bluuebunny/crossref_metadata_2025_split huggingface dataset:
African Swine Fever Virus CD2v protein promotes β-Interferon expression and apoptosis in swine cells
Authors: Chaulagain Sabal , Delhon Gustavo , Khatiwada Sushil , Rock Daniel L. 
Published: November 2020

ABSTRACTAfrican swine fever (ASF) is a disease of swine characterized by massive lymphocyte depletion in lymphatic tissues due to apoptosis of B and T cells, most likely triggered by proteins or factors secreted by infected adjacent macrophages. Here we describe a role for the ASF virus (ASFV) protein CD2v in apoptosis induction in lymphocytes. CD2v is a viral homolog of host CD2 that has been implicated in viral virulence and immunomodulationin vitro; however, its actual function remains unknown. We show that CD2v is secreted into culture medium of CD2v-expressing swine cells; and expression of-or treatment with CD2v led to significant induction of IFN-β/ISGs transcription and antiviral state. CD2v expression led to enhanced NF-κB-p65 nuclear translocation in these cultures and incubation with a NF-κB inhibitor reduced CD2v-induced NF-κB-p65 nuclear translocation and IFN-β transcription. We show that CD2v binds CD58, the natural CD2 ligand, and that CD58 siRNA knock-down results in significant reduction in NF-κB-p65 nuclear translocation and IFN-β transcription. Treatment of swine PBMC with purified CD2v led to enhanced NF-κB-p65 nuclear translocation and induction of IFN-β transcription. Further, induction of caspase-3 and PARP1 cleavage was observed in these swine PBMC at later times, providing a mechanism for CD2v-induced apoptosis of lymphocytes. Finally, IFN-β induction and NF-κB activation was inhibited in swine PBMC treated with purified CD2v pre-incubated with antibodies against CD2v. Overall, our results indicate that ASFV CD2v is an immunomodulatory protein that, by promoting lymphocyte apoptosis, may contribute to bystander lymphocyte depletion observed during ASFV infection in pigs.IMPORTANCEASF, a severe hemorrhagic disease of domestic swine, represents a significant economic threat to swine industry worldwide. One critical pathological event observed in pigs infected with virulent isolates is an extensive destruction of lymphoid tissue and massive lymphocyte depletion. However, viral factor/s involved in this event are yet to be identified. Here we show that, by inducing NF-κB-dependent IFN signaling, ASFV CD2v is able to promote apoptosis in swine PBMC. We propose that CD2v released by ASFV-infected macrophages contributes to the massive depletion of lymphocytes observed in lymphoid tissues of infected pigs. Results here improve our understanding of ASFV pathogenesis and will encourage novel intervention approaches.
Sulfate import inSalmonellaTyphimurium impacts bacterial aggregation and the neutrophil respiratory burst
Authors: Westerman TL , Sheats MK , Elfenbein JR 
Published: November 2020

AbstractDuring enteric salmonellosis, neutrophil generated reactive oxygen species alter the gut microenvironment favoring survival ofSalmonellaTyphimurium. While the type-3 secretion system-1 (T3SS-1) and flagellar motility are potentSalmonellaTyphimurium agonists of the neutrophil respiratory burstin vitro, neither of these pathways alone are responsible for stimulation of a maximal respiratory burst. In order to identifySalmonellaTyphimurium genes that impact the magnitude of the neutrophil respiratory burst, we performed a two-step screen of defined mutant libraries in co-culture with neutrophils. We first screenedSalmonellaTyphimurium mutants lacking defined genomic regions, followed by the individual mutants mapping to genomic regions under selection. Mutants in four genes,STM1696(sapF),STM2201(yeiE),STM2112(wcaD), andSTM2441(cysA), induced an attenuated respiratory burst. We linked the altered respiratory burst to reduced T3SS-1 expression and/or altered flagellar motility for two mutants (ΔSTM1696and ΔSTM2201). The ΔSTM2441mutant, defective for sulfate transport, formed aggregates in minimal media and adhered to surfaces in rich media, suggesting a role for sulfur homeostasis in regulation of aggregation/adherence. We linked the aggregation/adherence phenotype of the ΔSTM2441mutant to biofilm-associated protein A and flagellins and hypothesize that aggregation caused the observed reduction in the magnitude of the neutrophil respiratory burst. Our data demonstrate thatSalmonellaTyphimurium has numerous mechanisms to limit the magnitude of the neutrophil respiratory burst. These data further inform our understanding of how Salmonellamay alter neutrophil antimicrobial defenses.
Chemoreceptor Co-Expression inDrosophilaOlfactory Neurons
Authors: Task Darya , Lin Chun-Chieh , Vulpe Alina , Afify Ali , Ballou Sydney , Brbić Maria , Schlegel Philipp , Jefferis Gregory S. X. E. , Li Hongjie , Menuz Karen , Potter Christopher J. 
Published: November 2020

AbstractDrosophila melanogasterolfactory neurons have long been thought to express only one chemosensory receptor gene family. There are two main olfactory receptor gene families inDrosophila, the Odorant Receptors (ORs) and the Ionotropic Receptors (IRs). The dozens of odorant binding receptors in each family require at least one co-receptor gene in order to function:Orcofor ORs, andIr25a,Ir8a, andIr76bfor IRs. Using a new genetic knock-in strategy, we targeted the four co-receptors representing the main chemosensory families inDrosophila(Orco, Ir8a, Ir76b, Ir25a). Co-receptor knock-in expression patterns were verified as accurate representations of endogenous expression. We find extensive overlap in expression among the different co-receptors. As defined by innervation into antennal lobe glomeruli,Ir25ais broadly expressed in 88% of all olfactory sensory neuron classes and is co-expressed in 82% of Orco+ neuron classes, including all neuron classes in the maxillary palp.Orco,Ir8a, andIr76bexpression patterns are also more expansive than previously assumed. Single sensillum recordings from Orco-expressingIr25amutant antennal and palpal neurons identify changes in olfactory responses. These results suggest co-expression of chemosensory receptors is common in olfactory neurons. Together, our data present the first comprehensive map of chemosensory co-receptor expression and reveal their unexpected widespread co-expression in the fly olfactory system.
Expansion of Human Papillomavirus-Specific T Cells in Periphery and Cervix in a Therapeutic Vaccine Recipient Whose Cervical High-Grade Squamous Intraepithelial Lesion Regressed
Authors: Shibata Takeo , Shah Sumit , Evans Teresa , Coleman Hannah , Lieblong Benjamin J. , Spencer Horace J. , Quick C. Matthew , Sasagawa Toshiyuki , Stephens Owen W. , Peterson Erich , Johann Donald , Lu Yong-Chen , Nakagawa Mayumi 
Published: November 2020

AbstractAdvances in high-throughput sequencing have revolutionized the manner with which we can study T cell responses. We describe a woman who received a human papillomavirus (HPV) therapeutic vaccine called PepCan, and experienced complete resolution of her cervical high-grade squamous intraepithelial lesion. By performing bulk T cell receptor (TCR) β deep sequencing of peripheral blood mononuclear cells before and after 4 vaccinations, 70 putatively vaccine-specific clonotypes were identified for being significantly increased using a beta-binomial model. Interferon-γ enzyme-linked immunospot assay identified significantly increased HPV-specific T cell response in the HPV 16 E6 91-115 region after 4 vaccinations (p=0.023). T cells with specificity to this region were sorted and analyzed using single-cell RNA-seq and TCR sequencing, HPV specificity in 60 of the 70 clonotypes identified to be vaccine-specific was demonstrated. TCR β bulk sequencing of the cervical liquid-based cytology samples and cervical formalin-fixed paraffin-embedded samples before and after 4 vaccinations demonstrated the presence of these HPV-specific T cells in the cervix. Combining traditional and cutting-edge immunomonitoring techniques enabled us to demonstrate expansion of HPV-antigen specific T cells in the periphery and cervix.
Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection
Authors: Brouwer Philip J. M. , Brinkkemper Mitch , Maisonnasse Pauline , Dereuddre-Bosquet Nathalie , Grobben Marloes , Claireaux Mathieu , de Gast Marlon , Marlin Romain , Chesnais Virginie , Diry Ségolène , Allen Joel D. , Watanabe Yasunori , Giezen Julia M. , Kerster Gius , Turner Hannah L. , van der Straten Karlijn , van der Linden Cynthia A. , Aldon Yoann , Naninck Thibaut , Bontjer Ilja , Burger Judith A. , Poniman Meliawati , Mykytyn Anna Z. , Okba Nisreen M. A. , Schermer Edith E. , van Breemen Marielle J. , Ravichandran Rashmi , Caniels Tom G. , van Schooten Jelle , Kahlaoui Nidhal , Contreras Vanessa , Lemaître Julien , Chapon Catherine , Ho Tsong Fang Raphaël , Villaudy Julien , Sliepen Kwinten , van der Velden Yme U. , Haagmans Bart L. , de Bree Godelieve J. , Ginoux Eric , Ward Andrew B. , Crispin Max , King Neil P. , van der Werf Sylvie , van Gils Marit J. , Grand Roger Le , Sanders Rogier W. 
Published: November 2020

SummaryThe SARS-CoV-2 pandemic is continuing to disrupt personal lives, global healthcare systems and economies. Hence, there is an urgent need for a vaccine that prevents viral infection, transmission and disease. Here, we present a two-component protein-based nanoparticle vaccine that displays multiple copies of the SARS-CoV-2 spike protein. Immunization studies show that this vaccine induces potent neutralizing antibody responses in mice, rabbits and cynomolgus macaques. The vaccine-induced immunity protected macaques against a high dose challenge, resulting in strongly reduced viral infection and replication in upper and lower airways. These nanoparticles are a promising vaccine candidate to curtail the SARS-CoV-2 pandemic.
TRAF6 and TAK1 contribute to SAMHD1-mediated negative regulation of NF-κB signaling
Authors: Espada Constanza E. , Gelais Corine St. , Bonifati Serena , Maksimova Victoria V. , Cahill Michael P. , Kim Sun Hee , Wu Li 
Published: November 2020

AbstractSterile alpha motif and HD-domain–containing protein 1 (SAMHD1) restricts HIV-1 replication by limiting the intracellular dNTP pool. SAMHD1 also suppresses the activation of NF-κB in response to viral infections and inflammatory stimuli. However, the mechanisms by which SAMHD1 negatively regulates this pathway remain unclear. Here we show that SAMHD1-mediated suppression of NF-κB activation is modulated by two key mediators of NF-κB signaling, tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and transforming growth factor-β-activated kinase-1 (TAK1). We compared NF-κB activation stimulated by interleukin (IL)-1β in monocytic THP-1 control and SAMHD1 knockout (KO) cells with and without partial TRAF6 knockdown (KD), or in cells treated with TAK1 inhibitors. Relative to control cells, IL-1β-treated SAMHD1 KO cells showed increased phosphorylation of the inhibitor of NF-κB (IκBα), an indication of pathway activation, and elevated levels ofTNF-αmRNA. Moreover, SAMHD1 KO combined with TRAF6 KD or pharmacological TAK1 inhibition reduced IκBα phosphorylation andTNF-αmRNA to the level of control cells. SAMHD1 KO cells infected with single-cycle HIV-1 showed elevated infection andTNF-αmRNA levels compared to control cells, and the effects were significantly reduced by TRAF6 KD or TAK1 inhibition. We further demonstrated that overexpressed SAMHD1 inhibited TRAF6-stimulated NF-κB reporter activity in HEK293T cells in a dose-dependent manner. SAMHD1 contains a nuclear localization signal (NLS), but an NLS-defective SAMHD1 exhibited a suppressive effect similar to the wild-type protein. Our data suggest that the TRAF6-TAK1 axis contributes to SAMHD1-mediated suppression of NF-κB activation and HIV-1 infection.ImportanceCells respond to pathogen infection by activating a complex innate immune signaling pathway, which culminates in the activation of transcription factors and secretion of a family of functionally and genetically related cytokines. However, excessive immune activation may cause tissue damage and detrimental effects on the host. Therefore, in order to maintain host homeostasis, the innate immune response is tightly regulated during viral infection. We have reported SAMHD1 as a novel negative regulator of the innate immune response. Here, we provide new insights into SAMHD1-mediated negative regulation of the NF-κB pathway at the TRAF6-TAK1 checkpoint. We show that SAMHD1 inhibits TAK1 activation and TRAF6 signaling in response to proinflammatory stimuli. Interestingly, TRAF6 knockdown in SAMHD1-deficient cells significantly inhibited HIV-1 infection and activation of NF-κB induced by virus infection. Our research reveals a new negative regulatory mechanism by which SAMHD1 participates in the maintenance of cellular homeostasis during HIV-1 infection and inflammation.
Candidate Explorer: a tool for discovery, evaluation, and display of mutations causing significant immune phenotypes
Authors: Xu Darui , Lyon Stephen , Bu Chun Hui , Hildebrand Sara , Choi Jin Huk , Zhong Xue , Liu Aijie , Turer Emre E. , Zhang Zhao , Nair-Gill Evan , Shi Hexin , Wang Ying , Zhang Duanwu , Yue Tao , SoRelle Jeff , Misawa Takuma , Sun Lei , Wang Jianhui , Farokhnia Roxana , Sakla Andrew , Schneider Sara , Stewart Nathan , Coco Hannah , Coolbaugh Gabrielle , Hayse Braden , Mazal Sara , Medler Dawson , Nguyen Brandon , Rodriguez Edward , Wadley Andrew , Tang Miao , Li Xiaohong , Anderton Priscilla , Keller Katie , Scott Lindsay , Quan Jiexia , Cooper Sydney , Qin Baifang , Cardin Jennifer , Simpson Rochelle , Tadesse Meron , Sun Qihua , Santoyo John , Bronikowski Amy , Johnson Alexyss , Moresco Eva Marie Y. , Beutler Bruce 
Published: November 2020

AbstractWhen applied to immunity, forward genetic studies use meiotic mapping to provide strong statistical evidence that a particular mutation is causative of a particular immune phenotype. Notwithstanding this, co-segregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the selection of authentic causative mutations using a machine learning software tool, Candidate Explorer (CE), which integrates 65 data features into a single numeric score, mathematically convertible to the likelihood of verification of any putative mutation-phenotype association. CE has identified most genes within which mutations can be causative of flow cytometric phenovariation inMus musculus. The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.
Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos
Authors: Takasugi Paige R. , Wang Shengzhou , Truong Kimberly T. , Drage Evan P. , Kanishka Sahar N. , Higbee Marissa A. , Bamidele Nathan , Ojelabi Ogooluwa , Sontheimer Erik J. , Gagnon James A. 
Published: November 2020

AbstractThe CRISPR-Cas universe continues to expand. The type II CRISPR-Cas system fromStreptococcus pyogenes(SpyCas9) is the most widely used for genome editing due to its high efficiency in cells and organisms. However, concentrating on a single CRISPR-Cas system imposes limits on target selection and multiplexed genome engineering. We hypothesized that CRISPR-Cas systems originating from different bacterial species could operate simultaneously and independently due to their distinct single-guide RNAs (sgRNAs) or CRISPR-RNAs (crRNAs), and protospacer adjacent motifs (PAMs). Additionally, we hypothesized that CRISPR-Cas activity in zebrafish could be regulated through the expression of inhibitory anti-CRISPR (Acr) proteins. Here, we use a simple mutagenesis approach to demonstrate that CRISPR-Cas systems fromStreptococcus pyogenes(SpyCas9),Streptococcus aureus(SauCas9),Lachnospiraceae bacterium(LbaCas12a, previously known as LbCpf1), are orthogonal systems capable of operating simultaneously in zebrafish. CRISPR systems fromAcidaminococcussp. (AspCas12a, previously known as AsCpf1) andNeisseria meningitidis(Nme2Cas9) were also active in embryos. We implemented multichannel CRISPR recording using three CRISPR systems and show that LbaCas12a may provide superior information density compared to previous methods. We also demonstrate that type II Acrs (anti-CRISPRs) are effective inhibitors of SpyCas9 in zebrafish. Our results indicate that at least five CRISPR-Cas systems and two anti-CRISPR proteins are functional in zebrafish embryos. These orthogonal CRISPR-Cas systems and Acr proteins will enable combinatorial and intersectional strategies for spatiotemporal control of genome editing and genetic recording in animals.
Simultaneous, cell-intrinsic downregulation of PD-1 and TIGIT enhances the effector function of CD19-targeting CAR T cells and promotes an early-memory phenotype
Authors: Lee Young-Ho , Lee Hyeong Ji , Kim Hyung Cheol , Lee Yujean , Nam Su Kyung , Hupperetz Cedric , Ma Jennifer SY , Wang Xinxin , Singer Oded , Kim Won Seog , Kim Seok Jin , Koh Youngil , Jung Inkyung , Kim Chan Hyuk 
Published: November 2020

AbstractCD19-targeting chimeric antigen receptor (CAR) T cells have become an important therapeutic option for patients with relapsed and refractory B cell malignancies. However, recent clinical data indicate that a significant portion of patients still do not benefit from the therapy owing to various resistance mechanisms, including high expression of multiple inhibitory immune checkpoint receptors on activated CAR T cells. Here, we report a lentiviral two-in-one CAR T approach in which two checkpoint receptors are downregulated simultaneously by a dual short-hairpin RNA (shRNA) cassette integrated into a CAR vector. Using this system, we evaluated CD19-targeting CAR T cells in the context of four different checkpoint combinations—PD-1/TIM-3, PD-1/LAG-3, PD-1/CTLA-4 and PD-1/TIGIT—and found that CAR T cells with PD-1/TIGIT downregulation uniquely exerted synergistic antitumor effects in mouse xenograft models compared with PD-1 single downregulation, and maintained cytolytic and proliferative capacity upon repeated antigen exposure. Importantly, functional and phenotypic analyses of CAR T cells as well as analyses of transcriptomic profiles suggested that downregulation of PD-1 enhances short-term effector function, whereas downregulation of TIGIT is primarily responsible for maintaining a less-differentiated/exhausted state, providing a potential mechanism for the observed synergy. The PD-1/TIGIT–downregulated CAR T cells generated from diffuse large B-cell lymphoma patient-derived T cells using a clinically applicable manufacturing process also showed robust antitumor activity and significantly improved persistencein vivocompared with conventional CD19-targeting CAR T cells. Overall, our results demonstrate that the cell-intrinsic PD-1/TIGIT dual downregulation strategy may prove effective in overcoming immune checkpoint-mediated resistance in CAR T therapy.
A marine bacterial community that degrades poly(ethylene terephthalate) and polyethylene
Authors: Gao Rongrong , Sun Chaomin 
Published: November 2020

AbstractPlastic wastes have become the most common form of marine debris and present a growing global pollution problem. Recently, microorganisms-mediated degradation has become a most promising way to accomplish the eventual bioremediation of plastic wastes due to their prominent degradation potentials. Here, a marine bacterial community which could efficiently colonize and degrade both poly (ethylene terephthalate) (PET) and polyethylene (PE) was discovered through a screening with hundreds of plastic waste associated samples. Using absolute quantitative 16S rRNA sequencing and cultivation methods, we obtained the abundances and pure cultures of three bacteria mediating plastic degradation. We further reconstituted a tailored bacterial community containing above three bacteria and demonstrated its efficient degradation of PET and PE through various techniques. The released products from PET and PE degraded by the reconstituted bacterial community were determined by the liquid chromatography-mass spectrometry. Finally, the plastic degradation process and potential mechanisms mediated by the reconstituted bacterial community were elucidated through transcriptomic methods. Overall, this study establishes a stable and effective marine bacterial community for PET and PE degradation and sheds light on the degradation pathways and associated mechanistic processes, which paves a way to develop a microbial inoculant against plastic wastes.
Bacteroidetes contribute to the carbon and nutrient cycling of deep sea through breaking down diverse glycans
Authors: Zheng Rikuan , Cai Ruining , Liu Rui , Liu Ge , Sun Chaomin 
Published: November 2020

AbstractBacteroidetes are thought to be specialized for the degradation of algae-derived ocean polysaccharides and are a major contributor to the marine carbon and nutrient cycling. Here, we first show Bacteroidetes are the second most abundant phylum bacteria in deep-sea cold seep and possess more genes associated with polysaccharides degradation than other bacteria through metagenomics methods. We further isolate a novel Bacteroidetes species,Maribellus comscasisWC007T, which can efficiently degrade numerous different polysaccharides including: cellulose, pectin, fucoidan, mannan, xylan and starch. These results are verified by transcriptomic analyses and growth assays. Notably, we find cellulose promotes abundant bacterial growth, and using transcriptomics and metabolomics we finally report on the underlying mechanisms of cellulose degradation and utilization, as well as potential contributions to the carbon cycling. Overall, our results suggest Bacteroidetes play key roles in the deep-sea carbon and nutrient cycling, likely due to their high abundance and prominent polysaccharide degradation capabilities.One Sentence SummaryBacteroidetes contribute to ocean carbon and nutrient cycle.
Enhancing the prediction of protein coding regions in biological sequence via a deep learning framework with hybrid encoding★,★★
Authors: Wei Chao , Zhang Junying , Yuan Xiguo 
Published: November 2020

ABSTRACTProtein coding regions prediction is a very important but overlooked subtask for tasks such as prediction of complete gene structure, coding/noncoding RNA. Many machine learning methods have been proposed for this problem, they first encode a biological sequence into numerical values and then feed them into a classifier for final prediction. However, encoding schemes directly influence the classifier’s capability to capture coding features and how to choose a proper encoding scheme remains uncertain. Recently, we proposed a protein coding region prediction method in transcript sequences based on a bidirectional recurrent neural network with non-overlapping 3-mer feature, and achieved considerable improvement over existing methods, but there is still much room to improve the performance. First, 3-mer feature that counts the occurrence frequency of trinucleotides in a biological sequence only reflect local sequence order information between the most contiguous nucleotides, which loses almost all the global sequence order information. Second, kmer features of lengthklarger than three (e.g., hexamer) may also contain useful information. Based on the two points, we here present a deep learning framework with hybrid encoding for protein coding regions prediction in biological sequences, which effectively exploit global sequence order information, non-overlapping gapped kmer (gkm) features and statistical dependencies among coding labels. 3-fold cross-validation tests on human and mouse biological sequences demonstrate that our proposed method significantly outperforms existing state-of-the-art methods.