bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Injury Response to DNA Damage Promotes Anti-Tumor Immunity
Authors: Sriram Ganapathy , Milling Lauren , Chen Jung-Kuei , Abraham Wuhbet , Handly Erika D. , Irvine Darrell J. , Yaffe Michael B. 
Published: April 2020

ABSTRACTInhibition of immune checkpoints has shown promising results in the treatment of certain tumor types. However, the majority of cancers do not respond to immune checkpoint inhibition (ICI) treatment, indicating the need to identify additional modalities that enhance the response to immune checkpoint blockade. In this study, we identified a tumor-tailored approach usingex-vivoDNA damaging chemotherapy-treated tumor cells as a live injured cell adjuvant. Using an optimizedex vivosystem for dendritic cell-mediated T-cell IFN-γ induction in response to DNA-damaged tumor cells, we identified specific dose-dependent treatments with etoposide and mitoxantrone that markedly enhance IFN-γ production by T-cells. Unexpectedly, the immune-enhancing effects of DNA damage failed to correlate with known markers of immunogenic cell death or with the extent of apoptosis or necroptosis. Furthermore, dead tumor cells alone were not sufficient to promote DC cross-presentation and induce IFN-γ in T-cells. Instead, the enhanced immunogenicity resided in the fraction of injured cells that remained alive, and required signaling through the RIPK1, NF-kB and p38MAPK pathways. Directin vivotranslation of these findings was accomplished by intra-tumoral injection ofex vivoetoposide-treated tumor cells as an injured cell adjuvant, in combination with systemic anti-PD1/CTLA4 antibodies. This resulted in increased intra-tumoral CD103+dendritic cells and circulating tumor antigen-specific CD8+T-cells, leading to enhanced anti-tumor immune responses and improved survival. The effect was abrogated in BATF3-deficient mice indicating that BATF3+DCs are required for appropriate T-cell stimulation by live but injured DNA-damaged tumor cells. Notably, injection of the free DNA-damaging drug directly into the tumor failed to elicit such an enhanced anti-tumor response as a consequence of simultaneous damage to dendritic cells and T-cells. Finally, the DNA damage induced injured cell adjuvant and systemic ICI combination, but not ICI alone, induced complete tumor regression in a subset of mice who were then able to reject tumor re-challenge, indicating induction of a long-lasting anti-tumor immunological memory by the injured cell adjuvant treatmentin vivo.
Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice
Authors: Aryal Sameer , Longo Francesco , Klann Eric 
Published: April 2020

AbstractLoss of the fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS). FMRP is widely thought to repress protein synthesis, but its translational targets and modes of control remain in dispute. We previously showed that genetic removal of p70 S6 kinase 1 (S6K1) corrects altered protein synthesis as well as synaptic and behavioral phenotypes in FXS mice. In this study, we examined the gene-specificity of altered mRNA translation in FXS and the mechanism of rescue with genetic reduction of S6K1 by carrying out ribosome profiling and RNA-Seq on cortical lysates from wild-type, FXS, S6K1 knockout, and double knockout mice. We observed reduced ribosome footprint abundance in the majority of differentially translated genes in the cortices of FXS mice. We used molecular assays to discover evidence that the reduction in ribosome footprint abundance reflects an increased rate of ribosome translocation, which is captured as a decrease in the number of translating ribosomes at steady state, and is normalized by inhibition of S6K1. We also found that genetic removal of S6K1 prevented a positive-to-negative gradation of alterations in translation efficiencies (RF/mRNA) with coding sequence length across mRNAs in FXS mouse cortices. Our findings reveal the identities of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.
In vitroEvolution of Antibody Affinity via Insertional Mutagenesis Scanning of an Entire Antibody Variable Region
Authors: Skamaki Kalliopi , Emond Stephane , Chodorge Matthieu , Andrews John , Rees D. Gareth , Cannon Daniel , Popovic Bojana , Buchanan Andrew , Minter Ralph , Hollfelder Florian 
Published: April 2020

AbstractWe report the first systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD was used to generate large libraries with random in-frame InDels across the entire scFv gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (ISM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach and suggests that the results of this InDel approach and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.SignificanceInsertion/deletion (InDel) mutations play key roles in genome and protein evolution. Despite their prominence in evolutionary history, the potential of InDels for changing function in protein engineering by directed evolution remains unexplored. Instead point mutagenesis is widely used. Here we create antibody libraries containing InDels and demonstrate that affinity maturation can be achieved in this way, establishing an alternative to the point mutation strategies employed in all previous in vitro selections. These InDels mirror the observation of considerable length variation in loops of natural antibodies originating from the same germline genes and be combined with point mutations, making both natural sources of functional innovation available for artificial evolution in the test tube.
Flood-induced interspecific interactions in spring-fed tributary as an ecosystem function of heterogeneous river networks
Authors: Sakai Masaru , Wakiya Ryoshiro , Hoshi Gosuke 
Published: April 2020

AbstractUnderstanding the migratory community dynamics of river networks is important for maintaining lotic system integrity. River animals migrate to their preferred habitats in spatiotemporally heterogeneous river environments. Spring-fed habitats are uniquely characterized by stable temperature and flow regimes, which create suitable spawning habitats for the chum salmonOncorhynchus keta. O. ketaexhibits “run up” to its birthplace for spawning, especially during floods. Because the eggs deposited by this anadromous fish are nutritious and actively consumed by freshwater animals, the location and timing ofO. ketaspawning events affect the spatiotemporal accumulation of mobile consumers. In this study, we examined changes in temporal population density in spawningO. ketaand a mobile consumer (juvenileO. masou masou) in a lowland, spring-fed tributary in northern Japan during a 48.5-mm autumn rainfall event. In both species, population density increased, and then decreased, after the rainfall event. InO. keta, these changes were closely associated with rainfall intensity, whereas inO. masou masouthe peak was delayed until 3 days after the rainfall event. A comparison of the gut contents ofO. masou masousampled from a spring-fed tributary and an adjacent non-spring-fed tributary indicated greater consumption ofO. ketaeggs in the spring-fed tributary. These results suggested that preferential migration ofO. ketainto spring-fed tributaries for spawning induces subsequent accumulation of juvenileO. masou masou, in turn increasingO. ketaegg consumption. These findings improve our understanding of community dynamics during floods in a heterogeneous river network environment.
Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing
Authors: Shaw Alexander G. , Majumdar Manasi , Troman Catherine , O’Toole Áine , Benny Blossom , Abraham Dilip , Praharaj Ira , Kang Gagandeep , Sharif Salmaan , Masroor Alam Muhammad , Shaukat Shahzad , Angez Mehar , Khurshid Adnan , Mahmood Nayab , Arshad Yasir , Rehman Lubna , Mujtaba Ghulam , Akthar Ribqa , Salman Muhammad , Klapsa Dimitra , Hajarha Yara , Asghar Humayun , Bandyopadhyay Ananda , Rambaut Andrew , Martin Javier , Grassly Nicholas 
Published: April 2020

AbstractGlobal poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived and wild-type polioviruses and ensure an appropriate response. This cell-culture algorithm takes 2-3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity compared with cell-culture were 90.9% (95% Confidence Interval: 75.7-98.1%) and 99.2% (95.5-100.0%) for wild-type 1 poliovirus, 92.5% (79.6-98.4%) and 98.7% (95.4-99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2-93.5%) and 93.2% (88.6-96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell-culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.
Mycobacteriumphage Butters-encoded proteins contribute to host defense against viral attack
Authors: Mageeney Catherine M. , Mohammed Hamidu T. , Dies Marta , Anbari Samira , Cudkevich Netta , Chen Yanyan , Buceta Javier , Ware Vassie C. 
Published: April 2020

ABSTRACTA diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within Cluster N mycobacteriophages. In that context, we unveil a novel defense mechanism in Cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two component system articulated by interactions between protein products of genes30and31confers defense against heterotypic phage infection by PurpleHaze or Alma, but is insufficient to confer defense against attack by the heterotypic phage Island3. Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated.IMPORTANCEMany sequenced bacterial genomes including pathogenic bacteria contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems will be critical to development of phage therapy that circumvents these defenses. Additionally, such knowledge will help engineer phage-resistant bacteria of industrial importance.
Spatial Transcriptional Mapping of the Human Nephrogenic Program
Authors: Lindström Nils O. , Sealfon Rachel , Chen Xi , Parvez Riana , Ransick Andrew , De Sena Brandine Guilherme , Guo Jinjin , Hill Bill , Tran Tracy , Kim Albert D. , Zhou Jian , Tadych Alicja , Watters Aaron , Wong Aaron , Lovero Elizabeth , Grubbs Brendan H. , Thornton Matthew E. , McMahon Jill A. , Smith Andrew D. , Ruffins Seth W. , Armit Chris , Troyanskaya Olga G. , McMahon Andrew P. 
Published: April 2020

SummaryCongenital abnormalities of the kidney and urinary tract are amongst the most common birth defects affecting 3% of newborns. The human kidney develops over a 30-week period in which a nephron progenitor pool gives rise to around a million nephrons. To establish a framework for human nephrogenesis, we spatially resolved a stereotypical process by which equipotent nephron progenitors generate a nephron anlagen, then applied data-driven approaches to construct three-dimensional protein maps on anatomical models of the nephrogenic program. Single cell RNA sequencing identified novel progenitor states which were spatially mapped to the nephron anatomy enabling the generation of functional gene-networks predicting interactions within and between nephron cell-types. Network mining identified known developmental disease genes and predicts new targets of interest. The spatially resolved nephrogenic program made available through the Human Nephrogenesis Atlas (https://sckidney.flatironinstitute.org/) will facilitate an understanding of kidney development and disease, and enhance efforts to generate new kidney structures.
Anaerobic microbial degradation of protein and lipid macromolecules in subarctic marine sediment
Authors: Pelikan Claus , Wasmund Kenneth , Glombitza Clemens , Hausmann Bela , Herbold Craig W. , Flieder Mathias , Loy Alexander 
Published: April 2020

AbstractMicroorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet microorganisms that degrade them remain understudied. Here, we revealed identities, trophic interactions and genomic features of microorganisms that degraded 13C-labelled proteins and lipids in cold anoxic microcosms with sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas were prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides an improved understanding of the metabolic processes and functional partitioning of necromass macromolecules among microorganisms in the seafloor.
Expanding magnetic organelle biogenesis in the domainBacteria
Authors: Lin Wei , Zhang Wensi , Paterson Greig A. , Zhu Qiyun , Zhao Xiang , Knight Rob , Bazylinski Dennis A. , Roberts Andrew P. , Pan Yongxin 
Published: April 2020

AbstractThe discovery of membrane-enclosed, metabolically functional organelles inBacteriaandArchaeahas transformed our understanding of the subcellular complexity of prokaryotic cells. However, whether prokaryotic organelles emerged early or late in evolutionary history remains unclear and limits understanding of the nature and cellular complexity of early life. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Here, we reconstruct 168 metagenome-assembled MTB genomes from various aquatic environments and waterlogged soils. These genomes represent nearly a 3-fold increase over the number currently available, and more than double the known MTB species. Phylogenomic analysis reveals that these newly described genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domainBacteriathan previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. These gene clusters therefore represent a promising, diverse genetic resource for biosynthesizing novel magnetic nanoparticles. Finally, our phylogenetic analyses of the core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domainBacteria. These findings emphasize the potential biological significance of prokaryotic organelles on the early Earth and have important implications for our understanding of the evolutionary history of cellular complexity.
Modulation of macrophage defense responses by Mycobacterial persistence protein MprA (Rv0981) in human THP-1 cells: effect of single amino acid variation on host-pathogen interactions
Authors: Bhattacharyya Kausik , Bandopadhyay Upasana , Singh Aayushi , Prakash Amresh , Nemaysh Vishal , Jain Shruti , Varma-Basil Mandira , Lynn Andrew M , Bose Mridula , Luthra Pratibha Mehta , Natarajan Krishnamurthy , Brahmachari Vani 
Published: April 2020

SummaryM. tuberculosisis one of the most successful human pathogens causing tuberculosis that leads to highest daily morbidity worldwide. The evasion of the host immune responses is an important strategy thatM. tuberculosisadopts. MprA (Rv0981), the response regulator of two component system is known for DNA binding activity in the pathogen and its role in persistent infection in the host. MprA is recognized as a late stage antigen during infection. A variant form of the protein MprA with G70S polymorphism (MprA*) is observed in one of our local and in several global clinical isolates ofM. tuberculosis.Here we report the nuclear localization of MprA and MprA* in differentiated macrophages. MprA and MprA* increase the expression of TGF-β and IL-10, the immune suppressive cytokines in THP-1 derived macrophage cells. Concurrently the phago-lysosome fusion is significantly reduced as shown by infection withM.bovisBCG. We show that single nucleotide variation in clinical isolates lead to quantitative variations resulting in host immune suppression and support the survival and persistence of the pathogen.
A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains
Authors: Dearlove Bethany , Lewitus Eric , Bai Hongjun , Li Yifan , Reeves Daniel B. , Joyce M. Gordon , Scott Paul T. , Amare Mihret F. , Vasan Sandhya , Michael Nelson L. , Modjarrad Kayvon , Rolland Morgane 
Published: April 2020

AbstractThe magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spread away from its original epicenter in Wuhan, China. Importantly, there is little evidence that the virus has adapted to its human host since December 2019. Our findings suggest that a single vaccine should be efficacious against current global strains.One Sentence SummaryThe limited diversification of SARS-CoV-2 reflects drift and bottleneck events rather than adaptation to humans as the virus spread.
Digital twin of the rotor-shaft of a lightweight electric motor during aerobatics loads
Authors: Goraj Robert 
Published: April 2020

Purpose
This paper aims to present airworthiness considerations regarding a shaft of an electric motor. A fatigue lifetime prediction analysis based on one-step load spectrum is performed during high-cycle fatigue. Time-dependent normal and shear stress components are estimated using a high-fidelity digital twin built in Siemens PLM Nx Nastran as a finite element model (FEM). Linear and centrifugal acceleration as well as gyroscopic moment, motor torque, propeller thrust and thermal loads are considered. The equivalent cyclic degree of utilisation and a safety margin against the slip of a press-fitted shaft to rotor hub connection is estimated.

Design/methodology/approach
A load analysis using FEM is presented. The numerically obtained results are verified on an analytical and a semi-empirical basis.

Findings
The shaft of the electric motor can sustain 74 h of operation if burdened with aerobatic loads. Its load capacity equals 48% for the overall safety factor of 2.25.

Practical implications
The paper presents a specific, easily identifiable advance in knowledge that can be applicable in safety flight analysis issues.

Originality/value
The work presents a rotor of a novel lightweight electric motor for aircraft applications, which is a successor of the electric motor set recently in Extra 330E. The work delivers a computational estimation of the shaft life.
The accession of Latin American countries to the Asian Infrastructure Investment Bank: lessons from Brazil and Chile
Authors: Urdinez Francisco 
Published: April 2020

PurposeThe purpose of this paper is to discuss the motivations behind the accession of Latin American countries to the Asian Infrastructure Investment Bank (AIIB) with a focus on the cases of Brazil and Chile.Design/methodology/approachThe author collected data using a case study methodology, primarily through semi-structured interviews with decision-makers and through official government documentation.FindingsThe findings identified that, overall, the Brazilian politicians who made the decision to join the bank had an unclear perception of its economic benefit and believed that the clearest benefit from accession is political (to support China's initiative). After years of domestic political turmoil and economic crisis, Brazil experienced delayed incorporation into the bank, slow ratification processes in the domestic arena and a reduction in its capital commitment. Chilean decision-makers, on the other hand, seemed to have a clearer idea of the benefits from accessing the bank, which explains that their ratification process has been faster and smoother. Yet, a surprising socio-political crisis delayed incorporation into the bank. Both countries have delayed their accession to the bank due to domestic crises.Practical implicationsThree policy implications can be drawn from this study. First, the entry of Latin American countries into the bank reflects the persuasiveness of Chinese diplomacy in this region. Second, the author finds that interviewees are not always able to differentiate the AIIB from the Belt and Road Initiative (BRI) and hold the misguided idea that the AIIB is subordinated to the BRI rather than complementary to it. This might set overly high expectations of the benefits of entering the AIIB. Third, the author foresees that the largest potential of the AIIB in Latin America lies in the possibility of participating in co-financed projects, in particular with the Inter-American Development Bank and the Development Bank of Latin America.Originality/valueResearch on the AIIB has boomed in recent years, yet there are few in-depth studies about Latin American prospective members. The value of this study lies in offering in-depth data for two of the eight prospective members from this region.