bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral nudges increase COVID-19 vaccinations: Two randomized controlled trials
Authors: Dai Hengchen , Saccardo Silvia , Han Maria A , Roh Lily , Raja Naveen , Vangala Sitaram , Modi Hardikkumar , Pandya Shital , Croymans Daniel M
Published: April 2021

Fighting the COVID-19 pandemic requires quick and effective strategies to maximize vaccine uptake. We present two sequential randomized controlled trials (RCTs) that tackle this challenge with behavioral science insights. We deliver text-based nudges to UCLA Health patients one day (first RCT; N=113,229) and eight days (second RCT; N=90,662) after they receive notifications of vaccine eligibility. In the first RCT, text messages designed to make vaccination salient and easy to schedule boost appointment and vaccination rates by 86% and 26%, respectively. Nudges that make patients feel endowed with the vaccine heighten these effects, but addressing vaccine hesitancy via a video-based information intervention does not yield benefits beyond simple text. These results hold across ethnicity and age groups. By contrast, online experiments (N=2,003) soliciting hypothetical responses to the same messages reveal the opposite patterns, underscoring the importance of pilot-testing behavioral nudges in the real world before scaling them up. In the second RCT, we further find that receiving a second reminder boosts appointment and vaccination rates by 52% and 16%, respectively. Our findings suggest that text-based nudges can substantially increase and accelerate COVID-19 vaccinations at almost zero marginal cost, highlighting the promising role of behavioral science in addressing a critical component of the COVID-19 pandemic response.
Trends in National Opioid Prescribing for Dental Procedures among Medicaid Patients
Authors: Okunev Ilya , Frantsve-Hawley Julie , Tranby Eric
Published: April 2021

Background

We examine trends in opioid prescriptions by dentists for Medicaid-enrolled children and non-senior adults.

Methods

We utilized the IBM Watson Medicaid claims databases for 2012-2019 and the CDC conversion dataset. Opioid prescriptions were linked to a dental visit when prescribed within three days of the dental visit and if the patient had no medical visit reported during that period. We conducted descriptive analyses for age, procedures performed, treatment history, and prescription strength.

Results

Our study showed consistent decreases in opioid prescription rates in dentistry during the study period: from 2.7% to 1.6% among children (0-20), and from 28.6% to 12.2% for adults (21-64). The adult opioid prescription rate fell for nonsurgical dental procedures from 9.7% to 2.9%. For surgical procedures, the adult prescription rate fell from 48.0% to 28.7%. Most dental-related opioids were prescribed for oral surgeries (Children: 70.8%, Adults: 58.6%). By 2019, 23% of all opioid prescriptions for children were dental related.

Conclusion

We found that opioid prescription rates in dentistry for Medicaid enrollees declined significantly between 2012 and 2019 for both children and adults. The percent of prescriptions written for nonsurgical visits consistently declined over the observed timeframe. At the same time, opioid prescription rates for both dental surgical procedures and dental nonsurgical procedures decreased as well.

Practical Implications

Although the trends revealed in our analysis show declining opioid prescription patterns, these results suggest that the overall rate is still too high and prescriptions are being written unnecessarily.
The risk factors of COVID-19 in a longitudinal population-based study
Authors: Atergeleh Hozhabr Jamali , Emamian Mohammad Hassan , Goli Shahrbanoo , Rohani-Rasaf Marzieh , Hashemi Hassan , Fotouhi Akbar
Published: April 2021

The present longitudinal study aims to investigate the risk factors for getting COVID-19 in a population aged 50 to 74 years. Data were collected from Shahroud Eye Cohort Study and the electronic system of COVID-19 in Shahroud, northeast Iran. Participants were followed for about 13 months and predisposing factors for COVID-19 infection were investigated using log binomial model and by calculation of relative risks. From the beginning of the COVID-19 outbreak in Shahroud (February 20, 2020) to March 26, 2021, out of 4394 participants in the Eye Cohort Study, 271 (6.1%) were diagnosed with COVID-19 with a positive Reverse Transcription Polymerase Chain Reaction test on two nasopharyngeal and oropharyngeal swabs. Risk factors for getting COVID-19 were included male gender (Relative Risk (RR) = 1.51; 95% Confidence Intervals (CI), 1.15-1.99), BMI over 25 (RR = 1.03; 95% CI, 1.01-1.05) and diabetes (RR = 1.31; 95% CI, 1.02-1.67). Also, smoking (RR = 0.51; 95% CI, 0.28-0.93) and education (RR = 0.95; 95% CI, 0.92-0.98) had reverse associations. In conclusion men and diabetic patients and those who have BMI over 25, should be more alert to follow the health protocols related to COVID-19 and priority should be given to them considering COVID-19 vaccination.
Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells
Authors: Bednar Riley M. , Jana Subhashis , Kuppa Sahiti , Franklin Rachel , Beckman Joseph , Antony Edwin , Cooley Richard B. , Mehl Ryan A.
Published: April 2021

The ability to site-specifically modify proteins at multiple sitesin vivowill enable the study of protein function in its native environment with unprecedented levels of detail. Here, we present a versatile two-step strategy to meet this goal involving site-specific encoding of two distinct noncanonical amino acids bearing bioorthogonal handles into proteinsin vivofollowed by mutually orthogonal labeling. This general approach, that we calldualencodingand labeling (DEAL), allowed us to efficiently encoded tetrazine- and azide-bearing amino acids into a protein and demonstrate for the first time that the bioorthogonal labeling reactions with strained alkene and alkyne labels can function simultaneously and intracellularly with high yields when site-specifically encoded in a single protein. Using our DEAL system, we were able to perform topologically-defined protein-protein crosslinking, intramolecular stapling, and site-specific installation of fluorophores all inside livingEscherichia colicells, as well as study the DNA-binding properties of yeast Replication Protein Ain vitro. By enabling the efficient dual modification of proteinsin vivo, this DEAL approach provides a tool for the characterization and engineering of proteinsin vivo.
First description ofLotmaria passimandCrithidia mellificaehaptomonad stage in the honeybee hindgut
Authors: Buendía-Abad María , García-Palencia Pilar , de Pablos-Torró Luis Miguel , María Alunda José , Osuna Antonio , Martín-Hernández Raquel , Higes Mariano
Published: April 2021

The remodelling of flagella into attachment structures is a common and important event in the insect stages of the trypanosomatid life cycle. Among their hymenopteran hosts,Lotmaria passimandCrithidia mellificaecan parasitizeApis mellifera, and as a result they might have a significant impact on honeybee health. However, there are details of their life cycle and the mechanisms underlying their pathogenicity in this host that remain unclear. Here we show that bothL. passimpromastigotes andC. mellificaechoanomastigotes differentiate into haptomonad stage covering the ileum and rectum of honeybees. These haptomonad cells remain attached to the host surface via zonular hemidesmosome-like structures, as revealed by Transmission Electron Microscopy. Hence, for the first time this work describes the haptomonad morphotype of these species and their hemidesmosome-like attachment inApis mellifera, a key trait exploited by other trypanosomatid species to proliferate in the insect host hindgut.

Author summary

In recent years, the mortality of European Honeybees (Apis mellifera) has risen worldwide due to a variety of factors, including their infection by parasites. Former studies have linked the presence of several trypanosomatids species, beingLotmaria passimandCrithidia mellificaethe most prevalent ones, with this increase in mortality. Although previous studies have shown that trypanosomatid infection reduces the lifespan of bees, there is little information regarding their development in the gut when honeybees become infected. Here, for the first time we describe the haptomonad morphotype of these two trypanosomatid species inA. mellifera. The most characteristic feature of haptomonads is the extensive remodelling of the flagellum and the formation of junctional complexes at the host gut wall. The presence of this morphotype in the honeybee hindgut increases our understanding of the life cycle of these species and their possible pathogenic mechanisms. We found that they can multiply while attached and that their disposition, covering the hindgut walls, could hinder host nutrient uptake and consequently, represent a pathogenic mechanism itself. This attachment could also be a key stage in the life-cycle to prevent the trypanosomatids leaving the host prematurely, ensuring transmission through infective morphotypes.
The growth hormone gene has evolved independently inAfrican Pygmy Mouse Mus minutoides
Authors: Matsuya Sumito , Imai Hiroyuki , Kiso Yasuo , Kusakabe Ken Takeshi , Kano Kiyoshi
Published: April 2021

Mus minutoides(the African pygmy mouse) is one of the smallest mammals. We determined the nucleotide sequence of thegrowth hormone(Gh) gene and the sequence of the putative coding region inM. minutoides, where is predicted to be distinct in the functional and transcriptional regulatory regions betweenM. minutoidesandMus musculus(the House mouse). To investigate the evolutionary characteristics ofGhinM. minutoides, we constructed a phylogenetic tree based on the putative amino acid sequences ofGhinM. musculusand mammals by neighbor-joining method, suggesting thatGhdiverged relatively earlier than otherMusgenus and may have evolved independently inM. minutoides. Furthermore, analysis ofGhgene expression levels showed a tendency to be higher inM. minutoidesthan inM. musculus. Our results suggest thatGhmay have evolved independently inM. minutoidesand may have different functions and signaling inMusgenus.
CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens
Authors: Pursey Elizabeth , Dimitriu Tatiana , Paganelli Fernanda L. , Westra Edze R. , van Houte Stineke
Published: April 2021

The acquisition of antibiotic resistance genes via horizontal gene transfer is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of antibiotic resistance. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of antibiotic resistance. We analysed ~40,000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens includingEnterococcus,Staphylococcus,AcinetobacterandPseudomonas. We modelled the association between CRISPR-Cas and indicators of horizontal gene transfer, and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system. Analysis of the mobile genetic elements targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of antibiotic resistance. These results suggest a potential “immunocompromised” state for multidrug-resistant strains that may be exploited in tailored interventions that rely on mobile genetic elements, such as phage or phagemids, to treat infections caused by bacterial pathogens.
Is what you see what you get? The relationship between field observed and actual aphid parasitism rates in canola crops
Authors: Ward Samantha , Umina Paul A. , Parry Hazel , Balfour-Cunningham Amber , Cheng Xuan , Heddle Thomas , Holloway Joanne C. , Langley Caitlin , Severtson Dustin , Van Helden Maarten , Hoffmann Ary A.
Published: April 2021

BACKGROUND

Estimating parasitoid abundance in the field can be difficult, even more so when attempting to quantify parasitism rates and the ecosystem service of biological control that parasitoids can provide. To understand how ‘observed’ parasitism rates (in-field mummy counts) of the green peach aphid,Myzus persicae(Sulzer) (Homoptera: Aphididae) translate to ‘actual’ parasitism rates (laboratory-reared parasitoid counts), field work was undertaken in Australian canola fields over a growing season. Parasitoids were reared within a controlled laboratory setting.

RESULTS

Total observed and actual parasitism rates ofM. persicaevaried considerably across regions, but less so on a field level. Overall, actual parasitism was on average 2.4 times higher than that observed in the field, with rates an average of 4-fold higher in South Australia. As crop growth stage progressed, the percentage of mummies observed increased. Percentage of parasitoids reared also increased with crop growth stage, averaging 3.4% during flowering and reaching 14.4% during podding/senescing. Although there was a greater diversity of reared parasitoid species at later crop growth stages, actual parasitism rate was unaffected by parasitoid species.Diaeretiella rapaewas the most commonly reared parasitoid, increasing in abundance with crop growth stage.

CONCLUSION

These findings indicate that mummy counts alone do not provide a clear representation of parasitism within fields.
Comprehensive analysis of prime editing outcomes in human embryonic stem cells
Authors: Habib Omer , Habib Gizem , Hwang Gue-Ho , Bae Sangsu
Published: April 2021

Prime editing is a versatile and precise genome editing technique that can directly copy desired genetic modifications into target DNA sites without the need for donor DNA. This technique holds great promise for the analysis of gene function, disease modeling, and the correction of pathogenic mutations in clinically relevant cells such as human pluripotent stem cells (hPSCs). Here we comprehensively tested prime editing in hPSCs by generating a doxycycline-inducible prime editing platform. Prime editing successfully induced all types of nucleotide substitutions and small insertions and deletions, similar to observations in other human cell types. Moreover, we compared prime editing and base editing for correcting a disease-related mutation in induced pluripotent stem cells derived form a patient with α 1-antitrypsin (A1AT) deficiency. Finally, whole-genome sequencing showed that, unlike the cytidine deaminase domain of cytosine base editors, the reverse transcriptase domain of a prime editor does not lead to guide RNA-independent off-target mutations in the genome. Our results demonstrate that prime editing in hPSCs has great potential for complementing previously developed CRISPR genome editing tools.
Effect of diet modification in intestinal Escherichia coli population and antimicrobial resistance
Authors: Loayza-Villa Fernanda , García Daniela , Torres Alejandro , Trueba Gabriel
Published: April 2021

The fluctuations in the number of some intestinal bacterial lineages may be associated with increased antimicrobial resistance and disease. Adaptation to a given environment may select bacterial mutants that have reduced ability to adapt to new environments and changes in diet have been associated with alterations in microbiome taxon composition. We wanted to see the effect of diet change in linage composition and antimicrobial resistance profiles of numerically dominant E. coli. We subjected 50 chickens from an industrial operation (under corn-based diet supplemented with antimicrobials) to 2 antimicrobial-free diets; one based on corn and the other based on alfalfa. Fecal samples were obtained from all animals at arrival and after five weeks under different diets. Five E. coli colonies (from each sample) were subjected to genetic typing and antimicrobial susceptibility testing. We observed high diversity and high turnover rate of numerically dominant E. coli strains from animals from both diet groups. We did not find differences in antimicrobial resistance profiles in isolates from different diet groups. Our results suggest that there is high diversity and high turnover rate of E. coli strains in the intestines regardless of the diet. Chicken intestines seemed to contain many E. coli lineages able to thrive in different substrates. The absence of differences in antimicrobial resistance among bacteria, from animals in different diets, may indicate that the carriage of antimicrobial resistance genes does not affect the bacterial ability to adapt to different substrates.
Use of Modeling to Inform Decision-Making During the COVID-19 Pandemic: A Qualitative Study
Authors: Johnson Karl , Biddell Caitlin , Lich Kristen Hassmiller , Swann Julie , Delamater Paul , Mayorga Maria , Ivy Julie , Smith Raymond , Patel Mehul
Published: April 2021

Background

The COVID-19 Pandemic has popularized computer-based decision-support models as a tool for decision-makers to manage their organizations. It is unclear how decision-makers have considered these models to inform COVID-19-related decisions.

Methods

We interviewed decision-makers from North Carolina across diverse organizational backgrounds to assess major decision-making processes during COVID-19, including the use of modeling as an input to inform decision-making.

Results

Interviewees were aware of models during COVID-19, with some depending upon multiple models. Models were used to compare trends in disease spread across localities, allocate scarce resources, and track disease spread within small geographic areas. Decision-makers desired models to project disease spread within subpopulations and estimate where local outbreaks could occur as well as estimate the outcomes of social distancing policies, including consequences beyond typical health-related outcomes. Challenges to the use of modeling included doubts that models could reflect nuances of human behavior, concerns about the quality of data used in models, and the limited amount of modeling at the local level.

Conclusions

Throughout COVID-19, decision-makers perceived modeling as valuable for understanding disease spread within their communities and to inform organization decisions, yet there were variations in organizations’ ability and willingness to use models for these purposes.
Central obesity, smoking habit and hypertension are associated with a blunted serological response to COVID-19 mRNA vaccine
Authors: Watanabe Mikiko , Balena Angela , Tuccinardi Dario , Tozzi Rossella , Risi Renata , Masi Davide , Caputi Alessandra , Rossetti Rebecca , Spoltore Maria Elena , Filippi Valeria , Gangitano Elena , Manfrini Silvia , Mariani Stefania , Lubrano Carla , Lenzi Andrea , Mastroianni Claudio , Gnessi Lucio
Published: April 2021

Aims

To explore variables associated with the serological response following COVID-19 mRNA vaccine.

Methods

Healthcare workers adhering to the vaccination campaign against COVID-19 were enrolled in January-February 2021. All subjects underwent two COVID-19 mRNA vaccine inoculations (Pfizer/BioNTech) separated by three weeks. Blood samples were collected before the first and 1-4 weeks after the second inoculation. Clinical history, demographics, and vaccine side effects were recorded. Baseline anthropometric parameters were measured, and body composition was performed through dual-energy-X-ray absorptiometry.

Results

Eighty-six patients were enrolled. Those with central obesity had lower antibody (Ab) titers compared with those with no central obesity [1426(1436)vs1971(1819), p=0.04]; smokers had a blunted response compared to non-smokers [1099(1350)vs1921(1375), p=0.007], as well as hypertensive vs normotensive [650±1192vs1911(1364), p=0.001] and dyslipidemic compared to those with normal serum lipids [534(972)vs 1872(1406), p=0.005]. Multivariate analysis showed that higher waist circumference, smoking, hypertension and longer time elapsed since second vaccine inoculation were associated with lower Ab titers, independent of BMI, age and gender. The association between waist circumference and Ab titers was lost when controlling for body fat, suggesting that visceral accumulation may explain this result.

Conclusions

It is currently impossible to determine whether lower SARS CoV-2 Abs lead to higher likelihood of developing COVID-19. However, neutralizing abs correlate with protection against several viruses including SARS-CoV-2, and the finding that central obesity, hypertension and smoking are associated with a blunted response warrants further attention. Our findings must lead to a vigilant approach, as these subjects could benefit from earlier vaccine boosters or different vaccine schedules.
Cryptic survival and an unexpected recovery of the long-tailed mayflyPalingenia longicauda(Olivier, 1791) (Ephemeroptera: Palingeniidae) in Southeastern Europe
Authors: Dénes Avar L. , Vaida Romina , Szabó Emerencia , Martynov Alexander V. , Váncsa Éva , Ujvárosi Beáta , Keresztes L.
Published: April 2021

Once widespread in the large European rivers,Palingenia longicaudaunderwent a drastic range contraction as a result of the intense pollution and hydromorphological interventions of the 19thand 20thcenturies. For the last decades it was considered to be restricted only to the Tisa River and its tributaries, and to the Rába River, but new reports indicated its presence in the Danube River in Hungary, in the Danube Delta in Romania and Ukraine, and in the Prut River in the Republic of Moldova.

The objective of this study is to analyze the phylogeographic pattern between the two main eco-regions (Pannon and Pontic) of the species distribution, based on the combined mitochondrial COI (472 bp) and 16S (464 bp) sequences generated for individuals collected in Romania and Ukraine, and from publicly available ones, representing the Tisa catchment populations.

The presence of viable populations in the Danube Delta and on the Prut River in Romania is confirmed, and additional presence on the Mure□ and Bega rivers from Romania, and on the Styr and Horyn’ rivers in Northern Ukraine is shown.

The phylogeographic results indicate that the presence of the analyzed populations are not the result of recent founding events from the Pannon region, confirming the survival and expansion of cryptic local lineages.

The recent recovery of the species may be related to the improvement of water quality as a result of the implementation of the EU Water Framework Directive and the EU Floods Directive after 2000.
Epitope classification and RBD binding properties of neutralizing antibodies against SARS-CoV-2 variants of concern
Authors: Deshpande Ashlesha , Harris Bethany D. , Martinez-Sobrido Luis , Kobie James J. , Walter Mark R.
Published: April 2021

Severe acute respiratory syndrome coronavirus-2 (SAR-CoV-2) causes coronavirus disease 2019 (COVID19) that is responsible for short and long-term disease, as well as death, in susceptible hosts. The receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) protein binds to cell surface angiotensin converting enzyme type-II (ACE2) to initiate viral attachment and ultimately viral pathogenesis. The SARS-CoV-2 S RBD is a major target of neutralizing antibodies (NAbs) that block RBD - ACE2 interactions. In this report, NAb-RBD binding epitopes in the protein databank were classified as C1, C1D, C2, C3, or C4, using a RBD binding profile (BP), based on NAb-specific RBD buried surface area and used to predict the binding epitopes of a series of uncharacterized NAbs. Naturally occurring SARS-CoV-2 RBD sequence variation was also quantified to predict NAb binding sensitivities to the RBD-variants. NAb and ACE2 binding studies confirmed the NAb classifications and determined whether the RBD variants enhanced ACE2 binding to promote viral infectivity, and/or disrupted NAb binding to evade the host immune response. Of 9 single RBD mutants evaluated, K417T, E484K, and N501Y disrupted binding of 65% of the NAbs evaluated, consistent with the assignment of the SARS-CoV-2 P.1 Japan/Brazil strain as a variant of concern (VoC). RBD variants E484K and N501Y exhibited ACE2 binding equivalent to a Wuhan-1 reference SARS-CoV-2 RBD. While slightly less disruptive to NAb binding, L452R enhanced ACE2 binding affinity. Thus, the L452R mutant, associated with the SARS-CoV-2 California VoC (B.1.427/B.1.429-California), has evolved to enhance ACE2 binding, while simultaneously disrupting C1 and C2 NAb classes. The analysis also identified a non-overlapping antibody pair (1213H7 and 1215D1) that bound to all SARS-CoV-2 RBD variants evaluated, representing an excellent therapeutic option for treatment of SARS-CoV-2 WT and VoC strains.
Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
Authors: Cai Yongfei , Zhang Jun , Xiao Tianshu , Lavine Christy L. , Rawson Shaun , Peng Hanqin , Zhu Haisun , Anand Krishna , Tong Pei , Gautam Avneesh , Lu Shen , Sterling Sarah M. , Walsh Richard M. , Rits-Volloch Sophia , Lu Jianming , Wesemann Duane R. , Yang Wei , Seaman Michael S. , Chen Bing
Published: April 2021

Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains that continue to fuel the COVID-19 pandemic despite intensive vaccination efforts throughout the world. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Mutations in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement can account for the increased transmissibility and risk of mortality as the variant may begin to infect efficiently infect additional cell types expressing low levels of ACE2. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, rendering complete resistance to some potent neutralizing antibodies. These findings provide structural details on how the wide spread of SARS-CoV-2 enables rapid evolution to enhance viral fitness and immune evasion. They may guide intervention strategies to control the pandemic.
Dysfunctional vascular smooth muscle cells mediate early and late-stage neuroinflammation and Tau hyperphosphorylation
Authors: Aguilar-Pineda Jorge A. , Vera-Lopez Karin J. , Shrivastava Pallavi , Nieto-Montesinos Rita , Chávez-Fumagalli Miguel A. , Davila Del-Carpio Gonzalo , Valdez Badhin Gomez , Miller Clint L. , Malhotra Rajeev , Lindsay Mark E. , Lino Cardenas Christian L.
Published: April 2021

Despite the emerging evidence implying early vascular contributions to neurogenerative syndromes, the role of vascular smooth muscle cells (VSMCs) in the pathogenesis of Alzheimer’s disease is still not well understood. Herein, we show that VSMCs in brains of AD patients and the animal model of the disease, are deficient in multiple VSMC-contractile markers which correlated with Tau accumulation in brain arterioles.Ex vivoandin vitroexperiments demonstrated that VSMCs undergo dramatic phenotypic transitions under AD-like conditions, adopting pro-inflammatory and synthetic phenotypes. Notably, these changes coincided with Tau hyperphosphorylation at residues Y18, T205 and S262. We also observed that loss of VSMC markers occurred in an age-dependent manner, and that expression of Sm22α and α-Sma proteins were inversely correlated with CD68 and Tau accumulation in brain arterioles of 3xTg-AD mice. Together, these findings further support the contribution of VSMCs in AD pathogenesis, and nominate VSMCs as potential novel therapeutic target in AD.

Graphical Abstract
Males perceive honest information from female released sex pheromone in a moth
Authors: Yiftach Golov , Alexander Liberzon , Roi Gurka , Victoria Soroker , Russell Jurenka , Ally R Harari
Published: April 2021

There is accumulating evidence that male insects advertise their quality to conspecific females through pheromones. However, most studies of female released sex pheromone assume information transfer regarding merely the species of the female and her mating status. We show that more and precise information is conveyed through the female sex pheromone, positioning it as an honest sexual trait. We demonstrate that females in bad physical conditions (small, starved or old) lay significantly fewer eggs than females in good conditions (large, fed or young). The ratio of the sex pheromone blend in gland extracts of female pink bollworm moths accurately describes the female phenotypic condition whereas the pheromone amount in the glands fails to provide an honest signal of quality. Moreover, males use the female released pheromone blend to choose their mates and approach females that signal higher reproductive potential. In addition, surrogating the female effect, using synthetic pheromone blend that represents that of higher quality females (0.6:0.4 ZZ:ZE) more males were attracted to this blend than to the blend representing the population mean (0.5:0.5 ZZ:ZE). Both, female advertisement for males and the male choosiness, suggest that pheromones have evolved as sexual traits under directional, sexual selection.
Transcriptional Inactivation of TP53 and the BMP Pathway Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer
Authors: Han Hyunho , Wang Yan , Curto Josue , Gurrapu Sreeharsha , Laudato Sara , Rumandla Alekya , Chakraborty Goutam , Wang Xiaobo , Chen Hong , Jiang Yan , Kumar Dhiraj , Caggiano Emily , Zhang Boyu , Ji Yan , Maity Sankar N. , Hu Min , Bai Shanshan , Aparicio Ana , Efstathiou Eleni , Logothetis Christopher J. , Navin Nicholas , Navone Nora , Chen Yu , Giancotti Filippo G.
Published: April 2021

Unsupervised clustering and deconvolution analysis identifies a novel subtype of M-CRPC endowed with hybrid epithelial/mesenchymal (E/M) and luminal progenitor-like traits (Mesenchymal and Stem-like PC, MSPC). Analysis of patient datasets and mechanistic studies indicate that MSPC arises as a consequence of therapy-induced lineage plasticity. AR blockade instigates two separate and complementary processes: 1) transcriptional silencing ofTP53and hence acquisition of hybrid E/M and stem-like traits; and 2) inhibition of the BMP signaling, which promotes resistance to the pro-apoptotic and anti-proliferative effects of AR inhibition. The drug-tolerant prostate cancer cells generated through reprogramming are rescued by neuregulin and generate metastases in mice. Combined inhibition of HER2/3 and AR or mTORC1 exhibit efficacy in preclinical models of mixed ARPC/MSPC or MSPC, respectively. These results identify a novel subtype of M-CRPC, trace its origin to therapy-induced lineage plasticity, and reveal its dependency on HER2/3 signaling.
Towards a causal role of Broca’s area in language: A TMS-EEG study on syntactic prediction
Authors: Maran Matteo , Numssen Ole , Hartwigsen Gesa , Friederici Angela D. , Zaccarella Emiliano
Published: April 2021

Categorical predictions have been proposed as the key mechanism supporting the fast pace of syntactic composition in human language. Accordingly, grammar-based expectations facilitate the analysis of incoming syntactic information—e.g., hearing the determiner “the” enhances the prediction of a noun—which is then checked against a single or few other word categories. Previous functional neuroimaging studies point towards Broca’s area in the left inferior frontal gyrus (IFG) as one fundamental cortical region involved in categorical prediction during on-line language processing. Causal evidence for this hypothesis is however still missing. In this study, we combined Electroencephalography (EEG) and Transcranial Magnetic Stimulation (TMS) to test whether Broca’s area is functionally relevant in predictive mechanisms for language. Specifically, we transiently perturbed Broca’s area during the categorical prediction phase in two-word constructions, while simultaneously measuring the Event-Related Potential (ERP) correlates of syntactic composition. We reasoned that if Broca’s area is involved in predictive mechanisms for syntax, disruptive TMS during the processing of the first word (determiner/pronoun) would mitigate the difference in ERP responses for predicted and unpredicted categories when composing basic phrases and sentences. Contrary to our hypothesis, perturbation of Broca’s area at the predictive stage did not affect the ERP correlates of basic composition. The correlation strength between the electrical field induced by TMS and the magnitude of the EEG response on the scalp further confirmed this pattern. We discuss the present results in light of an alternative account of the role of Broca’s area in syntactic composition, namely the bottom-up integration of words into constituents.
Time grid-based isomer specific N-glycan analysis and detection of bi-secting Lewis X in human brain
Authors: Helm Johannes , Gruber Clemens , Thader Andreas , Urteil Jonathan , Führer Johannes , Stenitzer David , Maresch Daniel , Neumann Laura , Pabst Martin , Altmann Friedrich
Published: April 2021

The importance of protein glycosylation in the biomedical field demands for methods capable of resolving and identifying isomeric structures of N-glycans. However, the unambiguous identification of isomeric structures from complex mixtures is currently not reasonably realized even by the most sophisticated approaches. Here we present a novel approach which uses stable isotope labelled reference N-glycans to establish a retention time grid (glyco-TiGr) on porous graphitized carbon. This furthermore enables retention as the primary criterion for the structural assignment of isomeric N-glycans.

Moreover, we biosynthesized forty natural isomers of the fundamental N-glycan type consisting of five hexoses, four N-acetylhexosamines and one fucose residue. Nearly all of these isomers occupied unique positions on the retention time grid. Reference glycan assisted retention time determination with deci-minute accuracy narrowed the assignment space to very few, often only one possible glycan isomer.

Application of the glyco-TiGr approach revealed yet undescribed isomers of Lewis x determinants in multimeric human IgA and hybrid type N-glycans in human brain with galactose and even fucose linked to the bisecting N-acetylglucosamine. Thus, the brain N-glycome displayed a degree of sophistication commensurate with this organ’s role.
Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in the reef-building coralMontipora capitata
Authors: Chille E , Strand E , Neder M , Schmidt V , Sherman M , Mass T , Putnam HM
Published: April 2021

Background

Maternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral,Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 hours-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies.

Results

Weighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from ∼4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf-9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing enzymes (TET1) peak and remain stable past ∼4 hpf, indicating that methylome programming occurs before 4 hpf.

Conclusions

Our high-resolution insight into the coral maternal mRNA and MZT provides essential information regarding setting the stage for, and the sensitivity of, developmental success and parental carryover effects under increasing environmental stress.
INO-4800 DNA Vaccine Induces Neutralizing Antibodies and T cell Activity Against Global SARS-CoV-2 Variants
Authors: Andrade Viviane M. , Christensen-Quick Aaron , Agnes Joseph , Tur Jared , Reed Charles , Kalia Richa , Marrero Idania , Elwood Dustin , Schultheis Katherine , Purwar Mansi , Reuschel Emma , McMullan Trevor , Pezzoli Patrick , Kraynyak Kim , Sylvester Albert , Mammen Mammen P. , Tebas Pablo , Kim J. Joseph , Weiner David B. , Smith Trevor R.F. , Ramos Stephanie J. , Humeau Laurent M. , Boyer Jean D. , Broderick Kate E.
Published: April 2021

Global surveillance has identified emerging SARS-CoV-2 variants of concern (VOC) associated with broadened host specificity, pathogenicity, and immune evasion to vaccine induced immunity. Here we compared humoral and cellular responses against SARS-CoV-2 VOC in subjects immunized with the DNA vaccine, INO-4800. INO-4800 vaccination induced neutralizing antibodies against all variants tested, with reduced levels detected against B.1.351. IFNγ T cell responses were fully maintained against all variants tested.
Cost-precision trade-off relation determines the optimal morphogen gradient for accurate biological pattern formation
Authors: Song Yonghyun , Hyeon Changbong
Published: April 2021

Spatial boundaries growing into macroscopic structures through animal development originate from the pre-patterning of tissues by signaling molecules, called morphogens. To establish accurate boundaries, the morphogen concentration which thresholds the expression of target gene at the boundary should be precise enough, exhibiting large gradient and small fluctuations. Producing more morphogens would better serve to shape more precise target boundaries; however, it incurs more thermodynamic cost. In the classical diffusion-degradation model of morphogen profile formation, the morphogens synthesized from a local source display an exponentially decaying concentration profile with a characteristic length λ. Our theory suggests that in order to attain a precise morphogen profile with the minimal cost, λ should be roughly half the distance to the target boundary position from the source, so that the boundary is formed at the position where the morphogen concentration is ∼10 % of the value at the source. Remarkably, we find that the well characterized morphogens that pattern the fruit fly embryo and wing imaginal disk form profiles with nearly optimal λ, which underscores the thermodynamic cost as a key physical constraint in the morphogen profile formation.
Phosphorus stress induces the synthesis of novel glycolipids inPseudomonas aeruginosathat confer protection against a last-resort antibiotic
Authors: Jones Rebekah A. , Shropshire Holly , Zhao Caimeng , Murphy Andrew , Lidbury Ian , Wei Tao , Scanlan David J , Chen Yin
Published: April 2021

Pseudomonas aeruginosais a nosocomial pathogen with a prevalence in immunocompromised individuals and is particularly abundant in the lung microbiome of cystic fibrosis patients. A clinically important adaptation for bacterial pathogens during infection is their ability to survive and proliferate under phosphorus (P) limited growth conditions. Here, we demonstrate thatP. aeruginosaadapts to P-limitation by substituting membrane glycerophospholipids with sugar-containing glycolipids through a lipid renovation pathway involving a phospholipase and two glycosyltransferases. Combining bacterial genetics and multi-omics (proteomics, lipidomics and metatranscriptomic analyses), we show that the surrogate glycolipids monoglycosyldiacylglycerol and glucuronic acid-diacylglycerol are synthesised through the action of a new phospholipase (PA3219) and two glycosyltransferases (PA3218 and PA0842). Comparative genomic analyses revealed that this pathway is strictly conserved in allP. aeruginosastrains isolated from a range of clinical and environmental settings and actively expressed in the metatranscriptome of a cystic fibrosis patient. Importantly, this phospholipid-to-glycolipid transition comes with significant ecophysiological consequence in terms of antibiotic sensitivity. Mutants defective in glycolipid synthesis survive poorly when challenged with polymyxin B, a last-resort antibiotic for treating multi-drug resistantP. aeruginosa. Thus, we demonstrate an intriguing link between adaptation to environmental stress (nutrient availability) and antibiotic resistance, mediated through membrane lipid renovation that is an important new facet in our understanding of the ecophysiology of this bacterium in the lung microbiome of cystic fibrosis patients.

Classification

Integrated genomics and post-genomics approaches in microbial ecology
Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos
Authors: Paraiso Kitt D. , Blitz Ira L. , Cho Ken W.Y.
Published: April 2021

One of the first steps in cellular differentiation of vertebrate embryos is the formation of the three germ layers. Maternal pioneer transcription factors (TFs) bind to the regulatory regions of the embryonic genome prior to zygotic genome activation and initiate germ layer specification. While the involvement of maternal TFs in establishing epigenetic marks in whole embryos was addressed previously, how early pluripotent cells acquire spatially restricted epigenetic identity in embryos remain unknown. Here, we report that the H3K4me1 enhancer mark in each germ layer becomes distinct in germ layer specific regulatory regions, forming super-enhancers (SEs), by early gastrula stage. Distinct SEs are established in these germ layers near robustly regulated germ layer identity genes, suggesting that SEs are important for the canalization of development. Establishment of these enhancers requires a sequential function of maternal and zygotic TFs. By knocking down the expression of a critical set of maternal endodermal TFs, an overwhelming majority of the endodermal H3K4me1 marks are lost. Interestingly, this disappearance of endodermal marking coincides with the appearance of ectodermal and mesodermal H3K4me1 marks in the endoderm, suggesting a transformation in the chromatin state of these nuclei towards a more ecto-mesodermal state.De novomotif analysis to identify TFs responsible for the transformation recovers a profile for endodermal maternal TFs as well as their downstream target TFs. We demonstrate the importance of coordinated activities of maternal and zygotic TFs in defining a spatially resolved dynamic process of chromatin state establishment.
High resolution analysis of the cytosolic Ca2+events in beta cell collectives in situ
Authors: Postić Sandra , Sarikas Srdjan , Pfabe Johannes , Pohorec Viljem , Bombek Lidija Križančić , Sluga Nastja , Klemen Maša Skelin , Dolenšek Jurij , Korošak Dean , Stožer Andraž , Evans-Molina Carmella , Johnson James D , Rupnik Marjan Slak
Published: April 2021

The release of peptide hormones is predominantly regulated by a transient increase in cytosolic Ca2+concentration ([Ca2+]c). To trigger exocytosis, Ca2+ions enter the cytosol from intracellular Ca2+stores or from the extracellular space. The molecular events of late stages of exocytosis, and their dependence on [Ca2+]c, were extensively described in isolated single cells from various endocrine glands. Notably less work has been done on endocrine cells in situ to address the heterogeneity of [Ca2+]cevents contributing to a collective functional response of a gland. For this beta cell collectives in a pancreatic islet are particularly well suited as they are the smallest, experimentally manageable functional unit, where [Ca2+]cdynamics can be simultaneously assessed on both cellular and collective level. Here we measured [Ca2+]ctransients across all relevant timescales, from a sub-second to a minute time range, using high-resolution imaging with low-affinity Ca2+sensor. We quantified the recordings with a novel computational framework for semi-automatic image segmentation and [Ca2+]cevent identification. Our results demonstrate that under physiological conditions the duration of [Ca2+]cevents is variable, and segregated into 3 reproducible modes, sub-second, second and tens of seconds time range, and are a result of a progressive temporal summation of the shortest events. Using pharmacological tools we show that activation of intracellular Ca2+receptors is both sufficient and necessary for glucose-dependent [Ca2+]coscillations in beta cell collectives, and that a subset of [Ca2+]cevents could be triggered even in the absence of Ca2+influx across the plasma membrane. In aggregate, our experimental and analytical platform was able to readily address the involvement of intracellular Ca2+receptors in shaping the heterogeneity of [Ca2+]cresponses in collectives of endocrine cells in situ.
Associations between recurrent mutations and blast immunophenotype in acute myeloid leukemia
Authors: Kuželová Kateřina , Brodská Barbora , Marková Jana , Petráčková Martina , Ransdorfová Šárka , Gašová Zdenka , Šálek Cyril
Published: April 2021

The immune system undoubtly plays an important role in final elimination of residual leukemic cells during acute myeloid leukemia (AML) therapy. However, the anti-leukemia immune response can be inhibited by a variety of mechanisms enabling immune escape and eventual disease relapse. We analyzed selected markers of immune escape on AML cells at diagnosis (N = 53) and used them for hierarchical clustering analysis, which yielded distinct clusters with different incidence of mutations in nucleophosmin 1 (NPM1) and in the methyltransferase DNMT3A. More detailed analysis showed that in the absence of DNMT3A mutation, NPM1 mutation is associated with decreased HLA expression and also with low levels of other markers (CLIP, PD-L1, TIM-3). On the other hand, samples with concomitant DNMT3A mutation had high CLIP surface amount suggesting reduced antigen presentation. Higher CLIP exposition was also found in patients with internal tandem duplications in FLT3 (FLT3-ITD). TIM-3 transcript correlated not only with TIM-3 protein surface amount, but also with CLIP and PD-L1, suggesting acquisition of a complex immunoresistant phenotype. Our results indicate that AML genotype is to some extent related to the blast immunophenotype, and the established predictive values of particular mutations might also reflect an inherent cell resistance to the immune system.
Effects of tumor mutation burden on the antigen presentation pathway
Authors: Garcia-Rivera Enrique M. , Park Jiho , Desai Aakash , Boidot Romain , Chevrier Sandy , Truntzer Caroline , Ghiringhelli François , Borad Mitesh , Mansfield Aaron S.
Published: April 2021

Tumor mutation burden (TMB) is used to select patients to receive immune checkpoint inhibitors (ICIs) but has mixed predictive capabilities. We hypothesized that inactivation of antigen presenting genes (APGs) that result from increased TMBs would result in inherent resistance to ICIs. We observed that somatic mutations in APGs were associated with increasing TMBs across 9,418 tumor samples of 33 different histological subtypes. In adenocarcinomas of the lung,ITGAXandCD1Bwere some of the most commonly mutated APGs. In 62 patients with non-small cell lung cancers treated with a PD-1 inhibitor in second or later lines of therapy, there was an association of increased TMB with mutations in APGs; however, mutations in one or more APGs were associated with improved progression-free survival. Contrary to our hypothesis, mutations in APGs were associated with improved progression-free survival with nivolumab, possibly due to the involvement of single alleles rather than complete loss.