bluuebunny/crossref_metadata_2025 huggingface dataset:
Injustices in pandemic vulnerability: A spatial-statistical analysis of the CDC Social Vulnerability Index and COVID-19 outcomes in the U.S.
Authors: Song Jamie , South Eugenia , Solomon Sara , Wiebe Douglas
Published: May 2021

Background

The COVID-19 pandemic has exacerbated health injustices in the U.S. driven by racism and other forms of structural violence. Research has shown the disproportionate impacts of COVID-19 morbidity and mortality in the most marginalized communities.

Objectives

We examined the associations between COVID-19 cumulative incidence (CI) and case-fatality risk (CFR) and the CDC’s Social Vulnerability Index (SVI), a composite score assessing historical marginalization and thus vulnerability to disaster events.

Methods

Using county-level data from national databases, we used population density, Gini index, percent uninsured, and average annual temperature as covariates, and employed negative binomial regression to evaluate relationships between SVI and COVID-19 outcomes. Optimized hot spot analysis identified hot spots of COVID-19 CI and CFR, which were compared in terms of SVI using logistic regression.

Results

As of 2/3/21, 26,452,031 cases of and 448,786 deaths from COVID-19 had been reported in the U.S. Negative binomial regression showed that counties in the top SVI quintile reported 13.7% higher CI (p<0.001) than those in the bottom SVI quintile. Additionally, each unit increase in a county’s SVI score was associated with a 0.2% increase in CFR (p<0.001). Logistic regression analysis showed that counties in the lowest SVI quintile had significantly greater odds of being in a CI hot spot than all other counties, yet counties in the highest SVI quintile had 63% greater odds (p=0.008) of being in a CFR hot spot than counties in the lowest SVI quintile.

Conclusion

We demonstrated a significant relationship between SVI and CFR, but the relationship between SVI and CI is complex and warrants further investigation. SVI may help elucidate unequal impacts of COVID-19 and guide prioritization of vaccines to communities most impacted by structural injustices.
How can we increase notification of exposure to STIs between gay and bisexual men?: intervention development using stakeholder engagement, qualitative methods and behavioural science
Authors: Flowers Paul , Gerressu Makeda , McLeod Julie , McQueen Jean , Vojt Gabriele , Symonds Merle , Woode-Owusu Melvina , Estcourt Claudia
Published: May 2021

Rationale

The first key step in contact tracing for sexually transmitted infections (STIs) is tonotifyrecent exposed sex partners. Gay and bisexual men and other men who have sex with men (GBMSM) bear a high burden of STIs and one-off partners contribute disproportionately to community transmission, posing a particular challenge to contact tracing. Here we explore and theorise the barriers and facilitators of GBMSM telling their ‘one-off’ sexual partners about their exposure to STIs.

Design

Using focus groups with diverse GBMSM from Leeds, Glasgow, London and on-line (n=28) we used a multi-level approach to intervention development to enhance contact tracing. This framework included initial stakeholder engagement; deductive thematic analysis to identify key barriers and facilitators to contact tracing with one-off partners; the use of the theoretical domains framework (TDF) to theorise these barriers and facilitators and subsequently the use of the behaviour change wheel (BCW), incorporating the behaviour change technique taxonomy (BCTT), to suggest intervention content to enhance the key step of notifying partners; and final stakeholder input to ensure this content was fit for purpose and satisfied the APEASE criteria.

Results

In relation to the TDF, the barriers and facilitators primarily related to ‘beliefs about consequences’. Having used the BCW and further stakeholder engagement, our final intervention recommendations related to focussed efforts to change the culture and corresponding norms and social practice of notifying sex partners about the risk of infection in GBMSM communities. This could usefully be achieved through dedicated community engagement and partnership work, through focussed mass and social media interventions twinned with focussed peer-led work to normalise and destigmatise contact tracing.

Conclusion

Through systematically working with key stakeholders, GBMSM communities and using a range of tools from the behavioural sciences, we have developed a suite of evidence-based and theoretically informed intervention content which, if developed further, could enhance GBMSM’s willingness to notify sex partners about their risk of infection.
Trends in medical and surgical admission length of stay by race/ethnicity and socioeconomic status: a time series analysis
Authors: Ghosh Arnab K. , Unruh Mark A. , Soroka Orysya , Shapiro Martin
Published: May 2021

Length of stay, a metric of hospital efficiency, differs by race/ethnicity and socioeconomic status (SES). Longer LOS is associated with adverse health outcomes. We assessed differences in average adjusted length of stay (aALOS) over time by race/ethnicity, and SES stratified by discharge destination (home or non-home). Using the 2009-2014 State Inpatient Datasets from three states, we examined trends in aALOS differences by race/ethnicity, and SES (defined first vs fourth quartile of median income by zip code) controlling for patient, disease and hospital characteristics. For those discharged home, racial/ethnic and SES aALOS differences remained stable. Notably, for those discharged to non-home destinations, Black vs White, and low vs high SES aALOS differences increased significantly from 2009 to 2013, more sharply after Q3 2011, the Affordable Care Act’s (ACA) introduction. Further research to understand the ACA’s policy impact on hospital efficiencies, and relationship to racial/ethnic and SES differences in LOS is warranted.
Estimates of cases and hospitalizations averted by COVID-19 case investigation and contact tracing in 14 health jurisdictions in the United States
Authors: Jeon Seonghye , Rainisch Gabriel , Lash R. Ryan , Moonan Patrick K. , Oeltmann John E. , Greening Bradford , Adhikari Bishwa B. ,   Contact Tracing Impact Group, Meltzer Martin I.
Published: May 2021

Context

The implementation of case investigation and contact tracing (CICT) for controlling COVID-19 (caused by SARS-Cov-2 virus) has proven challenging due to varying levels of public acceptance and initially constrained resources, especially enough trained staff. Evaluating the impacts of CICT will aid efforts to improve such programs.

Objectives

Estimate the number of COVID-19 cases and hospitalizations averted by CICT and identify CICT processes that could improve overall effectiveness.

Design

We used data on proportion of cases interviewed, contacts notified or monitored, and days from testing to contact notification from 14 jurisdictions to model the impact of CICT on cumulative cases counts and hospitalizations over a 60-day period. Using the Centers for Disease Control and Prevention (CDC)’s COVIDTracer tool, we estimated a range of impacts by assuming either contacts would quarantine only if monitored or would do so upon notification of potential exposure. We also varied the observed program metrics to assess their relative influence.

Results

Performance by jurisdictions varied widely. Jurisdictions isolated between 12 and 86% of cases (including contacts which became cases) within 6 to 10 days after exposure-and-infection. We estimated that CICT-related reductions in transmission ranged from 0.4% to 32%. For every 100 cases prevented by nonpharmaceutical interventions, CICT averted between 4 and 97 additional cases. Reducing time to case isolation by one day increased averted case estimates by up to 15 percentage points. Increasing the proportion of cases interviewed or contacts notified by 20 percentage points each resulted in at most 3 or 6 percentage point improvements in averted cases.

Conclusions

We estimated that case investigation and contact tracing reduced the number of COVID-19 cases and hospitalizations among all jurisdictions studied. Reducing time to isolation produced the greatest improvements in impact of CICT.
Modeling the impact of COVID-19 vaccination in Lebanon: A call to speed-up vaccine roll out
Authors: Mumtaz Ghina R. , El-Jardali Fadi , Jabbour Mathilda , Harb Aya , Abu-Raddad Laith J. , Makhoul Monia
Published: May 2021

Background

Amidst a very difficult economic and political situation, and after a large first SARS-CoV-2 wave near the end of 2020, Lebanon launched its vaccination campaign on 14 February 2021. To date, only 6.7% of the population have received at least one dose of the vaccine, raising serious concerns over the speed of vaccine roll-out and its impact in the event of a future surge.

Objective

Using mathematical modeling, we assessed the short-term impact (by end of 2021) of various vaccine roll-out scenarios on SARS-CoV-2 epidemic course in Lebanon.

Results

At current immunity levels in the population, estimated by the model at 40% on 15 April 2021, a large epidemic wave is predicted if all social distancing restrictions are gradually eased and variants of concern are introduced. Reaching 80% vaccine coverage by end of 2021 will flatten the epidemic curve and will result in a 37% and 34% decrease in the peak daily numbers of severe/critical disease cases and deaths, respectively; while reaching intermediate coverage of 40% will result in only 10-11% decrease in each. Reaching 80% coverage by end of 2021 will avert 3 times more hospitalizations and deaths over the course of this year compared with 40% coverage. Impact of vaccination was substantially enhanced with rapid scale-up. Reaching 80% vaccine coverage by August would prevent twice as many severe/critical disease cases and deaths than if it were reached by December. Finally, a longer duration over which restrictions are eased resulted in a more favorable impact of vaccination.

Conclusion

For vaccination to have an impact on the predicted epidemic course and associated disease burden in Lebanon, vaccination has to be rapid and reach high coverage (at least 70%), while sustaining social distancing measures during roll-out. At current vaccination pace, this is unlikely to be achieved. Concerted efforts need to be put to overcome local challenges and substantially scale up vaccination to avoid a surge that the country, with its multiple crises and limited health-care capacity, is largely unprepared for.
Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation
Authors: Lee Hye Kyung , Knabl Ludwig , Knabl Ludwig , Wieser Manuel , Mur Anna , Zabernigg August , Schumacher Jana , Kaiser Norbert , Furth Priscilla A. , Hennighausen Lothar
Published: May 2021

Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 20211. This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies2,3. However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.
Predicting EGFR mutation status in lung adenocarcinoma presenting as ground-glass opacity: utilizing radiomics model in clinical translation
Authors: Cheng Bo , Deng Hongsheng , Zhao Yi , Xiong Junfeng , Liang Peng , Li Caichen , Liang Hengrui , Shi Jiang , Li Jianfu , Xiong Shan , Lai Ting , Chen Zhuxing , Wu Jianrong , Qian Tianyi , Huan Wenjing , Alexander Ng Man Tat , Wang Guotai , He Jianxing , Liang Wenhua
Published: May 2021

Objectives

This study aimed to establish a noninvasive radiomics model based on computed tomography (CT), with favorable sensitivity and specificity to predict EGFR mutation status in GGO-featured lung adenocarcinoma that subsequently guiding the administration of targeted therapy.

Method

Clinical-pathological information and preoperative CT-images of 636 lung adenocarcinoma patients (464, 100, and 72 in the training, internal, and external validation sets, respectively) that underwent GGO lesions resection were included. A total of 1476 radiomic features were extracted with gradient boosting decision tree (GBDT).

Results

The established radiomics model containing 252 selected features showed an encouraging discrimination performance of EGFR mutation status (mutant or wild-type), and the predictive ability was superior to that of the clinical model (AUC: 0.901 vs. 0.674, 0.813 vs. 0.730, and 0.801 vs. 0.746 the training, internal, and external validation sets, respectively). The combined radiomics plus clinical model showed no additional benefit over the radiomics model in predicting EGFR status (AUC: 0.909 vs. 0.901, 0.803 vs. 0.813, 0.808 vs. 0.801, respectively, in three cohorts). Uniquely, this model was validated in a cohort of lung adenocarcinoma patients who undertaken adjuvant EGFR-TKIs and harbored unresected GGOs, leading to a significantly improved potency of EGFR-TKIs (response rate: 33.9% vs. 62.5%, P =0.04; before- and after-prediction, respectively).

Conclusion

This presented radiomics model can be served as a noninvasive and time-saving approach for predicting the EGFR mutation status in lung adenocarcinoma presenting as GGO.

Key points

We developed a GGO-specific radiomics model containing 252 radiomics features for EGFR mutation status differentiation.

An AUC of 0.813 and 0.801 in the internal and external validation cohort, respectively, were achieved.

The radiomics model was utilized in clinical translation in an adjuvant EGFR-TKIs cohort with unresected GGOs. A significant improvement in the potency of EGFR-TKIs was achieved (response rate: 33.9% vs. 62.5%, P =0.04; before- and after-prediction).
Effectiveness of the Covid-19 vaccines in preventing infection in dental practitioners – results of a cross-sectional ‘questionnaire-based’ survey
Authors: Kumar Sanjeev , Saxena Susmita , Atri Mansi , Chamola Sunil Kumar
Published: May 2021

India started its vaccination program at the beginning of 2021, the main beneficiaries being health workers and frontline workers including police, paramilitary forces, sanitation workers, and disaster management volunteers in the first phase. By the time, the second wave of Covid-19 impacted India, approximately 14 million healthcare and frontline workers, including dentists had been vaccinated.

Aim

To study the effectiveness of vaccination on a subset of high-risk healthcare workers i.e. dentists in preventing Covid-19 during the second wave of the pandemic.

Study design

A questionnaire based pan-India online survey was carried out to record the Covid-related experiences of dentists prior to and after vaccination.

Result

The sample size for this survey was 4493 respondents from across India. During the second wave, 9.18% (n=364) respondents became positive in spite of the vaccine, while 14.69%(n=78) became positive in the unvaccinated group. A chi-square test of independence was performed to examine the relation between vaccination and the Covid positivity rate in all age groups. The relation between these variables was highly significant, [X2 (1, N = 4493) = 15.9809, p=.000064].

Conclusion

Our pan-India online survey inferred that vaccination has a definitive role to play in reducing the positivity rate amongst dentists during the second wave of the pandemic across all age groups.
Extraction of bouton-like structures from neuropil calcium imaging data
Authors: Fukumasu Kazushi , Nose Akinao , Kohsaka Hiroshi
Published: May 2021

The neuropil, the plexus of axons and dendrites, plays a critical role in operating the circuit processing of the nervous system. Revealing the spatiotemporal activity pattern within the neuropil would clarify how the information flows throughout the nervous system. However, calcium imaging to examine the circuit dynamics has mainly focused on the soma population due to their discrete distribution. The development of a methodology to analyze the calcium imaging data of a densely packed neuropil would provide us with new insights into the circuit dynamics. Here, we propose a new method to decompose calcium imaging data of the neuropil into populations of bouton-like synaptic structures with a standard desktop computer. To extract bouton-like structures from calcium imaging data, we introduced a new type of modularity, a widely used quality measure in graph theory, and optimized the clustering configuration by a simulated annealing algorithm, which is established in statistical physics. To assess this method’s performance, we conducted calcium imaging of the neuropil of Drosophila larvae. Based on the obtained data, we established artificial neuropil imaging datasets. We applied the decomposition procedure to the artificial and experimental calcium imaging data and extracted individual bouton-like structures successfully. Based on the extracted spatiotemporal data, we analyzed the network structure of the central nervous system of fly larvae and found it was scale-free. These results demonstrate that neuropil calcium imaging and its decomposition could provide new insight into our understanding of neural processing.
Strategy for detecting off-target sites in genome-edited rice
Authors: Narushima Jumpei , Kimata Shinya , Shiwa Yuh , Gondo Takahiro , Akimoto Satoru , Soga Keisuke , Yoshiba Satoko , Nakamura Kosuke , Shibata Norihito , Kondo Kazunari
Published: May 2021

Genome-editing using the CRISPR-Cas9 system can substantially accelerate crop breeding. Because off-target editing is the main problem with this system, a reliable method for comprehensively detecting off-target sites is required for the editing of food crop genomes. However, a method that accurately predicts off-target sites has not been established. In this study, we performed a SITE-Seq analysis to predict potential off-target sites. SITE-Seq is an unbiased method applicable for the in vitro detection of double-strand breaks (DSBs). To analyze SITE-Seq data, we developed a novel Galaxy system, which can perform simple and reproducible analyses without a command line operation. We conducted a SITE-Seq analysis of a rice genome modified by OsFH15 gRNA-Cas9, and identified 41 DSB sites in the annotated regions. Amplicon-sequencing revealed mutations at one off-target site in the genome-edited rice. The presence of an uncommon protospacer adjacent motif (NTG PAM) likely makes this off-target site difficult to identify using in silico methods. Of the six tested programs, only CRISPRdirect predicted this off-target site, but it also predicted 6,080 off-target sites in total. These results suggest the SITE-Seq method presented herein can efficiently predict off-target sites and is useful for assessing the safety of genome-edited food.
Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle
Authors: Ham Daniel J. , Börsch Anastasiya , Chojnowska Kathrin , Lin Shuo , Leuchtmann Aurel B. , Ham Alexander S. , Thürkauf Marco , Delezie Julien , Furrer Regula , Burri Dominik , Sinnreich Michael , Handschin Christoph , Tintignac Lionel A. , Zavolan Mihaela , Mittal Nitish , Rüegg Markus A.
Published: May 2021

As global life expectancy continues to climb, maintaining skeletal muscle function is increasingly essential to ensure a good life quality for aging populations. Calorie restriction (CR) is the most potent and reproducible intervention to extend health and lifespan, but is largely unachievable in humans. Therefore, identification of “CR mimetics” has received much attention. CR targets nutrient-sensing pathways centering on mTORC1. The mTORC1 inhibitor, rapamycin, has been proposed as a potential CR mimetic and is proven to counteract age-related muscle loss. Therefore, we tested whether rapamycin acts via similar mechanisms as CR to slow muscle aging. Contrary to our expectation, long-term CR and rapamycin-treated geriatric mice display distinct skeletal muscle gene expression profiles despite both conferring benefits to aging skeletal muscle. Furthermore, CR improved muscle integrity in a mouse with nutrient-insensitive sustained muscle mTORC1 activity and rapamycin provided additive benefits to CR in aging mouse muscles. Therefore, RM and CR exert distinct, compounding effects in aging skeletal muscle, opening the possibility of parallel interventions to counteract muscle aging.
Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA barcoding and molecular phylogenetic reconstruction
Authors: Katoh Takehiro K. , Chen Ji-Min , Yang Jin-Hua , Zhang Guang , Wang Lu , Suwito Awit , Toda Masanori J. , Zhang Ya-Ping , Gao Jian-Jun
Published: May 2021

The genus Dichaetophora is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we challenged to delimit species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, which were tentatively classified into the species groups of Dichaetophora, Mulgravea and Dudaica based on the morphological diagnoses for these supraspecific taxa. Then, we selected representative specimen(s) for each morpho-species and subjected them to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ABGD (automatic barcode gap discovery) algorithm estimated a total of 222 MOTUs (molecular operational taxonomic units). Although most of the morpho-species were recognized as individual MOTUs, some others were divided into multiple MOTUs or combined into a single MOTU, suggesting the existence of cryptic sibling species, subspecies or intraspecific genetic varieties. Out of the 222 MOTUs, 88 representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group (four species from the tribe Colocasiomyini as out-group) for phylogenetic reconstruction. We analyzed a dataset of concatenated nucleotide sequences of 12 nuclear gene markers by the maximum likelihood and Bayesian inference methods. As a result, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade, which we called the “pan-Dichaetophora”. Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped MOTUs of Dichaetophora. Thus, the present study has uncovered some problems in the taxonomy of the pan-Dichaetophora. Solving such problems will be challenged in Part II of this serial work.
Network instability dynamics drive a transient bursting period in the developing hippocampus in vivo
Authors: Graf Jürgen , Rahmati Vahid , Majoros Myrtill , Witte Otto W. , Geis Christian , Kiebel Stefan J. , Holthoff Knut , Kirmse Knut
Published: May 2021

Spontaneous correlated activity is a universal hallmark of immature neural circuits. However, the cellular dynamics and intrinsic mechanisms underlying network burstiness in the intact developing brain are largely unknown. Here, we use two-photon Ca2+ imaging to comprehensively map the developmental trajectories of spontaneous network activity in hippocampal area CA1 in vivo. We unexpectedly find that network burstiness peaks after the developmental emergence of effective synaptic inhibition in the second postnatal week. We demonstrate that the enhanced network burstiness reflects an increased functional coupling of individual neurons to local population activity. However, pairwise neuronal correlations are low, and network bursts (NBs) recruit CA1 pyramidal cells in a virtually random manner. Using a dynamic systems modeling approach, we reconcile these experimental findings and identify network bi-stability as a potential regime underlying network burstiness at this age. Our analyses reveal an important role of synaptic input characteristics and network instability dynamics for NB generation. Collectively, our data suggest a mechanism, whereby developing CA1 performs extensive input-discrimination learning prior to the onset of environmental exploration.
Resolving the molecular architecture of the photoreceptor active zone by MINFLUX nanoscopy
Authors: Grabner Chad P. , Jansen Isabelle , Neef Jakob , Weiss Tobias , Schmidt Roman , Riedel Dietmar , Wurm Christian A. , Moser Tobias
Published: May 2021

Cells assemble macromolecular complexes into scaffoldings that serve as substrates for catalytic processes. Years of molecular neurobiology indicate that neurotransmission depends on such optimization strategies, yet the molecular topography of the presynaptic Active Zone (AZ) where transmitter is released upon synaptic vesicle (SV) fusion remains to be visualized. Therefore, we implemented MINFLUX optical nanoscopy to resolve the AZ of rod photoreceptors. To facilitate MINFLUX nanoscopy of the AZ, we developed and verified an immobilization technique, we name Heat Assisted Rapid Dehydration (HARD). Here fresh retinal slices are directly stamped onto glass coverslips yielding a single layer of rod AZs. These AZs exhibited excellent labeling efficiency and minimal signal redundancy in the Z-direction. Our data indicate that the SV release site is a molecular complex of bassoon-Rab3-binding molecule 2 (RIM2)-ubMunc13-2-CAST. The complexes are serially duplicated longitudinally, and reflected in register along the axis of symmetry of the synaptic ribbon.

One sentence summary

Structural motifs formed by active zone proteins at the photoreceptor synapse.
Single-cell Transcriptomic Profiling Unveils Cardiac Cell-type Specific Response to Maternal Hyperglycemia Underlying the Risk of Congenital Heart Defects
Authors: Manivannan Sathiyanarayanan , Mansfield Corrin , Zhang Xinmin , Kodigepalli Karthik. M. , Majumdar Uddalak , Garg Vidu , Basu Madhumita
Published: May 2021

Congenital heart disease (CHD) is the most prevalent structural malformations of the heart affecting ∼1% of live births. To date, both damaging genetic variations and adverse environmental exposure such as maternal diabetes have been found to cause CHD. Clinical studies show ∼fivefold higher risk of CHD in the offspring of mothers with pregestational diabetes. Maternal pregestational diabetes affects the gene regulatory networks key to proper cardiac development in the fetus. However, the cell-type specificity of these gene regulatory responses to maternal diabetes and their association with the observed cardiac defects in the fetuses remains unknown. To uncover the transcriptional responses to maternal diabetes in the early embryonic heart, we used an established murine model of pregestational diabetes. In this model, we have previously demonstrated an increased incidence of CHD. Here, we show maternal hyperglycemia (matHG) elicits diverse cellular responses during heart development by single-cell RNA-sequencing in embryonic hearts exposed to control and matHG environment. Through differential gene-expression and pseudotime trajectory analyses of this data, we identified changes in lineage specifying transcription factors, predominantly affecting Isl1+ second heart field progenitors and Tnnt2+ cardiomyocytes with matHG. Using in vivo cell-lineage tracing studies, we confirmed that matHG exposure leads to impaired second heart field-derived cardiomyocyte differentiation. Finally, this work identifies matHG-mediated transcriptional determinants in cardiac cell lineages elevate CHD risk and show perturbations in Isl1-dependent gene-regulatory network (Isl1-GRN) affect cardiomyocyte differentiation. Functional analysis of this GRN in cardiac progenitor cells will provide further mechanistic insights into matHG-induced severity of CHD associated with diabetic pregnancies.
Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered tropical birds
Authors: Costantini Maria S. , Medeiros Matthew C.I. , Crampton Lisa H. , Reed Floyd A.
Published: May 2021

The gut microbiome of an animal has a strong influence on the health, fitness, and behavior of its host, and is thus a critical component of the animal itself. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai‘i, several threats have caused widespread population declines of Hawaiian honeycreepers (subfamily Carduelinae). These threats, and the environmental changes that result, can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, no previous study has explored the natural patterns of the gut microbiome of a honeycreeper species in the wild. This project used amplicon-based sequencing of the 16S rRNA gene to characterize the gut microbiome of two critically endangered species of Hawaiian honeycreepers. The two species differed significantly in both alpha and beta diversity. Intraspecific variation of the gut microbiome among individual birds was a major factor. However, small but significant differences also exist between sampling location and sexes. This baseline knowledge will help inform management decisions for these honeycreeper species both in their native habitats and in captivity.
Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat
Authors: Zheng Zhi-Zhong , Hua Rong , Xu Guo-Qiang , Yang Hui , Shi Peng
Published: May 2021

The naked mole-rats (Heterocephalus glaber, NMRs) and the blind mole-rats (Spalax galili, BMRs) are representative subterranean rodents that evolved many extraordinary traits, including hypoxia tolerance, longevity and cancer resistance. Although a batch of candidate loci responsible for these intriguing traits have been uncovered by genomic studies, many of them are limited to functional modifications of intact genes and little is known about the contributions of other genetic makeups. Here, to address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, as well as their respective terrestrial relatives, guinea pigs and rats, in a genome-wide scale. 167, 139, 341 and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. The pseudogenes in these EFGs might be associated with either regressive (e.g. visual system) or adaptive (e.g. altered DNA damage response) traits. In addition, several pseudogenes including TNNI3K and PDE5A, might be associated with their specific cardiac features observed in subterranean linages. Furthermore, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of TRIM17 in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating TRIM17 function in hypoxia adaptation. We also demonstrated that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively. Overall, our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution.
Molecular mechanisms of sperm motility are conserved in a basal metazoan
Authors: Speer Kelsey F. , Allen-Waller Luella , Novikov Dana R. , Barott Katie L.
Published: May 2021

Efficient and targeted sperm motility is essential for animal reproductive success. Studies in mammals and echinoderms have uncovered a highly conserved signaling mechanism in which sperm motility is stimulated by pH-dependent activation of the cAMP-producing enzyme soluble adenylyl cyclase (sAC). However, the presence of this pathway in basal metazoans has, until now, been unexplored. Here we found that cytoplasmic alkalinization induced a rapid burst of cAMP signaling and the full activation of motility in sperm from the reef-building coral Montipora capitata. Coral sperm expressed sAC in the flagellum, midpiece, and acrosomal regions, indicating that this molecular pH sensor may play a role in regulating mitochondrial respiration and flagellar beating. In bilaterians, sAC is a central node of a broader pH-dependent signaling pathway that alters cellular behavior in response to changes to the extracellular environment. We present transcript-level evidence that a homologous pathway is present in coral sperm, including the Na+/H+ exchanger SLC9C1, protein kinase A, and the CatSper Ca2+ channel conserved even in mammalian sperm. Our discovery of this pathway in a basal metazoan species highlights the ancient origin of the pH-sAC-cAMP signaling node in sperm physiology and suggests that it may be present in many other marine invertebrate taxa for which sperm motility mechanisms remain unexplored. These results emphasize our need to better understand the role of pH-dependent signaling in marine reproductive success, particularly as worsening ocean acidification and warming due to climate change continue to impair the physiology of corals and other marine invertebrates.

Statement of significance

Reef-building corals are the keystone species of the world’s most biodiverse yet threatened marine ecosystems. Corals reproduce by broadcast spawning, making the ability of their sperm to swim through the water column essential for fertilization. However, little is known about the mechanisms that regulate coral sperm motility. Here we found that elevated intracellular pH promotes the production of the second messenger cAMP in coral sperm and triggers the onset of motility. This study reveals the deep conservation of a sperm activation pathway from humans to corals, presenting the first comprehensive examination of the molecular mechanisms regulating sperm motility in an ancestral animal. These results are critical for understanding the resilience of this sensitive life stage to a changing marine environment.
Astrocyte GluN2C NMDA receptors control basal synaptic strengths of hippocampal CA1 pyramidal neurons in thestratum radiatum
Authors: Chipman Peter H. , Fernandez Alejandra Pazo , Fung Chi Chung Alan , Tedoldi Angelo , Kawai Atsushi , Gautam Sunita Ghimire , Kurosawa Mizuki , Abe Manabu , Sakimura Kenji , Fukai Tomoki , Goda Yukiko
Published: May 2021

Experience-dependent plasticity is a key feature of brain synapses for which neuronal N-Methyl-D-Aspartate receptors (NMDARs) play a major role, from developmental circuit refinement to learning and memory. Astrocytes also express NMDARs although their exact function has remained controversial. Here we identify a circuit function for GluN2C NMDAR, a subtype highly expressed in astrocytes, in layer-specific tuning of synaptic strengths in mouse hippocampal CA1 pyramidal neurons. Interfering with astrocyte NMDAR or GluN2C NMDAR activity reduces the range of presynaptic strength distribution specifically in thestratum radiatuminputs without an appreciable change in the mean presynaptic strength. Mathematical modeling shows that narrowing of the width of presynaptic release probability distribution compromises the expression of long-term synaptic plasticity. Our findings suggest a novel feedback signaling system that uses astrocyte GluN2C NMDARs to adjust basal synaptic weight distribution of Schaffer collateral inputs, which in turn impacts computations performed by the CA1 pyramidal neuron.
Synthetic antigen-presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses
Authors: Céspedes Pablo F. , Jainarayanan Ashwin , Fernández-Messina Lola , Saliba David G. , Valvo Salvatore , Kvalvaag Audun , Chen Lina , Kurz Elke , Ganskow Charity , Colin-York Huw , Fritzsche Marco , Peng Yanchun , Dong Tao , Johnson Errin , Siller-Farfán Jesús A. , Dushek Omer , Sezgin Erdinc , Peacock Ben , Law Alice , Aubert Dimitri , Engledow Simon , Attar Moustafa , Hester Svenja , Fischer Roman , Sánchez-Madrid Francisco , Dustin Michael L.
Published: May 2021

The T cell Immunological Synapse (IS) is a pivotal hub for the regulation of adaptive immunity by endowing the exchange of information between cells engaged in physical contacts. Beyond the integration of antigen (signal one), co-stimulation (signal two), and cytokines (signal three), the IS facilitates the delivery of T-cell effector assemblies including supramolecular attack particles (SMAPs) and extracellular vesicles (EVs). How these particulate outputs differ among T -cell subsets and how subcellular compartments and signals exchanged at the synapse contribute to their composition is not fully understood. Here we harnessed bead-supported lipid bilayers (BSLBs) as a tailorable and versatile technology for the study of synaptic particle biogenesis and composition in different T-cell subsets, including CART. These synthetic antigen-presenting cells (APCs) facilitated the characterisation of trans-synaptic vesicles (tSV) as a heterogeneous population of EVs comprising among others PM-derived synaptic ectosomes and CD63+exosomes. We harnessed BSLB to unveil the factors influencing the vesicular release of CD40L, as a model effector, identifying CD40 trans presentation, T-cell activation, ESCRT upregulation/recruitment, antigen density/potency, co-repression by PD-1 ligands, and its processing by ADAM10 as major determinants. Further, BSLB made possible the comparison of microRNA (miR) species associated with tSV and steadily released EVs. Altogether, our data provide evidence for a higher specialisation of tSV which are enriched not only in effector immune receptors but also in miR and RNA-binding proteins. Considering the molecular uniqueness and functional complexity of the tSV output, which is also accompanied by SMAPs, we propose their classification as signal four.

Graphical abstract

Highlights

Bead Supported Lipid Bilayers (BSLB) reconstituting antigen-presenting cells support synapse assembly by T cells and the release of effector particles.

BSLB facilitate the dissection of the cellular machineries and synapse composition shaping the released tSV.

tSV and their steadily released counterparts have a different composition. TSV show a higher enrichment of effectors including immune receptors, miR, RNA- and other nucleic acid-binding proteins, than EVs.
Oligodendrocyte precursor cells prune axons in the mouse neocortex
Authors: Buchanan JoAnn , Elabbady Leila , Collman Forrest , Jorstad Nikolas L. , Bakken Trygve E. , Ott Carolyn , Glatzer Jenna , Bleckert Adam A. , Bodor Agnes L. , Brittan Derrick , Bumbarger Daniel J. , Mahalingam Gayathri , Seshamani Sharmishtaa , Schneider-Mizell Casey , Takeno Marc M. , Torres Russel , Yin Wenjing , Hodge Rebecca D. , Castro Manuel , Dorkenwald Sven , Ih Dodam , Jordan Chris S. , Kemnitz Nico , Lee Kisuk , Lu Ran , Macrina Thomas , Mu Shang , Popovych Sergiy , Silversmith William M. , Tartavull Ignacio , Turner Nicholas L. , Wilson Alyssa M. , Wong William , Wu Jingpeng , Zlateski Aleksandar , Zung Jonathan , Lippincott-Schwartz Jennifer , Lein Ed S. , Seung H. Sebastian , Bergles Dwight E. , Reid R. Clay , da Costa Nuno Maçarico
Published: May 2021

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form1. This transformation is facilitated by the engulfment and degradation of excess axonal branches and inappropriate synapses by surrounding glial cells, including microglia and astrocytes2,3. However, the small size of phagocytic organelles and the complex, highly ramified morphology of glia has made it difficult to determine the contribution of these and other glial cell types to this process. Here, we used large scale, serial electron microscopy (ssEM) with computational volume segmentation to reconstruct the complete 3D morphologies of distinct glial types in the mouse visual cortex. Unexpectedly, we discovered that the fine processes of oligodendrocyte precursor cells (OPCs), a population of abundant, highly dynamic glial progenitors4, frequently surrounded terminal axon branches and included numerous phagolysosomes (PLs) containing fragments of axons and presynaptic terminals. Single- nucleus RNA sequencing indicated that cortical OPCs express key phagocytic genes, as well as neuronal transcripts, consistent with active axonal engulfment. PLs were ten times more abundant in OPCs than in microglia in P36 mice, and declined with age and lineage progression, suggesting that OPCs contribute very substantially to refinement of neuronal circuits during later phases of cortical development.
Tumor growth of neurofibromin-deficient cells is driven by decreased respiration and hampered by NAD+ and SIRT3
Authors: Masgras Ionica , Cannino Giuseppe , Ciscato Francesco , Sanchez-Martin Carlos , Pizzi Marco , Menga Alessio , Castegna Alessandra , Rasola Andrea
Published: May 2021

Neurofibromin loss drives neoplastic growth and a rewiring of mitochondrial metabolism. Here, we report that neurofibromin ablation dampens expression and activity of NADH dehydrogenase, the respiratory chain complex I, in an ERK-dependent fashion. This provides cells with resistance to pro-oxidants targeting complex I and decreases both respiration and intracellular NAD+. Expression of the alternative NADH dehydrogenase NDI1 raises NAD+/NADH ratio, enhances the activity of the mitochondrial NAD+-dependent deacetylase SIRT3 and interferes with tumorigenicity in neurofibromin-deficient cells. This anti-neoplastic effect is mimicked both in vitro and in vivo by administration of NAD+ precursors or by rising expression of the NAD+ deacetylase SIRT3, and is synergistic with ablation of the mitochondrial chaperone TRAP1, which augments succinate dehydrogenase activity further contributing to block pro-neoplastic metabolic changes of these cells. These findings shed light on chemotherapeutic resistance and on bioenergetic adaptations of tumors lacking neurofibromin, linking complex I inhibition to mitochondrial NAD+/NADH unbalance and SIRT3 inhibition, as well as to down-regulation of succinate dehydrogenase. This metabolic rewiring could unveil attractive therapeutic targets for neoplasms related to neurofibromin loss.
Trikafta therapy alters the CF lung mucus metabolome reshaping microbiome niche space
Authors: Sosinski Lauren M. , Martin H Christian , Neugebauer Kerri A. , Ghuneim Lydia-Ann J. , Guzior Douglas V. , Castillo-Bahena Alicia , Mielke Jenna , Thomas Ryan , McClelland Marc , Conrad Doug , Quinn Robert A.
Published: June 2021

Background

Novel small molecule therapies for cystic fibrosis (CF) are showing promising efficacy and becoming more widely available since recent FDA approval. The newest of these is a triple therapy of Elexacaftor-Tezacaftor-Ivacaftor (ETI, Trikafta®). Little is known about how these drugs will affect polymicrobial lung infections, which are the leading cause of morbidity and mortality among people with CF (pwCF).

Methods

we analyzed the sputum microbiome and metabolome from pwCF (n=24) before and after ETI therapy using 16S rRNA gene amplicon sequencing and untargeted metabolomics.

Results

The lung microbiome diversity, particularly its evenness, was increased (p = 0.044) and the microbiome profiles were different between individuals before and after therapy (PERMANOVA F=1.92, p=0.044). Despite these changes, the microbiomes were more similar within an individual than across the sampled population. There were no specific microbial taxa that were different in abundance before and after therapy, but collectively, the log-ratio of anaerobes to classic CF pathogens significantly decreased. The sputum metabolome also showed changes due to ETI. Beta-diversity increased after therapy (PERMANOVA F=4.22, p=0.022) and was characterized by greater variation across subjects while on treatment. This significant difference in the metabolome was driven by a decrease in peptides, amino acids, and metabolites from the kynurenine pathway. Metabolism of the three small molecules that make up ETI was extensive, including previously uncharacterized structural modifications.

Conclusions

This study shows that ETI therapy affects both the microbiome and metabolome of airway mucus. This effect was stronger on sputum biochemistry, which may reflect changing niche spaces for microbial residency in lung mucus as the drug’s effects take hold, which then leads to changing microbiology.

Funding

This project was funded by a National Institute of Allergy and Infectious Disease Grant R01AI145925
AR-V7 exhibits non-canonical mechanisms of nuclear import and chromatin engagement in Castrate-Resistant Prostate Cancer
Authors: Kim Seaho , Bin Jamalruddin Mohd Azrin , Au CheukMan Cherie , Mukhtar Eiman , Portella Luigi , Berger Adeline , Worroll Daniel , Rickman David S. , Nanus David M. , Giannakakou Paraskevi
Published: June 2021

Expression of the AR splice variant, AR-V7, in prostate cancer is correlated with poor patient survival and resistance to AR targeted therapies and taxanes. Currently, there is no specific inhibitor of AR-V7, while the molecular mechanisms regulating its biological function are not well elucidated. Here we report that AR-V7 has unique biological features that functionally differentiate it from canonical AR-fl or from the second most prevalent variant, AR-v567. First, AR-V7 exhibits fast nuclear import kinetics via a pathway distinct from the nuclear localization signal dependent importin-α /β pathway used by AR-fl and AR-v567. We also show that the dimerization box domain, known to mediate AR dimerization and transactivation, is required for AR-V7 nuclear import but not for AR-fl. Once in the nucleus, AR-V7 is transcriptionally active, yet exhibits unusually high intranuclear mobility and transient chromatin interactions, unlike the stable chromatin association of liganded AR-fl. The high intranuclear mobility of AR-V7 together with its high transcriptional output, suggest a Hit-and-Run mode of transcription. Our findings reveal unique mechanisms regulating AR-V7 activity, offering the opportunity to develop selective therapeutic interventions.