bluuebunny/crossref_metadata_2025 huggingface dataset:
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
Authors: Brůna Tomáš , Hoff Katharina J , Lomsadze Alexandre , Stanke Mario , Borodovsky Mark
Published: January 2021

The task of eukaryotic genome annotation remains challenging. Only a few genomes could serve as standards of annotation achieved through a tremendous investment of human curation efforts. Still, the correctness of all alternative isoforms, even in the best-annotated genomes, could be a good subject for further investigation. The new BRAKER2 pipeline generates and integrates external protein support into the iterative process of training and gene prediction by GeneMark-EP+ and AUGUSTUS. BRAKER2 continues the line started by BRAKER1 where self-training GeneMark-ET and AUGUSTUS made gene predictions supported by transcriptomic data. Among the challenges addressed by the new pipeline was a generation of reliable hints to protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. In comparison with other pipelines for eukaryotic genome annotation, BRAKER2 is fully automatic. It is favorably compared under equal conditions with other pipelines, e.g. MAKER2, in terms of accuracy and performance. Development of BRAKER2 should facilitate solving the task of harmonization of annotation of protein-coding genes in genomes of different eukaryotic species. However, we fully understand that several more innovations are needed in transcriptomic and proteomic technologies as well as in algorithmic development to reach the goal of highly accurate annotation of eukaryotic genomes.
Clinical, molecular, metabolic, and immune features associated with oxidative phosphorylation in melanoma brain metastases
Authors: Fischer Grant M , Guerrieri Renato A , Hu Qianghua , Joon Aron Y , Kumar Swaminathan , Haydu Lauren E , McQuade Jennifer L , Vashisht Gopal Y N , Knighton Barbara , Deng Wanleng , Hudgens Courtney W , Lazar Alexander J , Tetzlaff Michael T , Davies Michael A
Published: January 2021

Background

Recently, we showed that melanoma brain metastases (MBMs) are characterized by increased utilization of the oxidative phosphorylation (OXPHOS) metabolic pathway compared to melanoma extracranial metastases (ECMs). MBM growth was inhibited by a potent direct OXPHOS inhibitor, but observed toxicities support the need to identify alternative therapeutic strategies. Thus, we explored the features associated with OXPHOS to improve our understanding of the pathogenesis and potential therapeutic vulnerabilities of MBMs.

Methods

We applied an OXPHOS gene signature to our cohort of surgically resected MBMs that had undergone RNA-sequencing (RNA-seq) (n = 88). Clustering by curated gene sets identified MBMs with significant enrichment (High-OXPHOS; n = 21) and depletion (Low-OXPHOS; n = 25) of OXPHOS genes. Clinical data, RNA-seq analysis, and immunohistochemistry were utilized to identify significant clinical, molecular, metabolic, and immune associations with OXPHOS in MBMs. Preclinical models were used to further compare melanomas with High- and Low-OXPHOS and for functional validation.

Results

High-OXPHOS MBMs were associated with shorter survival from craniotomy compared to Low-OXPHOS MBMs. High-OXPHOS MBMs exhibited an increase in glutamine metabolism, and treatment with the glutaminase inhibitor CB839 improved survival in mice with MAPKi-resistant, High-OXPHOS intracranial xenografts. High-OXPHOS MBMs also exhibited a transcriptional signature of deficient immune activation, which was reversed in B16-F10 intracranial tumors with metformin treatment, an OXPHOS inhibitor.

Conclusions

OXPHOS is associated with distinct clinical, molecular, metabolic, and immune phenotypes in MBMs. These associations suggest rational therapeutic strategies for further testing to improve outcomes in MBM patients.
A novel loss-of-function mutation in LACC1 underlies hereditary juvenile arthritis with extended intra-familial phenotypic heterogeneity
Authors: Butbul Aviel Yonatan , Ofir Ayala , Ben-Izhak Ofer , Vlodavsky Euvgeni , Karbian Netanel , Brik Riva , Mevorach Dror , Magen Daniella
Published: January 2021

Objective

To investigate phenotypic and molecular characteristics of a consanguineous family with autosomal-recessive, polyarticular, juvenile isiopathic arthriris (JIA) with extra-articular manifestations, including renal amyloidosis and Crohn’s disease, associated with a novel homozygous truncating variant in LACC1.

Methods

Whole exome sequencing (WES) or targeted Sanger verification were performed in 15 participants. LACC1 expression and cytokine array were analysed in patient-derived and CRISPR/Cas9-generated LACC1-knockout macrophages (Mϕ).

Results

A homozygous truncating variant (p.Glu348Ter) in LACC1 was identified in three affected and one asymptomatic family member, and predicted harmful by causing premature stop of the LACC1 protein sequences, and by absence from ethnically-matched controls and public variation databases. Expression studies in patient-derived macrophages (Mϕ) showed no endogenous p.Glu348Ter-LACC1 RNA transcription or protein expression, compatible with nonsense-mediated mRNA decay. WES analysis in the asymptomatic homozygous subject for p. Glu348Ter-LACC1 detected an exclusive heterozygous variant (p.Arg928Gln) in complement component C5. Further complement activity analysis suggested a protective role for the p.Arg928Gln-C5 variant as a phenotypic modifier of LACC1-associated disease. Finally, cytokine profile analysis indicated increased levels of pro-inflammatory cytokines in LACC1-disrupted as compared with wild-type Mϕ.

Conclusions

Our findings reinforce the role of LACC1 disruption in autosomal-recessive JIA, extend the clinical spectrum and intra-familial heterogeneity of the disease-associated phenotype, indicate a modulatory effect of complement factor C5 on phenotypic severity, and suggest an inhibitory role for wild-type LACC1 on pro-inflammatory pathways.
Rapid online teaching: movement of animal science courses online during COVID-19. Case study: pedagogical decisions in transitioning animal science courses online
Authors: Barnes Taylor L , Ramsey W Shawn , Dunlap Kathrin A
Published: January 2021

Traditionally, earning a degree in animal science requires many face-to-face, hands-on courses; however, the COVID-19 pandemic created a situation in which traditional delivery of these courses may not be feasible as they provide a health risk to our students, teaching assistants, and instructors alike. This examination of two pedagogically different courses and how each was transitioned to an online format highlights the types of teaching decisions that are required to effectively teach animal science in an online format. The Farm Animal Production Systems lab was an animal handling and production practices lab, and although the transition to online delivery did not allow for students to participate in traditional hands-on development of skills, various resources were utilized that still achieved the development of animal handling concepts that will prepare students for later courses and work with live animals. In contrast, the Animal Science Laboratory Teaching Methods course remained consistent in format through the transition to online because students were still able to participate in discussion-based activities via Zoom meetings each week due to the small class size, which helped to maintain student engagement. However, the final teaching experience was modified to an alternative assignment. The alternate assignment included self-reflection and course evaluation that will help to improve both the Farm Animal Production Systems laboratory and the Animal Science Teaching Methods course in the future. Although COVID-19 has been a challenge that disrupted traditional courses, it has provided opportunities for a traditionally hands-on discipline, such as animal science, to more effectively engage students via an online platform.
The Demand for Advice: Theory and Empirical Evidence from Farmers in Sub-Saharan Africa
Authors: Naeher Dominik , Schündeln Matthias
Published: January 2021

Low levels of investment into modern technologies, and limited use of measures that have low monetary cost but the potential for high yields, are often regarded as obstacles to further agricultural development. This paper investigates farmers’ demand for one such measure, namely agricultural advisory services. These have modest (most frequently zero) monetary user cost but, according to some recent research, have the potential to result in large increases of yields. Yet demand for these extension services is often low. We propose that costly attention may be part of the explanation for this. In our model, advisory services are available free of charge, but positive effects on production are only realized if farmers devote attention to listening to and implementing the provided advice. Modeling farmers as rational decision makers facing scarce attention, we identify the circumstances under which farmers may optimally abstain from demanding advisory services. The model complements the insights of other theories commonly used to explain suboptimal farm decisions and outcomes, and generates testable predictions, which are consistent with empirical evidence based on a large farm-level panel dataset from Sub-Saharan Africa.
Pregnancy Loss and Cardiovascular Disease: A Nationwide Cohort Study
Authors: Mikkelsen Anders P. , Egerup Pia , Kolte Astrid M. , Westergaard David , Torp-Pedersen Christian , Nielsen Henriette S. , Lidegaard øjvind
Published: January 2021

Objectives

To examine how pregnancy loss influences the risk of cardiovascular disease later in life.

Design

Prospective historical cohort study.

Setting

Danish nationwide health registries.

Participants

All Danish women with a recorded pregnancy from 1977 to 2017.

Main outcome measures

Venous thromboembolism, myocardial infarction, or ischemic stroke.

Results

In this two-part study, part one evaluated the 20-year absolute risk of cardiovascular disease from age 40 among 596,699 women with a full registered reproductive history. Adjusting for calendar year, diabetes, autoimmune disease, live births, and education, the absolute risk of an outcome after 0 and ≥4 pregnancy losses, respectably was: venous thromboembolism 3.0% (95% CI 2.8 to 3.2%) and 5.0% (3.4 to 6.8%); myocardial infarction 1.5% (1.4 to 1.6%) and 2.4% (1.4 to 3.6%); ischemic stroke 2.0% (1.9 to 2.1%) and 2.6% (1.5 to 3.6%). Prior stillbirth increased the absolute risk of later venous thromboembolism by 1.1% (0.2 to 2.3%); myocardial infarction by 1.1% (0.3 to 2.0%).

In study part two, we included 966,490 women from first pregnancy in a time-dependent Cox regression model. Adjusted for confounders, each additional pregnancy loss increased the hazard ratio of venous thromboembolism 1.10 (95% CI 1.07 to 1.13); myocardial infarction 1.12 (1.07 to 1.18); and ischemic stroke 1.10 (1.06 to 1.14). Stillbirth was strongly associated with myocardial infarction before age 40, adjusted hazard ratio of 4.60 (2.65 to 8.00).

Conclusion

Pregnancy loss was associated with later venous thromboembolism, myocardial infarction, and ischemic stroke. The absolute and relative risk of outcomes increased in a dose-response manner with increasing numbers of prior pregnancy losses. Stillbirth was strongly associated with myocardial infarction before age 40.
Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation of long non-coding RNAs
Authors: Lelong Emeline I. J. , Adjibade Pauline , Joncas France-Hélène , Khelifi Gabriel , Grenier Valerie ST.-Sauveur , Zoubedi Amina , Lambert Jean-Philippe , Toren Paul , Mazroui Rachid , Hussein Samer M. I.
Published: January 2021

Emerging evidence associates translation factors and regulators to tumorigenesis. Recent advances in our ability to perform global translatome analyses indicate that our understanding of translational changes in cancer resistance is still limited. Here, we generated an enzalutamide-resistant prostate cancer (PCa) model, which recapitulated key features of clinical enzalutamide-resistant PCa. Using this model and polysome profiling, we investigated global translation changes that occur during the acquisition of PCa resistance. We found that enzalutamide-resistant cells exhibit a discordance in biological pathways affected in their translatome relative to their transcriptome, a deregulation of proteins involved in translation, and an overall decrease in translational efficiency. We also show that genomic alterations in proteins with high translational efficiency in enzalutamide-resistant cells are good predictors of poor patient prognosis. Additionally, long non-coding RNAs in enzalutamide-resistant cells show increased association with ribosomes, higher translation efficiency, and an even stronger correlation with poor patient prognosis. Taken together, this suggests that aberrant translation of coding and non-coding genes are strong indicators of PCa enzalutamide-resistance. Our findings thus point towards novel therapeutic avenues that may target enzalutamide resistant PCa.
How social engagement against Covid-19 in a Brazilian Slum helped mitigate rising statistics
Authors: Evangelista Heitor , Gonçalves Sérgio J. , Sodré Eduardo Delfino , Nogueira Juliana , Goldenberg-Barbosa Rodrigo , Magalhães Newton , dos Santos Angela M.G. , Godoi Ricardo H.M. , Amaral Cesar , da Silva Marcio Cataldo G. , de Oliveira Daniel A. Junger , Porto Luís Cristóvão
Published: January 2021

Objectives

For many underdeveloped countries, strategies implemented by social communities allied to scientific knowledge may be a rote to attenuate the rapid spread of Covid-19 cases and allow services to the population. This work presents a joint effort collaboration between scientists and underserved community groups from a Brazilian slum/Santa Marta in Rio de Janeiro City in the fight against Covid-19. Measurements of contamination in the air near the ground, georeferencing of data of infected people, were regressed with sanitization activities aiming at reducing the Covid-19 incidence.

Methods

We monitored aerosol containing SARS-Cov-2 virus in outdoor ambient air using various virus collection mediums (solid, liquid, and gelatinous substrates) at different aerodynamic sizes. We implemented a local statistics survey for the Covid-19 database correlated with varying sanitization levels between April 2020 and June 2021 developed in the Santa Marta slum.

Findings

We detected the SARS-CoV-2 virus in the air near the ground in diameters ranging from 0.25 to 0.5 µm, demonstrating that there is a circulation of the virus in the slum atmosphere. We demonstrate that Covid-19 cases for the Santa Marta slum were significatively lowered with improved sanitization levels (r = −0.74).

Conclusions

Despite previous publications that discarded the use of sanitization as a relevant tool in the fight against Covid-19, our results suggest that profits can be achieved in mitigating Covid-19 in underserved community sites. Furthermore, a permanent sanitization activity may induce positive social behavior for the sake of combating Covid-19.
Single cell proteomics of tumor compartments identifies differential kinase activities defining sensitivity to mTOR-PI3-kinase inhibition
Authors: Karabacak Nezihi Murat , Zheng Yu , Dubash Taronish D. , Burr Risa , Micalizzi Douglas S. , Wittner Ben S. , Wiley Devon , Comaills Valentine , Emmons Erin , Niederhoffer Kira , Ho Uyen , Nieman Linda , Haas Wilhelm , Stott Shannon L. , Ting David T. , Miyamoto David T. , Haber Daniel A. , Toner Mehmet , Maheswaran Shyamala
Published: January 2021

Cancer therapy often results in heterogeneous responses in different metastatic lesions in the same patient. Inter- and intra-tumor heterogeneity in proteomic signaling within the various tumor compartments and its impact on therapy are not well characterized due to the limited sensitivity of single cell proteomic approaches. To overcome this barrier, we applied single cell mass cytometry with a customized 29-antibody panel [against cell states, receptor tyrosine kinases (RTK) and phosphoinositide 3-kinase/mammalian target of rapamycin (PI3K/mTOR)-, mitogen-activated protein kinase (MAPK)-, and cytokine-signaling] to PTEN-deleted orthotopic prostate cancer xenograft models to measure the evolution of kinase activities in different tumor compartments during metastasis and upon drug treatment. Compared with primary tumors and circulating tumor cells (CTCs), bone metastases but not lung and liver metastases exhibited elevated PI3K/mTOR signaling and RTKs including c-Met protein, which, when suppressed, impaired tumor growth in the bone. Intra-tumoral heterogeneity within tumor compartments also arises from highly proliferative EpCAMhighepithelial cells with increased PI3K and mTOR kinase activities co-existing with poorly proliferating EpCAMlowmesenchymal populations with reduced kinase activities, findings recapitulated in epithelial and mesenchymal CTC populations in metastatic prostate and breast cancer patients. Increased kinase activity in EpCAMhighcells rendered them more sensitive to PI3K/mTOR inhibition and drug resistant EpCAMlowpopulations with reduced kinase activity emerged over time. Taken together, single cell proteomics identified microenvironment- and cell state-dependent activation of kinase networks creating heterogeneity and differential drug sensitivity among and within tumor populations across different sites, defining a new paradigm of drug responses to kinase inhibitors.
Role of T cells in intrauterine administration of activated peripheral blood mononuclear cells in recurrent implantation failure
Authors: Ricaud Guillaume , Vaillancourt Cathy , Blais Véronique , Disdier Marjorie , Joao Fabien , Johnson Bruno , Benkhalifa Moncef , Miron Pierre , Bernier Jacques
Published: January 2021

Over the last few years, intrauterine administration of autologous peripheral blood mononuclear cells (PBMC) has been proposed as new immunotherapy for patients with unexplained recurrent implantation failure (RIF). In these patients, administration of activated PBMC before embryo transfer results in a 2-fold increase in live birth rates(Yang et al., 2020). In this study we evaluated the role of T cells to promotes human endometrial receptivity. On the day of ovulation, PBMC were isolated from and activated with T cells mitogen, the phytohemagglutinin (PHA) and hCG for 48-h in a conditioned culture medium. Distributions of CD4+T cells were characterized in 157 patients by flow cytometry before and after PHA/hCG activation. Cytokine production was analyzed by cytometric beads array. We observed in RIF patients a significant decrease in Th2 and natural Treg cells before activation with PHA/hCG and an increase of Th17 cells after activation compared to intrauterine sperm insemination (IUI) and in vitro fertilization (IVF) groups. Furthermore, the hCG/PHA treatment increases anti-inflammatory T cells (Th2 and Treg cells) compared to non-treated T cells. Principal component analysis (PCA) performed on CD4 T cell subtypes revealed a different cellular profile in the RIF compared to the IUI and IVF groups. This inflammatory state change could explain how endometrium immunomodulation by hCG-activated PBMC helps patients with unexplained RIF to reach implantation.
Multiplexed Imaging Analysis of the Tumor-Immune Microenvironment Reveals Predictors of Outcome in Triple-Negative Breast Cancer
Authors: Patwa Aalok , Yamashita Rikiya , Long Jin , Angelo Michael , Keren Leeat , Rubin Daniel L.
Published: January 2021

Triple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach for the discovery of methods to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion-beam imaging that produces interpretable results, and is generalizable to other cancer types.
Barth syndrome cellular models have dysregulated respiratory chain complex I and mitochondrial quality control due to abnormal cardiolipin
Authors: Anzmann Arianna F. , Sniezek Olivia L. , Pado Alexandra , Busa Veronica , Vaz Frédéric Maxime , Kreimer Simion D. , Cole Robert Norman , Le Anne , Kirsch Brian James , Claypool Steven M. , Vernon Hilary J.
Published: January 2021

Barth syndrome (BTHS) is an X-linked genetic condition caused by defects inTAZ, which encodes a transacylase involved in the remodeling of the inner mitochondrial membrane phospholipid, cardiolipin (CL). As such, CL has been implicated in numerous mitochondrial functions, and the role of defective CL in the clinical pathology of BTHS is under intense investigation. We used untargeted proteomics, shotgun lipidomics, gene expression analysis, and targeted metabolomics to identify novel areas of mitochondrial dysfunction in a new model of TAZ deficiency in HEK293 cells. Functional annotation analysis of proteomics data revealed abnormal regulation of mitochondrial respiratory chain complex I (CI), driven by the reduced abundance of 6 CI associated proteins in TAZ-deficient HEK293 cells: MT-ND3, NDUFA5, NDUFAB1, NDUFB2, NDUFB4, and NDUFAF1. This resulted in reduced assembly and function of CI in TAZ-deficient HEK293 cells as well as BTHS patient derived lymphoblast cells. We also identified increased abundance of PARL, a rhomboid protein involved in the regulation of mitophagy and apoptosis, and abnormal downstream processing of PGAM5, another mediator of mitochondrial quality control, in TAZ-deficient cells. Lastly, we modulated CL via the phospholipase inhibitor bromoenol lactone and the CL targeted SS-peptide, SS-31, and showed that each is able to remediate abnormalities in CI abundance as well as PGAM5 processing. Thus, mitochondrial respiratory chain CI and PARL/PGAM5 regulated mitochondrial quality control, both of whose functions localize to the inner mitochondrial membrane, are dysregulated due to TAZ deficiency and are partially remediated via modulation of CL.
Onset of sexual maturity of sexually propagated and wildFavites abditacolonies in northwestern Philippines
Authors: Bonilla KG , Guest JR , dela Cruz DW , Baria-Rodriguez MV
Published: January 2021

Scleractinian corals are modular colonial organisms and are the main framework builders of coral reefs. Most corals reproduce by broadcast spawning with external fertilization and these processes are essential to replenish reef coral populations. Despite decades of research, many aspects of coral reproductive biology remain poorly studied. For example, two important reproductive life history traits, colony size and age at the onset of sexual maturity, are mostly unknown for many reef-building corals. In this study, wild colonies of different size classes and colonies of a known age (i.e. colonies sexually cultured and reared from larvae to adults) of the massive scleractinianFavites abditawere examined for the presence or absence of mature oocytes to determine size and age at the onset of sexual reproduction. Fecundity at the onset of reproductive maturity across size classes of wild colonies was also determined. Surveyed and sampled colonies were grouped into three size classes based on maximum colony diameter (A = 0.1-4.0 cm, B = 4.1-8.0 cm, and C = >8.1 cm). For both wild and sexually propagated colonies, the smallest colonies containing gametes were 1.8 cm in diameter, suggesting that this is the minimum colony size at onset of sexual maturity. Colonies of size class A had lower mean oocyte counts per polyp (44 ± 6.08; mean ± SE) compared to colonies of classes B and C (469 ± 62.41, 278 ± 57.15, respectively). However, mean oocyte geometric mean diameter of size class A colonies was greater (340.38 ± 7.68 μm) than classes B and C (283.96 ± 6.94 μm, 317.57 ± 9.18 μm, respectively). Results of this study bring in to question the widely applied operational definition of coral juveniles being colonies ≤4.0 cm diameter and suggest that even quite small colonies may play a role in contributing to the natural larval pool on reefs than previously thought.
Frog nest foams exhibit pharmaceutical foam-like properties
Authors: Brozio Sarah , O’Shaughnessy Erin M. , Woods Stuart , Hall-Barrientos Ivan , Martin Patricia E. , Kennedy Malcolm W. , Lamprou Dimitrios A. , Hoskisson Paul A.
Published: January 2021

Foams have frequently been used as systems for the delivery of cosmetic and therapeutic molecules; however, there is high variability in the foamability and long-term stability of synthetic foams. The development of pharmaceutical foams that exhibit desirable foaming properties, delivering appropriate amounts of the active pharmaceutical ingredient (API) and that have excellent biocompatibility is of great interest. The production of stable foams is rare in the natural world; however, certain species of frogs have adopted foam production as a means of providing a protective environment for their eggs and larvae from a predators and parasites, to prevent desiccation, to control gaseous exchange, temperature extremes, and to reduce UV damage. These foams show great stability (up to 10 days in tropical environments) and are highly biocompatible due to the sensitive nature of amphibian skin. This work demonstrates for the first time, that nests of the Túngara frog (Engystomops pustulosus) is stableex situwith useful physiochemical and biocompatible properties and is capable of encapsulating a range of compounds, including antibiotics. These protein foam mixtures share some properties with pharmaceutical foams and may find utility in a range of pharmaceutical applications such as a topical drug delivery systems (DDS).
Structural Brain Correlates of Creative Personality
Authors: Sadana Divya , Gupta Rajnish K. , Kumaran S. S. , Jain Sanjeev , Rajeswaran Jamuna
Published: January 2021

Creative individuals and their enigmatic personalities have always been a subject of fascination. The current study explored the neuroanatomical basis of creative personality using voxel-based morphometry. The sample comprised of two groups - Creative (CR) group (professional creative artists) and matched controls with no demonstrated artistic creativity (NC) with 20 participants in each group, in the age range of 20-40 years, right-handed, and had minimum average intelligence (IQ > 90). Participants in CR were selected using the creativity achievement questionnaire, creativity was assessed using the Wallach & Kogan test of creativity, and personality was administered using NEO-FFI. Results indicated significantly higher openness to new experiences in CR which positively correlates with the right middle frontal gyrus. An increased grey matter volume in the inferior frontal gyrus, anterior cingulate gyrus in CR, pointing towards the integration of cognitive and imaginative processes that might be implicated in creative personality.
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Authors: Ding Xinqiang , Lin Xingcheng , Zhang Bin
Published: January 2021

The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported fromin situexperiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded,in situconfigurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on thein siturelevance of the 30nm fiber.
Network Analysis Reveals Synergistic Genetic Dependencies for Rational Combination Therapy in Philadelphia Chromosome-like Acute Lymphoblastic Leukemia
Authors: Ding Yang-Yang , Kim Hannah , Madden Kellyn , Loftus Joseph P , Chen Gregory M , Allen David Hottman , Zhang Ruitao , Xu Jason , Hu Yuxuan , Tasian Sarah K , Tan Kai
Published: January 2021

Systems biology approaches can identify critical targets in complex cancer signaling networks to inform therapy combinations and overcome conventional treatment resistance. Herein, we developed a data-driven, network controllability-based approach to identify synergistic key regulator targets in Philadelphia chromosome-like B-acute lymphoblastic leukemia (Ph-like B-ALL), a high-risk leukemia subtype associated with hyperactive signal transduction and chemoresistance. Integrated analysis of 1,046 childhood B-ALL cases identified 14 dysregulated network nodes in Ph-like ALL involved in aberrant JAK/STAT, Ras/MAPK, and apoptosis pathways and other critical processes. Consistent with network controllability theory, combination small molecule inhibitor therapy targeting a pair of key nodes shifted the transcriptomic state of Ph-like ALL cells to become less like kinase-activatedBCR-ABL1-rearranged (Ph+) B-ALL and more similar to prognostically-favorable childhood B-ALL subtypes. Functional validation experiments further demonstrated enhanced anti-leukemia efficacy of combining the BCL-2 inhibitor venetoclax with tyrosine kinase inhibitors ruxolitinib or dasatinibin vitroin human Ph-like ALL cell lines andin vivoin multiple patient-derived xenograft models. Our study represents a broadly-applicable conceptual framework for combinatorial drug discovery, based on systematic interrogation of synergistic vulnerability pathways with pharmacologic targeted validation in sophisticated preclinical human leukemia models.
A Processed EEG based Brain Anesthetic Resistance Index Predicts Postoperative Delirium in Older Adults: A Dual Center Study
Authors: Cooter Mary , Bunning Thomas , Eleswarpu Sarada S. , Heflin Mitchell T. , McDonald Shelley , Lagoo-Deenadalayan Sandhya , Whitson Heather , Deiner Stacie G , Berger Miles
Published: January 2021

Background

Some older adults show exaggerated responses to drugs that act on the brain, such as increased delirium risk in response to anticholinergic drugs. The brain’s response to anesthetic drugs is often measured clinically by processed electroencephalogram (EEG) indices. Thus, we developed a processed EEG based-measure of the brain’s neurophysiologic resistance to anesthetic dose-related changes, and hypothesized that it would predict postoperative delirium.

Methods

We defined the Duke Anesthesia Resistance Scale (DARS) as the average BIS index divided by the quantity 2.5 minus the average age-adjusted end-tidal MAC (aaMAC) inhaled anesthetic fraction. The relationship between DARS and postoperative delirium was analyzed in derivation (Duke; N=69), validation (Mt Sinai; N=70), and combined estimation cohorts (N=139) of older surgical patients (age ≥65). In the derivation cohort, we identified a threshold relationship between DARS and for delirium and identified an optimal cut point for prediction.

Results

In the derivation cohort, the optimal DARS threshold for predicting delirium was 27.0. The delirium rate was 11/49 (22.5%) vs 11/20 (55.0%) and 7/57 (12.3%) vs 6/13 (46.2%) for those with DARS ≥ 27 vs those with DARS < 27 in the derivation and validation cohorts respectively. In the combined estimation cohort, multivariable analysis found a significant association of DARS <27.0 with postoperative delirium (OR=4.7; 95% CI: 1.87, 12.0; p=0.001). In the derivation cohort, the DARS had an AUC of 0.63 with sensitivity of 50%, specificity of 81%, positive predictive value of 0.55, and negative predictive value of 0.78. The DARS remained a significant predictor of delirium after accounting for opioid, midazolam, propofol, non-depolarizing neuromuscular blocker, phenylephrine and ketamine dosage, and for nitrous oxide and epidural usage.

Conclusions

These results suggest than an intraoperative processed EEG-based measure of lower brain anesthetic resistance (i.e. DARS <27) could be used in older surgical patients as an independent predictor of postoperative delirium risk.
Epidemiological differences in the impact of COVID-19 vaccination in the United States and China
Authors: Makhoul Monia , Chemaitelly Hiam , Ayoub Houssein H. , Seedat Shaheen , Abu-Raddad Laith J.
Published: January 2021

Background

The objective of this study was to forecast the impact of COVID-19 vaccination in the United States (US) and China, two countries at different epidemic phases.

Methods

A mathematical model describing SARS-CoV-2 transmission and disease progression was used to investigate vaccine impact. Impact was assessed both for a vaccine that prevents infection (VES = 95%) and a vaccine that prevents only disease (VEP = 95%).

Results

For VES = 95% and gradual easing of restrictions, vaccination in the US reduced the peak incidence of infection, disease, and death by >55% and cumulative incidence by >32%, and in China by >77% and >65%, respectively. Nearly three vaccinations were needed to avert one infection in the US, but only one was needed in China. For VEP = 95%, benefits of vaccination were half those for VES = 95%. In both countries, the impact of vaccination was substantially enhanced with rapid scale-up, vaccine coverage >50%, and slower or no easing of restrictions, particularly in the US.

Conclusions

COVID-19 vaccination can flatten, delay, and/or prevent future epidemic waves. However, vaccine impact is destined to be heterogeneous across countries because of an underlying “epidemiologic inequity” that reduces benefits for countries already at high incidence, such as the US. Despite 95% efficacy, actual vaccine impact could be meager in such countries, if vaccine scale-up is slow, acceptance of the vaccine is poor, or restrictions are eased prematurely.

One Sentence Summary

Vaccine impact will be heterogeneous across countries disadvantaging countries at high incidence. This heterogeneity can be alleviated with rapid vaccination scale-up and limited easing of restrictions.
Findings from Cardiovascular Evaluation of NCAA Division I Collegiate Student-Athletes after Asymptomatic or Mildly Symptomatic SARS-CoV-2 Infection
Authors: Hwang Calvin E , Kussman Andrea , Christle Jeffrey W , Froelicher Victor , Wheeler Matthew T , Moneghetti Kegan J
Published: January 2021

Objectives

The risk of myocardial damage after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been controversial. There is an urgent need for data to support the appropriate level of cardiovascular screening for safe return-to-play. The purpose of this study is to report the incidence of abnormal cardiovascular findings in National Collegiate Athletic Association (NCAA) Division I student-athletes with a history of SARS-CoV-2 infection.

Methods

This is a case series of student-athletes at a single NCAA Division I institution who tested positive for SARS-CoV-2 by polymerase chain reaction (PCR) or antibody testing (IgG) from 4/15/2020 to 10/31/2020. From 452 athletes who were screened, 5,124 PCR and 452 antibody tests were completed. Student-athletes were followed through 12/31/2020 (median 104 days, range 64-182 days). Cardiac work-up included clinical evaluation, troponin level, electrocardiogram (ECG), and echocardiogram. Additional work-up was ordered as clinically indicated.

Results

55 student-athletes tested positive for SARS-CoV-2. Of these, 38 (69%) had symptoms of Coronavirus Disease (COVID-19), 14 (26%) had a positive IgG test, and 41 (74%) had a positive PCR test. Eight abnormal cardiovascular screening evaluations necessitated further testing including cardiac magnetic resonance imaging (cMRI). Two athletes received new cardiac diagnoses, one probable early cardiomyopathy and one pericarditis, while the remaining six had normal cardiac MRIs.

Conclusion

These data support recent publications which recommend the de-escalation of cardiovascular testing for athletes who have recovered from asymptomatic or mildly symptomatic SARS-CoV-2 infection. Continued follow-up of these athletes for sequelae of SARS-CoV-2 is critical.
Center-Based Experiences Implementing Strategies to Reduce Risk of Horizontal Transmission of SARS-Cov-2: Potential for Compromise of Neonatal Microbiome Assemblage
Authors: Romano-Keeler Joann , Fiszbein Dana , Zhang Jilei , Horowitz Joseph , Hayani Karen , Buhimschi Irina , Lopez Christina , Kadhem Zaynab , Berman James , Rasamimari Phornphat , Raghavan Aarti , Pillers De-Ann M. , Sun Jun
Published: January 2021

Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units’ (NICU) policies minimize mother-infant contact to prevent transmission. We present our unit’s approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers’ deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents’ visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 60% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers’ similar policies influence this outcome.
Compartmentalized three-dimensional human neuromuscular tissue models fabricated on a well-plate-format microdevice
Authors: Yamamoto Kazuki , Yamaoka Nao , Imaizumi Yu , Nagashima Takunori , Furutani Taiki , Ito Takuji , Okada Yohei , Honda Hiroyuki , Shimizu Kazunori
Published: January 2021

Engineered three-dimensional models of neuromuscular tissues are promising for use in mimicking their disorder states in vitro. Although several models have been developed, it is still challenging to mimic the physically separated structures of motor neurons (MNs) and skeletal muscle (SkM) fibers in the motor units in vivo. In this study, we aimed to develop microdevices for precisely compartmentalized coculturing of MNs and engineered SkM tissues. The developed microdevices, which fit a well of 24 well plates, had a chamber for MNs and chamber for SkM tissues. The two chambers were connected by microtunnels for axons, permissive to axons but not to cell bodies. Human iPSC (hiPSC)-derived MN spheroids in one chamber elongated their axons into microtunnels, which reached the tissue-engineered human SkM in the SkM chamber, and formed functional neuromuscular junctions with the muscle fibers. The cocultured SkM tissues with MNs on the device contracted spontaneously in response to spontaneous firing of MNs. The addition of a neurotransmitter, glutamate, into the MN chamber induced contraction of the cocultured SkM tissues. Selective addition of tetrodotoxin or vecuronium bromide into either chamber induced SkM tissue relaxation, which could be explained by the inhibitory mechanisms. We also demonstrated the application of chemical or mechanical stimuli to the middle of the axons of cocultured tissues on the device. Thus, compartmentalized neuromuscular tissue models fabricated on the device could be used for phenotypic screening to evaluate the cellular type specific efficacy of drug candidates and would be a useful tool in fundamental research and drug development for neuromuscular disorders.
An awareness-dependent saliency map in the human visual system
Authors: Wang Lijuan , Huang Ling , Li Mengsha , Wang Xiaotong , Wang Shiyu , Lin Yuefa , Zhang Xilin
Published: January 2021

The bottom-up contribution to the allocation of exogenous attention is a saliency map. However, how the saliency map is distributed when multiple salient stimuli are presented simultaneously and how this distribution interacts with awareness remain unclear. These questions were addressed here using visible and invisible stimuli that consisting of two salient foregrounds: the high one served as the target and the low one served as the distractor, which did or did not interfere the target’ saliency, indicating a gradient or winner-take-all manner, respectively. By combining psychophysics, fMRI, and effective connectivity analysis, we found that the saliency map was distributed as a gradient or winner-take-all manner with and without awareness, respectively. Crucially, we further revealed that the gradient manner was derived by feedback from pIPS, whereas the winner-take-all manner was constructed in V1. Together, our findings indicate an awareness-dependent saliency map and reconcile previous, seemingly contradictory findings on the saliency map.
Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics
Authors: Kulkarni Mandar , Söderhjelm Pär
Published: January 2021

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around theCβ− Cγaxis (χ2dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate thatχ2as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues neededχ1(N − Cα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.
Coordinated overexpression ofOsSUT1, OsSWEET11andOsSWEET14in rice impairs carbohydrate metabolism that has implications in plant growth, yield and susceptibility toXanthomonas oryzae pv oryzae (Xoo)
Authors: Singh Jitender , James Donald , Murali Achary V Mohan , Patel Manish Kumar , Thakur Jitendra Kumar , Reddy M K , Tripathy Baishnab Charan
Published: January 2021

Enhancing carbohydrate export to sink tissues is considered as a feasible approach for improving photosynthetic efficiency and crop yield. InOryza sativaSucrose Transporter OsSUT1 located in companion cells and Sugars Will Eventually be Exported Transporters (SWEETs); OsSWEET11 and OsSWEET14 present in phloem parenchyma mesophyll cell plasma membranes are involved in long distance sucrose transport.OsSWEET11andOsSWEET14also play important role in host-pathogen interaction of rice plants andXanthomonas oryzaepvoryzae(Xoo) that causes bacterial leaf blight. Three genes,OsSUT1, OsSWEET11, andOsSWEET14were overexpressed under the control of their native promoters in rice to modulate long distance sugar transport and disease resistance. The transgenics displayed several phenotypic aberrations such as reduced plant height and seed weight due to altered sucrose transport and metabolism. Lower sucrose transport rate in transgenics than the WT resulted in reduced sucrose, fructose and glucose and increased starch accumulation in their leaves at the end of dark period. Transcriptional analysis revealed a reduction in the expression of genes involved in sucrose synthesis pathway in transgenics. Normal growth and development of transgenic seedlings were restored in growth media supplemented with 3% sucrose demonstratingin plantasucrose limitation. Remarkably, transgenic lines had diminished susceptibility toXoothan the WTs due to low sugar content in the leaves demonstrating that rice plants maintain an optimum level of SWEETs for proper plant growth and development, and upregulation of theseSWEETsin rice mimicksXooattack impelling plants to reduce sugar content in the apoplasm to inhibit pathogen growth.
Mapping cellular subpopulations within triple negative breast cancer tumors provides a tool for cancer sensitization to radiotherapy
Authors: Alkhatib Heba , Rubinstein Ariel M. , Vasudevan Swetha , Flashner-Abramson Efrat , Stefansky Shira , Oguche Solomon , Peretz-Yablonsky Tamar , Granit Avital , Granot Zvika , Ben-Porath Ittai , Sheva Kim , Meirovitz Amichay , Kravchenko-Balasha Nataly
Published: January 2021

Triple negative breast cancer (TNBC) is an aggressive type of cancer that is known to be resistant to radiotherapy (RT). Evidence is accumulating that is indicative of the plasticity of TNBC, where one cancer subtype switches to another in response to various treatments, including RT. In this study we aim to overcome tumor resistance by designing TNBC-sensitizing targeted therapies that exploit the plasticity occurring due to radiation exposure. Using single cell analysis of molecular changes occurring in irradiated TNBC tumors, we identified two initially undetected distinct subpopulations, represented by overexpressed Her2 and cMet, expanding post-RT and persisting in surviving tumors. Using murine cancer models and patient-derived TNBC tumors, we showed that only simultaneous targeting of Her2 and cMet was successful in sensitizing TNBC to RT and preventing its regrowth. The strategy presented herein holds the potential to be broadly applicable in clinical use.

Highlights

Sensitization of TNBC to radiotherapy (RT) is a clinically unmet need

Single cell strategy creates a precise map of subpopulations expanding post-RT

Evolution of intra-tumor heterogeneity is turned into a therapeutic advantage

Simultaneous targeting of expanding subpopulations sensitizes TNBC to radiotherapy