bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy of shoot production of cassava using the multiple shoot removal technique for rapid propagation
Authors: Murray F. V. N. , Cohen J. E.
Published: May 2021

One thrust in increasing food security in Jamaica is expansion of cassava production. The multiple shoot removal technique (MSRT) for rapid propagation of cassava can help address limitations in planting material. Shoots sprouting from cuttings of hardwood stem are severed in such a way as to induce further sprouting, and then put to root for subsequent transfer to the field. The effects of age and fertilization of parent plants and nodal age of stems were studied. Six Colombian varieties were planted in fertilized and unfertilized field plots with similar growing conditions to provide stems for MSRT propagation. Volume of two-node cuttings increased from apical to basal nodal age, but cutting density was a better predictor of shoot production. On average, three to six viable shoots were produced per cutting over 3 months in a greenhouse. All nodal ages of stems from parent plants aged 6, 7 and 9 months were suitable if the quality of the planting stakes producing parent plants was adequate. If stake quality is uncertain, it is recommended that apical pieces are not used from parents younger than 9 months. The variety CM 6119-5 consistently produced most shoots, suggesting a strong genotypic effect, but other varieties, particularly CM 849, were less consistent, indicating the role of environmental interactions. The physiological status of cuttings as influenced by stem maturity, parent plant age, nutrition and growing conditions of both grandparent and parent stems was as important as genotypic characteristics in determining shoot production from two-node cuttings of cassava stem.
Comorbid Affective Symptomatology and Neurocognitive Performance in College Athletes
Authors: Thomas Garrett A. , Guty Erin T. , Riegler Kaitlin E. , Arnett Peter A.
Published: May 2021

Objectives:

The current study aims to examine the prevalence rates and the relationship of symptoms of depression, anxiety, and comorbid depression/anxiety with neurocognitive performance in college athletes at baseline. We hypothesizeda priorithat the mood disturbance groups would perform worse than healthy controls, with the comorbid group performing worst overall.

Methods:

Eight hundred and thirty-one (M= 620,F= 211) collegiate athletes completed a comprehensive neuropsychological test battery at baseline which included self-report measures of anxiety and depression. Athletes were separated into four groups [Healthy Control (HC) (n= 578), Depressive Symptoms Only (n= 137), Anxiety Symptoms Only (n= 54), and Comorbid Depressive/Anxiety Symptoms (n= 62)] based on their anxiety and depression scores. Athletes’ neurocognitive functioning was analyzed viaZscore composites of Attention/Processing Speed and Memory.

Results:

One-way analysis of variance revealed that, compared to HC athletes, the comorbid group performedsignificantlyworse on measures of Attention/Processing Speed but not Memory. However, those in the depressive symptoms only and anxiety symptoms only groups were not significantly different from one another or the HC group on neurocognitive outcomes. Chi-square analyses revealed that a significantly greater proportion of athletes in all three affective groups were neurocognitively impaired compared to the HC group.

Conclusions:

These results demonstrate that collegiate athletes with comorbid depressive/anxiety symptoms should be identified, as their poorer cognitive performance at baseline could complicate post-concussion interpretation. Thus, assessing for mood disturbance at baseline is essential to obtain an accurate measurement of baseline functioning. Further, given the negative health outcomes associated with affective symptomatology, especially comorbidities, it is important to provide care as appropriate.
The impact of a discourse context on bilingual cross-language lexical activation
Authors: Schwartz Ana I. , Tarin Karla S.
Published: May 2021

Four hypotheses regarding the impact of discourse context on cross-language lexical activation were tested. Highly-proficient, Spanish–English bilinguals read all-English paragraphs containing non-identical and identical cognates or noncognate controls while their eye-movements were tracked. There were four paragraph conditions based on a full crossing of semantic bias from the topic sentence and sentence containing the critical word. In analyses in which cognate status was treated categorically there was an interaction between global bias and cognates status such that the observed inhibitory effects of cognate status were attenuated in global-neutral contexts. Follow-up analyses on the non-identical cognates in which orthographic overlap was treated continuously revealed a U-shaped function between orthographic overlap and processing time, which was more pronounced in global-neutral contexts. The overall pattern of findings is consistent with a combined operation of resonant-based and feature-restriction mechanisms of context effects.
Does the neighbourhood food environment contribute to ethnic differences in diet quality? Results from the HELIUS study in Amsterdam, the Netherlands
Authors: Poelman Maartje P , Nicolaou Mary , Dijkstra S Coosje , Mackenbach Joreintje D , Lu Meng , Karssenberg Derek , Snijder Marieke B , Vaartjes Ilonca , Stronks Karien
Published: May 2021

Objective:

The aim of the current study was to establish whether the neighbourhood food environment, characterised by the healthiness of food outlets, the diversity of food outlets and fast-food outlet density within a 500 m or 1000 m street network buffer around the home address, contributed to ethnic differences in diet quality.

Design:

Cross-sectional cohort study.

Setting:

Amsterdam, the Netherlands.

Participants:

Data on adult participants of Dutch, South-Asian Surinamese, African Surinamese, Turkish and Moroccan descent (n total 4728) in the HELIUS study were analysed.

Results:

The neighbourhood food environment of ethnic minority groups living in Amsterdam is less supportive of a healthy diet and of less diversity than that of participants of Dutch origin. For example, participants of Turkish, Moroccan and South-Asian Surinamese descent reside in a neighbourhood with a significantly higher fast-food outlet density (≤1000 m) than participants of Dutch descent. However, we found no evidence that neighbourhood food environment characteristics directly contributed to ethnic differences in diet quality.

Conclusion:

Although ethnic minority groups lived in less healthy food environments than participants of ethnic Dutch origin, this did not contribute to ethnic differences in diet quality. Future research should investigate other direct or indirect consequences of residing in less supportive food environments and gain a better understanding of how different ethnic groups make use of their neighbourhood food environment.
Specific fruit but not total fruit intake during early pregnancy is inversely associated with gestational diabetes mellitus risk: a prospective cohort study
Authors: Sun Hong , Dong Hongli , Zhang Yiqi , Lan Xi , Pang Xinxin , Cai Congjie , Bai Dan , Zhang Ju , Li Fei , Zeng Guo
Published: May 2021

Objectives:

Fruit intake may influence gestational diabetes mellitus (GDM) risk. However, prospective evidence remains controversial and limited. The current study aimed to investigate whether total fruit and specific fruit intake influence GDM risk.

Design:

A prospective cohort study was conducted. Dietary information was collected by a 3-d 24-h dietary recall. All participants underwent a standard 75-g oral glucose tolerance test at 24–28 gestational weeks. Log-binomial models were used to estimate the association between fruit intake and GDM risk, and the results are presented as relative risks (RR) and 95 % CI.

Setting:

Southwest China.

Participants:

Totally, 1453 healthy pregnant women in 2017.

Results:

Total fruit intake was not associated with lower GDM risk (RR of 1·03 (95 % CI 0·83, 1·27) (Ptrend = 0·789)). The RR of GDM risk was 0·73 for the highest anthocyanin-rich fruit intake quartile compared with the lowest quartile (95 % CI 0·56, 0·93; Ptrend = 0·015). A higher grape intake had a linear inverse association with GDM risk (Q4 v. Q1: RR = 0·65; 95 % CI 0·43, 0·98; Ptrend = 0·044), and after further adjustment for anthocyanin intake, the inverse association tended to be non-linear (Q4 v. Q1: RR = 0·65; 95 % CI 0·44, 0·98; Ptrend = 0·079). However, we did not find an association between glycaemic index-grouped fruit, glycaemic load-grouped fruit or other fruit subtype intake and GDM risk.

Conclusions:

In conclusion, specific fruit intake (particularly anthocyanin-rich fruit and grapes) but not total fruit intake was inversely associated with GDM risk.
The effect of playing games with toys made with medical materials in children with cancer on pain during intravenous treatment
Authors: Aslan Hakime , Erci Behice
Published: May 2021

Objective

This research aims to examine the effect of playing games with toys made of medical materials in children with cancer on pain that occurs during intravenous (IV) treatment.

Methods

The randomized controlled clinical trial was conducted between May 2016 and February 2018. The study sample comprised 110 children (experimental group 55; control group 55), determined using power analysis from the study population. The data were collected by the researcher, using face-to-face interview techniques, the Information Form, and Wong–Baker FACES Pain Rating Scale (WBS).

Results

The pre- and post-test pain mean scores of patients in the experimental group were 2.27 ± 0.91 and 0.43 ± 0.66, respectively (p= 0.0001). The pre- and post-test pain mean scores of patients in the control group were 1.72 ± 0.82 and 3.34 ± 0.77, respectively (p= 0.0001).

Significance of results

The experience of playing with toys made from materials used for invasive procedures relieves pain the during IV treatment.
Reversible dementia due to vitamin B12 deficiency in a lung cancer patient: Relevance of preoperative evaluation
Authors: Ishida Mayumi , Taguchi Ryo , Sakaguchi Hirozo , Itami Kumi , Yoshioka Akira , Sato Izumi , Uchida Nozomu , Onishi Hideki
Published: May 2021

Objective

Cognitive dysfunction has a negative effect on cancer treatment; however, in a cancer setting, specific treatments can restore cognitive function. Such conditions are known as reversible dementia, with one of these being vitamin B12 (VB12) deficiency. However, there have been no reports of VB12 deficiency identified by preoperative evaluation in cancer patients.

Method

We studied a patient who was referred to the Department of Psycho-oncology on suspicion of cognitive decline prior to lung cancer surgery. Preoperative evaluation revealed VB12 deficiency.

Results

The patient was an 82-year-old woman diagnosed with lung cancer. She also presented with cognitive decline and, therefore, was referred to the Department of Psycho-oncology for preoperative evaluation. The patient scored 19 points on a Mini-Mental State Examination (MMSE), which is indicative of cognitive decline. As the onset of symptoms occurred several months previously and they were subacute, the possibility of reversible dementia was considered. Extensive examination revealed VB12 deficiency, and VB12 replacement therapy normalized the MMSE score to 25 points before surgery.

Significance of the results

When cognitive decline is observed in cancer patients, it is necessary to actively evaluate the serum levels of some B vitamins, including VB12.
Why Learning Opportunities From Aviation Incidents Are	Lacking
Authors: Sieberichs Sebastian , Kluge Annette
Published: May 2021

Abstract. The rising trend of fatal aircraft accidents since 2018 suggests a limited safety capability of airlines in terms of learning from incidents (LFI). We evaluated 2,208 voluntary incident reports from commercial European pilots using qualitatively driven mixed methods to investigate LFI “bottlenecks.” The results showed that the report frequency depends on the type of pilots’ active failure causing the incident (performance‐based errors, judgment and decision‐making errors and violations). Learning opportunities were lacking, especially for incidents caused by pilots’ inadequate decision-making. Confidential reporting has positive effects on LFI, as these reports contained more information about latent failures. Furthermore, we identified several latent failures that are risk factors for certain unsafe acts. Our results may support airlines in various LFI activities.
Ranking Pictorial Cues in Simulated Landing Flares
Authors: Benbassat Danny , Konopasky Abigail , Dong Ting
Published: May 2021

Abstract. Two-dimensional pictorial cues provide depth perception information that help pilots initiate the landing flare 10–20 ft from the ground. Although prior studies established the importance of three specific cues, they failed to rank-order their importance. This exploratory paper presents two studies, with different methodologies, that examine the effect of these pictorial cues on depth perception. In both studies, participants experienced simulated scenarios and attempted to initiate the landing flare 10–20 ft above ground level. Study 1 included 121, and Study 2 included 141, naïve participants with no prior flight experience. Combined, the findings suggest that flight instructors, training literature, and airport architects should emphasize the runway above all other pictorial cues.
Science Storms the Cloud
Authors: Gentemann C. L. , Holdgraf C. , Abernathey R. , Crichton D. , Colliander J. , Kearns E. J. , Panda Y. , Signell R. P.
Published: May 2021

The core tools of science (data, software, and computers) are undergoing a rapid and historic evolution, changing what questions scientists ask and how they find answers. Earth science data are being transformed into new formats optimized for cloud storage that enable rapid analysis of multi‐petabyte data sets. Data sets are moving from archive centers to vast cloud data storage, adjacent to massive server farms. Open source cloud‐based data science platforms, accessed through a web‐browser window, are enabling advanced, collaborative, interdisciplinary science to be performed wherever scientists can connect to the internet. Specialized software and hardware for machine learning and artificial intelligence are being integrated into data science platforms, making them more accessible to average scientists. Increasing amounts of data and computational power in the cloud are unlocking new approaches for data‐driven discovery. For the first time, it is truly feasible for scientists to bring their analysis to data in the cloud without specialized cloud computing knowledge. This shift in paradigm has the potential to lower the threshold for entry, expand the science community, and increase opportunities for collaboration while promoting scientific innovation, transparency, and reproducibility. Yet, we have all witnessed promising new tools which seem harmless and beneficial at the outset become damaging or limiting. What do we need to consider as this new way of doing science is evolving?
Alignment of High‐Latitude Ionospheric and Thermospheric Lagrangian Coherent Structures
Authors: Wang Ningchao , Dang Tong , Lei Jiuhou , Wang Wenbin , Datta‐Barua Seebany
Published: May 2021

The storm‐time ionospheric‐thermospheric (IT) state is of great interest, since the IT dynamics change dramatically as energy is input and dissipated in the upper atmosphere. Lagrangian coherent structures (LCSs), which are objective ridges in time‐evolving flows that describe the tendency of neighboring fluid elements to separate, provides a unique opportunity to infer the dynamics in the IT system. In this work, we model IT flows with the Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model and identify the LCSs. We compare the LCSs in the neutral winds and plasma drifts during quiet times versus during active times. We find that LCSs are largely aligned in the modeled IT flows, with a dawn‐dusk asymmetry in their latitudinal position. During a geomagnetic storm, the thermospheric LCSs (T‐LCSs) and ionospheric LCSs (I‐LCSs) shift equatorward, align more closely with each other, and maintain a dawn‐dusk asymmetry. The collocation of T‐LCSs and I‐LCSs and their analogous response to the geomagnetic storm provide evidence of energy input into the thermosphere and ionosphere simultaneously, and the ion drag is the dominant effect causing LCS alignment during a geomagnetic storm.
Investigation on Two Mw 3.6 and Mw 4.1 Earthquakes Triggered by Poroelastic Effects of Hydraulic Fracturing Operations Near Crooked Lake, Alberta
Authors: Hui Gang , Chen Shengnan , Chen Zhangxin , He Yongming , Wang Shuhua , Gu Fei
Published: May 2021

A coupled approach of fluid flow and geomechanics is proposed in this study to quantitatively understand the hydraulic fracturing‐induced poroelastic effects that activate pre‐existing faults and trigger earthquake swarms near Crooked Lake, Alberta. The 3D poroelastic simulation of the seismogenic fault zone is then conducted to characterize the pressure diffusion and stress perturbation that led to fault activation. Results show that the poroelastic effects on the high‐permeable damage zones of a conductive‐barrier fault triggered the sequential activation of the seismogenic fault in the basement and Winterburn Formation. In addition, the high‐permeable damage zones act as conduits for pore pressure diffusion along the fault, whereas the fault core functions as a barrier to prevent crossing flow. The poroelastic effects in terms of pressure diffusion and stress perturbation in response to fluid injection facilitated the fault slip and hence triggered the Mw 3.6 earthquake in the basement formation 40 days after the fracturing operations. Moreover, the mainshock created negative Coulomb failure stress changes, inhibiting further fault slip in the basement formation. Subsequently, the stimulation of another well facilitated poroelastic effects on the fault damage zone in top Winterburn Formation, reactivating the same fault with an Mw 4.1 earthquake 8 days after the initiation of treatments. It is essential to optimize the injection site selection near the existing faults to reduce risks of the induced earthquakes near Crooked Lake.
Imaging the Deep Crustal Structure of Central Oklahoma Using Stacking and Inversion of Local Earthquake Waveforms
Authors: Ratre Pranshu , Behm Michael
Published: May 2021

The southern Granite‐Rhyolite province (SGRP) contains a comprehensive record of lithospheric evolution in North America. During the last decade, increased seismicity along with improved seismic monitoring in Oklahoma provided a rich catalog of local earthquakes. The source‐receiver geometry of this data set is well posed to illuminate the middle and lower crust through long offset recordings of the Pg phase. We present a 3‐D P‐wave velocity model for central and northern Oklahoma developed through a non‐standard processing scheme applied to local earthquake waveforms recorded from 2010 to 2017, focusing on the deeper crust. We employed common mid‐point sorting, stacking, and inversion of Pg phases which resulted in a set of localized velocity‐depth functions up to depths of 40 km. Using this methodology, we significantly increased the S/N ratio for far offset (∼200 km) local earthquake waveforms which led to the increase in depth of investigation in the final 3‐D velocity model. We find high velocity (>7 km/s) lower crust throughout the investigated area which suggests a mafic lower crust. The high velocities support previously established models which state that the lower crust of the SGRP was derived from melting of older crust. We further relate shallow and middle crustal velocity anomalies to other data sets such as gravimetric and magnetic anomalies, and the spatial distribution of earthquakes. We do not find clear evidence for the existence of the Midcontinent Rift in northern Oklahoma.
State Regulatory Heterogeneity and Compliance With the Clean Water and Safe Drinking Water Acts
Authors: Elbakidze Levan , Beeson Quinn
Published: May 2021

We examine the implications of state water quality regulatory heterogeneity for waste and drinking water violations in the continental US using Environmental Protection Agency data from 2007 to 2017. Using discrete regression analyses, we find some evidence that cumulative violations are higher when additional state water quality standards are introduced. However, one year after a new standard is implemented, cumulative violations seem to decline relative to the number of violations before introducing additional regulations. Compliance may improve after introducing new standards as operations and procedures are modified, the use of inputs like disinfectants is adjusted, or technologies are upgraded in response to new standards.
3D Carbonate Digital Rock Reconstruction Using Progressive Growing GAN
Authors: You Nan , Li Yunyue Elita , Cheng Arthur
Published: May 2021

The development of digital rock physics relies on the availability of high‐quality 3D digital rock images, which can be directly obtained with X‐ray micro‐Computed Tomography (μCT). However, X‐ray μCT is hampered by its high expenses, small sample size (several millimeters in diameter) and low resolution (in micron scale). Although Scanning Electron Microscope (SEM) provides higher resolution on larger rock samples, it only images the 2D rock surface structure. Thus, 3D digital rock reconstruction from 2D cross‐section images becomes promising in saving imaging cost for μCT scan and improving image quality by enabling the incorporation of SEM images in 3D digital rock reconstruction. Here, we propose a machine learning method to reconstruct 3D digital rocks from 2D cross‐section images taken at large constant intervals along the axial direction of the rock sample. The key idea is to train a Progressive Growing Generative Adversarial Network (PG‐GAN) to generate high‐quality gray‐scale cross‐section images, and then reconstruct the 3D digital rock by linearly interpolating the inverted latent vectors corresponding to the sparsely scanned images. We apply our method to reconstructing a large‐size high‐resolution 3D image of an Estaillades carbonate rock sample. We demonstrate that both the reconstructed image and the extracted pore network are visually indistinguishable from the ground truth. Overall, our method achieves nine times speedup of the imaging process, and greater than 4,500 times compression of the image data for the Estaillades carbonate rock sample. The PG‐GAN can enlarge the digital rock repository and enable efficient imaging editing in its linear latent space.
Determining chemical air equivalency using silicone personal monitors
Authors: O’Connell Steven G. , Anderson Kim A. , Epstein Marc I.
Published: May 2021

Background

Silicone personal samplers are increasingly being used to measure chemical exposures, but many of these studies do not attempt to calculate environmental concentrations.

Objective

Using measurements of silicone wristband uptake of organic chemicals from atmospheric exposure, create log Ksa and ke predictive models based on empirical data to help develop air equivalency calculations for both volatile and semi-volatile organic compounds.

Methods

An atmospheric vapor generator and a custom exposure chamber were used to measure the uptake of organic chemicals into silicone wristbands under simulated indoor conditions. Log Ksa models were evaluated using repeated k-fold cross-validation. Air equivalency was compared between best-performing models.

Results

Log Ksa and log ke estimates calculated from uptake data were used to build predictive models from boiling point (BP) and other parameters (all models: R2 = 0.70–0.94). The log Ksa models were combined with published data and refined to create comprehensive and effective predictive models (R2: 0.95–0.97). Final estimates of air equivalency using novel BP models correlated well over an example dataset (Spearman r = 0.984) across 5-orders of magnitude (<0.05 to >5000 ng/L).

Significance

Data from silicone samplers can be translated into air equivalent concentrations that better characterize environmental concentrations associated with personal exposures and allow direct comparisons to regulatory levels.
Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria
Authors: Jiao Jian-Yu , Fu Li , Hua Zheng-Shuang , Liu Lan , Salam Nimaichand , Liu Peng-Fei , Lv Ai-Ping , Wu Geng , Xian Wen-Dong , Zhu Qiyun , Zhou En-Min , Fang Bao-Zhu , Oren Aharon , Hedlund Brian P , Jiang Hong-Chen , Knight Rob , Cheng Lei , Li Wen-Jun
Published: May 2021

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b–3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.
Spatial segregation and cooperation in radially expanding microbial colonies under antibiotic stress
Authors: Sharma Anupama , Wood Kevin B
Published: May 2021

Antibiotic resistance in microbial communities reflects a combination of processes operating at different scales. In this work, we investigate the spatiotemporal dynamics of bacterial colonies comprised of drug-resistant and drug-sensitive cells undergoing range expansion under antibiotic stress. Using the opportunistic pathogen Enterococcus faecalis with plasmid-encoded β-lactamase, we track colony expansion dynamics and visualize spatial patterns in fluorescently labeled populations exposed to antibiotics. We find that the radial expansion rate of mixed communities is approximately constant over a wide range of drug concentrations and initial population compositions. Imaging of the final populations shows that resistance to ampicillin is cooperative, with sensitive cells surviving in the presence of resistant cells at otherwise lethal concentrations. The populations exhibit a diverse range of spatial segregation patterns that depend on drug concentration and initial conditions. Mathematical models indicate that the observed dynamics are consistent with global cooperation, despite the fact that β-lactamase remains cell-associated. Experiments confirm that resistant colonies provide a protective effect to sensitive cells on length scales multiple times the size of a single colony, and populations seeded with (on average) no more than a single resistant cell can produce mixed communities in the presence of the drug. While biophysical models of drug degradation suggest that individual resistant cells offer only short-range protection to neighboring cells, we show that long-range protection may arise from synergistic effects of multiple resistant cells, providing surprisingly large protection zones even at small population fractions.
Ecologically coherent population structure of uncultivated bacterioplankton
Authors: Sjöqvist Conny , Delgado Luis Fernando , Alneberg Johannes , Andersson Anders F
Published: May 2021

Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations’ existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.
Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria
Authors: Thomas François , Le Duff Nolwen , Wu Ting-Di , Cébron Aurélie , Uroz Stéphane , Riera Pascal , Leroux Cédric , Tanguy Gwenn , Legeay Erwan , Guerquin-Kern Jean-Luc
Published: May 2021

Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced 13C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm−3 h−1. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated 13C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.
Ablation of dynamin-related protein 1 promotes diabetes-induced synaptic injury in the hippocampus
Authors: Park Gyeongah , Lee Jong Youl , Han Hye Min , An Hyeong Seok , Jin Zhen , Jeong Eun Ae , Kim Kyung Eun , Shin Hyun Joo , Lee Jaewoong , Kang Dawon , Kim Hyun Joon , Bae Yong Chul , Roh Gu Seob
Published: May 2021

Dynamin-related protein 1 (Drp1)-mediated mitochondrial dysfunction is associated with synaptic injury in the diabetic brain. However, the dysfunctional mitochondria by Drp1 deletion in the diabetic brain are poorly understood. Here, we investigated the effects of neuron-specific Drp1 deletion on synaptic damage and mitophagy in the hippocampus of a high-fat diet (HFD)/streptozotocin (STZ)-induced diabetic mice. HFD/STZ-induced diabetic mice exhibited metabolic disturbances and synaptic damages. Floxed Drp1 mice were crossed with Ca2+/calmodulin-dependent protein kinase IIα (CaMKIIα)-Cre mice, to generate neuron-specific Drp1 knockout (Drp1cKO) mice, which showed marked mitochondrial swelling and dendritic spine loss in hippocampal neurons. In particular, diabetic Drp1cKO mice exhibited an increase in dendritic spine loss and higher levels of oxidative stress and neuroinflammation compared with diabetic wild-type (WT) mice. Diabetic WT mice generally displayed increased Drp1-induced small mitochondrial morphology in hippocampal neurons, but large mitochondria were prominently observed in diabetic Drp1cKO mice. The levels of microtubule-associated protein 1 light-chain 3 and lysosomal-associated membrane protein 1 proteins were significantly increased in the hippocampus of diabetic Drp1cKO mice compared with diabetic WT mice. The inhibition of Drp1 adversely promotes synaptic injury and neurodegeneration in the diabetic brain. The findings suggest that the exploratory mechanisms behind Drp1-mediated mitochondrial dysfunction could provide a possible therapeutic target for diabetic brain complications.
SOX2 promotes chemoresistance, cancer stem cells properties, and epithelial–mesenchymal transition by β-catenin and Beclin1/autophagy signaling in colorectal cancer
Authors: Zhu Yin , Huang Shimiao , Chen Shengyuan , Chen Jiaxuan , Wang Zhiqing , Wang Yadong , Zheng Haoxuan
Published: May 2021

Sex-determining region Y-box2 (SOX2), a master regulator of embryonic and induced pluripotent stem cells, drives cancer stem cells (CSCs) properties, fuels tumor initiation, and contributes to tumor aggressiveness. Our previous study has demonstrated the oncogenic role of SOX2 in colorectal cancer (CRC). In this study, we sought to elucidate the underlying mechanisms. Cell function experiments were performed to detect chemoresistance, proliferation, stemness, migration, and invasion in vitro. Chromatin immunoprecipitation, co-immunoprecipitation, luciferase reporter assay, and immunofluorescence were performed to explore the regulation of ABCC2, β-catenin, and Beclin1 by SOX2. The carcinogenic role of SOX2-β-catenin/Beclin1-ABCC2 axis in vivo was analyzed by CRC tissues and xenograft models. Here, we reported that SOX2 sustained chemoresistance by transcriptional activation of ABCC2 expression. Suppressing either β-catenin or autophagy signaling curbed SOX2-driven chemoresistance, stemness, and epithelial–mesenchymal transition (EMT). Mechanistically, SOX2 combined with β-catenin and increased its nuclear expression and transcriptional activity. Transcriptional activation of Beclin1 expression by SOX2 consequently activating autophagy and inducing malignant phenotype. Furthermore, overexpression of β-catenin or Beclin1 facilitated ABCC2 expression. The clinical analyses showed that high expression of ABCC2 and Beclin1 were positively correlated with SOX2 and were associated with poor prognosis in CRC patients. Finally, xenograft models revealed that inhibition of SOX2 expression and autophagy restrained tumor growth and chemoresistance in vivo. Conclusively, we demonstrated a novel mechanism by which the SOX2-β-catenin/Beclin1/autophagy signaling axis regulates chemoresistance, stemness, and EMT in CRC. Our findings provide novel insights into CRC carcinogenesis and may help develop potential therapeutic candidates for CRC.
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells
Authors: Cole Lauren , Kurscheid Sebastian , Nekrasov Maxim , Domaschenz Renae , Vera Daniel L. , Dennis Jonathan H. , Tremethick David J.
Published: May 2021

Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Here, we prepare high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for all human Pol II promoters in epithelial, mesenchymal and isogenic cancer cell lines. We find that, in contrast to the prevailing model, many different types of active and inactive promoter structures are observed that differ in their nucleosome organization and sensitivity to MNase digestion. Key aspects of an active chromatin structure include positioned H2A.Z MNase resistant nucleosomes upstream or downstream of the TSS, and a MNase sensitive nucleosome at the TSS. Furthermore, the loss of H2A.Z leads to a dramatic increase in the accessibility of transcription factor binding sites. Collectively, these results suggest that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
The lncRNA Caren antagonizes heart failure by inactivating DNA damage response and activating mitochondrial biogenesis
Authors: Sato Michio , Kadomatsu Tsuyoshi , Miyata Keishi , Warren Junco S. , Tian Zhe , Zhu Shunshun , Horiguchi Haruki , Makaju Aman , Bakhtina Anna , Morinaga Jun , Sugizaki Taichi , Hirashima Kaname , Yoshinobu Kumiko , Imasaka Mai , Araki Masatake , Komohara Yoshihiro , Wakayama Tomohiko , Nakagawa Shinichi , Franklin Sarah , Node Koichi , Araki Kimi , Oike Yuichi
Published: May 2021

In the past decade, many long noncoding RNAs (lncRNAs) have been identified and their in vitro functions defined, although in some cases their functions in vivo remain less clear. Moreover, unlike nuclear lncRNAs, the roles of cytoplasmic lncRNAs are less defined. Here, using a gene trapping approach in mouse embryonic stem cells, we identify Caren (short for cardiomyocyte-enriched noncoding transcript), a cytoplasmic lncRNA abundantly expressed in cardiomyocytes. Caren maintains cardiac function under pathological stress by inactivating the ataxia telangiectasia mutated (ATM)-DNA damage response (DDR) pathway and activating mitochondrial bioenergetics. The presence of Caren transcripts does not alter expression of nearby (cis) genes but rather decreases translation of an mRNA transcribed from a distant gene encoding histidine triad nucleotide-binding protein 1 (Hint1), which activates the ATM-DDR pathway and reduces mitochondrial respiratory capacity in cardiomyocytes. Therefore, the cytoplasmic lncRNA Caren functions in cardioprotection by regulating translation of a distant gene and maintaining cardiomyocyte homeostasis.
Cohesin-protein Shugoshin-1 controls cardiac automaticity via HCN4 pacemaker channel
Authors: Liu Donghai , Song Andrew Taehun , Qi Xiaoyan , van Vliet Patrick Piet , Xiao Jiening , Xiong Feng , Andelfinger Gregor , Nattel Stanley
Published: May 2021

Endogenous cardiac pacemaker function regulates the rate and rhythm of cardiac contraction. The mutation p.Lys23Glu in the cohesin protein Shugoshin-1 causes severe heart arrhythmias due to sinoatrial node dysfunction and a debilitating gastrointestinal motility disorder, collectively termed the Chronic Atrial and Intestinal Dysrhythmia Syndrome, linking Shugoshin-1 and pacemaker activity. Hyperpolarization-activated, cyclic nucleotide-gated cation channel 4 (HCN4) is the predominant pacemaker ion-channel in the adult heart and carries the majority of the “funny” current, which strongly contributes to diastolic depolarization in pacemaker cells. Here, we study the mechanism by which Shugoshin-1 affects cardiac pacing activity with two cell models: neonatal rat ventricular myocytes and Chronic Atrial and Intestinal Dysrhythmia Syndrome patient-specific human induced pluripotent stem cell derived cardiomyocytes. We find that Shugoshin-1 interacts directly with HCN4 to promote and stabilize cardiac pacing. This interaction enhances funny-current by optimizing HCN4 cell-surface expression and function. The clinical p.Lys23Glu mutation leads to an impairment in the interaction between Shugoshin-1 and HCN4, along with depressed funny-current and dysrhythmic activity in induced pluripotent stem cell derived cardiomyocytes derived from Chronic Atrial and Intestinal Dysrhythmia Syndrome patients. Our work reveals a critical non-canonical, cohesin-independent role for Shugoshin-1 in maintaining cardiac automaticity and identifies potential therapeutic avenues for cardiac pacemaking disorders, in particular Chronic Atrial and Intestinal Dysrhythmia Syndrome.
Calcium isotope evidence for early Archaean carbonates and subduction of oceanic crust
Authors: Antonelli Michael A. , Kendrick Jillian , Yakymchuk Chris , Guitreau Martin , Mittal Tushar , Moynier Frédéric
Published: May 2021

Continents are unique to Earth and played a role in coevolution of the atmosphere, hydrosphere, and biosphere. Debate exists, however, regarding continent formation and the onset of subduction-driven plate tectonics. We present Ca isotope and trace-element data from modern and ancient (4.0 to 2.8 Ga) granitoids and phase equilibrium models indicating that Ca isotope fractionations are dominantly controlled by geothermal gradients. The results require gradients of 500–750 °C/GPa, as found in modern (hot) subduction-zones and consistent with the operation of subduction throughout the Archaean. Two granitoids from the Nuvvuagittuq Supracrustal Belt, Canada, however, cannot be explained through magmatic processes. Their isotopic signatures were likely inherited from carbonate sediments. These samples (> 3.8 Ga) predate the oldest known carbonates preserved in the rock record and confirm that carbonate precipitation in Eoarchaean oceans provided an important sink for atmospheric CO2. Our results suggest that subduction-driven plate tectonic processes started prior to ~3.8 Ga.
Mastocytosis-derived extracellular vesicles deliver miR-23a and miR-30a into pre-osteoblasts and prevent osteoblastogenesis and bone formation
Authors: Kim Do-Kyun , Bandara Geethani , Cho Young-Eun , Komarow Hirsh D. , Donahue Danielle R. , Karim Baktiar , Baek Moon-Chang , Kim Ho Min , Metcalfe Dean D. , Olivera Ana
Published: May 2021

Osteoporosis and other manifestations of bone disease are frequent in patients with systemic mastocytosis (SM) in association with the presence of mast cell infiltrates in bone marrow, although the mechanisms behind bone disease remain poorly understood. We find that extracellular vesicles (EVs) released by neoplastic mast cells and present in the serum of patients with SM (SM-EVs) block osteoblast differentiation and mineralization in culture, and when injected into mice diminish the expression of osteoblast markers, and trabecular bone volume and microarchitecture. We demonstrate that miRNA-30a and miRNA-23a, increased in SM-EVs and neoplastic mast cell-derived EVs, attenuate osteoblast maturation by suppressing expression of RUNX2 and SMAD1/5, essential drivers of osteogenesis. Thus, SM-EVs carry and deliver miRNAs that epigenetically interfere with bone formation and can contribute to bone mass reduction in SM. These findings also suggest possibilities for novel approaches to the management of bone disease in mast cell proliferative disorders.
Quantification of FRET-induced angular displacement by monitoring sensitized acceptor anisotropy using a dim fluorescent donor
Authors: Laskaratou Danai , Fernández Guillermo Solís , Coucke Quinten , Fron Eduard , Rocha Susana , Hofkens Johan , Hendrix Jelle , Mizuno Hideaki
Published: May 2021

Förster resonance energy transfer (FRET) between fluorescent proteins has become a common platform for designing genetically encoded biosensors. For live cell imaging, the acceptor-to-donor intensity ratio is most commonly used to readout FRET efficiency, which largely depends on the proximity between donor and acceptor. Here, we introduce an anisotropy-based mode of FRET detection (FADED: FRET-induced Angular Displacement Evaluation via Dim donor), which probes for relative orientation rather than proximity alteration. A key element in this technique is suppression of donor bleed-through, which allows measuring purer sensitized acceptor anisotropy. This is achieved by developing Geuda Sapphire, a low-quantum-yield FRET-competent fluorescent protein donor. As a proof of principle, Ca2+ sensors were designed using calmodulin as a sensing domain, showing sigmoidal dose response to Ca2+. By monitoring the anisotropy, a Ca2+ rise in living HeLa cells is observed upon histamine challenging. We conclude that FADED provides a method for quantifying the angular displacement via FRET.
CD200–CD200R immune checkpoint engagement regulates ILC2 effector function and ameliorates lung inflammation in asthma
Authors: Shafiei-Jahani Pedram , Helou Doumet Georges , Hurrell Benjamin P. , Howard Emily , Quach Christine , Painter Jacob D. , Galle-Treger Lauriane , Li Meng , Loh Yong-Hwee Eddie , Akbari Omid
Published: May 2021

The prevalence of asthma and airway hyperreactivity (AHR) is increasing at an alarming rate. Group 2 innate lymphoid cells (ILC2s) are copious producers of type 2 cytokines, which leads to AHR and lung inflammation. Here, we show that mouse ILC2s express CD200 receptor (CD200R) and this expression is inducible. CD200R engagement inhibits activation, proliferation and type 2 cytokine production, indicating an immunoregulatory function for the CD200–CD200R axis on ILC2s. Furthermore, CD200R engagement inhibits both canonical and non-canonical NF-κB signaling pathways in activated ILC2s. Additionally, we demonstrate both preventative and therapeutic approaches utilizing CD200R engagement on ILC2s, which lead to improved airway resistance, dynamic compliance and eosinophilia. These results show CD200R is expressed on human ILC2s, and its engagement ameliorates AHR in humanized mouse models, emphasizing the translational applications for treatment of ILC2-related diseases such as allergic asthma.
A dual-target molecular mechanism of pyrethrum repellency against mosquitoes
Authors: Liu Feng , Wang Qiang , Xu Peng , Andreazza Felipe , Valbon Wilson R. , Bandason Elizabeth , Chen Mengli , Yan Ru , Feng Bo , Smith Leticia B. , Scott Jeffrey G. , Takamatsu Genki , Ihara Makoto , Matsuda Kazuhiko , Klimavicz James , Coats Joel , Oliveira Eugenio E. , Du Yuzhe , Dong Ke
Published: May 2021

Pyrethrum extracts from flower heads of Chrysanthemum spp. have been used worldwide in insecticides and repellents. While the molecular mechanisms of its insecticidal action are known, the molecular basis of pyrethrum repellency remains a mystery. In this study, we find that the principal components of pyrethrum, pyrethrins, and a minor component, (E)-β-farnesene (EBF), each activate a specific type of olfactory receptor neurons in Aedes aegypti mosquitoes. We identify Ae. aegypti odorant receptor 31 (AaOr31) as a cognate Or for EBF and find that Or31-mediated repellency is significantly synergized by pyrethrin-induced activation of voltage-gated sodium channels. Thus, pyrethrum exerts spatial repellency through a novel, dual-target mechanism. Elucidation of this two-target mechanism may have potential implications in the design and development of a new generation of synthetic repellents against major mosquito vectors of infectious diseases.