bluuebunny/crossref_metadata_2025 huggingface dataset:
Resurrection of a viral internal ribosome entry site from a 700 year old ancient Northwest Territories cripavirus
Authors: Wang Xinying , Jan Eric
Published: January 2021

The dicistrovirus intergenic region internal ribosome entry site (IGR IRES) uses an unprecedented streamlined mechanism whereby the IRES adopts a triple-pseudoknot (PK) structure to directly bind to the conserved core of the ribosome and drive translation from a non-AUG codon. The origin of this IRES mechanism is not known. Previously, a partial fragment of a divergent dicistrovirus RNA genome, named ancient Northwest territories cripavirus (aNCV), was extracted from 700-year-old caribou feces trapped in a subarctic ice patch. Structural prediction of the aNCV IGR sequence generated a secondary structure similar to contemporary IGR IRES structures. There are, however, subtle differences including 105 nucleotides upstream of the IRES of unknown function. Using filter binding assays, we showed that the aNCV IGR IRES could bind to purified salt-washed human ribosomes and compete with a prototypical IGR IRES for ribosomes. Toeprinting analysis using primer extension pinpointed the putative start site of the aNCV IGR at a GCU alanine codon adjacent to PKI. Using a bicistronic reporter RNA, the aNCV IGR IRES can direct internal ribosome entryin vitroin a manner dependent on the integrity of the PKI domain. Lastly, we generated a chimeric virus clone by swapping the aNCV IRES into the cricket paralysis virus infectious clone. The chimeric infectious clone with an aNCV IGR IRES supported translation and virus infection. The characterization and resurrection of a functional IGR IRES from a divergent 700-year-old virus provides a historical framework in the importance of this viral translational mechanism.

IMPORTANCE

Internal ribosome entry sites are RNA structures that are used by some positive-sense monopartite RNA viruses to drive viral protein synthesis. The origin of internal ribosome entry sites is not known. Using biochemical approaches, we demonstrate that an RNA structure from an ancient viral genome that was discovered from a 700-year-old caribou feces trapped in subarctic ice is functionally similar to modern internal ribosome entry sites. We resurrect this ancient RNA mechanism by demonstrating that it can support virus infection in a contemporary virus clone, thus providing insights into the origin and evolution of this viral strategy.
Structure of a Plant-Specific Partitivirus Capsid Reveals a Novel Coat Protein Architecture with a Hypervariable Protrusion
Authors: Byrne Matthew , Kashyap Aseem , Esquirol Lygie , Ranson Neil , Sainsbury Frank
Published: January 2021

Persistent plant viruses may be the most common viruses in wild plants. A growing body of evidence for mutualism between such viruses and their hosts, suggests that they play an important role in ecology and agriculture. Here we present the structure of a plant-specific partitivirus capsid at 2.9 Å resolution by Cryo-EM. Structural features, including theT=1 arrangement of 60 coat protein dimers, are shared with fungal partitiviruses and the picobirnavirus lineage of dsRNA viruses. However, the topology of the capsid is markedly different with protrusions emanating from, and partly comprising, the binding interface of coat protein dimers. We show that a disordered region at the apex of the protrusion is not required for capsid assembly and represents a hypervariable site characteristic of the plant-specific partitiviruses. These results suggest a structural basis for the acquisition of additional functions by partitivirus coat proteins that enables mutualistic relationships with diverse plant hosts.
LBH is a cancer stem cell- and metastasis-promoting oncogene essential for WNT stem cell function in breast cancer
Authors: Garikapati Koteswararao , Ashad-Bishop Kilan , Hong Sunhwa , Qureshi Rehana , Rieger Megan E. , Lindley Linsey E. , Wang Bin , Azzam Diana J. , Khanlari Mahsa , Nadji Mehrad , Jain Chaitanya , Kwon Deukwoo , Ban Yuguang , Gao Zhen , Chen Steven X. , Sims Andrew H. , Kesmodel Susan B. , Slingerland Joyce M. , Briegel Karoline J.
Published: January 2021

Cancer stem cells (CSCs) initiate tumors, resist treatment, and seed lethal metastases; yet CSC-specific treatments are lacking. Aggressive, treatment-resistant triple-negative breast cancers (TNBC) exhibit WNT pathway activation and are CSC enriched. Here, we show that Limb-Bud- and-Heart (LBH), a WNT/β-catenin target required for normal mammary stem cell self-renewal, marks poor prognosis, stem-like TNBC, and is a key controller of breast cancer stemness. LBH is specifically expressed in tumor-initiating CD44+CD24-/lowbreast CSCs. LBH overexpression confers stem-like, metastatic traits on both TNBC and luminal origin, non-TNBC breast cancer cells by activating stem cell transcriptional programs. Importantly, silencing LBH potently suppresses tumor initiation and metastasisin vivo, and sensitizes TNBC cells to chemotherapy. LBH knockout in the MMTV-Wnt1 breast cancer mouse model, furthermore, revealed LBH is required for WNT-driven breast CSC expansion. Our findings identify LBH as an essential CSC driver downstream of WNT, and a new molecular target for anti-cancer stem cell therapy.
Comparative Genomics and Environmental Distribution of Large dsDNA viruses in the familyAsfarviridae
Authors: Karki Sangita , Moniruzzaman Mohammad , Aylward Frank O.
Published: January 2021

TheAsfarviridaeis a family of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) of which African swine fever virus (ASFV) is the most well-characterized. Recently the discovery of severalAsfarviridaemembers other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found thatAsfarviridaegenomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and different eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that threeAsfarviridaeMAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with >95% amino acid identity to genes sequenced from a virus that infects the dinoflagellateHeterocapsa circularisquama(HcDNAV). This suggests a potential host for this MAG, which would thereby represent a near-complete genome of a dinoflagellate-infecting giant virus. Together, these results show thatAsfarviridaeare ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.
TAK1 blockade as a therapy for retinal neovascularization
Authors: Lin Fan-Li , Wang Jiang-Hui , Chen Jinying , Zhu Linxin , Chuang Yu-Fan , Tu Leilei , Ma Chenkai , Lama Suraj , Ling Damien , Wong Raymond Ching-Bong , Hewitt Alex W. , Tseng Ching-Li , Bui Bang V. , van Wijngaarden Peter , Dusting Gregory J. , Wang Peng-Yuan , Liu Guei-Sheung
Published: January 2021

Retinal neovascularization, or pathological angiogenesis in the retina, is a leading cause of blindness in developed countries. Transforming growth factor-β-activated kinase 1 (TAK1) is a mitogen-activated protein kinase kinase kinase (MAPKKK) activated by TGF-β1 and other pro-inflammatory cytokines. TAK1 is also a key mediator of inflammation, innate immune responses, apoptosis and tissue homeostasis and plays an important role in physiological angiogenesis. Its role in pathological angiogenesis, particularly in retinal neovascularization, remains unclear. We investigated the regulatory role of TAK1 in pathological angiogenesis in the retina. Transcriptome analysis of human retina featuring retinal neovascularization revealed enrichment of known TAK1-mediated signaling pathways. Selective inhibition of TAK1 activation by 5Z-7-oxozeaenol attenuated aberrant retinal angiogenesis in rats following oxygen-induced retinopathy. Transcriptome profiling revealed that TAK1 activation in human microvascular endothelial cells under TNFα stimulation led to increase the gene expression related to cytokines and leukocyte-endothelial interaction, mainly through nuclear factor kappa B (NFκB) signaling pathways. These results reveal that inhibition of TAK1 signaling may have therapeutic value for the treatment of pathological angiogenesis in the retina.
Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+tumor immunity
Authors: Sidiropoulos Dimitrios N. , Rafie Christine , Christmas Brian J. , Davis-Marcisak Emily F. , Sharma Gaurav , Bigelow Emma , Gupta Anuj , Yegnasubramanian Srinivasan , Stearns Vered , Connolly Roisin M. , Gaykalova Daria A. , Kagohara Luciane T. , Jaffee Elizabeth M. , Fertig Elana J. , Roussos Torres Evanthia T.
Published: January 2021

Understanding how novel therapeutic combinations alter solid tumor microenvironments (TME) in immunosuppressive tumors such as breast cancer is essential to improve their responses to immune checkpoint inhibitors (ICIs). Entinostat, an oral histone deacetylase inhibitor (HDACi), has been shown to improve responses to ICIs in various tumor models with immunosuppressive TMEs, but the precise alterations induced by entinostat and mechanisms of synergy with ICIs remain unknown. Here, we employ single-cell RNA-sequencing on HER2 overexpressing breast tumors from mice treated with entinostat + ICIs to characterize these changes across cell types in the TME. This analysis demonstrates that treatment with entinostat induces a shift from a pro-tumor to an anti-tumor TME signature characterized predominantly by changes in the myeloid cells. Notably, myeloid-derived suppressor cells (MDSCs) are shifted toward the less suppressive granulocytic phenotype in association with reduced signaling through the STAT3 pathway. In addition, tumor-associated macrophages are shifted toward an anti-tumor M1 phenotype by epigenetic reprogramming. Overall, these entinostat-induced TME changes reduce immunosuppression and increase mechanisms of tumor cell killing to improve ICI responses and broaden the population of patients who could potentially benefit from immunotherapy.
Pseudomonascan prevent the parasitic fungus, while keeping the crop fungus unaffected, in the gardens ofOdontotermes obesus
Authors: Agarwal Renuka , Gupta Manisha , Antony Abin , Sen Ruchira , Raychoudhury Rhitoban
Published: January 2021

Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, takes over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the parasitic fungusPseudoxylaria. The mechanism by whichPseudoxylariais suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth ofPseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India,Odontotermes obesus. From the 38 bacterial cultures tested, a strain ofPseudomonasshowed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealedPseudomonasto be a part of the core microbiota ofOdontotermes obesus. A meta-analysis of microbiota composition across different species ofOdontotermesalso confirms the wide-spread prevalence ofPseudomonaswithin this termite. These evidence indicate thatPseudomonascould be playing the role of defensive mutualist withinOdontotermes.
Circadian dynamics of the teleost skin immune-microbiome interface
Authors: Ellison Amy R , Wilcockson David , Cable Jo
Published: January 2021

Circadian rhythms of host immune activity and their microbiomes are likely pivotal to health and disease resistance. The integration of chronotherapeutic approaches to disease mitigation in managed animals, however, is yet to be realised. In aquaculture, light manipulation is commonly used to enhance growth and control reproduction but may have unknown negative consequences for animal health. Infectious diseases are a major barrier to sustainable aquaculture and understanding the circadian dynamics of fish immunity and crosstalk with the microbiome is urgently needed. We demonstrate daily rhythms in fish skin immune expression and microbiomes, that are modulated by photoperiod and parasitic infection. We identify putative associations of host clock and immune gene profiles with microbial composition. Our results suggest circadian perturbation that shifts the magnitude and timing of immune and microbiota activity, is detrimental to fish health. This study represents a valuable foundation for investigating the utility of chronotherapies in aquaculture, and more broadly contributes to our understanding of circadian health in vertebrates.
Effect of concentration and hydraulic reaction time on the removal of pharmaceutical compounds in a membrane bioreactor inoculated with activated sludge
Authors: Rios-Miguel Ana B. , Jetten Mike S.M. , Welte Cornelia U.
Published: January 2021

Pharmaceuticals are often not fully removed in wastewater treatment plants (WWTPs) and are thus being detected at trace levels in water bodies all over the world posing a risk to numerous organisms. These organic micropollutants (OMPs) reach WWTPs at concentrations sometimes too low to serve as growth substrate for microorganisms, thus co-metabolism is thought to be the main conversion mechanism. In this study, the microbial removal of six pharmaceuticals was investigated in a membrane bioreactor at increasing concentrations (4-800 nM) of the compounds and using three different hydraulic retention times (HRT; 1, 3.5, 5 days). The bioreactor was inoculated with activated sludge from a Dutch WWTP and fed with ammonium, acetate, and methanol as main growth substrates to stimulate and mimic co-metabolism in a WWTP. Each pharmaceutical compound had a different average removal efficiency: acetaminophen (100%) > fluoxetine (50%) > metoprolol (25%) > diclofenac (20%) > metformin (15%) > carbamazepine (10%). Higher pharmaceutical influent concentrations proportionally increased the removal rate of each compound, but surprisingly not the removal percentage. Furthermore, only metformin removal improved to 80-100% when HRT or biomass concentration was increased in the reactor. Microbial community changes were followed with 16S rRNA gene amplicon sequencing in response to the increment of supplied pharmaceutical concentration: it was found thatNitrospiraeandPlanctomycetes16S rRNA relative gene abundance decreased, whereasAcidobacteriaandBacteroidetesincreased. Remarkably, theDokdonellagenus, previously implicated in acetaminophen metabolism, showed a 30-fold increase in abundance at the highest (800 nM) concentration of pharmaceuticals applied. Taken together, these results suggest that the incomplete removal of most pharmaceutical compounds in WWTPs is neither dependent on concentration nor HRT. Accordingly, we propose a chemical equilibrium or a growth substrate limitation as the responsible mechanisms of the incomplete removal. Finally,Dokdonellacould be the main acetaminophen degrader under activated sludge conditions, and non-antimicrobial pharmaceuticals might still be toxic to relevant WWTP bacteria.
Doxorubicin Induces Senescence in Intestinal Epithelial Cells
Authors: Biraud Mandy , Cortes Jocsa , Cray Paul , Kunzmann Guy , Mohammed Javid , Dekaney Christopher M.
Published: January 2021

Doxorubicin treatment induces DNA damage and apoptosis in rapidly dividing cell types like intestinal epithelial cells. This has been demonstrated bothin vivoandin vitro. In certain cell types some cells do not undergo DNA damage-induced apoptosis in response to doxorubicin but instead become senescent. Induction of senescence in these cells can lead to dysfunction and chronic inflammation, which can lead to more damage. We questioned whether a single dose of doxorubicin would be able to induce apoptosis and senescence in intestinal epithelial cellsin vitro. For these studies, we exposed IEC-6 small intestinal epithelial cells to doxorubicin to evaluate whether senescence is induced in a relatively homogeneous population of intestinal epithelial cells. Although some cells underwent apoptosis, those that did not showed traits of senescence. Our studies showed that doxorubicin treatment increased cell size and increased expression of senescence-associated β-galactosidase. Concomitantly, we observed increased mRNA expression of several genes associated with a senescence-associated secretory phenotype includingIL-6,Ptges,Faim2, andCdkn1aand decreased expression ofSirt1. We also observed release of HMGB1, a cellular alarmin, from treated cells. Together, these data suggest that doxorubicin induces senescence in intestinal epithelial cells. Furthermore, our data indicate that cellular responses to a DNA damaging agent, such as doxorubicin, can differ within a population of cells suggesting differing levels of sensitivity within a relatively homogenous cell population. Further studies are needed to delineate the mechanisms that determine whether a cell moves down an apoptotic or senescent pathway following DNA damage.
Serum hormone levels in infertile women between conceived with and without hormone replacement therapy: Safety of estradiol and progesterone replacement therapy in frozen-thawed embryo transfer cycles for breast cancer survivors
Authors: Ito Ayumu , Katagiri Yukiko , Fukuda Yusuke , Morita Mineto
Published: January 2021

Objective

Recent advances in cancer treatment and reproductive medicine have made the post-treatment quality of life an important concern for cancer survivors. We aimed to evaluate the safety of sex hormone (estradiol and progesterone) replacement therapy (HRT) in women who conceived by assisted reproductive technology (ART) with hormone receptor-positive breast cancer.

Methods

We measured serum E2 and P4 levels at 4–10 weeks of gestation in women who conceived naturally or after timed intercourse or intrauterine insemination for infertility without HRT for luteal support (non-HR group; n=135). We conducted a retrospective comparison of the values from the non-HR group with those of women who conceived by ART with HRT for infertility (HR group; n=75).

Results

Serum E2 levels were significantly higher in the non-HR group than in the HR group at 5, 6, and 8 weeks of gestation. Similarly, serum P4 levels were significantly higher in the non-HR group than in the HR group at 4, 5, and 6 weeks of gestation.

Conclusions

This study suggests that in cancer reproductive medicine for hormone-dependent breast cancer survivors, HRT administered during the first trimester of a pregnancy after primary disease treatment may not increase the sex hormone levels to levels above those seen in spontaneous pregnancy.
White matter hyperintensity volume and early-onset post-stroke depression in Thai older patients
Authors: Jaroonpipatkul Chaichana , Onwanna Jaruwan , Tunvirachaisakul Chavit , Jittapiromsak Nutchawan , Rakvongthai Yothin , Chutinet Aurauma , Supasitthumrong Thitiporn
Published: January 2021

Objective

Post-stroke depression (PSD) is one of the most frequent psychiatric symptoms after a stroke event. The role of white matter hyperintensities (WMHs) associated with PSD in older patients remains unclear. This study aimed to examine the volume and location of white matter microstructure abnormalities among older patients with early-onset PSD.

Methods

Older (≥55 years) patients with acute cerebral infarction and hospitalized in King Chulalongkorn Memorial Hospital’s stroke unit from October 2019 to September 2020 were recruited. Participants were assessed with the Montgomery-Åsberg Depression Rating Scale (MADRS) within three months after the onset of stroke. All patients had MRI scans. The brain images were segmented into four regions via left/right, frontal/dorsal plains. Two WMHs volume detections (visual rating vs. semi-automated WMHs volumetric detection) were employed on the fluid-attenuated inversion recovery images (FLAIR) for each segment. The study then investigated the association between WMHs volume and MADRS score with regression analysis.

Results

The study included twenty-nine patients with acute stroke. Total WMHs volume and segmented regions were not statistically associated with the MADRS score. However, there was a trend in different WHMs volume of the left anterior segment between depressed and non-depressed groups (t-test 2.058, p = 0.055). Further, demographic and clinical data showed no association with depressive symptoms.

Conclusion

The volume of WHMs might not contribute to the development of early-onset PSD in older patients. This study showed a potential of a quantitative MRI analysis in clinical practice. Further investigation with a larger group of patients is needed.
m6A RNA methylation facilitates pre-mRNA 3’-end formation and is essential for viability ofToxoplasma gondii
Authors: Holmes Michael J. , Padgett Leah R. , Bastos Matheus S. , Sullivan William J.
Published: January 2021

Toxoplasma gondiiis an obligate intracellular parasite that can cause serious opportunistic disease in the immunocompromised or through congenital infection. To progress through its life cycle,Toxoplasmarelies on multiple layers of gene regulation that includes an array of transcription and epigenetic factors. Over the last decade, the modification of mRNA has emerged as another important layer of gene regulation called epitranscriptomics. Here, we report that epitranscriptomics machinery exists inToxoplasma,namely the methylation of adenosines (m6A) in mRNA transcripts. We identified novel components of the m6A methyltransferase complex and determined the distribution of m6A marks within the parasite transcriptome. m6A mapping revealed the modification to be preferentially located near the 3’-boundary of mRNAs within the consensus sequence, YGCAUGCR. Knockdown of the m6A writer enzyme METTL3 resulted in diminished m6A marks, loss of a target transcript, and a complete arrest of parasite replication. Furthermore, we examined the two proteins inToxoplasmathat possess YTH domains, which bind m6A marks, and showed them to be integral members of the cleavage and polyadenylation machinery that catalyzes the 3’-end processing of pre-mRNAs. Together, these findings establish that the m6A epitranscriptome is essential for parasite viability by contributing to the processing of mRNA 3’-ends.

Author Summary

Toxoplasma gondiiis a parasite of medical importance that causes disease upon immuno-suppression. Uncovering essential pathways that the parasite uses for its basic biological processes may reveal opportunities for new anti-parasitic drug therapies. Here, we describe the machinery thatToxoplasmauses to modify specific adenosine residues within its messenger RNAs (mRNA) by N6-adenosine methylation (m6A). We discovered that m6A mRNA methylation is prevalent in multiple stages of the parasite life cycle and is required for parasite replication. We also establish that m6A plays a major role in the proper maturation of mRNA. Two proteins that bind m6A modifications on mRNA associate with factors responsible for the cleavage and final processing steps of mRNA maturation. Since all of the machinery is conserved from plants toToxoplasmaand other related parasites, we propose that this system operates similarly in these organisms.
Metabolic flexibility via mitochondrial BCAA carrier SLC25A44 is required for optimal fever
Authors: Yoneshiro Takeshi , Kataoka Naoya , Walejko Jacquelyn M. , Ikeda Kenji , Brown Zachary , Yoneshiro Momoko , Crown Scott B. , McGarrah Robert W. , White Phillip J. , Nakamura Kazuhiro , Kajimura Shingo
Published: January 2021

Importing necessary metabolites into the mitochondrial matrix is a crucial step of fuel choice during stress adaptation. Branched chain-amino acids (BCAA, Valine, Leucine, and Isoleucine) are essential for anabolic processes like protein synthesis, but they are also imported into the mitochondria for catabolic reactions. What controls the distinct subcellular BCAA utilization during stress adaptation is insufficiently understood. The present study reports the role of SLC25A44, a recently identified mitochondrial BCAA carrier (MBC), in the regulation of mitochondrial BCAA catabolism and adaptive response to fever. We found that mitochondrial BCAA oxidation in brown adipose tissue (BAT) is significantly enhanced during fever in response to the pyrogenic mediator prostaglandin E2(PGE2) and psychological stress. Genetic deletion of MBC in a BAT-specific manner blunts mitochondrial BCAA oxidation and non-shivering thermogenesis following intracerebroventricular PGE2administration. At a cellular level, MBC is required for mitochondrial BCAA deamination as well as the synthesis of mitochondrial amino acids and TCA intermediates. Together, these results illuminate the role of MBC as a determinant of metabolic flexibility to mitochondrial BCAA catabolism and optimal febrile responses. This study also offers an opportunity to control fever by rewiring the subcellular BCAA fate.
GATA2 deficiency during embryogenesis elevates Interferon Regulatory Factor-8 to subvert a progenitor cell differentiation program
Authors: Johnson Kirby D. , Bresnick Emery H.
Published: January 2021

Cell type-specific transcription factors control stem and progenitor cell transitions by establishing networks containing hundreds of genes and proteins. Network complexity renders it challenging to discover essential versus modulatory or redundant components. This scenario is exemplified by GATA2 regulation of hematopoiesis during embryogenesis. Previously, we demonstrated that loss ofGata2, −77 enhancer disrupts the GATA2-dependent genetic network governing erythro-myeloid differentiation. The aberrant network includes the transcription factor Interferon Regulatory Factor-8 and a host of innate immune regulators. Mutant progenitors lose the capacity to balance production of diverse myelo-erythroid progeny. To elucidate mechanisms, we asked if IRF8 is essential, contributory or not required.Irf8ablation, in the context of the −77 mutant allele, reversed granulocytic deficiencies of −77−/−embryos and rescued an imbalance of dendritic cell progenitors. Despite many dysregulated components that control vital processes, including transcription and signaling, aberrant elevation of a single transcription factor deconstructed the differentiation program.
Antagonistic relationship of NuA4 with the Non-Homologous End-Joining machinery at DNA damage sites
Authors: Ahmad Salar , Côté Valerie , Cheng Xue , Bourriquen Gaëlle , Sapountzi Vasileia , Altaf Mohammed , Côté Jacques
Published: January 2021

The NuA4 histone acetyltransferase complex, apart from its known role in gene regulation, has also been directly implicated in the repair of DNA double-strand breaks (DSBs), favoring homologous recombination (HR) in S/G2 during the cell cycle. Here, we investigate the antagonistic relationship of NuA4 with non-homologous end joining (NHEJ) factors. We show that budding yeast Rad9, the 53BP1 ortholog, can inhibit NuA4 acetyltransferase activity when bound to chromatinin vitro. While we previously reported that NuA4 is recruited at DSBs during the S/G2 phase, we can also detect its recruitment in G1 when genes for NHEJ factors Rad9, Yku80 and Nej1 are mutated. This is accompanied with the binding of single-strand DNA binding protein RPA and Rad52, indicating DNA end resection in G1 as well as recruitment of the HR machinery. This NuA4 recruitment to DSBs in G1 depends on both Xrs2 and Lcd1/Ddc2 and is linked to the hyper-resection phenotype of NHEJ mutants. It also implicates NuA4 in the resection-based single-strand annealing (SSA) repair pathway along Rad52. Interestingly, we identified two novel non-histone acetylation targets of NuA4, Nej1 and Yku80. Acetyl-mimicking mutant of Nej1 inhibits repair of DNA breaks by NHEJ, decreases its interaction with other core NHEJ factors such as Yku80 and Lif1 and favors end resection. Altogether, these results establish a strong reciprocal antagonistic regulatory function of NuA4 and NHEJ factors in repair pathway choice and suggests a role of NuA4 in alternative repair mechanism that involves DNA-end resection in G1.

Author Summary

DNA double-strand breaks (DSBs) are one of the most harmful form of DNA damage. Cells employ two major repair pathways to resolve DSBs: Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ). Here we wanted to dissect further the role played by the NuA4 (Nucleosome acetyltransferase of histone H4) complex in the repair of DSBs. Budding yeast NuA4 complex, like its mammalian homolog TIP60 complex, has been shown to favor repair by HR. Here, we show that indeed budding yeast NuA4 and components of the NHEJ repair pathway share an antagonistic relationship. Deletion of NHEJ components enables increased recruitment of NuA4 in the vicinity of DSBs, possible through two independent mechanisms, where NuA4 favors the end resection process which implicates it in repair by single-strand annealing (SSA), an alternate homology-based repair pathway. Additionally, we also present two NHEJ core components as new targets of NuA4 acetyltransferase activity and suggest that these acetylation events can disassemble the NHEJ repair complex from DSBs, favoring repair by HR. Our study demonstrates the importance of NuA4 in the modulation of DSB repair pathway choice.
From heterogeneity to homogeneity: coordination of siderophore gene expression among clonal cells of the bacteriumPseudomonas aeruginosa
Authors: Mridha Subham , Kümmerli Rolf
Published: January 2021

There has been great progress in understanding how bacterial groups coordinate social actions, such as biofilm formation, swarming and public-goods secretion. Less clear, however, is whether the seemingly coordinated responses observed at the group level actually mirror what individual cells do. Here, we use a microscopy approach to simultaneously quantify the investment of individual cells of the bacteriumPseudomonas aeruginosainto two public goods, the siderophores pyochelin and pyoverdine. Using gene expression as a proxy for investment, we initially observed no coordination but high heterogeneity and bimodality in siderophore gene expression across cells. With increasing cell density, gene expression became homogenized across cells, accompanied by a shift from pyochelin to pyoverdine expression. We found positive correlations in the expression of pyochelin and pyoverdine genes across cells, and show that cell-to-cell variation is driven by differences in cellular metabolic states. We propose a model explaining how variation in internal iron stocks can spur initial erratic gene expression, while siderophore-mediated signalling and intra-cellular feedbacks later on can induce highly coordinated gene expression and synchronized shifts from pyochelin to pyoverdine. Our work provides new insights into bacterial collective decision-making processes and reveals a three-phase chronobiological siderophore investment cycle inP. aeruginosa.
MMP12 Knockout Prevent Weight and Muscle Loss Induced by Cancer Cachexia
Authors: Jiang Lingbi , Yang Mingming , He Shihui , Li Zhengyang , Li Haobin , Niu Ting , Xie Dehuan , Mei Yan , He Xiaodong , Wei Lili , Huang Pinzhu , Huang Mingzhe , Zhang Rongxin , Wang Lijing , Li Jiangchao
Published: January 2021

Weight loss and muscle wasting can have devastating impacts on survival and quality of life of patients with cancer cachexia. Here, we have established a hybrid mouse of ApcMin/+mice and MMP12 knockout mice (ApcMin/+; MMP12-/-) and found that knockout MMP12 can suppress the weight and muscle loss of ApcMin/+mice. In detail, we found that interleukin 6 was highly upregulated in the serum of cancer patients and MMP12 was increased in muscle of tumor-bearing mice. Interestingly, the interleukin 6 secreted by tumor cells led to MMP12 overexpression in the macrophages, which further resulted in degradation of insulin and insulin-like growth factor 1 and interruption of glycolipid metabolism. Notably, depletion of MMP12 prevented weight loss of ApcMin/+mice. Our study uncovers the critical role of MMP12 in controlling weight and highlights the great potential of MMP12 in the treatment of cancer cachexia.
Information retrieval in an infodemic: the case of COVID-19 publications
Authors: Teodoro Douglas , Ferdowsi Sohrab , Borissov Nikolay , Kashani Elham , Alvarez David Vicente , Copara Jenny , Gouareb Racha , Naderi Nona , Amini Poorya
Published: January 2021

The COVID-19 pandemic has led to an exponential surge and an enormous amount of published literature, both accurate and inaccurate, a term usually coined as an infodemic. In the context of searching for COVID-19 related scientific literature, we present an information retrieval methodology for effectively finding relevant publications for different information needs. Our multi-stage information retrieval architecture combines probabilistic weighting models and re-ranking algorithms based on neural masked language models. The methodology was evaluated in the context of the TREC-COVID challenge, achieving competitive results with the top ranking teams participating in the competition. Particularly, the ranking combination of bag-of-words and language models significantly outperformed a BM25-based baseline model (16 percentage points for the NDCG@20 metric), correctly retrieving more than 16 out of the top 20 documents retrieved. The proposed pipeline could thus support the effective search and discovery of relevant information in the case of an infodemic.
Behavioral and brain mechanisms mediating conditioned flight behavior in rats
Authors: Totty Michael S. , Warren Naomi , Huddleston Isabella , Ramanathan Karthik R. , Ressler Reed L. , Oleksiak Cecily R. , Maren Stephen
Published: January 2021

Environmental contexts and associative learning can inform animals of potential threats, though it is currently unknown how contexts bias defensive transitions. Here we investigated context-dependent flight responses in the Pavlovian serial-compound stimulus (SCS) paradigm. We show here that SCS-evoked flight behavior in male and female rats is dependent on contextual fear. Flight was reduced in the conditioning context after context extinction and could be evoked in a different shock-associated context. Although flight was exclusive to white noise stimuli, it was nonetheless associative insofar as rats that received an equal number of unpaired USs did not show flight-like behavior. Finally, we found that inactivation of either the central nucleus of the amygdala (CeA) or bed nucleus of the stria terminalis (BNST) attenuated both contextual fear and flight responses. This work demonstrates that contextual fear summates with cued and innate fear to drive a high fear state and freeze-to-flight transitions.
Smoothened and ARL13B are critical in mouse for superior cerebellar peduncle targeting
Authors: Suciu Sarah K. , Long Alyssa B. , Caspary Tamara
Published: January 2021

Patients with the ciliopathy Joubert syndrome present with physical anomalies, intellectual disability, and a hindbrain malformation described as the “molar tooth sign” due to its appearance on an MRI. This radiological abnormality results from a combination of hypoplasia of the cerebellar vermis and inappropriate targeting of the white matter tracts of the superior cerebellar peduncles. ARL13B is a cilia-enriched regulatory GTPase established to regulate cell fate, cell proliferation and axon guidance through vertebrate Hedgehog signaling. In patients, mutations in ARL13B cause Joubert syndrome. In order to understand the etiology of the molar tooth sign, we used mouse models to investigate the role of ARL13B during cerebellar development. We found ARL13B regulates superior cerebellar peduncle targeting and these fiber tracts require Hedgehog signaling for proper guidance. However, in mouse the Joubert-causing R79Q mutation in ARL13B does not disrupt Hedgehog signaling nor does it impact tract targeting. We found a small cerebellar vermis in mice lacking ARL13B function but no cerebellar vermis hypoplasia in mice expressing the Joubert-causing R79Q mutation. Additionally, mice expressing a cilia-excluded variant of ARL13B that transduces Hedgehog normally, showed normal tract targeting and vermis width. Taken together, our data indicate that ARL13B is critical for control of cerebellar vermis width as well as superior cerebellar peduncle axon guidance, likely via Hedgehog signaling. Thus, our work highlights the complexity of ARL13B in molar tooth sign etiology.

Summary statement

Joubert syndrome is diagnosed by the hindbrain “molar tooth sign” malformation. Using mouse models, we show loss of the ciliary GTPase ARL13B, mutations in which lead to Joubert syndrome, result in two features of the molar tooth sign: hypoplasia of the cerebellar vermis and inappropriate targeting of the superior cerebellar peduncles. Furthermore, we demonstrate that loss of vertebrate Hedgehog signaling may be the underlying disrupted mechanism as we extend its role in axon guidance to the superior cerebellar peduncles.
A Cas-BCAR3 co-regulatory circuit controls lamellipodia dynamics
Authors: Steenkiste Elizabeth M. , Berndt Jason D. , Pilling Carissa , Simpkins Christopher , Cooper Jonathan A.
Published: January 2021

Integrin adhesion complexes regulate cytoskeletal dynamics during cell migration. Adhesion activates phosphorylation of integrin-associated signaling proteins, including Cas (p130Cas, BCAR1), by Src-family kinases. Cas regulates leading-edge protrusion and migration in cooperation with its binding partner, BCAR3. However, it has been unclear how Cas and BCAR3 cooperate. Here, using normal epithelial cells, we find that BCAR3 localization to integrin adhesions requires Cas. In return, Cas phosphorylation, as well as lamellipodia dynamics and cell migration, requires BCAR3. These functions require the BCAR3 SH2 domain and a specific phosphorylation site, Tyr 117, that is also required for BCAR3 downregulation by the ubiquitin-proteasome system. These findings place BCAR3 in a co-regulatory positive-feedback circuit with Cas, with BCAR3 requiring Cas for localization and Cas requiring BCAR3 for activation and downstream signaling. The use of a single phosphorylation site in BCAR3 for activation and degradation ensures reliable negative feedback by the ubiquitin-proteasome system.
Mechanism of Debris Ejection in Atomized Dielectric-Based Electrical Discharge Machining
Authors: Tanveer Asif , Kapoor Shiv
Published: January 2021

Atomized dielectric-based electrical discharge machining (EDM) is a novel machining process in which a thin film of moving fluid resulting from a spray acts as the dielectric in the interelectrode gap. In addition to acting as the dielectric, the thin film also helps to flush the debris away from EDM crater features and requires very small quantity of fluid in doing so. This results in significantly less dielectric consumption compared to the conventional EDM while yielding higher material removal rates and better debris flushing. This paper presents a model-based investigation of the mechanism of debris flushing in atomized dielectric-based EDM. A material removal model is used to predict the amount of debris removed in terms of number of particles ejected during a single EDM discharge. The dielectric material properties and atomization spray parameters are varied in order to produce different ejection conditions and crater geometries, respectively. Particles are ejected from the bottom of crater geometries. The model captures the asymmetry in particle motion caused by the dielectric film flow and predicts the percentage of debris flushed away from the crater center. It is also observed that crater shape and size of debris particles play a role in the amount of debris flushed away.
Structural Dynamic and Inherent Damping Characterization of Additively Manufactured Airfoil Components
Authors: Goldin Andrew , Scott-Emuakpor Onome , George Tommy , Runyon Brian , Cobb Richard
Published: January 2021

The push for low cost and higher performance/efficient turbine engines has introduced a demand for novel technologies to improve robustness to vibrations resulting in high cycle fatigue (HCF). There have been many proposed solutions to this, some passive and some active. With the advent of additive manufacturing (AM), new damping techniques can now be incorporated directly into the design and manufacture process to suppress the vibrations that cause HCF. Recent work has been investigating new ways of using AM for turbine engine applications. A specifically innovative approach using laser powder bed fusion (LPBF) is of particular note. The use of internal pockets filled with the build powder but left unfused has proved to have damping quality with >90% force response reduction. This study will investigate the as-manufactured parts, damping endurance, and structural dynamic changes when this technology is applied to a compressor-like blade. This will be done by using multiple testing methods to investigate the performance and dynamics of the blade. The study will use a computed tomography (CT) scans to investigate the pockets, structured light scans to investigate the external geometry, modal assurance criteria (MAC) to investigate the structural dynamics, and a sinusoidal strain step test to investigate endurance. This study found similar endurance and damping capabilities as previously observed, in addition to finding that the inclusion of the unfused powder pockets did not affect mode shapes measured by the MAC.
Fluoxetine-induced hepatic lipid accumulation is linked to elevated serotonin production
Authors: Ayyash Ahmed , Holloway Alison C.
Published: January 2021

Fluoxetine, a commonly prescribed selective serotonin reuptake inhibitor antidepressant, has been shown to increase hepatic lipid accumulation, a key factor in the development of nonalcoholic fatty liver disease. Interestingly, fluoxetine has also been reported to increase peripheral serotonin synthesis. As emerging evidence suggests that serotonin may be involved in the development of nonalcoholic fatty liver disease, we sought to determine if fluoxetine-induced hepatic lipid accumulation is mediated via altered serotonin production. Fluoxetine treatment increased lipid accumulation in association with increased mRNA expression of tryptophan hydroxylase 1 (Tph1, serotonin biosynthetic enzyme) and intracellular serotonin content. Serotonin alone had a similar effect to increase lipid accumulation. Moreover, blocking serotonin synthesis reversed the fluoxetine-induced increases in lipid accumulation. Collectively, these data suggest that fluoxetine-induced lipid accumulation can be mediated, in part, by elevated serotonin production. These results suggest a potential therapeutic target to ameliorate the adverse metabolic effects of fluoxetine exposure.
Observation of gravitational waves by light polarization
Authors: Park Chan , Kim Dong-Hoon
Published: January 2021

We provide analysis to determine the effects of gravitational waves on electromagnetic waves, using perturbation theory in general relativity. Our analysis is performed in a completely covariant manner without invoking any coordinates. For a given observer, using the geometrical-optics approach, we work out the perturbations of the phase, amplitude, frequency and polarization properties–axes of ellipse and ellipticity of light, due to gravitational waves. With regard to the observation of gravitational waves, we discuss the measurement of Stokes parameters, through which the antenna patterns are presented to show the detectability of the gravitational wave signals.
Energy map and effective metric in an effective-one-body theory based on the second-post-Minkowskian approximation
Authors: He Xiaokai , Sun Manman , Jing Jiliang , Cao Zhoujian
Published: January 2021

Effective-one-body (EOB) theory was originally proposed based on the post-Newtonian (PN) approximation and plays an important role in the analysis of gravitational wave signals. Recently, the post-Minkowskian (PM) approximation has been applied to the EOB theory. The energy map and the effective metric are the two key building blocks of the EOB theory, and in PN approximation radial action variable correspondence is employed to construct the energy map and the effective metric. In this paper, we employ the PM approximation up to the second order, and use the radial action variable correspondence and the precession angle correspondence to construct the energy map and the effective metric. We find that our results based on the radial action variable correspondence, are exactly the same with those obtained based on the precession angle correspondence. Furthermore, we compare the results obtained in this work to the previous existing ones.
Effects of a new extended uncertainty principle on Schwarzschild and Reissner–Nordström black holes thermodynamics
Authors: Hassanabadi H. , Chung W. S. , Lütfüoğlu B. C. , Maghsoodi E.
Published: January 2021

In this paper, we employ a new form of the extended uncertainty principle to investigate the thermal properties of the Schwarzschild and Reissner–Nordström. After we construct the formalism, we obtain the mass-temperature function for the Schwarzschild black hole. We follow a heuristic method to derive the entropy function after we obtained the heat capacity function. Then, we derive the mass-temperature and mass-charge-temperature functions of the Reissner–Nordström black hole in the new formalism. After we obtain the heat capacity and entropy functions, we present a comprehensive and comparative analysis of all these functions. We find that the deformation parameter changes drastically some of the thermodynamic function characteristics.
Computational investigation of non-uniform magnetic field on thermal characteristic of nanofluid stream inside 180∘ elbow pipe
Authors: Chu Yu-Ming , Moradi Rasoul , Abazari Amir Musa
Published: January 2021

The thermal efficiency of the heat exchanger is substantial in chemical and mechanical systems. The presence of the non-homogeny magnetic field considerably enhances the heat rate of nanofluid stream. In this exploration, the presence of the non-uniform magnetic intensity on the heat rate of nanofluid stream is noted inside the [Formula: see text] elbow pipe. FVM is used to model the flow characteristics and temperature distribution through the [Formula: see text] elbow pipe. Our major focus is to demonstrate the main influences of the non-uniform FHD on flow stream and heat transfer of nanofluid in various inlet velocities and magnetic intensities. Achieved outcomes display that growing the magnetic intensity from 1e + 6 to 4e + 6 enhances the average Nusselt number about 30%. Our findings show that increasing the inlet velocity to Re = 100 decreases the magnetic effects about 17% on the heat transfer growth.