bluuebunny/crossref_metadata_2025_split huggingface dataset:
High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection
Authors: Colles Frances M. , Karasova Daniela , Crhanova Magdalena , Preston Stephen G. , Smith Adrian L. , Dawkins Marian S. , Rychlik Ivan , Gebhardt-Henrich Sabine G. 
Published: March 2022

ABSTRACTContaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 weeks of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh faecal samples collected from broiler flocks aged 23-28 days. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant amongst flocks that would be determined to be Campylobacter ‘positive’ by conventional means, but a diverse pattern was seen amongst flocks that were Campylobacter ‘negative’. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.
Maximizing the Anti-tumor Potential of Immune Checkpoint Blockade through Modulation of Myeloid-specific CXCL16 and STAT1 Signaling
Authors: Palakurthi Bhavana , Guldner Ian H. , Liu Xiyu , Martino Anna K. , Wang Qingfei , Fross Shaneann , Neff Ryan A. , Golomb Samantha M. , Howe Erin N. , Zhang Siyuan 
Published: March 2022

ABSTRACTSensitivity to immune checkpoint blockades (ICB) depends on the overall balance of immunogenic and immunosuppressive signals in the tumor immune microenvironment (TIME). Chemotherapy as an immunostimulatory strategy showed potential in improving ICB’s clinical efficacy. Yet, evolution of highly plastic tumor-associated myeloid cells hinders ICB’s potential to reach its full therapeutic potential. In this study, we leveraged single-cell transcriptomic and trajectory analyses to delineate TIME dynamics after chemotherapy priming. We found that metronomic chemotherapy (MCT) treatment led to an accelerated T cell exhaustion through CXCL16-mediated recruitment of peripheral immature myeloid cells and expansion of STAT1-driven PD-L1 expressing myeloid cells. Inhibiting STAT1 signaling in MCT-primed breast cancer relieved T cell exhaustion and significantly enhanced the efficacy of anti-PD-1 ICB treatment. Our study leveraged single-cell analyses to dissect the dynamics of breast cancer TIME and provides a pre-clinical rationale to translate the anti-STAT1 plus anti-PD-1 combinatorial immunotherapy regimen to maximize ICB’s efficacy.Manuscript SummarySingle-cell analyses on low dose chemotherapy primed breast tumor-associated immune cells demonstrates a parallel coexistence of immunogenic and immunosuppressive myeloid cell subsets. Modulating STAT1 signaling in the tumor microenvironment fine-tunes immunogenic and immunosuppressive balance and maximizes the anti-PD-1 immunotherapy efficacy in chemotherapy-primed breast cancer.
Transient Water Wires Mediate Selective Proton Transport in Designed Channel Proteins
Authors: Kratochvil Huong T. , Watkins Laura C. , Mravic Marco , Somberg Noah H. , Thomaston Jessica L. , Nicoludis John M. , Liu Lijun , Hong Mei , Voth Gregory A. , DeGrado William F. 
Published: March 2022

Summary paragraphSelective proton transport through proteins is essential for forming and utilizing proton gradients in cells. Protons are conducted along hydrogen-bonded “wires” of water molecules and polar sidechains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways inferred from static protein structures. We hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess proton itself in the water wire. To test this hypothesis, we used molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+over Na+. These studies inform mechanisms of biological proton conduction and principles for engineering proton-conductive materials.
A unifiedin vitrotoin vivofluorescence lifetime screening platform yields amyloid β aggregation inhibitors
Authors: Collins Súil , van Vliet Liisa , Gielen Fabrice , Janeček Matej , Valladolid Sara Wagner , Poudel Chetan , Fusco Giuliana , De Simone Alfonso , Michel Claire , Kaminski Clemens F. , Spring David R , Hollfelder Florian , Kaminski Schierle Gabriele S 
Published: March 2022

AbstractInhibiting the aggregation of amyloid β (1-42) is a promising strategy for the development of disease-modifying Alzheimer’s disease therapeutics. To date, however, no sufficiently efficacious inhibitors have been identified, despite the best efforts of >200 advanced drug development campaigns. This failure can be attributed to limitations in current compound screening andin vivovalidation assays. Here, we report anin vitrotoin vivoscreening platform based on the use of a fluorescence lifetime aggregation sensor. The microfluidic “nanoFLIM” assay developed circumvents issues that plague conventional assays, such as lack of reproducibility, high cost and artefactual false read-outs. The fluorescence lifetime sensor can also dynamically monitor peptide aggregation in cellular andCaenorhabditis elegansdisease models, providing directly comparable aggregation kinetics, which is not achievable by any other method. The power of this unified system for accelerating hit-to-lead strategies, lowering attrition rates and expeditingin vivoscreening, was demonstrated with a pilot screening campaign of 445 compounds, revealing a new inhibitor that can inhibit amyloid β self-assemblyin vitroas well as in cellular and whole organism disease models.
Deciphering TP53 mutant Cancer Evolution with Single-Cell Multi-Omics
Authors: Rodriguez-Meira Alba , Norfo Ruggiero , Wen Wei Xiong , Chédeville Agathe L. , Rahman Haseeb , O’Sullivan Jennifer , Wang Guanlin , Louka Eleni , Kretzschmar Warren W. , Paterson Aimee , Brierley Charlotte , Martin Jean-Edouard , Demeule Caroline , Bashton Matthew , Sousos Nikolaos , Hamblin Angela , Guermouche Helene , Pasquier Florence , Marzac Christophe , Girodon François , Drummond Mark , Harrison Claire , Plo Isabelle , Jacobsen Sten Eirik W. , Psaila Bethan , Thongjuea Supat , Antony-Debré Iléana , Mead Adam J 
Published: March 2022

SummaryTP53 is the most commonly mutated gene in human cancer, typically occurring in association with complex cytogenetics and dismal outcomes. Understanding the genetic and non-genetic determinants of TP53-mutation driven clonal evolution and subsequent transformation is a crucial step towards the design of rational therapeutic strategies. Here, we carry out allelic resolution single-cell multi-omic analysis of haematopoietic stem/progenitor cells (HSPC) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukaemia (AML), a tractable model of TP53-mutant cancer evolution. All patients showed dominant TP53 ‘multi-hit’ HSPC clones at transformation, with a leukaemia stem cell transcriptional signature strongly predictive of adverse outcome in independent cohorts, across both TP53-mutant and wild-type AML. Through analysis of serial samples and antecedent TP53-heterozygous clones, we demonstrate a hitherto unrecognised effect of chronic inflammation, which supressed TP53 wild-type HSPC whilst enhancing the fitness advantage of TP53 mutant cells. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukaemia, and are of broader relevance to other cancer types.
The hidden intricacies of aquaporins: Remarkable details in a common structural scaffold
Authors: Gössweiner-Mohr Nikolaus , Siligan Christine , Pluhackova Kristyna , Umlandt Linnea , Köfler Sabina , Trajkovska Natasha , Horner Andreas 
Published: March 2022

AbstractEvolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of 4 representatives, we identify key aspects of AQP stability, gating, selectivity, pore geometry and oligomerization, with a potential impact on channel functionality. We challenge the general view of AQPs possessing a continuous open water pore and depict that AQPs selectivity is not exclusively shaped by pore lining residues but also by the relative arrangement of transmembrane helices. Moreover, our analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, we establish a novel numbering scheme of the conserved AQP scaffold facilitating direct comparison and prediction of potential structural effects of e.g. disease-causing mutations. Additionally, our results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.
LTD-inducing low frequency stimulation enhances p-Tau181 and p-Tau217 in an age-dependent manner in live rats
Authors: Zhang Yangyang , Yang Yin , Hu Zhengtao , Zhu Manyi , Qin Shuangying , Yu Pengpeng , Li Bo , Xu Jitian , Rowan Michael J. , Hu Neng-Wei 
Published: March 2022

AbstractThe progressive cognitive decline in Alzheimer’s disease (AD) patients correlates with the extent of tau pathology, in particular tau hyperphosphorylation, which is strongly age-associated. Although elevation of phosphorylated tau (p-Tau) on residues Thr181 (p-Tau181), Thr217 (p-Tau217), and Thr231 (p-Tau231) in cerebrospinal fluid or blood are recently proposed to be particularly sensitive markers of early AD, the generation of p-Tau during brain activity is poorly understood. A major form of synaptic plasticity, long-term depression (LTD), has recently been linked to the enhancement of tau phosphorylation. Here we show that low frequency stimulation (LFS), used to induce LTD, enhances p-Tau181 and p-Tau217 in an age-dependent manner in the hippocampus of live rats. In contrast, phosphorylation at residues Thr231, Ser202/Thr205, and Ser396 is less sensitive to LFS. Pharmacological antagonism of either NMDA or metabotropic glutamate 5 (mGluR5) receptors inhibits the elevation of both p-Tau181 and p-Tau217. Targeting ageing with a small molecule cognitive enhancer ISRIB (trans-isomer) prevents the enhancement of p-Tau by LFS in aged rats. Together, our data provide anin vivomeans to uncover brain plasticity-related cellular and molecular processes of tau phosphorylation in health and ageing conditions.
Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria
Authors: Uzun Maria , Koziaeva Veronika , Dziuba Marina , Leão Pedro , Krutkina Maria , Grouzdev Denis 
Published: March 2022

AbstractMagnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. MTB belonging to one of such phyla,Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g.,mam, mms) andmangenes, which were considered to be specific for this group. However, the recent discovery ofmangenes in MTB from theThermodesulfobacteriotaphylum has raised several questions about the inheritance of these genes in MTB. In this work, three newmangenes containing MTB genomes affiliated withNitrospirotaandThermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of allNitrospirotawas most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylumNitrospirotaby horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from theMagnetobacteriaceaeto theDissulfurispiraceaefamily withinNitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.
Serotonin Modulates an Inhibitory Input to the Central Amygdala from the Ventral Periaqueductal Gray
Authors: Hon Olivia J. , DiBerto Jeffrey F. , Mazzone Christopher M. , Sugam Jonathan , Bloodgood Daniel W. , Hardaway J. Andrew , Husain Mariya , Kendra Alexis , McCall Nora M. , Lopez Alberto J. , Kash Thomas L. , Lowery-Gionta Emily G. 
Published: March 2022

ABSTRACTFear is an adaptive state that drives defensive behavioral responses to specific and imminent threats. The central nucleus of the amygdala (CeA) is a critical site of adaptations that are required for the acquisition and expression of fear, in part due to alterations in the activity of inputs to the CeA. Here, we characterize a novel GABAergic input to the CeA from the ventral periaqueductal gray area (vPAG) using fiber photometry and ex vivo whole-cell slice electrophysiology combined with optogenetics and pharmacology. GABA transmission from this ascending vPAG-CeA input was enhanced by bath application of serotonin via activation of serotonin type 2C (5HT2C) receptors. Results indicate that these receptors are presynaptic. Interestingly, we found that GABA release from the vPAG-CeA input is enhanced following fear learning via activation of 5HT2C receptors and that this pathway is dynamically engaged during fear learning. Additionally, we characterized serotonin release in the CeA during fear learning and recall for the first time using fiber photometry coupled to a serotonin biosensor. Together, these findings describe a mechanism by which serotonin modulates GABA release from ascending vPAG GABA inputs to the CeA and characterize a role for this pathway in fear learning.
Excitatory-Inhibitory Recurrent Dynamics Produce Robust Visual Grids and Stable Attractors
Authors: Zhang Xiaohan , Long Xiaoyang , Zhang Sheng-Jia , Chen Zhe Sage 
Published: March 2022

AbstractSpatially modulated grid cells has been recently found in the rat secondary visual cortex (V2) during activation navigation. However, the computational mechanism and functional significance of V2 grid cells remain unknown, and a theory-driven conceptual model for experimentally observed visual grids is missing. To address the knowledge gap and make experimentally testable predictions, here we trained a biologically-inspired excitatory-inhibitory recurrent neural network (E/I-RNN) to perform a two-dimensional spatial navigation task with multisensory (e.g., velocity, acceleration, and visual) input. We found grid-like responses in both excitatory and inhibitory RNN units, and these grid responses were robust with respect to the choices of spatial cues, dimensionality of visual input, activation function, and network connectivity. Dimensionality reduction analysis of population responses revealed a low-dimensional torus-like manifold and attractor, showing the stability of grid patterns with respect to new visual input, new trajectory and relative speed. We found that functionally similar receptive fields with strong excitatory-to-excitatory connection appeared within fully connected as well as structurally connected networks, suggesting a link between functional grid clusters and structural network. Additionally, multistable torus-like attractors emerged with increasing sparsity in inter- and intra-subnetwork connectivity. Finally, irregular grid patterns were found in a convolutional neural network (CNN)-RNN architecture while performing a visual sequence recognition task. Together, our results suggest new computational mechanisms of V2 grid cells in both spatial and non-spatial tasks.HighlightsGrid patterns emerge in trained RNNs with multisensory inputsGrid patterns are robust to the RNN input and network connectivityPopulation responses show emergent ring-like manifolds and attractorsGrid-like patterns persist in RNNs while performing a non-spatial task.
Improving the Safety of Cultured Meat Using Basal Medium Prepared using Food Ingredients
Authors: Kanayama Takanori , Tanaka Keita , Shimada Haruna , Ichiyama Koji , Higuchi Sadaharu , Kawashima Ikko 
Published: March 2022

AbstractCurrently, meat production involves environmental issues and high costs; one solution to address this may be to produce meat via cell culture. Therefore, there is an urgent demand for the development of cell culture methods that replace raw materials with food materials to produce cultured meat as food. In this study, we designed food-grade-Dulbecco’s Modified Eagle’s Medium (FG-DMEM); when the cells cultured in FG-DMEM and regular DMEM were compared, there was no significant difference in cell growth or differentiation. Therefore, FG-DMEM can be used for research and safe production of cultured meat.
Telomere-to-telomere human DNA replication timing profiles
Authors: Massey Dashiell J. , Koren Amnon 
Published: March 2022

AbstractThe spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.
An engineered ACE2 decoy receptor can be administered by inhalation and potently targets the BA.1 and BA.2 omicron variants of SARS-CoV-2
Authors: Zhang Lianghui , Narayanan Krishna K. , Cooper Laura , Chan Kui K. , Devlin Christine A. , Aguhob Aaron , Shirley Kristie , Rong Lijun , Rehman Jalees , Malik Asrar B. , Procko Erik 
Published: March 2022

ABSTRACTMonoclonal antibodies targeting the SARS-CoV-2 spike (S) glycoprotein neutralize infection and are efficacious for the treatment of mild-to-moderate COVID-19. However, SARS-CoV-2 variants have emerged that partially or fully escape monoclonal antibodies in clinical use. Notably, the BA.2 sublineage of B.1.1.529/omicron escapes nearly all monoclonal antibodies currently authorized for therapeutic treatment of COVID-19. Decoy receptors, which are based on soluble forms of the host entry receptor ACE2, are an alternative strategy that broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22.v2.4-IgG1 was previously shown to be effective in vivo against SARS-CoV-2 variants when administered intravenously. Here, the inhalation of sACE22.v2.4-IgG1 is found to increase survival and ameliorate lung injury in K18-hACE2 transgenic mice inoculated with a lethal dose of the virulent P.1/gamma virus. Loss of catalytic activity reduced the decoy’s therapeutic efficacy supporting dual mechanisms of action: direct blocking of viral S and turnover of ACE2 substrates associated with lung injury and inflammation. Binding of sACE22.v2.4-IgG1 remained tight to S of BA.1 omicron, despite BA.1 omicron having extensive mutations, and binding exceeded that of four monoclonal antibodies approved for clinical use. BA.1 pseudovirus and authentic virus were neutralized at picomolar concentrations. Finally, tight binding was maintained against S from the BA.2 omicron sublineage, which differs from S of BA.1 by 26 mutations. Overall, the therapeutic potential of sACE22.v2.4-IgG1 is further confirmed by inhalation route and broad neutralization potency persists against increasingly divergent SARS-CoV-2 variants.
Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance
Authors: Naito Ken , Wakatake Takanori , Shibata Tomoko F. , Iseki Kohtaro , Shigenobu Shuji , Takahashi Yu , Ogiso-Tanaka Eri , Muto Chiaki , Teruya Kuniko , Shiroma Akino , Shimoji Makiko , Satou Kazuhito , Hirano Takashi , Nagano Atsushi J. , Tomooka Norihiko , Hasebe Mitsuyasu , Fukushima Kenji , Sakai Hiroaki 
Published: March 2022

AbstractHarnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.