bluuebunny/crossref_metadata_2025_split huggingface dataset:
E proteins orchestrate dynamic transcriptional cascades to suppress ILC2 differentiation
Authors: Peng Vincent , Georgescu Constantin , Bakowska Anna , Qian Liangyue , Wren Jonathan D , Sun Xiao-Hong 
Published: March 2020

AbstractThe basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of group2 innate lymphoid cells from bone marrow and thymic progenitors. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such asCbfa2t3andJdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.SummaryDifferentiation of group 2 innate lymphoid cells is forcefully repressed by E protein transcription factors. This report elucidates how E proteins repress a transcriptional network important for ILC2 differentiation by up-regulating the expression of transcriptional repressors.
Identification of lactate as a potential inhibitory factor within epithelial cell supernatant and its effects on type 2 T cell populations
Authors: Hughes Francis , Pavord Ian D , Powell Timothy J 
Published: March 2020

Abstract / Short SummaryEpithelial cells have been shown previously to inhibit release of type 2 cytokines from T cells and this process could be important in a type 2-mediated diseases such as asthma. Factors secreted by epithelial cells could regulate inflammatory responses and release an ‘all is well’ signal such that the immune system is controlled. Here we show that lung epithelial cells are able to inhibit IL-2 driven type 2 cytokine release by PBMC cells across a transwell indicating the involvement of soluble mediators. We then fractionate the mediators within the conditioned media using methanol chloroform separation and size fractionation. Inhibitory activity was demonstrated within the polar fraction of supernatant separated by methanol chloroform extraction. We then found that lactate, a component within the polar fraction was able to mediate inhibition of the type 2 cytokines. The inhibitory activity of lactate deserves further study and could play a role in the inhibition of T cell derived cytokines in vivo.
Convective forces increase rostral delivery of intrathecal antisense oligonucleotides in the cynomolgus monkey nervous system
Authors: Sullivan Jenna M. , Mazur Curt , Wolf Daniel A. , Horky Laura , Currier Nicolas , Fitzsimmons Bethany , Hesterman Jacob , Pauplis Rachel , Haller Scott , Powers Berit , Tayefeh Leighla , DeBrosse-Serra Bea , Hoppin Jack , Kordasiewicz Holly , Swayze Eric E. , Verma Ajay 
Published: March 2020

ABSTRACTBackgroundThe intrathecal (IT) dosing route introduces drugs directly into the CSF to bypass the blood-brain barrier and gain direct access to the CNS. We evaluated the use of convective forces acting on the cerebrospinal fluid as a means for increasing rostral delivery of IT dosed radioactive tracer molecules and antisense oligonucleotides (ASO) in the monkey CNS. We also measured the cerebral spinal fluid (CSF) volume in a group of cynomolgus monkeys.MethodsThere are three studies presented, in each of which cynomolgus monkeys were injected into the IT space with radioactive tracer molecules and/or ASO by lumbar puncture in either a low or high volume. The first study used the radioactive tracer64Cu-DOTA and PET imaging to evaluate the effect of the convective forces. The second study combined the injection of the radioactive tracer99mTc-DTPA and ASO, then used SPECT imaging and ex vivo tissue analysis of the effects of convective forces to bridge between the tracer and the ASO distributions. The third experiment evaluated the effects of different injection volumes on the distribution of an ASO. In the course of performing these studies we also measured the CSF volume in the subject monkeys by Magnetic Resonance Imaging.ResultsIt was consistently found that larger bolus dose volumes produced greater rostral distribution along the neuraxis. Thoracic percussive treatment also increased rostral distribution of low volume injections. There was little added benefit on distribution by combining the thoracic percussive treatment with the high-volume injection. The CSF volume of the monkeys was found to be 11.9 ± 1.6 cm3.ConclusionsThese results indicate that increasing convective forces after IT injection increases distribution of molecules up the neuraxis. In particular, the use of high IT injection volumes will be useful to increase rostral CNS distribution of therapeutic ASOs for CNS diseases in the clinic.
CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning
Authors: Shang Jiayu , Sun Yanni 
Published: March 2020

ABSTRARCTThe fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used alignment-based methods are not ideal choices for detecting new viral species. In this work, we present a novel hierarchical classification model named CHEER, which can conduct read-level taxonomic classification from order to genus for new species. By combining k-mer embedding-based encoding, hierarchically organized CNNs, and carefully trained rejection layer, CHEER is able to assign correct taxonomic labels for reads from new species. We tested CHEER on both simulated and real sequencing data. The results show that CHEER can achieve higher accuracy than popular alignment-based and alignment-free taxonomic assignment tools. The source code, scripts, and pre-trained parameters for CHEER are available via GitHub:https://github.com/KennthShang/CHEER.
Medicago truncatula Yellow Stripe-Like7encodes a peptide transporter required for symbiotic nitrogen fixation
Authors: Castro-Rodríguez Rosario , Reguera María , Escudero Viviana , Gil-Díez Patricia , Quintana Julia , Prieto Rosa Isabel , Kumar Rakesh K. , Brear Ella , Grillet Louis , Wen Jiangqi , Mysore Kirunkamar S. , Walker Elsbeth L. , Smith Penelope M. C. , Imperial Juan , González-Guerrero Manuel 
Published: March 2020

ABSTRACTYellow Stripe-Like (YSL) proteins are a family of plant transporters typically involved in transition metal homeostasis. The substrate of three of the four YSL clades (clades I, II, and IV) are metal complexes with non-proteinogenic amino acid nicotianamine or its derivatives. No such transport capabilities have been shown for any member of the remaining clade (clade III), which is able to translocate short peptides across the membranes instead. The connection between clade III YSL members and metal homeostasis might have been masked by the functional redundancy characteristic of this family. This might have been circumvented in legumes through neofunctionalization of YSLs to ensure a steady supply of transition metals for symbiotic nitrogen fixation in root nodules. To test this possibility,Medicago truncatulaclade III transporter MtYSL7 has been studied both when the plant was fertilized with ammonium nitrate or when nitrogen had to be provided by endosymbiotic rhizobia within the root nodules. MtYSL7 is a plasma membrane protein expressed in the vasculature and in the nodule cortex. This protein is able to transport short peptides into the cytosol, although none with known metal homeostasis roles. ReducingMtYSL7expression levels resulted in diminished nitrogen fixation rates. In addition, nodules of mutant lines lackingYSL7accumulated more copper and iron, the later the likely result of increased expression in roots of iron uptake and delivery genes. The available data is indicative of a role of MtYSL7, and likely other clade III YSLs, in transition metal homeostasis.ONE SENTENCE SUMMARYMedicago truncatulaYSL7 is a peptide transporter required for symbiotic nitrogen fixation in legume nodules, likely controlling transition metal allocation to these organs.
Top-down coordination of local cortical state during selective attention
Authors: van Kempen Jochem , Gieselmann Marc A. , Boyd Michael , Steinmetz Nicholas A. , Moore Tirin , Engel Tatiana A. , Thiele Alexander 
Published: March 2020

AbstractSpontaneous fluctuations in cortical excitability influence sensory processing and behavior. These fluctuations, long known to reflect global changes in cortical state, were recently found to be modulated locally within a retinotopic map during spatially selective attention. We found that periods of vigorous (On) and faint (Off) spiking activity, the signature of cortical state fluctuations, were coordinated across brain areas along the visual hierarchy and tightly coupled to their retinotopic alignment. During top-down attention, this interareal coordination was enhanced and progressed along the reverse cortical hierarchy. The extent of local state coordination between areas was predictive of behavioral performance. Our results show that cortical state dynamics are shared across brain regions, modulated by cognitive demands and relevant for behavior.One Sentence SummaryInterareal coordination of local cortical state is retinotopically precise and progresses in a reverse hierarchical manner during selective attention.
Forced Abstinence from Alcohol Induces Sex-Specific Depression-like Behavioral and Neural Adaptations in Somatostatin Neurons in Cortical and Amygdalar Regions
Authors: Dao Nigel C. , Nair Malini S. , Magee Sarah N. , Moyer J. Brody , Sendao Veronica , Brockway Dakota F. , Crowley Nicole A. 
Published: March 2020

ABSTRACTForced abstinence (FA) from alcohol has been shown to produce a variety of anxiety- and depression- like symptoms in animal models. Somatostatin (SST) neurons, a subtype of GABAergic neurons found throughout the brain, are a novel neural target with potential treatment implications in affective disorders, yet their role in alcohol use disorders (AUD) remains to be explored. Here, we examined the neuroadaptations of SST neurons during forced abstinence from voluntary alcohol consumption. Following six weeks of two-bottle choice alcohol consumption and protracted forced abstinence, male and female C57BL/6J mice exhibited a heightened, but sex-specific, depressive-like behavioral profile in the sucrose preference test (SPT) and forced swim test (FST), without changes in anxiety-like behaviors in the elevated plus maze (EPM) and open field test (OFT). FST-induced cFos expressions in the prefrontal cortex (PFC) and ventral bed nucleus of the stria terminalis (vBNST) were altered in FA-exposed female mice only, suggesting a sex-specific effect of forced abstinence on the neural response to acute stress. SST immunoreactivity in these regions was unaffected by forced abstinence, while differences were seen in SST/cFos co-expression in the vBNST. No differences in cFos or SST immunoreactivity were seen in the lateral central nucleus of the amygdala (CEA) and the basolateral amygdala (BLA). Additionally, SST neurons displayed opposing alterations in the PFC and vBNST, with heightened intrinsic excitability in the PFC and diminished intrinsic excitability in the vBNST. These findings provide an overall framework of forced abstinence-induced neuroadaptations in these key brain regions involved in emotional regulation and processing.
The potential SARS-CoV-2 entry inhibitor
Authors: Lung Jrhau , Lin Yu-Shih , Yang Yao-Hsu , Chou Yu-Lun , Chang Geng-He , Tsai Ming-Shao , Hsu Cheng-Ming , Yeh Reming-Albert , Shu Li-Hsin , Cheng Yu-Ching , Liu Hung Te , Wu Ching-Yuan 
Published: March 2020

ABSTRACTOutbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and has rapidly spread to almost all parts of world. In coronaviruses, the receptor binding domain (RBD) in the distal part of S1 subunit of SARS-CoV-2 spike protein can directly bind to angiotensin converting enzyme 2 (ACE2). RBD promote viral entry into the host cells and is an important therapeutic target. In this study, we discovered that theaflavin showed the lower idock score (idock score: −7.95 kcal/mol). To confirm the result, we discovered that theaflavin showed FullFitness score of −991.21 kcal/mol and estimated ΔG of −8.53 kcal/mol for the most favorable interaction with contact area of SARS-CoV-2 RBD by SwissDock service. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were formed between theaflavin and Arg454, Phe456, Asn460, Cys480, Gln493, Asn501 and Val503 of SARS-CoV-2 RBD, near the direct contact area with ACE2. Our results suggest that theaflavin could be the candidate of SARS-CoV-2 entry inhibitor for further study.
Inflammatory and oxidative status in European captive black rhinoceroses: a link with Iron Overload Disorder?
Authors: Pouillevet Hanae , Soetart Nicolas , Boucher Delphine , Wedlarski Rudy , Jaillardon Laetitia 
Published: March 2020

AbstractIron Overload Disorder (IOD) is a syndrome developed by captive browsing rhinoceroses like black rhinoceroses (Diceros bicornis) in which hemosiderosis settles in vital organs while free iron accumulates in the body, potentially predisposing to various secondary diseases. Captive grazing species like white rhinoceroses (Ceratotherium simum) do not seem to be affected. The pro-oxidant and pro-inflammatory properties of iron, associated with the poor antioxidant capacities of black rhinoceroses, could enhance high levels of inflammation and oxidative stress leading to rapid ageing and promoting diseases. In this prospective study, 15 black (BR) and 29 white rhinoceroses (WR) originating from 22 European zoos were blood-sampled and compared for their iron status (serum iron), liver/muscle biochemical parameters (AST, GGT, cholesterol), inflammatory status (total proteins, protein electrophoresis) and oxidative stress markers (SOD, GPX, dROMs). Results showed higher serum iron and liver enzyme levels in black rhinoceroses (P<0.01), as well as higher GPX (P<0.05) and dROM (P<0.01) levels. The albumin/globulin ratio was lower in black rhinoceroses (P<0.05) due to higher α2-globulin levels (P<0.001). The present study suggests a higher inflammatory and oxidative profile in captive BR than in WR, possibly in relation to iron status. This could be either a consequence or a cause of iron accumulation, potentially explaining rapid ageing and various diseases. Further investigations are needed to assess the prognostic value of the inflammatory and oxidative markers in captive black rhinoceroses, particularly for evaluating the impact of reduced-iron and antioxidant-supplemented diets.
Analyses of cancer incidence and other morbidities in gamma irradiated B6CF1 mice
Authors: Zander Alia , Paunesku Tatjana , Woloschak Gayle 
Published: March 2020

ABSTRACTWith increasing medical radiation exposures, it is important to understand how different modes of delivery of ionizing radiation as well as total doses of exposure impact health outcomes. Our lab studied the risks associated with ionizing radiation by analyzing the Northwestern University Radiation Archive for animals (NURA). NURA contains detailed data from a series of 10 individual neutron and gamma irradiation experiments conducted on over 50,000 mice. Rigorous statistical testing on control mice from all Janus experiments enabled us to select studies that could be compared to one another and uncover unexpected differences among the controls as well as experimental animals. For controls, mice sham irradiated with 300 fractions died significantly earlier than those with fewer sham fractions. Using the integrated dataset of gamma irradiated and control mice, we found that fractionation significantly decreased the death hazard for animals dying of lymphomas, tumors, non-tumors, and unknown causes. Gender differences in frequencies of causes of death were identified irrespective of irradiation and dose fractionation, with female mice being at a greater risk for all causes of death, except for lung tumors. Irradiated and control male mice were at a significantly greater risk for lung tumors, the opposite from observations noted in humans. Additionally, we discovered that lymphoma deaths can occur quickly after exposures to high doses of gamma rays. This study systematically cross-compared outcomes of different modes of fractionation across a wide span of total doses to demonstrate that protraction modulated survival and disease status differently based on the total dose, cause of death, and sex of an animal. This novel method for analyzing the Janus datasets will lead to insightful new mechanistic hypotheses and research in the fields of radiation biology and protection.
Analyses of cancer incidence and other morbidities in neutron irradiated B6CF1 mice
Authors: Zander Alia , Paunesku Tatjana , Woloschak Gayle 
Published: March 2020

ABSTRACTThe Department of Energy conduced ten large-scale neutron irradiation experiments at Argonne National Laboratory between 1972 and 1989. Using a new approach to utilize experimental controls to determine whether a cross comparison between experiments was appropriate, we amalgamated data on neutron exposures to discover that fractionation significantly improved overall survival. A more detailed investigation showed that fractionation only had a significant impact on the death hazard for animals that died from solid tumors, but did not significantly impact any other causes of death. Additionally, we compared the effects of sex, age first irradiated, and radiation fractionation on neutron irradiated mice versus cobalt 60 gamma irradiated mice and found that solid tumors were the most common cause of death in neutron irradiated mice, while lymphomas were the dominant cause of death in gamma irradiated mice. Most animals in this study were irradiated before 150 days of age but a subset of mice was first exposed to gamma or neutron irradiation over 500 days of age. Advanced age played a significant role in decreasing the death hazard for neutron irradiated mice, but not for gamma irradiated mice. Mice that were 500 days old before their first exposures to neutrons began dying later than both sham irradiated or gamma irradiated mice.
Characterization and establishment of a novel EBV strain simultaneously associated with nasopharyngeal carcinoma and B-cell lymphoma
Authors: Yu Fenggang , Syn Nicholas L. , Lu Yanan , Chong Qing Yun , Lai Junyun , Tan Wei Jian , Goh Boon Cher , MacAry Paul A. , Wang Lingzhi , Loh Kwok Seng 
Published: March 2020

ABSTRACTEpstein-Barr virus (EBV) – the prototypical human tumor virus – is responsible for 1-2% of the global cancer burden, but divergent strains seem to exist in different geographical regions with distinct predilections for causing lymphoid or epithelial malignancies. Here we report the establishment and characterization of Yu103, an Asia Pacific EBV strain with a highly remarkable provenance of being derived from nasopharyngeal carcinoma biopsy but subsequently propagated in human B-lymphoma cells and xenograft models. Unlike previously characterized EBV strains which are either predominantly B-lymphotropic or epitheliotropic, Yu103 evinces an uncanny capacity to infect and transform both B-lymphocytes and nasopharyngeal epithelial cells. Genomic and phylogenetic analyses indicated that Yu103 EBV lies midway along the spectrum of EBV strains known to drive lymphomagenesis or carcinogenesis, and harbors molecular features which likely account for its unusual properties. To our knowledge, Yu103 EBV is currently the only EBV isolate shown to drive human nasopharyngeal carcinoma and B-lymphoma, and should therefore provide a powerful novel platform for research on EBV-driven hematological and epithelial malignancies.
Biochemical characterizations of ER-resident peroxidases, GPx7 and GPx8, reveal their distinct and regulated oxidative activities
Authors: Kanemura Shingo , Sofia Elza Firdiani , Hirai Naoya , Okumura Masaki , Kadokura Hiroshi , Inaba Kenji 
Published: March 2020

AbstractIn the mammalian endoplasmic reticulum (ER), the diverse network comprising more than 20 members of the protein disulfide isomerase (PDI) family and more than five PDI oxidases has evolved to promote oxidative protein folding. While the canonical disulfide bond formation pathway constituted by Ero1α and PDI has been well studied so far, mechanistic and physiological bases of newly identified PDI oxidases, glutathione peroxidase-7 (GPx7) and -8 (GPx8), are only poorly understood. We here demonstrated that human GPx7 has much higher reactivity with H2O2than human GPx8, leading to efficient PDI oxidation. GPx7 forms a catalytic tetrad at the redox active site to react with H2O2efficiently and stabilize a resultantly generated sulfenylated species. While it was previously postulated that the GPx7 catalysis involved a highly reactive peroxidatic cysteine, a resolving cysteine was found to act to regulate the PDI oxidation activity of GPx7. The present study also revealed that GPx7 formed complexes preferentially with PDI and P5 in H2O2-treated cells. Altogether, human GPx7 functions as an H2O2-dependent PDI oxidase in cells whereas PDI oxidation may not be the central physiological role of human GPx8.
A regulatory program for initiation of Wnt signaling during posterior regeneration
Authors: Ramirez Alyson N. , Loubet-Senear Kaitlyn , Srivastava Mansi 
Published: March 2020

SummaryWhole-body regeneration requires the re-establishment of body axes for appropriate patterning of new and old tissue. Wnt signaling has been utilized to correctly regenerate tissues along the primary axis in many animals. However, the causal molecular mechanisms that first launch Wnt signaling during regeneration are poorly characterized. We used the acoel wormHofstenia miamiato identify processes that initiate Wnt signaling. Transcriptome profiling,in situhybridization, and functional studies revealed a Wnt ligand,wnt-3, as an early wound-induced gene specifically activated in posterior-facing wound sites and was required for establishing posterior identity during regeneration.wnt-3was upregulated upon amputation in stem cells, and its inhibition affected stem cell proliferation. Ectopic expression of anterior markers inwnt-3RNAi head fragments was stem cell dependent. Chromatin accessibility data revealed thatwnt-3activation during regeneration required input from the general wound response. Additionally, the expression of a different Wnt ligand,wnt-1, prior to amputation was required for activation of wound-inducedwnt-3expression. Our study establishes a gene regulatory network for initiating Wnt signaling in posterior tissues in a bilaterian.