bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Representation in the DARPA SD2 Program
Authors: Roehner Nicholas , Beal Jacob , Bartley Bryan , Markeloff Richard , Mitchell Tom , Nguyen Tramy , Sumorok Daniel , Walczak Nicholas , Myers Chris , Zundel Zach , Scholz James , Hatch Benjamin , Weston Mark , Colonna-Romano John 
Published: September 2021

1SUMMARYModern scientific enterprises are often highly complex and multidisciplinary, particularly in areas like synthetic biology where the subject at hand is itself inherently complex and multidisciplinary. Collaboration across many organizations is necessary to efficiently tackle such problems [6, 15], but remains difficult. The challenge is further amplified by automation that increases the pace at which new information can be produced, and particularly so for matters of fundamental research, where concepts and definitions are inherently fluid and may rapidly change as an investigation evolves [7].The DARPA program Synergistic Discovery and Design (SD2) aimed to address these challenges by organizing the development of data-driven methods to accelerate discovery and improve design robustness, with one of the key domains under study being synthetic biology. The program was specifically organized such that teams provided complementary types of expertise and resources, and without any team being in a dominant organizational position, such that subject-matter investigations would necessarily require peer-level collaboration across multiple team boundaries. With more than 100 researchers across more than 20 organizations, several of which ran experimental facilities with high-throughput automation, participants were forced to confront challenges around effective data sharing.The default architecture for scientific collaboration is essentially one of anarchy, with ad-hoc bilateral relations between pairs of collaborators or experimental phases (Figure 1(a)). This was by necessity the case during early phases of the SD2 program as well, in which incorporating new tools into pipelines was ad-hoc and time-consuming, and data was generally disconnected from genetic designs and experimental plans. The other typical approach for collaboration is one of “command and control”, in which a dominant organization determines the data sharing content and format for all participants (Figure 1(b)). This can be efficient, but tends to be limited in flexibility and extensibility, rendering it unsuitable for research collaboration, as indeed was found when we attempted this approach during the first year of the SD2 program. We addressed these problems with the application of distributed standards to create a “flexible rendezvous” model of collaboration (Figure 1(c)), enabling information flow to track evolving collaborative relationships, improving the sharing and utility of information across the community and supporting accelerated rates of experimentation.
Sister chromatid exchanges induced by perturbed replication are formed independently of homologous recombination factors
Authors: Heijink Anne Margriet , Stok Colin , Porubsky David , Manolika Eleni M. , Kok Yannick P. , Everts Marieke , de Boer H. Rudolf , Audrey Anastasia , Wierenga Elles , Guryev Victor , Spierings Diana C.J. , Knipscheer Puck , Chaudhuri Arnab Ray , Lansdorp Peter M. , van Vugt Marcel A.T.M. 
Published: September 2021

SummarySister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, upon generation of irradiation-induced DNA breaks, SCE induction was compromised in cells deficient for canonical HR factors BRCA1, BRCA2 and RAD51. Contrarily, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs were enriched at common fragile sites (CFSs), and were accompanied by post-replicative single-stranded DNA (ssDNA) gaps. Moreover, PARP inhibitor-induced replication lesions were transmitted into mitosis, suggesting that SCEs originate from mitotic processing of under-replicated DNA. We found that DNA polymerase theta (POLQ) was recruited to mitotic DNA lesions, and loss of POLQ resulted in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Combined, our data show that PARP inhibition generates under-replicated DNA, which is transferred into mitosis and processed into SCEs, independently of canonical HR factors.
Inter-species comparison of the orientation algorithm directing larval chemotaxis in the genus Drosophila
Authors: Fink Elie , Louis Matthieu 
Published: September 2021

AbstractAnimals differ in their appearances and behaviors. While many genetic studies have addressed the origins of phenotypic differences between fly species, we are still lacking a quantitative assessment of the variability in the way different fly species behave. We tackled this question in one of the most robust behaviors displayed by Drosophila: chemotaxis. At the larval stage, Drosophila melanogaster navigate odor gradients by combining four sensorimotor routines in a multilayered algorithm: a modulation of the overall locomotor speed and turn rate; a bias in turning during down-gradient motion; a bias in turning toward the gradient; the local curl of trajectories toward the gradient (“weathervaning”). Using high-resolution tracking and behavioral quantification, we characterized the olfactory behavior of eight closely related species of the Drosophila group in response to 19 ecologically-relevant odors. Significant changes are observed in the receptive field of each species, which is consistent with the rapid evolution of the peripheral olfactory system. Our results reveal substantial inter-species variability in the algorithms directing larval chemotaxis. While the basic sensorimotor routines are shared, their parametric arrangements can vary dramatically across species. The present analysis sets the stage for deciphering the evolutionary relationships between the structure and function of neural circuits directing orientation behaviors in Drosophila.
MinION nanopore sequencing provides similar methylation estimates to Sanger bisulfite sequencing in the TRPA1 promoter region
Authors: Gombert Sara , Jahn Kirsten , Pathak Hansi , Burkert Alexandra , Schmidt Gunnar , Wiehlmann Lutz , Davenport Colin , Brändl Björn , Müller Franz-Josef , Leffler Andreas , Deest Maximilian , Frieling Helge 
Published: September 2021

AbstractBisulfite sequencing has long been considered the gold standard for measurement of DNA methylation at single CpG resolution. In the meantime, several new approaches have been developed, which are regarded as less error-prone. Since these errors were shown to be sequence-specific, we aimed to verify the methylation data of a particular region of the TRPA1 promoter obtained from our previous studies. For this purpose, we compared methylation rates obtained via direct bisulfite sequencing and nanopore sequencing. Thus, we were able to confirm our previous findings to a large extent.
Accumulation of the GSK3 target protein β-catenin is lethal for B cell precursors and malignant B cells
Authors: Jumaa Huda , Kistner Klaus M. , Setz Corinna , Taketo M. Mark , Jumaa Hassan , Jellusova Julia 
Published: September 2021

SummaryGlycogen synthase kinase 3 (GSK3) is a ubiquitously expressed kinase involved in a myriad of biological processes. Although GSK3 mediated phosphorylation has been shown to induce the degradation of many pro-survival and pro-proliferation factors, cancer cells of different origin show reduced proliferation or survival after GSK3 inhibition. Our current understanding of the role GSK3 plays in normal mature B cells, B cell precursors and transformed B cells is incomplete and does not allow to assess whether GSK3 inhibitors can be used to treat B cell derived malignancies. Here we identify β-catenin as the major factor driving GSK3-inhibition induced changes in B cells. We show that β-catenin accumulation has opposing effects on cell metabolism and survival in mature B cells and B cell precursors. Moreover, we demonstrate that β-catenin destabilizes the commitment to the B cell lineage. In summary, our study identifies β-catenin induced signaling as a factor that can be exploited to limit the survival of malignant B cells.
Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants
Authors: Sandholm Niina , Rubio García Arcadio , Pekalski Marcin L , Inshaw Jamie RJ , Cutler Antony J , Todd John A 
Published: September 2021

AbstractWe recently mapped a genetic susceptibility locus on chromosome 6q22.33 for type 1 diabetes diagnosed below age of 7 years near the gene Protein tyrosine phosphatase receptor type K (PTPRK) and the thymocyte selection associated gene (THEMIS). As the thymus plays a central role in shaping the T cell repertoire, we aimed to identify the most likely causal genetic factors behind the association using thymocyte genomic data. In four thymocyte populations we identified 253 DNA sequence motifs underlying histone modifications. The G insertion allele of rs138300818, associated with protection from diabetes, created thymocyte motifs for multiple histone modifications and thymocyte types. The insertion also disrupted a predicted RFX5/7 transcription factor binding site. RFX7 is abundantly expressed in thymus. Chromatin state and RNA sequencing data suggested strong transcription overlapping rs138300818 in fetal thymus, while eQTL and chromatin conformation data indicated that the rs138300818 insertion is associated with lower THEMIS expression. Taken together, our results support a role for thymic THEMIS gene expression and the rs138300818 variant in promoting the development and diagnosis of type 1 diabetes at an earlier age.
CUX2 deficiency causes facilitation of excitatory synaptic transmission onto hippocampus and increased seizure susceptibility to kainate
Authors: Suzuki Toshimitsu , Tatsukawa Tetsuya , Sudo Genki , Delandre Caroline , Pai Yun Jin , Miyamoto Hiroyuki , Raveau Matthieu , Shimohata Atsushi , Ohmori Iori , Hamano Shin-ichiro , Haginoya Kazuhiro , Uematsu Mitsugu , Takahashi Yukitoshi , Morimoto Masafumi , Fujimoto Shinji , Osaka Hitoshi , Oguni Hirokazu , Osawa Makiko , Ishii Atsushi , Hirose Shinichi , Kaneko Sunao , Inoue Yushi , Moore Adrian Walton , Yamakawa Kazuhiro 
Published: September 2021

AbstractCUX2 gene encodes a transcription factor that controls neuronal proliferation, dendrite branching and synapse formation, locating at the epilepsy-associated chromosomal region 12q24 that we previously identified by a genome-wide association study (GWAS) in Japanese population. A CUX2 recurrent de novo variant p.E590K has been described in patients with rare epileptic encephalopathies and the gene is a candidate for the locus, however the mutation may not be enough to generate the genome-wide significance in the GWAS and whether CUX2 variants appear in other types of epilepsies and physiopathological mechanisms are remained to be investigated. Here in this study, we conducted targeted sequencings of CUX2, a paralog CUX1 and its short isoform CASP harboring a unique C-terminus on 271 Japanese patients with a variety of epilepsies, and found that multiple CUX2 missense variants, other than the p.E590K, and some CASP variants including a deletion, predominantly appeared in patients with temporal lobe epilepsy (TLE). The CUX2 variants showed abnormal localization in human cell culture analysis. While wild-type CUX2 enhances dendritic arborization in fly neurons, the effect was compromised by some of the variants. Cux2- and Casp-specific knockout mice both showed high susceptibility to kainate, increased excitatory cell number in the entorhinal cortex, and significant enhancement in glutamatergic synaptic transmission to the hippocampus. CASP and CUX2 proteins physiologically bound to each other and co-expressed in excitatory neurons in brain regions including the entorhinal cortex. These results suggest that CUX2 and CASP variants contribute to the TLE pathology through a facilitation of excitatory synaptic transmission from entorhinal cortex to hippocampus.
Reversing chemorefraction in colorectal cancer cells by controlling mucin secretion
Authors: Cantero-Recasens G , Alonso-Marañón J , Lobo-Jarne T , Garrido M , Iglesias M , Espinosa L , Malhotra V 
Published: September 2021

ABSTRACT15% of colorectal cancers (CRC) cells exhibit a mucin hypersecretory phenotype, which is suggested to provide resistance to immune surveillance and chemotherapy. We now formally show that colorectal cancer cells build a barrier to chemotherapeutics by increasing mucins’ secretion. We show that low levels of KChIP3, a negative regulator of mucin secretion (Cantero-Recasens et al., 2018), is a risk factor for CRC patients’ relapse in subset of untreated tumours. Our results also reveal that cells depleted of KChIP3 are four times more resistant (measured as cell viability and DNA damage) to chemotherapeutics 5-Fluorouracil plus Irinotecan (5-FU+iri.) compared to control cells, whereas KChIP3 overexpressing cells are 10 times more sensitive to killing by chemotherapeutics. Similar increase in tumour cell death is observed upon chemical inhibition of mucin secretion by the sodium/calcium exchanger (NCX) blockers (Mitrovic et al., 2013). Finally, sensitivity of CRC patient-derived organoids to 5-FU+iri increases 40-fold upon mucin secretion inhibition. Reducing mucin secretion thus provides a means to control chemoresistance of mucinous colorectal cancer cells and other mucinous tumours.
The effect of pre-analytical and physiological variables on cell-free DNA fragmentation
Authors: van der Pol Ymke , Moldovan Norbert , Verkuijlen Sandra , Ramaker Jip , Boers Dries , Onstenk Wendy , de Rooij Johan , Bahce Idris , Pegtel D. Michiel , Mouliere Florent 
Published: September 2021

AbstractAssays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve the performance of liquid biopsy. However, pre-analytic and physiological differences between individuals on fragmentomic analysis are poorly defined.We analyzed the impact of collection tube, plasma processing time and physiology on the size distribution of cfDNA, their genome-wide representation and sequence diversity at the cfDNA fragment-ends using shallow Whole Genome Sequencing.We observed that using different stabilizing collection tubes, or processing times does not affect the cfDNA fragment sizes, but can impact the genome-wide fragmentation patterns and fragment-end sequences of cfDNA. In addition, beyond differences depending on the gender, the physiological conditions tested between 63 individuals (age, body mass index, use of medication and chronic conditions) minimally influenced the outcome of fragmentomic methods.Our results highlight that fragmentomic approaches have potential for implementation in the clinic, pending clear traceability of analytical and physiological factors.
Transcriptional and translational regulation of pathogenesis in Alzheimer’s disease model mice
Authors: Eastman Guillermo , Sharlow Elizabeth R. , Lazo John S. , Bloom George S. , Sotelo-Silveira José R. 
Published: September 2021

ABSTRACTBackgroundDefining the cellular mechanisms that drive Alzheimer’s disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and the ensuing periods of steadily declining cognition. Previous studies have emphasized changes in transcriptional regulation, but not translational regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD.ObjectiveTo identify genes whose expression might be regulated at the transcriptional, and especially at the translational levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2-/-) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling).MethodsIdentical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptional and translational levels separately, and also at the translational efficiency level. Regulated genes were functionally evaluated by gene ontology tools.ResultsCompared to WT mice, AD model mice had similar levels of transcriptional regulation, but displayed differences in translational regulation. A specific microglial signature associated with early stages of Aβ accumulation was up-regulated at both transcriptome and translatome levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to APP metabolism associated with neurotoxicity and neuroprotection.ConclusionThis work represents the first genome-wide study of brain translational regulation in animal models of AD, and provides evidence of a tight and early translational regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.
In Silico Electrophysiology of Inner-Ear Mechanotransduction Channel TMC1 Models
Authors: Walujkar Sanket , Lotthammer Jeffrey M. , Nisler Collin R. , Sudar Joseph C. , Ballesteros Angela , Sotomayor Marcos 
Published: September 2021

AbstractInner-ear sensory hair cells convert mechanical stimuli from sound and head movements into electrical signals during mechanotransduction. Identification of all molecular components of the inner-ear mechanotransduction apparatus is ongoing; however, there is strong evidence that TMC1 and TMC2 are pore-forming subunits of the complex. We present molecular dynamics simulations that probe ion conduction of TMC1 models built based on two different structures of related TMEM16 proteins. Unlike most channels, the TMC1 models do not show a central pore. Instead, simulations of these models in a membrane environment at various voltages reveal a peripheral permeation pathway that is exposed to lipids and that shows cation permeation at rates comparable to those measured in hair cells. Furthermore, our analyses suggest that TMC1 gating mechanisms involve protein conformational changes and tension-induced lipid-mediated pore widening. These results provide insights into ion conduction and activation mechanisms of hair-cell mechanotransduction channels essential for hearing and balance.
Structural analysis and construction of thermostable antifungal chitinase
Authors: Kozome Dan , Uechi Keiko , Taira Toki , Fukada Harumi , Kubota Tomomi , Ishikawa Kazuhiko 
Published: September 2021

ABSTRACTChitin is a biopolymer of N-acetyl-D-glucosamine with β-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the β-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme’s thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual applicable conditions. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. Based on the crystal structure and sequence alignment among other chitinases, we rationally introduced proline residues, a disulfide bond, and salt bridge in the chitinase using protein engineering methods. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family.IMPORTANCEWe solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9 °C higher than wild type (WT) and a half-life at 60°C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including five proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment
Authors: Schwabkey Zaker , Wiesnoski Diana H. , Chang Chia-Chi , Tsai Wen-Bin , Pham Dung , Ahmed Saira S. , Hayase Tomo , Ortega Turrubiates Miriam R. , El-Himri Rawan K. , Sanchez Christopher A. , Hayase Eiko , Frenk Oquendo Annette C. , Miyama Takahiko , Halsey Taylor M. , Heckel Brooke E. , Brown Alexandria N. , Jin Yimei , Lorenzi Philip L. , Warmoes Marc O. , Tan Lin , Swennes Alton G. , Jensen Vanessa B. , Peterson Christine B. , Do Kim-Anh , Zhang Liangliang , Shi Yushu , Wang Yinghong , Galloway-Pena Jessica R. , Okhuysen Pablo C. , Daniel-MacDougall Carrie R. , Shono Yusuke , da Silva Marina Burgos , Peled Jonathan U. , van den Brink Marcel R.M. , Ajami Nadim , Wargo Jennifer A. , Rondon Gabriela , Srour Samer A. , Mehta Rohtesh S. , Alousi Amin M. , Shpall Elizabeth J. , Champlin Richard E. , Shelburne Samuel A. , Molldrem Jeffrey J. , Jamal Mohamed A. , Karmouch Jennifer L. , Jenq Robert R. 
Published: September 2021

AbstractNot all cancer patients with severe neutropenia develop fever, and the fecal microbiome may play a role. In neutropenic hematopoietic cell transplant patients (n=119), 63 (53%) developed a subsequent fever and had increased fecal Akkermansia muciniphila, a mucus-degrading bacteria (p=0.006, corrected for multiple comparisons).In mouse models, two therapies, irradiation and melphalan, similarly expanded A. muciniphila. Dietary restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Azithromycin treatment depleted A. muciniphila and preserved colonic mucus.Dietary restriction raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila with lower pH and increased propionate prevented utilization of mucin. Treating irradiated mice with azithromycin or propionate preserved the mucus layer, lessened hypothermia, and reduced inflammatory cytokines in the colon. These results suggest that diet, metabolites and colonic mucus link the microbiome to neutropenic fever, and could guide future microbiome-based preventive strategies.