bluuebunny/crossref_metadata_2025 huggingface dataset:
Papillary Urothelial Carcinoma of Urinary Bladder Identified on 18F-Fluciclovine PET/CT
Authors: Meka Vamsi Mohan , Wankhar Baphiralyne , Ojili Vijayanadh , Batchala Prem P.
Published: March 2021

18F-fluciclovine is a radiolabeled synthetic amino acid recently approved by the Food and Drug Administration for evaluating recurrent prostate cancer. Upregulated amino acid transporters in prostate cancer cells result in elevated radiotracer uptake in sites of tumor recurrence. However, 18F-fluciclovine is not specific for prostate cancer. Nonprostatic malignancies and benign conditions can also demonstrate uptake. This information combined with the knowledge about common patterns of prostate cancer recurrence helps guide appropriate management. We present an 87-year-old man with biochemical recurrence for prostate cancer but found to have a urinary bladder wall mass on 18F-fluciclovine PET/CT with moderate avidity. Biopsy revealed papillary urothelial carcinoma.
International attitudes on COVID-19 vaccination: repeat national cross-sectional surveys across 15 countries
Authors: Crespo Roberto Fernandez , Shafat Manar , Melas-Kyriazi Natalie , Gould Lisa , Jones Sarah , Neves Ana Luisa , Leis Melanie S , Maheswaran Hendramoorthy , Darzi Ara
Published: March 2021

Objective

To examine the general public’s views around willingness to receive COVID-19 vaccines and concerns regarding their safety.

Design

Repeat cross-sectional surveys.

Setting

Online surveys in Australia, Canada, Denmark, Finland, France, Germany, Italy, Japan, Netherlands, Norway, Singapore, South Korea, Spain, Sweden and the United Kingdom

Participants

National samples of adults aged >=18 years in November 2020 and January 2021.

Main outcomes measures

The proportion of adults reporting: willingness to receive a COVID-19 vaccination; concern regarding side-effects from vaccinations; concerns over contraction COVID-19, and beliefs around vaccine provision in their country. Changes between the November and January surveys are also reported.

Results

Across the 15 countries, the proportion of respondents reporting they would have the COVID-19 vaccine increased from 40.7% (range: 25.0-55.1) to 55.2% (range: 34.8-77.5), proportion reporting worried about the side-effects of vaccine decreased from 53.3% (range: 42.1-66.7) to 47.9% (range: 28.0-66.1). On the second survey, willingness to receive vaccine remained low in females (49.4%, range: 30.2-79.1), aged 18-39 years (42.1%, range: 25.9-71.7), those not working or unemployed (48.9, range: 18.8-67.0), students (45.9%, range: 22.8-70.0), and those with children at home (46.5%, range: 32.4-68.9). Concerns regarding safety of vaccine remained high in females (53.7%, range: 31.8-70.4), aged 18-39 years (50.8%, range: 28.2-60.7), aged 40-64 years (51.3%, range: 30.7-68.5), those working (50.5%, range: 26.7-65.0), those not working or unemployed (53.3, range: 35.4-73.8) and those with children at home (55.8%, range: 36.5-64.7).

Conclusion

COVID-19 vaccine hesitancy decreased considerably over a relatively short time coinciding with the discovery of effective vaccines. The public remain concerned about their safety, and public health messaging will need to emphasis their safety especially amongst females, parents and younger adults.
Depressive Symptoms and Negative Experiences in School: A Network Analysis
Authors: Huang Yi , Macek Petr , Lu Jinjin
Published: March 2021

BACKGROUNDS

Negative experiences in school predict youth’s depression. However, the dynamic interactions of depressive symptoms with adolescents’ negative experiences in school remain unclear. This study aimed to applied network analysis to detect the complex relationships between early adolescents’ depressive symptoms and negative experiences in school.

METHODS

We adopted the data from a Chinese national survey conducted in 2018. Eight hundred ninety-seven adolescents from 10 to 15 years old were included. The measurements included an 8-item depression screener scale and a 14-item scale assessing negative experiences in school.

RESULTS

The centrality analysis suggested that Chinese adolescents’ core depressive symptoms were negative affections and negative cognition that “ I felt that everything I did was an effort. “ Regarding “negative experiences in the school,” the most central nodes were poor academic performance and peer relationships. The bridge-centrality results showed negative emotions in school and difficulties in peer relationships were significantly linked to depression.

CONCLUSION

Negative emotional experiences in school and peer relationships were the two most important factors linked to depression.
“Monozygotic twins discordant for severe clinical recurrence of COVID-19 show drastically distinct T cell responses to SARS-Cov-2”
Authors: Castro Mateus V. de , Santos Keity S. , Apostolico Juliana S. , Fernandes Edgar R. , Almeida Rafael R. , Levin Gabriel , Magawa Jhosiene Y. , S. Nunes João Paulo , Bruni Miriam , Yamamoto Marcio M. , Lima Ariane C. , Silva Monize V. R. , Matos Larissa R. B. , Coria Vivian R. , Castelli Erick C. , Scliar Marilia O. , Kuramoto Andreia , Bruno Fernanda R. , Jacintho Lucas C. , Nunes Kelly , Wang Jaqueline Y. T. , Coelho Veronica P. , Neto Miguel Mitne , Maciel Rui M. B. , Naslavsky Michel S. , Passos-Bueno Maria Rita , Boscardin Silvia B. , Rosa Daniela S. , Kalil Jorge , Zatz Mayana , Cunha-Neto Edecio
Published: March 2021

Background

Clinical recurrence of COVID-19 in convalescent patients has been reported, which immune mechanisms have not been thoroughly investigated. Presence of neutralizing antibodies suggests other types of immune response are involved.

Methods

We assessed the innate type I/III IFN response, T cell responses to SARS-CoV-2 with IFNγ ELISPOT, binding and neutralizing antibody assays, in two monozygotic twin pairs with one COVID-19 recurrence case.

Results

In pair 1, four months after a first mild episode of infection for both siblings, one displayed severe clinical recurrence of COVID-19. Twin pair 2 of siblings underwent non-recurring asymptomatic infection. All fours individuals presented similar overall responses, except for remarkably difference found in specific cellular responses. Recurring sibling presented a reduced number of recognized T cell epitopes as compared to the other three including her non-recurring sibling.

Conclusions

Our results suggest that an effective SARS-CoV-2-specific T cell immune response is key for complete viral control and avoidance of clinical recurrence of COVID-19. Besides, adaptive immunity can be distinct in MZ twins. Given the rising concern about SARS-CoV-2 variants that evade neutralizing antibodies elicited by vaccination or infection, our study stresses the importance of T cell responses in protection against recurrence/reinfection.

Key points

Immune parameters leading to COVID-19 recurrence/reinfection are incompletely understood. A COVID-19 recurrence case in a monozygotic twin pair is described with an intact antibody and innate type I/III Interferon response and drastically reduced number of recognized SARS-CoV-2 T cell epitopes.
Perceptions on undertaking regular asymptomatic self-testing for COVID-19 using lateral flow tests: A qualitative study of university students and staff
Authors: Wanat Marta , Logan Mary , Hirst Jennifer , Vicary Charles , Lee Joseph Jonathan , Perera Rafael , Tracey Irene , Duff Gordon , Tuffano Peter , Fanshawe Thomas R. , Mwandigha Lazaro , Nicholson Brian D. , Tonkin-Crine Sarah , Hobbs Richard
Published: March 2021

Background

There has been an increased interest from governments in implementing mass testing for COVID-19 of asymptomatic individuals using Lateral Flow Tests (LFTs). Successful implementation of such programmes depends on several factors, including feasibility, acceptability and how people act on test results. There is a paucity of studies examining these issues.

Objective

We aimed to examine experiences of university students and staff with experience of regular asymptomatic self-testing using LFTs, and their subsequent behaviours.

Methods

We invited people who were participating in a ‘weekly testing’ feasibility study. We conducted semi-structured remote interviews between December 2020 and January 2021. Additional qualitative data from a survey were also analysed. Data were analysed thematically.

Results

We interviewed 18 and surveyed 214 participants. Participants were motivated to regularly self-test as they wanted to know whether or not they were infected with SARS-CoV-2. Most reported that a negative test result did not change their behaviour but it did provide them with reassurance to engage with permitted activities. In contrast, some participants reported making decisions about visiting other people when they would not have done so otherwise, because they felt reassured by a negative test result. Participants valued the test training but some participants still doubted their ability to carry out the test. Participants were concerned about safety of attending test sites with lots of people and reported home testing was most convenient.

Conclusions

If governments want to increase uptake of LFT use, clear messages highlighting the benefits of regular testing for family, friends and society in identifying asymptomatic cases are needed. This should be coupled with transparent communication about accuracy of LFTs and how to act on either a positive or negative result. Concerns about safety, convenience of testing, and ability to do tests need to be addressed to ensure successful scaling up asymptomatic testing.
Intellectual disability and cerebellar hypoplasia in autism reported by associative learning
Authors: Welsh John P. , Munson Jeffrey , John Tanya St. , Meehan Christina N. , Tran Elise N. , Begay K. Kawena , Dager Stephen R. , Estes Annette M.
Published: March 2021

Objective

To determine how impairments in associative learning in autism spectrum disorder (ASD) relate to intellectual disability (ID) and early-childhood cerebellar hypoplasia.

Methods

Trace and long-delay eye blink conditioning (EBC) were performed in 62 children age 11.2 years having: 1) ASD with ID (ASD+ID); 2) ASD without ID (ASD-noID); or 3) typical development (TD). The sub-second timing of conditioned eye-blink responses (CRs) acquired to a tone paired with a corneal air puff was related to brain structure at age 2 years and clinical measures across ages 2-12 years. Because CR timing is influenced strongly by cerebellar function, EBC was used to test hypotheses relating cerebellar hypoplasia to ASD.

Results

Children with ASD+ID showed early-onset CRs during trace EBC that were related to early-childhood hypoplasia of the cerebellum but not of the cerebral cortex, hippocampus, or amygdala. Children with ASD-noID showed early-onset CRs only during long-delay EBC without cerebellar hypoplasia. Using EBC measures, logistic regression detected ASD with 81% sensitivity and 79% specificity while linear discriminant analysis separated ASD subgroups based on ID but not ASD severity. MRI of additional 2-year-olds with ASD indicated that early-onset CRs during trace EBC revealed ASD+ID more readily than cerebellar hypoplasia, per se.

Conclusions

Early-childhood cerebellar hypoplasia occurs in children with ASD+ID that demonstrate early-onset CRs during trace EBC. Trace EBC reveals the relationship between cerebellar hypoplasia and ASD+ID likely by engaging cerebro-cerebellar circuits involved in intellect. We emphasize that the cerebellum optimizes sensory-motor processing at sub-second intervals, impairments of which may contribute to ID.
Estimating COVID-19 cases and deaths prevented by non-pharmaceutical interventions, and the impact of individual actions: a retrospective model-based analysis
Authors: Fair Kathyrn R , Karatayev Vadim A , Anand Madhur , Bauch Chris T
Published: March 2021

Simulation models from the early COVID-19 pandemic highlighted the urgency of applying non-pharmaceutical interventions (NPIs), but had limited empirical data. Here we use data from 2020-2021 to retrospectively model the impact of NPIs in Ontario, Canada. Our model represents age groups and census divisions in Ontario, and is parameterised with epidemiological, testing, demographic, travel, and mobility data. The model captures how individuals adopt NPIs in response to reported cases. We compare a scenario representing NPIs introduced within Ontario (closures of workplaces/schools, reopening of schools/workplaces with NPIs in place, individual-level NPI adherence) to counterfactual scenarios wherein alternative strategies (e.g. no closures, reliance on individual NPI adherence) are adopted to ascertain the extent to which NPIs reduced cases and deaths. Combined school/workplace closure and individual NPI adoption reduced the number of deaths in the best-case scenario for the case fatality rate (CFR) from 178548 [CI: 171845, 185298] to 3190 [CI: 3095, 3290] in the Spring 2020 wave. In the Fall 2020/Winter 2021 wave, the introduction of NPIs in workplaces/schools reduced the number of deaths from 20183 [CI: 19296, 21057] to 4102 [CI: 4075, 4131]. Deaths were several times higher in the worst-case CFR scenario. Each additional 9−16 (resp. 285−578) individuals who adopted NPIs in the first wave prevented one additional infection (resp., death). Our results show that the adoption of NPIs prevented a public health catastrophe. A less comprehensive approach, employing only closures or individual-level NPI adherence, would have resulted in a large number of cases and deaths.
Assessment of serological assays for identifying high titer convalescent plasma
Authors: Farnsworth Christopher W. , Case James Brett , Hock Karl , Chen Rita E. , O’Halloran Jane A. , Presti Rachel , Goss Charles W. , Rauseo Adriana M. , Ellebedy Ali , Theel Elitza S. , Diamond Michael S. , Henderson Jeffrey P.
Published: March 2021

The COVID-19 pandemic has been accompanied by the largest mobilization of therapeutic convalescent plasma (CCP) in over a century. Initial identification of high titer units was based on dose-response data using the Ortho VITROS IgG assay. The proliferation of SARS-CoV-2 serological assays and non-uniform application has led to uncertainty about their interrelationships. The purpose of this study was to establish correlations and analogous cutoffs between commercially available serological tests (Ortho, Abbott, Roche), a spike ELISA, and a virus neutralization assay using convalescent plasma from a cohort of 79 donors from April 2020. Relationships relative to FDA-approved cutoffs under the CCP EUA were identified by linear regression and receiver operator characteristic curves. Relative to the Ortho VITROS assay, the r2 of the Abbott, Roche, the anti-Spike ELISA and the neutralizing assay were 0.58, 0.5, 0.82, and 0.44, respectively. The best correlative index for establishing high-titer units was 3.82 S/C for the Abbott, 10.89 COI for the Roche, 1:1,202 for the anti-Spike ELISA, and 1:200 by the neutralization assay. The overall agreement using derived cutoffs compared to the CCP EUA Ortho VITROS cutoff of 9.5 was 92.4% for Abbott, 84.8% for Roche, 87.3% for the anti-S ELISA and 78.5% for the neutralization assay. Assays based on antibodies against the nucleoprotein (Roche, Abbott) and neutralizing antibody tests were positively associated with the Ortho assay, although their ability to distinguish FDA high-titer specimens was imperfect. The resulting relationships help reconcile results from the large body of serological data generated during the COVID-19 pandemic.
In vivoregulation of fluorescent fusion proteins by engineered kinases
Authors: Lepeta Katarzyna , Roubinet Chantal , Kanca Oguz , Ochoa-Espinosa Amanda , Bieli Dimitri , Cabernard Clemens , Affolter Markus , Caussinus Emmanuel
Published: March 2021

Reversible protein phosphorylation by kinases in extensively used to control a plethora of processes essential for proper development and homeostasis of multicellular organisms. One main obstacle in studying the role of a defined kinase-substrate interaction is that kinases form complex signaling networks and most often phosphorylate multiple substrates involved in various cellular processes. In recent years, several new approaches have been developed to control the activity of a given kinase. However, most of them fail to regulate a single protein target, likely hiding the effect of a unique kinase-substrate by pleiotropic effects. To overcome this limitation, we have created protein binder-based engineered kinases for direct, robust and tissue-specific phosphorylation of target fluorescent protein fusionsin vivo. We show that synthetic Rok kinases, based on theDrosophilaortholog of Rho-associated protein kinase (ROCK), are functional enzymes and can activate myosin II through phosphorylation of Sqh::GFP or Sqh::mCherry in different morphogenetic processes in a developing fly embryo. We next use the system to study the impact of actomyosin activation specifically in the developing tracheal branches and showed that ectopic activation of actomyosin with engineered Rok kinase did not prevent cell intercalation nor the formation of autocellular junctions. We assume that this approach can be adapted to other kinases and targets in various eukaryotic genetic systems.
Identification and prediction of developmental enhancers in sea urchin embryos
Authors: Arenas-Mena César , Miljovska Sofija , Rice Edward J. , Gurges Justin , Shashikant Tanvi , Ercan Sevinç , Danko Charles G.
Published: March 2021

Background

The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.

Results

We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimentalcis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonic territories. Using the three functional genomic data types, machine learning models are trained and tested to classify and quantitatively predict the enhancer activity of several hundred genomic regions previously validated with reporter constructs invivo.

Conclusions

Overall, chromatin accessibility and transcription have substantial power for predicting enhancer activity. For promoter-overlapping cis-regulatory elements in particular, the distribution of Pol II is the best predictor of enhancer activity in blastula embryos. Furthermore, ATAC- and PRO-seq predictive value is stage dependent for the promoter-overlapping subset. This suggests that the sequence of regulatory mechanisms leading to transcriptional activation have distinct relevance at different levels of the developmental gene regulatory hierarchy deployed during embryogenesis.
Antidepressants stimulate lipoprotein(a) macropinocytosis via serotonin-enhanced cell surface binding
Authors: Deo Nikita , Siddiqui Halima , Madani Golnoush , Rutledge Malcolm , Williams Michael JA , McCormick Sally PA , Redpath Gregory MI
Published: March 2021

We recently found that plasminogen receptors regulate the plasma membrane binding and uptake of Lp(a) via macropinocytosis. In this study, we sought to further define lipoprotein(a) [Lp(a)] macropinocytosis, discovering an unexpected role for antidepressants and serotonin in the regulation of this process. We found that the tricyclic antidepressant imipramine enhanced Lp(a) uptake, in contradiction of its published role as a macropinocytosis inhibitor. Extending these experiments to the commonly used serotonin uptake inhibitors (SSRIs) citalopram and sertraline, we found that citalopram stimulated, while sertraline inhibited, Lp(a) uptake. Imipramine and citalopram enhanced cell surface binding of Lp(a) rather than upregulating macropinocytosis. Consistent with imipramine and citalopram boosting extracellular serotonin levels, serotonin itself also enhanced Lp(a) surface binding and uptake. Imipramine and serotonin increased expression of the plasminogen receptor with a C-terminal lysine (PlgRKT), a receptor known to enhance cell surface binding of Lp(a), likely accounting for their effects on Lp(a) uptake. Finally, imipramine and citalopram increased Lp(a) delivery into Rab11 recycling endosomes, but not degradative pathways in the cell. These findings indicate citalopram and imipramine may have utility as a potential Lp(a)-lowering therapeutic in people suffering from depression who often have elevated Lp(a) levels and an increased risk of cardiovascular disease.
High content 3D imaging method for quantitative characterization of organoid development and phenotype
Authors: Beghin Anne , Grenci Gianluca , Rajendiran Harini , Delaire Tom , Mohamad Raffi Saburnisha Binte , Blanc Damien , Mets Richard de , Ong Hui Ting , Acharya Vidhyalakshmi , Sahini Geetika , Racine Victor , Galland Remi , Sibarita Jean-Baptiste , Viasnoff Virgile
Published: March 2021

Quantitative analysis on a large number of organoids can provide meaningful information from the morphological variability observed in 3D organotypic cultures, called organoids. Yet, gathering statistics of growing organoids is currently limited by existing imaging methods and subsequent image analysis workflows that are either restricted to 2D, limited in resolution, or with a low throughput. Here, we present an automated high content imaging platform synergizing high density organoid cultures with 3D live light-sheet imaging. The platform is an add-on to a standard inverted microscope. We demonstrate our capacity to collect libraries of 3D images at a rate of 300 organoids per hour, enabling training of artificial intelligence-based algorithms to quantify the organoid morphogenetic organization at multiple scales with subcellular resolution. We validate our approach on different organotypic cell cultures (stem, primary, and cancer), and quantify the development of hundreds of neuroectoderm organoids (from human Embryonic Stem Cells) at cellular, multicellular and whole organoid scales.
Transcriptome-based phylogeny and whole-genome duplication in Theaceae
Authors: Zhang Qiong , Zhao Lei , Zhao Jian-Li , Folk Ryan A. , Zamora Nelson , Soltis Pamela S. , Soltis Douglas E. , Yang Shi-Xiong , Gao Lian-Ming , Peng Hua , Yu Xiang-Qin
Published: March 2021

Theaceae, with three tribes and nine genera, is a family of great economic and ecological importance. Recent phylogenetic analyses based on plastid genome resolved the relationship among three tribes and the intergeneric relationships within Gordonieae and Stewartieae. However, generic level relationships within the largest tribe Theeae were not fully resolved and potential hybridization among genera within Theeae revealed previously also remains to be tested further. Here we conducted a comprehensive phylogenomic study of Theaceae based on transcriptomes and low-depth whole-genome sequencing of 57 species as well as additional plastome sequence data from previous work. Phylogenetic analyses suggested that Stewartieae was the first-diverging clade in Theaceae, consistent with previous study using plastomic data. Within Theeae, the highly supportedApterosperma-Laplaceaclade grouped withPyrenariawith maximum support based on the partitioned and unpartitioned concatenation analyses using the 610 low-copy nuclear genes, leavingCamelliaandPolysporaas another sister genera in the tribe. PhyloNet analyses suggested one reticulation event withinCamelliaandPyrenariarespectively, but no intergeneric reticulations were detected in Theeae. Another introgression was found betweenGordonia lasianthusand the common ancestor of Gordonieae during the Late Oligocene. The existing land bridges (e.g. Bering land bridge) might have facilitated this ancient introgression. Further researches need to be conducted to uncover the interspecific introgression pattern withinCamellia.Ks distribution analyses supported the tea family shared one whole-genome duplication (WGD) event Ad-β, which was recently mapped to the clade containing core Ericales, Primuloids, Polemonioids and Lecythidaceae.
Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma
Authors: Izadi Fereshteh , Sharpe Benjamin P. , Breininger Stella P. , Secrier Maria , Gibson Jane , Walker Robert , Rahman Saqib , Devonshire Ginny , Lloyd Megan A , Walters Zoë S. , Fitzgerald Rebecca C. , Rose-Zerilli Matthew J. J. , Underwood Tim J.
Published: March 2021

Neoadjuvant therapy followed by surgery is the standard of care for locally advanced esophageal adenocarcinoma (EAC). Unfortunately, response to neoadjuvant chemotherapy (NAC) is poor (<20%), as is the overall survival benefit at 5 years (5%). The EAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns may result in chemotherapy sensitivity or resistance. To identify associations between genomic events and response to NAC in EAC, a comparative genomic analysis was performed in 65 patients with extensive clinical and pathological annotation using whole-genome sequencing (WGS). We defined response using Mandard Tumor Regression Grade (TRG), with responders classified as TRG1-2 (n=27) and non-responders classified as TRG4-5 (n=38). We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs 1.70/Mb,P=0.036) and elevated copy number variation in non-responders (282 vs 136/patient,P<0.001). We identified copy number variants unique to each group in our cohort, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of note,NAV3mutations were exclusively present in the non-responder group with a frequency of 22%. Thus, lower mutation burden, higher chromosomal instability and specific copy number alterations are associated with resistance to NAC.
Regulatory FOXP3+ T cells in uterine sarcomas are associated with favorable prognosis, low extracellular matrix expression and reduced YAP activation
Authors: Gultekin Okan , Gonzalez-Molina Jordi , Hardell Elin , Moyano-Galceran Lidia , Mitsios Nicholas , Mulder Jan , Kokaraki Georgia , Isaksson Anders , Sarhan Dhifaf , Lehti Kaisa , Carlson Joseph W.
Published: March 2021

Purpose

Uterine sarcomas are rare but deadly malignancies without effective treatment. The goal of this study was to characterize and identify potential mechanisms underlying observed variations in the immune microenvironment of different sarcoma subtypes, using integrated clinicopathological and molecular methods.

Experimental design

Fifty-eight cases of uterine sarcoma with full clinicopathological annotation were analyzed for their immune landscape in the tumor microenvironment, gene, and protein expression. Cases included leiomyosarcoma (LMS; n=13), low-grade endometrial stromal sarcoma (ESS; n=16), undifferentiated uterine sarcoma (UUS; n=26), and YWHAE-FAM22 translocation-bearing ESS (YFAM; n=3). Image analysis was used to quantify immune cells and immune regulatory proteins. Gene ontology and network enrichment analysis of matching transcriptomic data was used to relate over- and under expressed genes to pathways and further to the immune phenotype and clinicopathological findings.

Results

Immune cell characterization revealed overall prevalence of regulatory T cells and the pro-tumor M2-like macrophages. Cytotoxic T cells were only found in ESS and UUS tumors. Expression of immune regulatory proteins was heterogeneous, with PD-L1 being undetectable. Hierarchical clustering of patients showed four immune signatures independent of tumor type, where infiltration of non-exhausted FOXP3+cells and M1-like macrophages were associated with greater overall survival. High CD8+/FOXP3+ratio in UUS and ESS was associated with poor survival and upregulation of extracellular matrix (ECM)-related genes and proteins and YAP nuclear localization.

Conclusions

Uterine sarcomas present distinct immune signatures with prognostic value, independent of tumor type. This study suggests that the ECM is a potential regulator of the immune microenvironment in uterine sarcomas.
Quantifying evolutionary constraints on the intronic branch point sequence in the bovine and human genome
Authors: Kadri Naveen Kumar , Mapel Xena Marie , Pausch Hubert
Published: March 2021

The branch point sequence is a cis-acting intronic motif required for mRNA splicing. Despite their functional importance, branch point sequences are not routinely annotated. Here we predict branch point sequences in 179,476 bovine introns and investigate their variability using a catalogue of 29.4 million variants detected in 266 cattle genomes. We localize the bovine branch point within a degenerate heptamer “nnyTrAy”. An adenine residue at position 6, that acts as branch point, and a thymine residue at position 4 of the heptamer are more strongly depleted for mutations than coding sequences suggesting extreme purifying selection. We provide evidence that mutations affecting these evolutionarily constrained residues lead to alternative splicing. We confirm evolutionary constraints on branch point sequences using a catalogue of 115 million SNPs established from 3,942 human genomes of the gnomAD database.
Verticillium dahliaeeffector VDAL protects MYB6 from degradation by interacting with PUB25/26 E3 ligases for enhancing Verticillium wilt resistance inArabidopsis
Authors: Ma Aifang , Zhang Dingpeng , Wang Guangxing , Wang Kai , Li Zhen , Gao Yuanhui , Li Hengchang , Bian Chao , Cheng Jinkui , Han Yinan , Yang Shuhua , Gong Zhizhong , Qi Junsheng
Published: March 2021

Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophicVerticillium dahliae(V. dahliae)-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leavesin vitro,but enhances the resistance toV. dahliaewhen overexpressed inArabidopsisor cotton without affecting the plant growth and development. VDAL protein interacts withArabidopsisE3 ligases PUB25 and PUB26 (PUBs) and is ubiquitinated by PUBsin vitro. However, VDAL is not degraded by PUB25 or PUB26in planta. Besides, thepub25 pub26double mutant shows higher resistance toV. dahliaethan the wild type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist theV. dahliaeinfection without causing a hypersensitive response (HR), Alternatively, in order to take nutrients from host cells, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance.

One-sentence summary

Ectopically expressed VDAL inArabidopsisalleviates the degradation of a positive disease response factor MYB6 through its interaction with PUB25/26 E3 ligases.
RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization
Authors: Collombet Samuel , Rall Isabell , Dugast-Darzacq Claire , Heckert Alec , Halavatyi Aliaksandr , Le Saux Agnes , Dailey Gina , Darzacq Xavier , Heard Edith
Published: March 2021

Sub-nuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments, where transcription and epigenetic factors are either concentrated or depleted. The inactive X chromosome offers a paradigm for studying sub-nuclear compartmentalization. When the non-codingXistRNA coats the X chromosome, it recruits repressors and chromatin factors that trigger gene silencing, and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in X-chromosome inactivation (XCI) and might explain exclusion of the transcription machinery by preventing its diffusion into theXist-coated territory. Here, using quantitative fluorescence microscopy and single particle tracking, we show that RNA polymerase II (RNAPII) freely accesses theXistterritory during initiation of XCI, and that its diffusion is not prevented by biophysical constraints. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin bound fraction. These findings demonstrate that initial exclusion of RNA Pol2 from the inactive X is a consequence of its reduced binding rate at the chromatin and gene level, rather than the biophysical compartmentalization of the inactive X heterochromatin domain. The Xist silent compartment is thus a biochemical rather than a biophysical compartment, at least during initiation of XCI.
Robust, Fiducial-Free Drift Correction for Super-resolution Imaging
Authors: Wester Michael J. , Schodt David J. , Mazloom-Farsibaf Hanieh , Fazel Mohamadreza , Pallikkuth Sandeep , Lidke Keith A.
Published: March 2021

We describe a robust, fiducial-free method of drift correction for use in single molecule localization-based super-resolution methods. The method combines periodic 3D registration of the sample using brightfield images with a fast post-processing algorithm that corrects residual registration errors and drift between registration events. The method is robust to low numbers of collected localizations, requires no specialized hardware, and provides stability and drift correction for an indefinite time period.
Host genetic control of succession in the switchgrass leaf fungal microbiome
Authors: VanWallendael A. , Benucci G. M. N. , da Costa P. B. , Fraser L. , Sreedasyam A. , Fritschi F. , Juenger T. E. , Lovell J. T. , Bonito G. , Lowry D. B.
Published: March 2021

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.
Draft Genome of the Korean smeltHypomesus nipponensisand its transcriptomic responses to heat stress in the liver and muscle
Authors: Xuan Biao , Park Jongbin , Choi Sukjung , You Inhwan , Nam Bo-Hye , Noh Eun Soo , Kim Eun Mi , Song Mi-Young , Shin Younhee , Jeon Ji-Hyeon , Kim Eun Bae
Published: March 2021

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome ofH. nipponensisand transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome ofH. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic ofH. nipponensiswill be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.
Histone H3 dopaminylation in ventral tegmental area underlies heroin-induced maladaptive plasticity
Authors: Fulton Sasha L. , Mitra Swarup , Lepack Ashley E. , Martin Jennifer A. , Dietz David M. , Maze Ian
Published: March 2021

Persistent transcriptional eventsamples were incubated on ice for 30 min and then centrifugeds in ventral tegmental area (VTA) and other reward relevant brain regions contribute to enduring behavioral adaptations that characterize substance use disorder (SUD). Recent data from our laboratory indicate that aberrant accumulation of the newly discovered histone post-translational modification (PTM), H3 dopaminylation at glutamine 5 (H3Q5dop), contributes significantly to cocaine-seeking behavior following prolonged periods of abstinence. It remained unclear, however, whether this modification is important for relapse vulnerability in the context of other drugs of abuse, such as opioids. Here, we showed that H3Q5dop plays a critical role in heroin-mediated transcriptional plasticity in midbrain. In rats undergoing abstinence from heroin self-administration (SA), we found acute and persistent accumulation of H3Q5dop in VTA. By attenuating H3Q5dop during abstinence, we both altered gene expression programs associated with heroin withdrawal and reduced heroin-primed reinstatement behavior. These findings thus establish an essential role for H3Q5dop, and its downstream transcriptional consequences, in opioid-induced plasticity in VTA.

SIGNIFICANCE STATEMENT

Opioid addiction is a chronically relapsing disorder defined by pathological drug-seeking behavior. Persistent relapse vulnerability is hypothesized to reflect a functional “rewiring” of reward-processing circuitry in the brain. This phenomenon is precipitated by drug-induced alterations in transcriptional plasticity of midbrain dopamine neurons, indicating an important role for epigenetic regulatory mechanisms in opioid dependence. We found that the newly discovered histone modification, H3 dopaminylation at glutamine 5 (H3Q5dop), was increased in ventral tegmental area (VTA) during periods of abstinence. H3Q5dop accumulation was found to regulate transcriptional programs associated with chronic heroin exposure. Using viral-mediated gene therapy to reduce H3Q5dop accumulation during abstinence resulted in attenuated heroin-primed seeking behaviors. Together, our results indicate that H3Q5dop plays an abstinence-specific role in regulating heroin-induced behavioral plasticity during prolonged abstinence.
Dopaminergic regulation of vestibulo-cerebellar circuits through unipolar brush cells
Authors: Canton-Josh Jose Ernesto , Qin Joanna , Salvo Joseph , Kozorovitskiy Yevgenia
Published: March 2021

While multiple monoamines modulate cerebellar output, the mechanistic details of dopaminergic signaling in the cerebellum remain poorly understood. Here we show that Drd1 dopamine receptors are expressed in unipolar brush cells (UBCs) of the cerebellar vermis. Drd1 activation increases UBC firing rate and postsynaptic NMDA receptor-mediated currents. Using anatomical tracing andin situhybridization, we tested three hypotheses about the source of cerebellar dopamine. We exclude midbrain dopaminergic nuclei and tyrosine hydroxylase-positive Purkinje cells as potential sources, supporting the possibility of dopaminergic co-release from locus coeruleus (LC) axons. Using an optical dopamine sensor GRABDA, electrical stimulation, and optogenetic activation of LC fibers in the acute slice, we find evidence for monoamine release onto Drd1-expressing UBCs. Altogether, we propose that the LC regulates cerebellar cortex activity by co-releasing dopamine onto UBCs to modulate their response to cerebellar inputs. Purkinje neurons directly inhibit these Drd1-positive UBCs, forming a dopamine-sensitive recurrent vestibulo-cerebellar circuit.
Manifestations of genetic risk for Alzheimer’s Disease in the blood: a cross-sectional multi-omic analysis in healthy adults aged 18-90+
Authors: Heath Laura , Earls John C. , Magis Andrew T. , Kornilov Sergey A. , Lovejoy Jennifer C. , Funk Cory C. , Rappaport Noa , Logsdon Benjamin A. , Mangravite Lara M. , Kunkle Brian W. , Martin Eden R. , Naj Adam C. , Ertekin-Taner Nilüfer , Golde Todd E. , Hood Leroy , Price Nathan D. ,   Alzheimer’s Disease Genetics Consortium
Published: March 2021

Deeply phenotyped cohort data can elucidate differences associated with genetic risk for common complex diseases across an age spectrum. Previous work has identified genetic variants associated with Alzheimer’s disease (AD) risk from large-scale genome-wide association study meta-analyses. To explore effects of known AD-risk variants, we performed a phenome-wide association study on ~2000 clinical, proteomic, and metabolic blood-based analytes obtained from 2,831 cognitively normal adult clients of a consumer-based scientific wellness company. Results uncovered statistically significant SNP-analyte associations for five genetic variants after correction for multiple testing (for SNPs in or nearNYAP1, ABCA7, INPP5D, andAPOE). These effects were detectable from early adulthood. Sex modified the effects of four genetic variants, with multiple interrelated immune-modulating effects associated with thePICALMvariant. Sex-stratified GWAS results from an independent AD case-control meta-analysis supported sexspecific disease effects of thePICALMvariant, highlighting the importance of sex as a biological variable. These analyses support evidence from previous functional genomics studies in the identification of a causal variant within thePILRAgene. Taken together, this study highlights clues to the earliest effects of AD genetic risk variants in individuals where disease symptoms have not (yet) arisen.
Modulation masking and fine structure shape neural envelope coding to predict speech intelligibility across diverse listening conditions
Authors: Viswanathan Vibha , Bharadwaj Hari M. , Shinn-Cunningham Barbara G. , Heinz Michael G.
Published: March 2021

A fundamental question in the neuroscience of everyday communication is how scene acoustics shape the neural processing of attended speech sounds and in turn impact speech intelligibility. While it is well known that the temporal envelopes in target speech are important for intelligibility, how the neural encoding of target-speech envelopes is influenced by background sounds or other acoustic features of the scene is unknown. Here, we combine human electroencephalography with simultaneous intelligibility measurements to address this key gap. We find that the neural envelope-domain signal-to-noise ratio in target-speech encoding, which is shaped by masker modulations, predicts intelligibility over a range of strategically chosen realistic listening conditions unseen by the predictive model. This provides neurophysiological evidence for modulation masking. Moreover, using high-resolution vocoding to carefully control peripheral envelopes, we show that target-envelope coding fidelity in the brain depends not only on envelopes conveyed by the cochlea, but also on the temporal fine structure (TFS), which supports scene segregation. Our results are consistent with the notion that temporal coherence of sound elements across envelopes and/or TFS influences scene analysis and attentive selection of a target sound. Our findings also inform speech-intelligibility models and technologies attempting to improve real-world speech communication.
Insights intoin vivoadipocyte differentiation through cell-specific labeling in zebrafish
Authors: Lepanto Paola , Levin Florencia , Koziol Uriel , Malacrida Leonel , Badano José L.
Published: March 2021

White adipose tissue hyperplasia has been shown to be crucial for handling excess energy in healthy ways. Though adipogenesis mechanisms have been underscoredin vitro, we lack information on how tissue and systemic factors influence the differentiation of new adipocytes. While this could be studied in zebrafish, adipocyte identification currently relies on neutral lipid labeling, thus precluding access to cells in early stages of differentiation. Here we report the generation and analysis of a zebrafish line with the transgenefabp4(-2.7):EGFPcaax. In vivoconfocal microscopy of the pancreatic and abdominal visceral depots of transgenic larvae, revealed the presence of labeled mature adipocytes as well as immature cells in earlier stages of differentiation. Through co-labeling for blood vessels, we observed a close interaction of differentiating adipocytes with endothelial cells through cell protrusions. Finally, we implemented hyperspectral imaging and spectral phasor analysis in Nile Red labeled transgenic larvae and revealed the lipid metabolic transition towards neutral lipid accumulation of differentiating adipocytes. Altogether our work presents the characterization of a novel adipocyte-specific label in zebrafish and uncovers previously unknown aspects ofin vivoadipogenesis.

Summary statement

Analysis of the differentiation of adipocytesin vivothrough cell-specific labeling in zebrafish, revealed their early interaction with blood vessels as well as early lipid metabolic changes.