bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation is associated with codon degeneracy in a species of bumblebee
Authors: Marshall H. , Nicholas M. T. , van Zweden J. S. , Wäckers F. , Ross L. , Wenseleers T. , Mallon E. B. 
Published: January 2023

AbstractSocial insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebeeBombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.
Bioprinting microporous functional living materials from protein-based core-shell microgels
Authors: Ou Yangteng , Cao Shixiang , Zhang Yang , Zhu Hongjia , Guo Chengzhi , Yan Wei , Xin Fengxue , Dong Weiliang , Zhang Yanli , Narita Masashi , Yu Ziyi , Knowles Tuomas P. J. 
Published: January 2023

AbstractLiving materials bring together material science and biology to allow the engineering and augmenting of living systems with novel functionalities. Bioprinting promises accurate control over the formation of such complex materials through programmable deposition of cells in soft materials, but current approaches had limited success in fine-tuning cell microenvironments while generating robust macroscopic morphologies. Here, we address this challenge through the use of core-shell microgel ink to decouple cell microenvironments from the structural shell for further processing. Cells are microfluidically immobilized in the viscous core that can promote the formation of both microbial populations and mammalian cellular spheroids, followed by interparticle annealing to give covalently stabilized functional scaffolds with controlled microporosity. The results show that the core-shell strategy mitigates cell leakage while affording a favorable environment for cell culture. Furthermore, we demonstrate that different microbial consortia can be printed into scaffolds for a range of applications. By compartmentalizing microbial consortia in separate microgels, the collective bioprocessing capability of the scaffold is significantly enhanced, shedding light on strategies to augment living materials with bioprocessing capabilities.
Cytotoxic CD8+ T cells target citrullinated antigens in rheumatoid arthritis
Authors: Moon Jae-Seung , Younis Shady , Ramadoss Nitya S. , Iyer Radhika , Sheth Khushboo , Sharpe Orr , Rao Navin L. , Becart Stephane , Carman Julie A. , James Eddie A. , Buckner Jane H. , Deane Kevin D. , Holers V. Michael , Goodman Susan M. , Donlin Laura T. , Davis Mark M. , Robinson William H. 
Published: January 2023

AbstractThe immune mechanisms that mediate synovitis and joint destruction in rheumatoid arthritis (RA) remain poorly defined. Although increased levels of CD8+ T cells have been described in RA, their function in pathogenesis remains unclear. Here we perform single cell transcriptome and T cell receptor (TCR) sequencing of CD8+ T cells derived from anti-citrullinated protein antibodies (ACPA)+ RA blood. We identify GZMB+CD8+ subpopulations containing large clonal lineage expansions that express cytotoxic and tissue homing transcriptional programs, while a GZMK+CD8+ memory subpopulation comprises smaller clonal expansions that express effector T cell transcriptional programs. We demonstrate RA citrullinated autoantigens presented by MHC class I activate RA blood-derived GZMB+CD8+ T cells to expand, express cytotoxic mediators, and mediate killing of target cells. We also demonstrate that these clonally expanded GZMB+CD8+ cells are present in RA synovium. These findings suggest that cytotoxic CD8+ T cells targeting citrullinated antigens contribute to synovitis and joint tissue destruction in ACPA+ RA.
Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting
Authors: Morehouse Nicholas J. , Clark Trevor N. , McMann Emily J. , van Santen Jeffrey A. , Haeckl F. P. Jake , Gray Christopher A. , Linington Roger G. 
Published: January 2023

AbstractSpectral matching of MS2 fragmentation spectra has become a popular method for characterizing natural products libraries but identification remains challenging due to differences in MS2 fragmentation properties between instruments and the low coverage of current spectral reference libraries. To address this bottleneck we present Structural similarity Network Annotation Platform for Mass Spectrometry (SNAP-MS) which matches chemical similarity grouping in the Natural Products Atlas to grouping of mass spectrometry features from molecular networking. This approach assigns compound families to molecular networking subnetworks without the need for experimental or calculated reference spectra. We demonstrate SNAP-MS can accurately annotate subnetworks built from both reference spectra and an in-house microbial extract library, and correctly predict compound families from published molecular networks acquired on a range of MS instrumentation. Compound family annotations for the microbial extract library are validated by co-injection of standards or isolation and spectroscopic analysis. SNAP-MS is freely available at www.npatlas.org/discover/snapms.
Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition
Authors: Kimchi Ofer , King Ella M. , Brenner Michael P. 
Published: January 2023

AbstractRNA molecules aggregate under certain conditions. The resulting condensates are implicated in human neurological disorders, and can potentially be designed towards specified bulk properties in vitro. However, the mechanism for aggregation—including how aggregation properties change with sequence and environmental conditions—remains poorly understood. To address this challenge, we introduce an analytical framework based on multimer enumeration. Our approach reveals the driving force for aggregation to be the increased configurational entropy associated with the multiplicity of ways to form bonds in the aggregate. Our model uncovers rich phase behavior, including a sequence-dependent reentrant phase transition, and repeat parity-dependent aggregation. We validate our results by comparison to a complete computational enumeration of the landscape, and to previously published molecular dynamics simulations. Our work unifies and extends published results, both explaining the behavior of CAG-repeat RNA aggregates implicated in Huntington’s disease, and enabling the rational design of programmable RNA condensates.
Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay
Authors: Sanabria Gladys Estigarribia , Sequera Guillermo , Aguirre Sarita , Méndez Julieta , dos Santos Paulo César Pereira , Gustafson Natalie Weiler , Godoy Margarita , Ortiz Analía , Cespedes Cynthia , Martínez Gloria , García-Basteiro Alberto L. , Andrews Jason R. , Croda Julio , Walter Katharine S. 
Published: January 2023

AbstractRecent rises in incident tuberculosis (TB) cases in Paraguay and the increasing concentration of TB within prisons highlight the urgency of targeting strategies to interrupt transmission and prevent new infections. However, whether specific cities or carceral institutions play a disproportionate role in transmission remains unknown. We conducted prospective genomic surveillance, sequencing 471 Mycobacterium tuberculosis complex genomes, from inside and outside prisons in Paraguay’s two largest urban areas, Asunción and Ciudad del Este, from 2016 to 2021. We found genomic evidence of frequent recent transmission within prisons and transmission linkages spanning prisons and surrounding populations. We identified a signal of frequent M. tuberculosis spread between urban areas and marked recent population size expansion of the three largest genomic transmission clusters. Together, our findings highlight the urgency of strengthening TB control programs to reduce transmission risk within prisons in Paraguay, where incidence was 70 times that outside prisons in 2021.
Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing
Authors: Tavakoli Sepideh , Nabizadeh Mohammad , Makhamreh Amr , Gamper Howard , McCormick Caroline A. , Rezapour Neda K. , Hou Ya-Ming , Wanunu Meni , Rouhanifard Sara H. 
Published: January 2023

AbstractHere, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of coverage and specific k-mer sequences are critical parameters for accurate basecalling. By adjusting these parameters for high-confidence U-to-C basecalling errors, we identify many known sites of pseudouridylation and uncover previously unreported uridine-modified sites, many of which fall in k-mers that are known targets of pseudouridine synthases. Identified sites are validated using 1000-mer synthetic RNA controls bearing a single pseudouridine in the center position, demonstrating systematic under-calling using our approach. We identify mRNAs with up to 7 unique modification sites. Our workflow allows direct detection of low-, medium-, and high-occupancy pseudouridine modifications on native RNA molecules from nanopore sequencing data and multiple modifications on the same strand.
Electrochemical direct air capture of CO2 using neutral red as reversible redox-active material
Authors: Seo Hyowon , Hatton T. Alan 
Published: January 2023

AbstractDirect air capture of carbon dioxide is a viable option for the mitigation of CO2 emissions and their impact on global climate change. Conventional processes for carbon capture from ambient air require 230 to 800 kJ thermal per mole of CO2, which accounts for most of the total cost of capture. Here, we demonstrate electrochemical direct air capture using neutral red as a redox-active material in an aqueous solution enabled by the inclusion of nicotinamide as a hydrotropic solubilizing agent. The electrochemical system demonstrates a high electron utilization of 0.71 in a continuous flow cell with an estimated minimum work of 35 kJe per mole of CO2 from 15% CO2. Further exploration using ambient air (410 ppm CO2 in the presence of 20% oxygen) as a feed gas shows electron utilization of 0.38 in a continuous flow cell to provide an estimated minimum work of 65 kJe per mole of CO2.
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2
Authors: Huang Kuan-Ying A. , Chen Xiaorui , Mohapatra Arpita , Nguyen Hong Thuy Vy , Schimanski Lisa , Tan Tiong Kit , Rijal Pramila , Vester Susan K. , Hills Rory A. , Howarth Mark , Keeffe Jennifer R. , Cohen Alexander A. , Kakutani Leesa M. , Wu Yi-Min , Shahed-Al-Mahmud Md , Chou Yu-Chi , Bjorkman Pamela J. , Townsend Alain R. , Ma Che 
Published: January 2023

AbstractAntibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the “down” state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development
Authors: Yao Huan , Gao Chun-Chun , Zhang Danru , Xu Jiawei , Song Gege , Fan Xiu , Liang Dao-Bo , Chen Yu-Sheng , Li Qian , Guo Yanjie , Cai Yu-Ting , Hu Lulu , Zhao Yong-Liang , Sun Ying-Pu , Yang Ying , Han Jianyong , Yang Yun-Gui 
Published: January 2023

AbstractN6-methyladenosine (m6A) has been demonstrated to regulate RNA metabolism and various biological processes, including gametogenesis and embryogenesis. However, the landscape and function of m6A at single cell resolution have not been extensively studied in mammalian oocytes or during pre-implantation. In this study, we developed a single-cell m6A sequencing (scm6A-seq) method to simultaneously profile the m6A methylome and transcriptome in single oocytes/blastomeres of cleavage-stage embryos. We found that m6A deficiency leads to aberrant RNA clearance and consequent low quality of Mettl3Gdf9 conditional knockout (cKO) oocytes. We further revealed that m6A regulates the translation and stability of modified RNAs in metaphase II (MII) oocytes and during oocyte-to-embryo transition, respectively. Moreover, we observed m6A-dependent asymmetries in the epi-transcriptome between the blastomeres of two-cell embryo. scm6A-seq thus allows in-depth investigation into m6A characteristics and functions, and the findings provide invaluable single-cell resolution resources for delineating the underlying mechanism for gametogenesis and early embryonic development.
General low-temperature growth of two-dimensional nanosheets from layered and nonlayered materials
Authors: Qin Biao , Saeed Muhammad Zeeshan , Li Qiuqiu , Zhu Manli , Feng Ya , Zhou Ziqi , Fang Jingzhi , Hossain Mongur , Zhang Zucheng , Zhou Yucheng , Huangfu Ying , Song Rong , Tang Jingmei , Li Bailing , Liu Jialing , Wang Di , He Kun , Zhang Hongmei , Wu Ruixia , Zhao Bei , Li Jia , Liao Lei , Wei Zhongming , Li Bo , Duan Xiangfeng , Duan Xidong 
Published: January 2023

AbstractMost of the current methods for the synthesis of two-dimensional materials (2DMs) require temperatures not compatible with traditional back-end-of-line (BEOL) processes in semiconductor industry (450 °C). Here, we report a general BiOCl-assisted chemical vapor deposition (CVD) approach for the low-temperature synthesis of 27 ultrathin 2DMs. In particular, by mixing BiOCl with selected metal powders to produce volatile intermediates, we show that ultrathin 2DMs can be produced at 280–500 °C, which are ~200–300 °C lower than the temperatures required for salt-assisted CVD processes. In-depth characterizations and theoretical calculations reveal the low-temperature processes promoting 2D growth and the oxygen-inhibited synthetic mechanism ensuring the formation of ultrathin nonlayered 2DMs. We demonstrate that the resulting 2DMs exhibit electrical, magnetic and optoelectronic properties comparable to those of 2DMs grown at much higher temperatures. The general low-temperature preparation of ultrathin 2DMs defines a rich material platform for exploring exotic physics and facile BEOL integration in semiconductor industry.
Integrated interfacial design of covalent organic framework photocatalysts to promote hydrogen evolution from water
Authors: He Ting , Zhen Wenlong , Chen Yongzhi , Guo Yuanyuan , Li Zhuoer , Huang Ning , Li Zhongping , Liu Ruoyang , Liu Yuan , Lian Xu , Xue Can , Sum Tze Chien , Chen Wei , Jiang Donglin 
Published: January 2023

AbstractAttempts to develop photocatalysts for hydrogen production from water usually result in low efficiency. Here we report the finding of photocatalysts by integrated interfacial design of stable covalent organic frameworks. We predesigned and constructed different molecular interfaces by fabricating ordered or amorphous π skeletons, installing ligating or non-ligating walls and engineering hydrophobic or hydrophilic pores. This systematic interfacial control over electron transfer, active site immobilisation and water transport enables to identify their distinct roles in the photocatalytic process. The frameworks, combined ordered π skeletons, ligating walls and hydrophilic channels, work under 300–1000 nm with non-noble metal co-catalyst and achieve a hydrogen evolution rate over 11 mmol g–1h–1, a quantum yield of 3.6% at 600 nm and a three-order-of-magnitude-increased turnover frequency of 18.8 h–1compared to those obtained with hydrophobic networks. This integrated interfacial design approach is a step towards designing solar-to-chemical energy conversion systems.
Ultralow contact resistance in organic transistors via orbital hybridization
Authors: Zeng Junpeng , He Daowei , Qiao Jingsi , Li Yating , Sun Li , Li Weisheng , Xie Jiacheng , Gao Si , Pan Lijia , Wang Peng , Xu Yong , Li Yun , Qiu Hao , Shi Yi , Xu Jian-Bin , Ji Wei , Wang Xinran 
Published: January 2023

AbstractOrganic field-effect transistors (OFETs) are of interest in unconventional form of electronics. However, high-performance OFETs are currently contact-limited, which represent a major challenge toward operation in the gigahertz regime. Here, we realize ultralow total contact resistance (Rc) down to 14.0 Ω ∙ cm in C10-DNTT OFETs by using transferred platinum (Pt) as contact. We observe evidence of Pt-catalyzed dehydrogenation of side alkyl chains which effectively reduces the metal-semiconductor van der Waals gap and promotes orbital hybridization. We report the ultrahigh performance OFETs, including hole mobility of 18 cm2 V−1 s−1, saturation current of 28.8 μA/μm, subthreshold swing of 60 mV/dec, and intrinsic cutoff frequency of 0.36 GHz. We further develop resist-free transfer and patterning strategies to fabricate large-area OFET arrays, showing 100% yield and excellent variability in the transistor metrics. As alkyl chains widely exist in conjugated molecules and polymers, our strategy can potentially enhance the performance of a broad range of organic optoelectronic devices.
Sex-specificity of the C. elegans metabolome
Authors: Burkhardt Russell N. , Artyukhin Alexander B. , Aprison Erin Z. , Curtis Brian J. , Fox Bennett W. , Ludewig Andreas H. , Palomino Diana Fajardo , Luo Jintao , Chaturbedi Amaresh , Panda Oishika , Wrobel Chester J. J. , Baumann Victor , Portman Douglas S. , Lee Siu Sylvia , Ruvinsky Ilya , Schroeder Frank C. 
Published: January 2023

AbstractRecent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and sex determination mutants, we show thatC. eleganshermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporatingN,N-dimethyltryptophan, increases food consumption, reduces lifespan, and accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape theC. elegansmetabolome and provide a blueprint for the discovery of sex-dependent metabolites in other animals.
Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies
Authors: Kulczyk Arkadiusz W. , McKee Karen K. , Zhang Ximo , Bizukojc Iwona , Yu Ying Q. , Yurchenco Peter D. 
Published: January 2023

AbstractLaminin polymerization is the major step in basement membranes assembly. Its failures cause laminin N-terminal domain lamininopathies including Pierson syndrome. We have employed cryo-electron microscopy to determine a 3.7 Å structure of the trimeric laminin polymer node containing α1, β1 and γ1 subunits. The structure reveals the molecular basis of calcium-dependent formation of laminin lattice, and provides insights into polymerization defects manifesting in human disease.
Solids that are also liquids: elastic tensors of superionic materials
Authors: Materzanini Giuliana , Chiarotti Tommaso , Marzari Nicola 
Published: January 2023

AbstractSuperionics are fascinating materials displaying both solid- and liquid-like characteristics: as solids, they respond elastically to shear stress; as liquids, they display fast-ion diffusion at normal conditions. In addition to such scientific interest, superionics are technologically relevant for energy, electronics, and sensing applications. Characterizing and understanding their elastic properties is, e.g., urgently needed to address their feasibility as solid-state electrolytes in all-solid-state batteries. However, static approaches to elasticity assume well-defined reference positions around which atoms vibrate, in contrast with the quasi-liquid motion of the mobile ions in fast ionic conductors. Here, we derive the elastic tensors of superionics from ensemble fluctuations in the isobaric-isothermal ensemble, exploiting extensive Car-Parrinello simulations. We apply this approach to paradigmatic Li-ion conductors, and complement with a block analysis to compute statistical errors. Static approaches sampled over the trajectories often overestimate the response, highlighting the importance of a dynamical treatment in determining elastic tensors in superionics.