bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multifaceted architectural framework of the mouse claustrum complex
Authors: Grimstvedt Joachim S. , Shelton Andrew M. , Hoerder-Suabedissen Anna , Oliver David K. , Berndtsson Christin H. , Blankvoort Stefan , Nair Rajeevkumar R. , Packer Adam M. , Witter Menno P. , Kentros Clifford G. 
Published: June 2022

Accurate anatomical characterizations are necessary to investigate neural circuitry on a fine scale, but for the rodent claustrum complex (CC) this has yet to be fully accomplished. The CC is generally considered to comprise two major subdivisions, the claustrum (CL) and the dorsal endopiriform nucleus (DEn), but regional boundaries to these areas are highly debated. To address this, we conducted a multifaceted analysis of fiber- and cyto-architecture, genetic marker expression, and connectivity using mice of both sexes, to create a comprehensive guide for identifying and delineating borders to the CC. We identified four distinct subregions within the CC, subdividing both the CL and the DEn into two. Additionally, we conducted brain-wide tracing of inputs to the entire CC using a transgenic mouse line. Immunohistochemical staining against myelin basic protein (MBP), parvalbumin (PV), and calbindin (CB) revealed intricate fiber-architectural patterns enabling precise delineations of the CC and its subregions. Myelinated fibers were abundant in dorsal parts of the CL but absent in ventral parts, while parvalbumin labelled fibers occupied the entire CL. Calbindin staining revealed a central gap within the CL, which was also visible at levels anterior to the striatum. Furthermore, cells in the CL projecting to the retrosplenial-cortex were located within the myelin sparse area. By combining our own experimental data with digitally available datasets of gene expression and input connectivity, we could demonstrate that the proposed delineation scheme allows anchoring of datasets from different origins to a common reference framework.Significance statementMice are a highly tractable model for studying the claustrum complex (CC). However, without a consensus on how to delineate the CC in rodents, comparing results between studies is challenging. It is therefore important to expand our anatomical knowledge of the CC, to match the level of detail needed to study its functional properties. Using multiple strategies for identifying claustral borders, we created a comprehensive guide to delineate the CC and its subregions. This anatomical framework will allow researchers to anchor future experimental data into a common reference space. We demonstrated the power of this new structural framework by combining our own experimental data with digitally available data on gene expression and input connectivity of the CC.
Deletion of CD226 in Foxp3+ T cells Reduces Diabetes Incidence in Non-Obese Diabetic Mice by Improving Regulatory T Cell Stability and Function
Authors: Thirawatananond Puchong , Brown Matthew E. , Sachs Lindsey K. , Arnoletti Juan M. , Yeh Wen-I , Posgai Amanda L. , Shapiro Melanie R. , Chen Yi-Guang , Brusko Todd M. 
Published: June 2022

AbstractCo-stimulation serves as a critical checkpoint for T cell development and activation, and several genetic variants affecting co-stimulatory pathways confer risk for autoimmune diseases. A single nucleotide polymorphism in CD226 (rs763361; G307S) has been shown to increase susceptibility to type 1 diabetes, multiple sclerosis, and rheumatoid arthritis. CD226 competes with the co-inhibitory receptor TIGIT (T cell immunoreceptor with Ig and ITIM domains) to bind CD155 to amplify TCR signaling. We previously found that Cd226 knockout protected non-obese diabetic (NOD) mice from disease, but the impact of CD226 signaling on individual immune subsets remained unclear. We focused on regulatory T cells (Tregs) as a population of interest, as prior reports demonstrated that human CD226+ Tregs exhibit reduced FOXP3+Helios+ purity and suppressive function following expansion. Hence, we hypothesized that global deletion of Cd226 would increase Treg stability and accordingly, Treg-specific Cd226 deletion would inhibit diabetes in NOD mice. Indeed, crossing the NOD.Cd226-/- and NOD.Foxp3-GFP-Cre.R26-loxP-STOP-loxP-YFP Treg-fate tracking strains resulted in increased Treg induction and decreased FoxP3-deficient “ex-Tregs” in the pancreatic lymph nodes. We generated a Treg-conditional knockout (TregΔCd226) strain and found that female TregΔCd226 mice had decreased insulitis and diabetes incidence compared to TregWT mice. Additionally, we observed increased TIGIT expression on Tregs and conventional CD4+ T cells within the pancreas of TregΔCd226 versus TregWT mice. These findings demonstrate that an imbalance of CD226/TIGIT signaling may contribute to Treg destabilization in the NOD mouse and highlight the potential for therapeutic targeting of this pathway to prevent or reverse autoimmunity.
Single-hit genome edition for expression of single-chain immunoglobulins by edited B cells
Authors: Ueda Natsuko , Cahen Marine , Sirac Christophe , Galy Anne , Moreaux Jérôme , Danger Yannic , Cogné Michel 
Published: June 2022

ABSTRACTLymphocytes have become attractive agents for adoptive immunotherapy but only the reformatting of T cells is efficiently mastered. Despite some recent breakthroughs, B cells remain challenging targets, with regard to both their long-term survival after in vitro manipulation and the rewiring of immunoglobulin (Ig) expression. Working on these two aspects, we have designed a new format of single-chain Ig (“scFull-Ig”) coding cassette, the insertion of which at a single genomic position can redirect B cells toward a new antigen specificity, while preserving all functional domains of the B cell receptor. Precise genomic edition at a single locus then provides the most efficient and safe strategy to both disrupt endogenous Ig expression while encoding a new Ig paratope. As proofs of concept, functionality of such scFull BCR was validated by checking specific binding of two different classical targets of tumor immunotherapy, HER2 and CD20. Once the strategy validated in cell lines, it was also validated in primary B cells, again showing successful engineering of BCR expression. These results contribute to pave the way for future B cell-based adoptive cell therapy.
Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance
Authors: Jin Xin , Zhang Xiaowei , Ding Xuejing , Tian Tian , Tseng Chao-Kai , Luo Xinwei , Chen Xiao , Lo Chien-Jung , Leake Mark C. , Bai Fan 
Published: June 2022

AbstractAs an important free energy source, the membrane voltage (Vm) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial Vm sensors which allow single-cell recording of bacterial Vm dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically “excitable” and “resting” states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial Vm are observed, which facilitates increased antibiotic tolerance. In the electrically resting state, bacterial Vm displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment.
Variation in behaviour of native prey mediates the impact of an invasive species on plankton communities
Authors: Hasnain Sarah S. , Arnott Shelley E 
Published: June 2022

AbstractPopulation-level differences in predator trait expression influence predator impacts on prey species, altering ecological interactions and trophic dynamics. However, the effect of inter-population differences in prey traits on the impacts of predation on ecological communities remains poorly understood, especially for introduced predators where differences in prey traits could influence the outcome of biological invasions. We examined if differences inDaphniavertical position influenced the impacts of the invasive predatorBythotrephes cederströmiion major zooplankton and algal groups. Our results show differences inDaphniavertical position influencedBythotrephesimpacts on small cladocerans. Larger reductions in density were observed in mesocosms with greater proportion of hypolimneticDaphnia. Larger increases in algal biomass were also observed in invaded mesocosms with greater proportion of hypolimneticDaphnia. These results suggest that differences inDaphniavertical position influence the magnitude and type ofBythotrephesimpacts on zooplankton communities.
Advances in non-invasive tracking of wave-type electric fish in natural and laboratory settings
Authors: Raab Till , Madhav Manu S. , Jayakumar Ravikrishnan P. , Henninger Jörg , Cowan Noah J. , Benda Jan 
Published: June 2022

ABSTRACTRecent technological advances greatly improved the possibility to study freely behaving animals in natural conditions. However, many systems still rely on animal-mounted devices, which can already bias behavioral observations. Alternatively, animal behaviors can be detected and tracked in recordings of stationary sensors, e.g. video cameras. While these approaches circumvent the influence of animal-mounted devices, identification of individuals is much more challenging. We take advantage of the individual-specific electric fields electric fish generate by discharging their electric organ (EOD) to record and track their movement and communication behaviors without interfering with the animals themselves. EODs of complete groups of fish can be recorded with electrode arrays submerged in the water and then be tracked for individual fish. Here, we present an improved algorithm for tracking electric signals of wave-type electric fish with unprecedented accuracy. Our algorithm benefits from combining and refining previous approaches of tracking individual specific EOD frequencies (EODf) and spatial electric field properties. In this process, the similarity of signal pairs in extended data windows determines their tracking order, making the algorithm more robust against detection losses and intersections. We quantify the performance of the algorithm and show its application for a data set recorded with a 64-electrode array in a stream in the Llanos, Colombia, where we managed, for the first time, to track Apteronotus leptorhynchus over many days. These technological advances make electric fish a unique model system for a detailed analysis of social and communication behaviors, with strong implications for our research on sensory coding.
Dkk1 inhibition normalizes limb phenotypes in a mouse model ofFzd2associated omodysplasia Robinow syndromes
Authors: Liegel Ryan P. , Michalski Megan N. , Vaidya Sanika , Bittermann Elizabeth , Finnerty Erin , Menke Chelsea A. , Diegel Cassandra R. , Zhong Zhendong A. , Williams Bart O. , Stottmann Rolf W. 
Published: June 2022

ABSTRACTFRIZZLED-2 (FZD2) is a transmembrane Wnt ligand receptor. We previously identified a pathogenic humanFZD2variant, encoding for a protein with a premature stop and loss of 17 amino acids. This includes a portion of the consensus DISHEVELLED binding sequence required for Wnt signal transduction. Patients with this variant exhibited FZD2-associated autosomal dominant Robinow Syndrome. To model this variant, we utilized zygote microinjection andi-GONAD-based CRISPR/Cas9-mediated genome editing to generate an allelic series in the mouse. Embryos mosaic for humanizedFzd2W553*knock-in exhibited cleft palate and shortened limbs, consistent withFZD2W548*patient phenotypes. We also generated two germline mouse alleles with small deletions,Fzd2D3andFzd2D4. Homozygotes for each allele survive embryonic development at normal ratios but exhibit a highly penetrant cleft palate phenotype, shortened limbs compared to wild-type and perinatal lethality.Fzd2D4craniofacial tissues indicated decreased canonical WNT signaling.In uterotreatment with IIIC3a (DKK inhibitor) normalized the limb lengths inFzd2D4homozygotes. Thein vivoreplication represents an approach to further investigate the mechanism of FZD2 phenotypes and validates the utility of CRISPR knock-in mice as a tool for demonstrating pathogenicity of human genetic variants. We also present evidence for a potential therapeutic intervention.
Activation of trace amine-associated receptor 1 (TAAR1) transiently reduces alcohol drinking in socially housed mice
Authors: Frycz Bartosz Adam , Nowicka Klaudia , Konopka Anna , Hoener Marius Christian , Bulska Ewa , Kaczmarek Leszek , Stefaniuk Marzena 
Published: June 2022

AbstractAlcohol dependence is characterized by the abnormal release of dopamine in the brain reward-related areas. Trace amine-associated receptor 1 (TAAR1) is a G Protein-Coupled Receptor that negatively regulates dopamine neurotransmission and thus is a promising target in the treatment of drug addiction. However, the role of TAAR1 in the regulation of alcohol abuse remains understudied. Here, we assessed the effect of TAAR1 activation on alcohol-drinking behaviors of C57Bl/6J female mice housed in IntelliCages. The animals were administered with either vehicle or TAAR1 full selective agonist, RO5256390, and tested for alcohol consumption, alcohol preference, and motivation for alcohol seeking. We found that mice with the highest preference for alcohol (high drinkers) in the RO5256390 group consumed less alcohol and had lower alcohol preference in comparison to high drinkers in the vehicle group, during 20 h of free alcohol access (FAA). We also found decreased alcohol consumption and alcohol preference comparing all animals in the RO5256390 to all animals in the vehicle group, during 20 h of FAA performed after the abstinence. These effects of RO5256390 lasted for the first 24 hours after administration that roughly corresponded to the compound level in the brain, measured by mass spectrometry. Finally, we found that administration of RO5256390 may attenuate motivation for alcohol seeking. Taken together, our findings reveal that activation of TAAR1 may transiently reduce alcohol drinking; thus, TAAR1 is a promising target for the treatment of alcohol abuse and relapse.
The Nucleocapsid Protein Of SARS-CoV-2, Combined With ODN-39M, Is A Potential Component For An Intranasal Bivalent Pancorona Vaccine
Authors: Lobaina Yadira , Chen Rong , Suzarte Edith , Ai Panchao , Huerta Vivian , Musacchio Alexis , Silva Ricardo , Tan Changyuan , Martin Alejandro , Lazo Laura , Guillén Gerardo , Yang Ke , Perera Yasser , Hermida Lisset 
Published: June 2022

AbstractDespite the rapid development of vaccines and their reported efficacy for controlling the COVID-19 waves, two key challenges remain: the scope of the immunity against upcoming variants and zoonosis events, and the induction of mucosal immunity able to clear the virus in the upper respiratory tract for halting the transmission. The present study is aiming at assessing a potential component for a new generation of vaccines so as to overcome such limitations. The recombinant nucleocapsid (N) protein from SARS-CoV-2 Delta variant was combined with a phosphodiester backbone CpG ODN (ODN-39M), forming high molecular weight aggregates. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive Cell-Mediated-Immunity (CMI). In turn, this combination was able to induce anti-N IgA in lungs, which along with the specific IgG in sera and CMI in spleen, resulted cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N+ODN-39M preparation combined with the RBD Delta protein, as inductor of neutralizing Abs, enhanced the local and systemic immune response against RBD with a modulation toward a Th1 pattern. Taken together, these results make the N+ODN-39M preparation a suitable component for a future intranasal pancorona vaccine against Sarbecoviruses. Particularly, the bivalent vaccine formulation N+ODN-39M+RBD could be used as an effective nasal booster in previously vaccinated population.
Control of SIV infection in prophylactically vaccinated, ART-naïve macaques is required for the most efficacious CD8 T cell response during treatment with the IL-15 superagonist N-803
Authors: Ellis-Connell Amy L. , Balgeman Alexis J. , Harwood Olivia E. , Moriarty Ryan V. , Safrit Jeffrey T. , Weiler Andrea M. , Friedrich Thomas C. , O’Connor Shelby L. 
Published: June 2022

AbstractThe IL-15 superagonist N-803 has been shown to enhance the function of CD8 T cells and NK cells. We previously found that in a subset of vaccinated, ART-naïve, SIV+ rhesus macaques, N-803 treatment led to a rapid but transient decline in plasma viremia that positively correlated with an increase in the frequency of CD8 T cells. Here we tested the hypothesis that prophylactic vaccination was required for N-803 mediated suppression of SIV plasma viremia. We vaccinated rhesus macaques with a DNA prime/Ad5 boost regimen using vectors expressing SIVmac239 gag, with or without a plasmid expressing IL-12, or left them unvaccinated. Animals were then intravenously infected with SIVmac239M. Six months after infection, animals were treated with N-803. We found no differences in control of plasma viremia during N-803 treatment between vaccinated and unvaccinated macaques. Furthermore, the SIV-specific CD8 T cells displayed no differences in frequency or ability to traffic to the lymph nodes. Interestingly, when we divided the SIV+ animals based on plasma viral load set-point prior to N-803 treatment, N-803 increased the frequency of SIV-specific T cells expressing ki-67+ and granzyme B+ in animals with low plasma viremia (<104 copies/mL; SIV controllers) compared to animals with high plasma viremia (>104 copies/mL;SIV non-controllers). In addition, Gag-specific CD8 T cells from the SIV+ controllers had a greater increase in CD107a+CD8+ T cells when compared to SIV+ non-controllers. Overall, our results indicate that N-803 is most effective in SIV+ animals with a pre-existing immunological ability to control SIV replication.
Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic network
Authors: Zhou Zhiwei , Luo Mingdu , Zhang Haosong , Yin Yandong , Cai Yuping , Zhu Zheng-Jiang 
Published: June 2022

AbstractLiquid chromatography - mass spectrometry (LC-MS) based untargeted metabolomics allows to measure both known and unknown metabolites in the metabolome. However, unknown metabolite annotation is a grand challenge in untargeted metabolomics. Here, we developed an approach, namely, knowledge-guided multi-layer network (KGMN), to enable global metabolite annotation from knowns to unknowns in untargeted metabolomics. The KGMN approach integrated three-layer networks, including knowledge-based metabolic reaction network, knowledge-guided MS/MS similarity network, and global peak correlation network. To demonstrate the principle, we applied KGMN in an in-vitro enzymatic reaction system and different biological samples, with ∼100-300 putative unknowns annotated in each data set. Among them, >80% unknown metabolites were validated with in-silico MS/MS tools. Finally, we successfully validated 5 unknown metabolites through the repository-mining and the syntheses of chemical standards. Together, the KGMN approach enables efficient unknown annotations, and substantially advances the discovery of recurrent unknown metabolites towards deciphering dark matters in untargeted metabolomics.
Community interactions drive the evolution of antibiotic tolerance in bacteria
Authors: Mizrahi Sivan Pearl , Goyal Akshit , Gore Jeff 
Published: June 2022

AbstractThe emergence of antibiotic tolerance (prolonged survival against exposure) in natural bacterial populations is a major concern. Since it has been studied primarily in isogenic populations, we do not yet understand how ecological interactions in a diverse community impact the evolution of tolerance. To address this, we studied the evolutionary dynamics of a synthetic bacterial community composed of two interacting strains. In this community, an antibiotic-resistant strain protected the other, susceptible strain by degrading the antibiotic ampicillin in the medium. Surprisingly, we found that in the presence of antibiotics, the susceptible strain evolved tolerance. Tolerance was typified by an increase in survival as well as an accompanying decrease in growth rate, highlighting a trade-off between the two. A simple mathematical model explained that the observed decrease in death rate, even when coupled with a decreased growth rate, is beneficial in a community with weak protective interactions. In the presence of strong interactions, the model predicted that the trade-off would instead be detrimental and tolerance would not emerge, which we experimentally verified. By whole genome sequencing the evolved tolerant isolates, we identified three genetic hotspots which accumulated mutations in parallel lines, suggesting their association with tolerance. Our work highlights that ecological interactions can promote antibiotic tolerance in bacterial communities, which has remained understudied.SignificanceBacteria evolve to evade antibiotic pressure, leading to adverse infection outcomes. Understanding the evolutionary dynamics which lead to different antibiotic responses has thus far focused on single-strain bacterial populations, with limited attention to multi-strain communities which are more common in nature. Here, we experimentally evolved a simple two-strain community, comprising an antibiotic-resistant strain protecting a susceptible one, and found that susceptible populations evolve tolerance, helping them better survive long antibiotic exposure. Using the interplay between community interactions, antibiotic dynamics, and resource availability, we explain this finding with a simple mathematical model, and predict and experimentally verify that an increased resistant strain carrying capacity would render tolerance detrimental. Our results highlight that community interactions can alter bacterial evolutionary responses to antibiotics.
Genome-Wide Large-Scale Multi-Trait Analysis Characterizes Global Patterns of Pleiotropy and Unique Trait-Specific Variants
Authors: Qi Guanghao , Chhetri Surya B. , Ray Debashree , Dutta Diptavo , Battle Alexis , Bhattacharjee Samsiddhi , Chatterjee Nilanjan 
Published: June 2022

AbstractGenome-wide association studies (GWAS) have found widespread evidence of pleiotropy, but characterization of global patterns of pleiotropy remain highly incomplete due to insufficient power of current approaches. We develop fastASSET, an extension of the method ASSET, to allow computationally efficient detection of variant-level pleiotropic association across a large number of traits. We analyze GWAS summary statistics of 116 complex traits of diverse types collected from the NIH GRASP repository and a number of other large GWAS consortia. We identify a total of 2,293 independent loci at the genome-wide significance level and found that the lead variants in nearly all of these loci (∼99%) to be associated with to two or more (median = 6) traits. Further, the estimated degree of pleiotropy for the detected variants strongly predicted their degree of pleiotropy across a much larger number of traits (K=4,114) in the UK Biobank Study. Follow-up analyses of 21 unique trait-specific variants suggest that they are often linked to the expression in trait-related tissues for a small number of genes, some of which are well known to be involved in relevant biological processes. Our findings provide deeper insight into the nature of complex trait pleiotropy and leads to, for the first time, identification of highly unique trait-specific susceptibility variants.