bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica
Authors: Baisya Dipankar , Ramesh Adithya , Schwartz Cory , Lonardi Stefano , Wheeldon Ian 
Published: February 2022

AbstractGenome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
Density of states prediction for materials discovery via contrastive learning from probabilistic embeddings
Authors: Kong Shufeng , Ricci Francesco , Guevarra Dan , Neaton Jeffrey B. , Gomes Carla P. , Gregoire John M. 
Published: February 2022

AbstractMachine learning for materials discovery has largely focused on predicting an individual scalar rather than multiple related properties, where spectral properties are an important example. Fundamental spectral properties include the phonon density of states (phDOS) and the electronic density of states (eDOS), which individually or collectively are the origins of a breadth of materials observables and functions. Building upon the success of graph attention networks for encoding crystalline materials, we introduce a probabilistic embedding generator specifically tailored to the prediction of spectral properties. Coupled with supervised contrastive learning, our materials-to-spectrum (Mat2Spec) model outperforms state-of-the-art methods for predicting ab initio phDOS and eDOS for crystalline materials. We demonstrate Mat2Spec’s ability to identify eDOS gaps below the Fermi energy, validating predictions with ab initio calculations and thereby discovering candidate thermoelectrics and transparent conductors. Mat2Spec is an exemplar framework for predicting spectral properties of materials via strategically incorporated machine learning techniques.
Development and characterization of functional antibodies targeting NMDA receptors
Authors: Tajima Nami , Simorowski Noriko , Yovanno Remy A. , Regan Michael C. , Michalski Kevin , Gómez Ricardo , Lau Albert Y. , Furukawa Hiro 
Published: February 2022

AbstractN-methyl-D-aspartate receptors (NMDARs) are critically involved in basic brain functions and neurodegeneration as well as tumor invasiveness. Targeting specific subtypes of NMDARs with distinct activities has been considered an effective therapeutic strategy for neurological disorders and diseases. However, complete elimination of off-target effects of small chemical compounds has been challenging and thus, there is a need to explore alternative strategies for targeting NMDAR subtypes. Here we report identification of a functional antibody that specifically targets the GluN1-GluN2B NMDAR subtype and allosterically down-regulates ion channel activity as assessed by electrophysiology. Through biochemical analysis, x-ray crystallography, single-particle electron cryomicroscopy, and molecular dynamics simulations, we show that this inhibitory antibody recognizes the amino terminal domain of the GluN2B subunit and increases the population of the non-active conformational state. The current study demonstrates that antibodies may serve as specific reagents to regulate NMDAR functions for basic research and therapeutic objectives.
Functionally selective signaling and broad metabolic benefits by novel insulin receptor partial agonists
Authors: Wu Margaret , Carballo-Jane Ester , Zhou Haihong , Zafian Peter , Dai Ge , Liu Mindy , Lao Julie , Kelly Terri , Shao Dan , Gorski Judith , Pissarnitski Dmitri , Kekec Ahmet , Chen Ying , Previs Stephen F. , Scapin Giovanna , Gomez-Llorente Yacob , Hollingsworth Scott A. , Yan Lin , Feng Danqing , Huo Pei , Walford Geoffrey , Erion Mark D. , Kelley David E. , Lin Songnian , Mu James 
Published: February 2022

AbstractInsulin analogs have been developed to treat diabetes with focus primarily on improving the time action profile without affecting ligand-receptor interaction or functional selectivity. As a result, inherent liabilities (e.g. hypoglycemia) of injectable insulin continue to limit the true therapeutic potential of related agents. Insulin dimers were synthesized to investigate whether partial agonism of the insulin receptor (IR) tyrosine kinase is achievable, and to explore the potential for tissue-selective systemic insulin pharmacology. The insulin dimers induced distinct IR conformational changes compared to native monomeric insulin and substrate phosphorylation assays demonstrated partial agonism. Structurally distinct dimers with differences in conjugation sites and linkers were prepared to deliver desirable IR partial agonist (IRPA). Systemic infusions of a B29-B29 dimer in vivo revealed sharp differences compared to native insulin. Suppression of hepatic glucose production and lipolysis were like that attained with regular insulin, albeit with a distinctly shallower dose-response. In contrast, there was highly attenuated stimulation of glucose uptake into muscle. Mechanistic studies indicated that IRPAs exploit tissue differences in receptor density and have additional distinctions pertaining to drug clearance and distribution. The hepato-adipose selective action of IRPAs is a potentially safer approach for treatment of diabetes.
Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium
Authors: Yamaguchi Manako , Nakaoka Hirofumi , Suda Kazuaki , Yoshihara Kosuke , Ishiguro Tatsuya , Yachida Nozomi , Saito Kyota , Ueda Haruka , Sugino Kentaro , Mori Yutaro , Yamawaki Kaoru , Tamura Ryo , Revathidevi Sundaramoorthy , Motoyama Teiichi , Tainaka Kazuki , Verhaak Roel G. W. , Inoue Ituro , Enomoto Takayuki 
Published: February 2022

AbstractIt has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that “rhizome structures”, in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases.
In-situ transfer vat photopolymerization for transparent microfluidic device fabrication
Authors: Xu Yang , Qi Fangjie , Mao Huachao , Li Songwei , Zhu Yizhen , Gong Jingwen , Wang Lu , Malmstadt Noah , Chen Yong 
Published: February 2022

AbstractWhile vat photopolymerization has many advantages over soft lithography in fabricating microfluidic devices, including efficiency and shape complexity, it has difficulty achieving well-controlled micrometer-sized (smaller than 100 μm) channels in the layer building direction. The considerable light penetration depth of transparent resin leads to over-curing that inevitably cures the residual resin inside flow channels, causing clogs. In this paper, a 3D printing process — in-situ transfer vat photopolymerization is reported to solve this critical over-curing issue in fabricating microfluidic devices. We demonstrate microchannels with highZ-resolution (within 10 μm level) and high accuracy (within 2 μm level) using a general method with no requirements on liquid resins such as reduced transparency nor leads to a reduced fabrication speed. Compared with all other vat photopolymerization-based techniques specialized for microfluidic channel fabrication, our universal approach is compatible with commonly used 405 nm light sources and commercial photocurable resins. The process has been verified by multifunctional devices, including 3D serpentine microfluidic channels, microfluidic valves, and particle sorting devices. This work solves a critical barrier in 3D printing microfluidic channels using the high-speed vat photopolymerization process and broadens the material options. It also significantly advances vat photopolymerization’s use in applications requiring small gaps with high accuracy in theZ-direction.
Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots
Authors: Huang Zhen , De O. Furo Ivanete , Liu Jing , Peona Valentina , Gomes Anderson J. B. , Cen Wan , Huang Hao , Zhang Yanding , Chen Duo , Xue Ting , Zhang Qiujin , Yue Zhicao , Wang Quanxi , Yu Lingyu , Chen Youling , Suh Alexander , de Oliveira Edivaldo H. C. , Xu Luohao 
Published: February 2022

AbstractThe karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots.
RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity
Authors: Feng Sumin , Ma Sai , Li Kejiao , Gao Shengxian , Ning Shaokai , Shang Jinfeng , Guo Ruiyuan , Chen Yingying , Blumenfeld Britny , Simon Itamar , Li Qing , Guo Rong , Xu Dongyi 
Published: February 2022

AbstractThe 53BP1-RIF1 pathway antagonizes resection of DNA broken ends and confers PARP inhibitor sensitivity on BRCA1-mutated tumors. However, it is unclear how this pathway suppresses initiation of resection. Here, we identify ASF1 as a partner of RIF1 via an interacting manner similar to its interactions with histone chaperones CAF-1 and HIRA. ASF1 is recruited to distal chromatin flanking DNA breaks by 53BP1-RIF1 and promotes non-homologous end joining (NHEJ) using its histone chaperone activity. Epistasis analysis shows that ASF1 acts in the same NHEJ pathway as RIF1, but via a parallel pathway with the shieldin complex, which suppresses resection after initiation. Moreover, defects in end resection and homologous recombination (HR) in BRCA1-deficient cells are largely suppressed by ASF1 deficiency. Mechanistically, ASF1 compacts adjacent chromatin by heterochromatinization to protect broken DNA ends from BRCA1-mediated resection. Taken together, our findings identify a RIF1-ASF1 histone chaperone complex that promotes changes in high-order chromatin structure to stimulate the NHEJ pathway for DSB repair.
Stroke induces disease-specific myeloid cells in the brain parenchyma and pia
Authors: Beuker Carolin , Schafflick David , Strecker Jan-Kolja , Heming Michael , Li Xiaolin , Wolbert Jolien , Schmidt-Pogoda Antje , Thomas Christian , Kuhlmann Tanja , Aranda-Pardos Irene , A-Gonzalez Noelia , Kumar Praveen Ashok , Werner Yves , Kilic Ertugrul , Hermann Dirk M. , Wiendl Heinz , Stumm Ralf , Meyer zu Hörste Gerd , Minnerup Jens 
Published: February 2022

AbstractInflammation triggers secondary brain damage after stroke. The meninges and other CNS border compartments serve as invasion sites for leukocyte influx into the brain thus promoting tissue damage after stroke. However, the post-ischemic immune response of border compartments compared to brain parenchyma remains poorly characterized. Here, we deeply characterize tissue-resident leukocytes in meninges and brain parenchyma and discover that leukocytes respond differently to stroke depending on their site of residence. We thereby discover a unique phenotype of myeloid cells exclusive to the brain after stroke. These stroke-associated myeloid cells partially resemble neurodegenerative disease-associated microglia. They are mainly of resident microglial origin, partially conserved in humans and exhibit a lipid-phagocytosing phenotype. Blocking markers specific for these cells partially ameliorates stroke outcome thus providing a potential therapeutic target. The injury-response of myeloid cells in the CNS is thus compartmentalized, adjusted to the type of injury and may represent a therapeutic target.
Heterotypic interactions drive antibody synergy against a malaria vaccine candidate
Authors: Ragotte Robert J. , Pulido David , Lias Amelia M. , Quinkert Doris , Alanine Daniel G. W. , Jamwal Abhishek , Davies Hannah , Nacer Adéla , Lowe Edward D. , Grime Geoffrey W. , Illingworth Joseph J. , Donat Robert F. , Garman Elspeth F. , Bowyer Paul W. , Higgins Matthew K. , Draper Simon J. 
Published: February 2022

AbstractUnderstanding mechanisms of antibody synergy is important for vaccine design and antibody cocktail development. Examples of synergy between antibodies are well-documented, but the mechanisms underlying these relationships often remain poorly understood. The leading blood-stage malaria vaccine candidate, CyRPA, is essential for invasion of Plasmodium falciparum into human erythrocytes. Here we present a panel of anti-CyRPA monoclonal antibodies that strongly inhibit parasite growth in in vitro assays. Structural studies show that growth-inhibitory antibodies bind epitopes on a single face of CyRPA. We also show that pairs of non-competing inhibitory antibodies have strongly synergistic growth-inhibitory activity. These antibodies bind to neighbouring epitopes on CyRPA and form lateral, heterotypic interactions which slow antibody dissociation. We predict that such heterotypic interactions will be a feature of many immune responses. Immunogens which elicit such synergistic antibody mixtures could increase the potency of vaccine-elicited responses to provide robust and long-lived immunity against challenging disease targets.
Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells
Authors: Van Damme Ryan , Li Kongpan , Zhang Minjie , Bai Jianhui , Lee Wilson H. , Yesselman Joseph D. , Lu Zhipeng , Velema Willem A. 
Published: February 2022

AbstractThree-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a method, Spatial 2′-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D structure modeling at near-nanometer resolution. Integrating SHARC-exo with other crosslinking-based methods, we discover compact folding of the 7SK RNA, a critical regulator of transcriptional elongation. These results establish a strategy for measuring RNA 3D distances and alternative conformations in their native cellular context.
A cattle graph genome incorporating global breed diversity
Authors: Talenti A. , Powell J. , Hemmink J. D. , Cook E. A. J. , Wragg D. , Jayaraman S. , Paxton E. , Ezeasor C. , Obishakin E. T. , Agusi E. R. , Tijjani A. , Amanyire W. , Muhanguzi D. , Marshall K. , Fisch A. , Ferreira B. R. , Qasim A. , Chaudhry U. , Wiener P. , Toye P. , Morrison L. J. , Connelley T. , Prendergast J. G. D. 
Published: February 2022

AbstractDespite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
Ammonia pools in zeolites for direct fabrication of catalytic centers
Authors: Yao Jie , He Yingluo , Zeng Yan , Feng Xiaobo , Fan Jiaqi , Komiyama Shoya , Yong Xiaojing , Zhang Wei , Zhao Tiejian , Guo Zhongshan , Peng Xiaobo , Yang Guohui , Tsubaki Noritatsu 
Published: February 2022

AbstractReduction process is a key step to fabricate metal-zeolite catalysts in catalytic synthesis. However, because of the strong interaction force, metal oxides in zeolites are very difficult to be reduced. Existing reduction technologies are always energy-intensive, and inevitably cause the agglomeration of metallic particles in metal-zeolite catalysts or destroy zeolite structure in severe cases. Herein, we disclose that zeolites after ion exchange of ammonium have an interesting and unexpected self-reducing feature. It can accurately control the reduction of metal-zeolite catalysts, via in situ ammonia production from ‘ammonia pools’, meanwhile, restrains the growth of the size of metals. Such new and reliable ammonia pool effect is not influenced by topological structures of zeolites, and works well on reducible metals. The ammonia pool effect is ultimately attributed to an atmosphere-confined self-regulation mechanism. This methodology will significantly promote the fabrication for metal-zeolite catalysts, and further facilitate design and development of low-cost and high-activity catalysts.
TrkB agonist antibody ameliorates fertility deficits in aged and cyclophosphamide-induced premature ovarian failure model mice
Authors: Qin Xunsi , Zhao Yue , Zhang Tianyi , Yin Chenghong , Qiao Jie , Guo Wei , Lu Bai 
Published: February 2022

AbstractPremature ovarian failure (POF) is a leading cause of women’s infertility without effective treatment. Here we show that intravenous injection of Ab4B19, an agonistic antibody for the BDNF receptor TrkB, penetrates into ovarian follicles, activates TrkB signaling, and promotes ovary development. In both natural aging and cyclophosphamide-induced POF models, treatment with Ab4B19 completely reverses the reduction of pre-antral and antral follicles, and normalizes gonadal hormone. Ab4B19 also attenuates gonadotoxicity and inhibits apoptosis in cyclophosphamide-induced POF ovaries. Further, treatment with Ab4B19, but not BDNF, restores the number and quality of oocytes and enhances fertility. In human, BDNF levels are high in granulosa cells and TrkB levels increase in oocytes as they mature. Moreover, BDNF expression is down-regulated in follicles of aged women, and Ab4B19 activates TrkB signaling in human ovary tissue ex vivo. These results identify TrkB as a potential target for POF with differentiated mechanisms, and confirms superiority of TrkB activating antibody over BDNF as therapeutic agents.
CPEB1 directs muscle stem cell activation by reprogramming the translational landscape
Authors: Zeng Wenshu , Yue Lu , Lam Kim S. W. , Zhang Wenxin , So Wai-Kin , Tse Erin H. Y. , Cheung Tom H. 
Published: February 2022

AbstractSkeletal muscle stem cells, also called Satellite Cells (SCs), are actively maintained in quiescence but can activate quickly upon extrinsic stimuli. However, the mechanisms of how quiescent SCs (QSCs) activate swiftly remain elusive. Here, using a whole mouse perfusion fixation approach to obtain bona fide QSCs, we identify massive proteomic changes during the quiescence-to-activation transition in pathways such as chromatin maintenance, metabolism, transcription, and translation. Discordant correlation of transcriptomic and proteomic changes reveals potential translational regulation upon SC activation. Importantly, we show Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1), post-transcriptionally affects protein translation during SC activation by binding to the 3′ UTRs of different transcripts. We demonstrate phosphorylation-dependent CPEB1 promoted Myod1 protein synthesis by binding to the cytoplasmic polyadenylation elements (CPEs) within its 3′ UTRs to regulate SC activation and muscle regeneration. Our study characterizes CPEB1 as a key regulator to reprogram the translational landscape directing SC activation and subsequent proliferation.