factors
Authors: Allam Simon , Allam Bassem , Pales Espinosa Emmanuelle
Published: October 2020

Lectins are a large and diverse group of sugar-binding proteins involved in nonself recognition and cell-to-cell interactions. Suspension-feeding bivalves, such as the oyster Crassostrea virginica, are capable of using these molecules to bind cell surface carbohydrates of food particles, allowing particle capture and selection. The aim of this project was to assess whether the expression of mucosal lectins in C. virginica is constant or changes with the season, and to determine whether lectin expression is linked to environmental parameters and/or internal biological factors (gametogenesis). A total of 130 oysters were placed in submerged cages at a tidal estuary and monitored for changes in lectin gene expression over a 1-year period. In parallel, environmental parameters prevailing at the field site, including seawater physicochemical characteristics (temperature, salinity and dissolved oxygen), particulate organic matter and chlorophyll contents, were also monitored. Throughout the study, oysters were dissected and the gills were collected and used for the assessment of the expression of three different lectin genes (CvML, CvML3914 and CvML3912). Remaining tissues were processed for histology and the classification of the gonad development stage. Results showed that when food is abundant, such as during the spring bloom, lectin gene expressions are low, and inversely lectin levels increase with lower food levels. These findings suggest that oysters increase lectin expression to enhance the capture and ingestion of scarce food, while during spring, enough food is already being ingested and lectins are not needed. Furthermore, results showed that as the energy demands of oysters increase (gonad maturation), lectin gene expressions also increase to enhance selective ingestion of nutritious food particles. This study, therefore, demonstrates the seasonality of lectin gene expression in C. virginica, and suggests that lectin regulation is related to the reproduction process and abundance of high-quality food.
On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight
Authors: Platella Chiara , Trajkovski Marko , Doria Filippo , Freccero Mauro , Plavec Janez , Montesarchio Daniela
Published: October 2020

Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology. Interplay of different binding modes of NDI-5 to G-quadruplexes was observed for both parallel and hybrid topologies, with end-stacking always operative as the predominant binding event. While NDI-5 primarily targets the 5′-end quartet of the hybrid G-quadruplex model (m-tel24), the binding to a parallel G-quadruplex model (M2) occurs seemingly simultaneously at the 5′- and 3′-end quartets. With parallel G-quadruplex M2, NDI-5 formed stable complexes with 1:3 DNA:ligand binding stoichiometry. Conversely, when interacting with hybrid G-quadruplex m-tel24, NDI-5 showed multiple binding poses on a single G-quadruplex unit and/or formed different complexes comprising two or more G-quadruplex units. NDI-5 produced stabilizing effects on both G-quadruplexes, forming complexes with dissociation constants in the nM range.
Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis
Authors: Chai Peiwei , Yu Jie , Jia Ruobing , Wen Xuyang , Ding Tianyi , Zhang Xiaoyu , Ni Hongyan , Jia Renbing , Ge Shengfang , Zhang He , Fan Xianqun
Published: October 2020

Chromatin remodeling impacts the structural neighborhoods and regulates gene expression. However, the role of enhancer-guided chromatin remodeling in the gene regulation remains unclear. Here, using RNA-seq and ChIP-seq, we identified for the first time that neurotensin (NTS) serves as a key oncogene in uveal melanoma and that CTCF interacts with the upstream enhancer of NTS and orchestrates an 800 kb chromosomal loop between the promoter and enhancer. Intriguingly, this novel CTCF-guided chromatin loop was ubiquitous in a cohort of tumor patients. In addition, a disruption in this chromosomal interaction prevented the histone acetyltransferase EP300 from embedding in the promoter of NTS and resulted in NTS silencing. Most importantly, in vitro and in vivo experiments showed that the ability of tumor formation was significantly suppressed via deletion of the enhancer by CRISPR-Cas9. These studies delineate a novel onco-enhancer guided epigenetic mechanism and provide a promising therapeutic concept for disease therapy.
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
Authors: Manfredonia Ilaria , Nithin Chandran , Ponce-Salvatierra Almudena , Ghosh Pritha , Wirecki Tomasz K , Marinus Tycho , Ogando Natacha S , Snijder Eric J , van Hemert Martijn J , Bujnicki Janusz M , Incarnato Danny
Published: October 2020

SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5′ UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
Instability of CII is needed for efficient switching between lytic and lysogenic development in bacteriophage 186
Authors: Murchland Iain M , Ahlgren-Berg Alexandra , Pietsch Julian M J , Isabel Alejandra , Dodd Ian B , Shearwin Keith E
Published: October 2020

The CII protein of temperate coliphage 186, like the unrelated CII protein of phage λ, is a transcriptional activator that primes expression of the CI immunity repressor and is critical for efficient establishment of lysogeny. 186-CII is also highly unstable, and we show that in vivo degradation is mediated by both FtsH and RseP. We investigated the role of CII instability by constructing a 186 phage encoding a protease resistant CII. The stabilised-CII phage was defective in the lysis-lysogeny decision: choosing lysogeny with close to 100% frequency after infection, and forming prophages that were defective in entering lytic development after UV treatment. While lysogenic CI concentration was unaffected by CII stabilisation, lysogenic transcription and CI expression was elevated after UV. A stochastic model of the 186 network after infection indicated that an unstable CII allowed a rapid increase in CI expression without a large overshoot of the lysogenic level, suggesting that instability enables a decisive commitment to lysogeny with a rapid attainment of sensitivity to prophage induction.
GreenPhylDB v5: a comparative pangenomic database for plant genomes
Authors: Guignon Valentin , Toure Abdel , Droc Gaëtan , Dufayard Jean-François , Conte Matthieu , Rouard Mathieu
Published: October 2020

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.
VARAdb: a comprehensive variation annotation database for human
Authors: Pan Qi , Liu Yue-Juan , Bai Xue-Feng , Han Xiao-Le , Jiang Yong , Ai Bo , Shi Shan-Shan , Wang Fan , Xu Ming-Cong , Wang Yue-Zhu , Zhao Jun , Chen Jia-Xin , Zhang Jian , Li Xue-Cang , Zhu Jiang , Zhang Guo-Rui , Wang Qiu-Yu , Li Chun-Quan
Published: October 2020

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include ‘Variation information’, ‘Regulatory information’, ‘Related genes’, ‘Chromatin accessibility’ and ‘Chromatin interaction’. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.
Yi Zeng: promoting good governance of artificial intelligence
Authors: Jia Hepeng
Published: October 2020

Artificial intelligence (AI) has developed quickly in recent years, with applications expanding from automatic driving and smart manufacturing to personal healthcare and algorithm-based social media utilization. During the COVID-19 pandemic, AI has played an essential role in identifying suspected infections, ensuring epidemic surveillance and quickening drug screening. However, many questions accompanied AI’s development. How to protect citizens’ privacy and national information security? What measures can help AI learn and practice good human behaviors and avoid unethical use of AI technologies? To answer these questions, Nation Science Review (NSR) interviewed Yi Zeng, Professor and Deputy Director at the Research Center for Brain-inspired Artificial Intelligence at the Institute of Automation, Chinese Academy of Sciences (CAS). He is a board member for the National Governance Committee of Next-Generation Artificial Intelligence affiliated to the Ministry of Science and Technology of China (MOST). Zeng is also in AI ethics expert groups at the World Health Organization and the United Nations Educational, Scientific, and Cultural Organization (UNESCO). He jointly led the drafting of Beijing AI Principles (2019) and the National Governance Principles of New Generation AI of China (GPNGAI, 2019).
Impact of preconception, pregnancy, and postpartum culinary nutrition education interventions: a systematic review
Authors: Taylor Rachael M , Wolfson Julia A , Lavelle Fiona , Dean Moira , Frawley Julia , Hutchesson Melinda J , Collins Clare E , Shrewsbury Vanessa A
Published: October 2020

Context

Frequent consumption of home-prepared meals is associated with higher diet quality in children and adults. Therefore, increasing the culinary skills of women and couples during their childbearing years may be an effective strategy for the prevention of overweight and obesity.

Objective

To determine the impact of culinary nutrition-education interventions for women with or without their partners during preconception, pregnancy, or postpartum (PPP) on parental cooking skills, nutrition knowledge, parent/child diet quality, or health outcomes.

Data sources

Eligibility criteria were defined using a PICOS framework. A systematic search strategy was developed to identify eligible studies and was implemented in 11 electronic databases. Reference lists of selected systematic reviews were manually searched for additional studies.

Data extraction

Study characteristics and outcomes were extracted from eligible studies by 1 reviewer and checked by a second reviewer.

Data analysis

A narrative synthesis of the findings of eligible studies was prepared including descriptive statistics. Reporting was guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement and Synthesis Without Meta-Analysis in systematic reviews reporting guideline.

Results

A total of 6951 articles were identified from the search strategy and 31 studies during pregnancy or postpartum were included. By category, the number of studies with a favorable outcome per total number of studies measuring outcome were as follows: parental food/cooking skills (n = 5 of 5), nutrition knowledge (n = 6 of 11), parent/child diet quality (n = 10 of 19), infant feeding (n = 6 of 11), eating behavior (n = 2 of 5), maternal (n = 2 of 5) and child anthropometry (n = 6 of 10), mental health and development n = (2 of 3), and clinical indictors (n = 1 of 1).

Conclusions

Culinary nutrition-education interventions during pregnancy and the postpartum period show promise in improving cooking skills, diet quality, and a variety of health-related outcomes. The precise effect of these interventions during PPP is limited by the quality and heterogeneity of study designs to date.

Systematic review registration

PROSPERO registration number: CRD42020154966
Assessment of Respiratory Bacterial Coinfections Among Severe Acute Respiratory Syndrome Coronavirus 2-Positive Patients Hospitalized in Intensive Care Units Using Conventional Culture and BioFire, FilmArray Pneumonia Panel Plus Assay
Authors: Kolenda Camille , Ranc Anne-Gaëlle , Boisset Sandrine , Caspar Yvan , Carricajo Anne , Souche Aubin , Dauwalder Olivier , Verhoeven Paul O , Vandenesch François , Laurent Frédéric
Published: October 2020

Background

Approximately 15% of patients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present with severe forms of the disease and require hospitalization in intensive care units, which has been associated with high mortality rates. The prevalence of bacterial infections in these patients is not well established, and more data are needed to guide empiric antibiotic therapy and improve patient outcomes.

Methods

In this prospective multicenter study, we assessed bacterial coinfections identified in culture from 99 French patients infected by SARS-Cov-2 and hospitalized in intensive care units. We concomitantly evaluated an innovative molecular diagnostic technology technique, the BioFire, FilmArray Pneumonia Panel plus (FA-pneumo) assay, to identify these coinfections at an early stage, and its concordance with conventional culture.

Results

We showed that a bacterial coinfection was detected in 15% of patients based on conventional culture. Staphylococcus aureus and Haemophilus influenzae were the most prevalent pathogens. The sensitivity of FA-pneumo compared with culture was 100%. In contrast, the specificity varied between 88.4% and 100% according to the pathogen, and our results highlighted that 60.5% of bacterial targets reported using this assay were not recovered by culture; 76.9% of discordant results corresponded to bacteria belonging to commensal oral flora and/or reported with ≤105 copies/mL bacterial nucleic acids.

Conclusions

Based on its excellent sensitivity, the FA-pneumo assay is useful to rule out bacterial coinfections in the context of severe SARS-CoV-2 infection and avoid the inappropriate prescription of antibiotics. However, positive tests should be interpreted carefully, taking into consideration deoxyribonucleic acid bacterial load and all clinical and biological signs.
Concepts
Authors: Spitzer Michael
Published: October 2020

After reviewing some recent writing by philosophers and psychologists of emotion (including Patrik Juslin and David Huron), this chapter proposes an “attitudinal theory” of emotion as “felt bodily stance,” grounded in Nico Frijda’s behavioral theory of “action tendencies” (or “action readiness”). It proposes emotional “attitudes” displayed within musical “personas,” following persona theorists such as Jenefer Robinson and Charles Nussbaum. It builds on Nussbaum’s model of the musical persona navigating a landscape of tonal forces, adjusting it so as to project discrete emotional categories. It reconciles Nussbaum’s ecological theory with Jenefer Robinson’s “process model” of emotion, arguing that musical emotion emerges gradually through a cycle of primary and secondary appraisals.
Passions
Authors: Spitzer Michael
Published: October 2020

This chapter begins that part of the book devoted to the period of “affective realism,” when the modern concept of musical emotion crystallized. Dedicated to the Baroque period, the chapter focuses on the four musical-emotional communities of Italy (Vivaldi), England (Handel), Germany (J. S. Bach), and France (Rameau). Arching over all four emotional styles is the dialogue between emotional models developed by Descartes and Spinoza; and, more broadly, the dialectic between “passion” and “action,” stemming from Aquinas. The chapter reviews Descartes’ theory of emotional expression, and Spinoza’s therapeutic model of emotion, especially his theory of Conatus. The prevailing idea of Affektenlehre is thereby placed into context. The chapter concludes with an extended consideration of Rameau’s opera, Hippolyte et Aricie, in the context of Descartes’ theory of wonder.
Children, Childhood, and Development in Evolutionary Perspective
Authors: Bjorklund David F.
Published: October 2020

This chapter highlights the principles of evolutionary psychology and evolutionary developmental psychology, emphasizing that adaptations occurred at all life stages, not just in adults, and may have been especially important early in life. Infants, children, and adolescents evolved sets of behaviors, emotions, and cognitions adapted to their immediate environments and not necessarily to future ones. These adaptations are inherited but only develop properly through interaction with a supportive context. Humans evolved most of their unique psychological features over the last 2 million years or so, living as hunter-gatherers on the savannahs of Africa, and these are the environments in which human nature evolved. Many scholars contend that hunter-gatherer childhoods are the models upon which we should judge the practices we use in raising children today.
Embryos and Ancestors
Authors: Bjorklund David F.
Published: October 2020

Evolutionary developmental biology, or Evo Devo, examines how developmental mechanisms affect evolutionary change. Heterochrony refers to genetic-based differences in developmental timing. One important type of heterochrony for humans is neoteny, which refers to the retention of juvenile traits into later development. Humans are a neotenous species, as seen in infants’ features of “babyness,” which promote attention and caring from adults, extending the primate prenatal brain growth rate well past birth, and a reduction of reactive aggression relative to great apes, which facilitated increased cooperation among group members. Homo sapiens extended the time it takes to reach adulthood by inventing new two life stages—childhood and adolescence. The social and cognitive abilities of Homo sapiens’ youth may be well suited to the childhood and adolescent stages and to the attainment of skills necessary for developing into functional adults.
Developing the Evolved Social Brain
Authors: Bjorklund David F.
Published: October 2020

For human hypersociality to evolve required that natural selection operate both at the levels of the individual and the group as described by multilevel selection theory. According to the social brain hypothesis, increased social cognition was the driving force in human social-cognitive evolution. Infants evolved “psychological weapons” designed to obtain attention and caregiving from adults. According to Tomasello’s shared intentionality theory, infants view others as intentional agents, as reflected in shared attention beginning around 9 months, and later, between 3 and 5 years of age, in collective intentionality, in which children establish a group-minded “we” with other people. The development and evolution of hypersociality is reflected in: treating others as intentional agents, perspective taking, empathy, normativity, social learning, prosociality (helping, sharing, sense of fairness), and collaboration. Each of these and other social-cognitive abilities were necessary for the evolution of a hypersocial species and evolved as a result of changes in great ape ontogeny.