bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification and progress over time of specific antibodies against SARS-CoV-2 in breast milk of lactating women vaccinated with BNT162b2 Pfizer-BioNTech COVID-19 vaccine (LacCOVID)
Authors: Esteve-Palau Erika , Gonzalez-Cuevas Araceli , Guerrero M. Eugenia , Garcia-Terol Clara , Alvarez M. Carmen , Garcia Geneva , Moreno Encarna , Medina Francisco , Casadevall David , Diaz-Brito Vicens 
Published: November 2021

ABSTRACTImportanceTo our knowledge, this is the first study to analyze long–term passage (6 months after immunization) of specific antibodies induced by BNT162b2 COVID-19 vaccine through breast milk.ObjectivesMain objective: to determine SARS-CoV-2 vaccine induced antibody levels in the breast milk of lactating women 4 weeks after mRNA BNT162b2 Pfizer-BioNTech COVID-19 complete vaccination.Secondary objectives: to analyze SARS-CoV-2 antibody levels (breast milk and serum) at different time-points after vaccination, examine the correlation of SARS-CoV-2 antibody levels between serum and breast milk, describe adverse events related to vaccination (AErV) in both mothers and infants and determine the rate of COVID-19 infections.DesignProspective cohort study between February and September 2021.SettingParc Sanitari Sant Joan de Déu, an urban hospital in Spain.ParticipantsDuring our health worker vaccination campaign at our hospital between January and March 2, we recruited 33 lactating women vaccinated with BNT162b2 Pfizer-BioNTech COVID-19.ResultsA total of 33 volunteers were included in the study. The median (IQR) age of mothers was 38 (36-39) years and 15 (10-22) months for the infants.Primary end-point: at 4 w after second dose median (IQR) IgG-S1 levels for serum–milk pairs were 12,478 (6,870-20,801) to 50.4 (24.3-104) arbitrary units (AU) per mL.Secondary end-pointsSARS-CoV-2 antibody levels at different time-points were (serum-milk): 519 (234-937) to 1 (0-2.9) AU/mL at 2w after first dose, 18,644 (9,923-29,264) to 78 (33.7-128) AU/mL at 2w, 4,094 (2,413-8,480) to 19.9 (10.8-51.9) AU/mL at 12w, and 1,350 (831-2,298) to 8.9 (7.8-31.5) at 24w after second dose.We found a positive correlation of SARS-CoV-2 antibody levels between serum and breast milk (Pearson correlation coefficient 0.68).No serious AErV were observed.We found two (6%) COVID-19 vaccine breakthrough infections.ConclusionsPfizer-BioNTech COVID-19 vaccination is safe during breastfeeding and it transmits antibodies into breast milk with a positive correlation with serum levels, and both decrease over time in a 6-month follow-up. Infants of breastfeeding vaccinated women could be protected for at least six months after vaccination and serum determination of SARS-CoV-2 IgG-S1 could indicate the breastmilk levels of antibodies during this period.
ANALYSIS OF IMMUNE ESCAPE VARIANTS FROM ANTIBODY-BASED THERAPEUTICS AGAINST COVID-19
Authors: Focosi Daniele , Maggi Fabrizio , Franchini Massimo , McConnell Scott , Casadevall Arturo 
Published: November 2021

AbstractAccelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID19 convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), the few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of Spike protein (e.g, ΔHV69-70, ΔLGVY141-144 and ΔAL243-244). Continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and fitness of emerging variants.
50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA
Authors: Laughlin Zane T. , Nandi Suparno , Dey Debayan , Zelinskaya Natalia , Witek Marta A. , Srinivas Pooja , Nguyen Ha An , Kuiper Emily G. , Comstock Lindsay R. , Dunham Christine M. , Conn Graeme L. 
Published: November 2021

AbstractChanges in bacterial ribosomal RNA methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2’-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a post-catalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144 which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.Significance StatementThe bacterial ribosome is an important target for antibiotics used to treat infection. However, resistance to these essential drugs can arise through changes in ribosomal RNA (rRNA) modification patterns through the action of intrinsic or acquired rRNA methyltransferase enzymes. How these antibiotic resistance-associated enzymes recognize their ribosomal targets for site-specific modification is currently not well defined. Here, we uncover the molecular basis for large ribosomal (50S) subunit substrate recognition and modification by the Mycobacterium tuberculosis methyltransferase TlyA, necessary for optimal activity of the antitubercular drug capreomycin. From this work, recognition of complex rRNA structures distant from the site of modification and “flipping” of the target nucleotide base both emerge as general themes in ribosome recognition for bacterial rRNA modifying enzymes.
Intestinal Transgene Delivery with Native E. coli Chassis Allows Persistent Physiological Changes
Authors: Russell Baylee J. , Brown Steven D. , Saran Anand R. , Mai Irene , Lingaraju Amulya , Siguenza Nicole , Maissy Erica , Dantas Machado Ana C. , Pinto Antonio F. M. , Miyamoto Yukiko , Richter R. Alexander , Ho Samuel B. , Eckmann Lars , Hasty Jeff , Saghatelian Alan , Knight Rob , Zarrinpar Amir 
Published: November 2021

ABSTRACTLive bacterial therapeutics (LBT) could reverse disease by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally-raised (CR) hosts have been unsuccessful, because engineered microbial organisms (i.e., chassis) cannot colonize the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli isolated from stool cultures of CR mice were modified to express functional bacterial (bile salt hydrolase) and eukaryotic (Interleukin-10) genes. Reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect host physiology and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock-in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts, and enables LBT with curative intent.
Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32
Authors: Mi Chenchen , Zhang Li , Sun Shan , Huang Guoqiang , Shao Guangcan , Yang Fan , You Xin , Dong Meng-Qiu , Sui Sen-Fang 
Published: November 2021

AbstractTransport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and have three forms- TRAPPI, TRAPPII and TRAPPIII, which share a core of six TRAPPI proteins. TRAPPII facilitates intra-Golgi and endosome-to-Golgi transports by activating GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor (GEF) in yeast. Here we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle shaped monomers, while the monomer in the apo structure exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both TRAPPI and Trs120 via its nucleotide binding domain and binds with Trs31 of TRAPPI via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.One Sentence SummaryStructures of TRAPPII in different states reveal the mechanism of the specific activation of Ypt32 by TRAPPII.
POTATO: An automated pipeline for batch analysis of optical tweezers data
Authors: Buck Stefan , Pekarek Lukas , Caliskan Neva 
Published: November 2021

ABSTRACTOptical tweezers is a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein–nucleic acid interactions and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (Practical Optical Tweezers Analysis TOol). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to worm-like chain and freely-jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface (https://github.com/REMI-HIRI/POTATO), which allows researchers without programming knowledge to perform sophisticated data analysis.SIGNIFICANCEStudying (un)folding of biopolymer structures with optical tweezers under different conditions generates very large datasets for statistical data analysis. Recent technical improvements accelerated data acquisition by coupling modern instruments with microfluidic systems, at the same time creating the need for a high-throughput, and unbiased data analysis. We developed Practical Optical Tweezers Analysis TOol (POTATO); an open-source python-based tool that can process data gathered by any OT force-ramp experiment in an automated fashion. POTATO is principally designed for data preprocessing, identification of (un)folding events and the fitting of the force-distance curves. In addition, all parameters for preprocessing, statistical analysis and fitting of the curves can be adapted to suit the dataset under analysis in an easy-to-use graphical user interface.
Evolution of a new testis-specific functional promotor within the highly conservedMap2k7gene of the mouse
Authors: Heinen Tobias , Xie Chen , Keshavarz Maryam , Stappert Dominik , Künzel Sven , Tautz Diethard 
Published: November 2021

AbstractMap2k7(synonymMkk7) is a conserved regulatory kinase gene and a central component of the JNK signaling cascade with key functions during cellular differentiation. It shows complex transcription patterns and different transcript isoforms are known in the mouse (Mus musculus). We have previously identified a newly evolved testis specific transcript for theMap2k7gene in the subspeciesM. m. domesticus. Here, we identify the new promotor that drives this transcript and find that its transcript codes for an open reading frame (ORF) of 50 amino acids. The new promotor was gained in the stem lineage of closely related mouse species, but was secondarily lost in the subspeciesM. m. musculusandM. m. castaneus. A single mutation can be correlated with its transcriptional activity inM. m. domesticusand cell culture assays demonstrate the capability of this mutation to drive expression. A mouse knock-out line in which the promotor region of the new transcript is deleted reveals a functional contribution of the newly evolved promotor to sperm motility and to the spermatid transcriptome. Our data show that a new functional transcript (and possibly protein) can evolve within an otherwise highly conserved gene, supporting the notion of regulatory changes contributing to the emergence of evolutionary novelties.
Are island plants really poorly defended? No support for the loss of defense hypothesis in domatia-bearing plants
Authors: Biddick M. 
Published: November 2021

1.AbstractThe loss of defense hypothesis posits that island colonizers experience a release from predation on the mainland and subsequently lose their defensive adaptations. While support for the hypothesis is abundant, it has never been tested in domatia-bearing plants. Leaf domatia are cave-like structures produced on the underside of leaves that facilitate a defensive mutualism with predatory and fungivorous mites. I tested the loss of defense hypothesis in six domatia-bearing taxa inhabiting New Zealand and its offshore islands. No support for the loss of defense hypothesis was found. Changes in domatia investment were instead associated with changes in leaf size – a trait that has been repeatedly observed to undergo rapid evolution on islands. Overall results demonstrate that not all types of defense are lost on islands, suggesting a higher-resolution approach is needed when studying the evolution of defense on islands.
MICS1 is the Ca2+/H+ antiporter of mammalian mitochondria
Authors: Austin Shane , Mekis Ronald , Mohammed Sami E. M. , Scalise Mariafrancesca , Pfeiffer Christina , Galluccio Michele , Borovec Tamara , Parapatics Katja , Vitko Dijana , Dinhopl Nora , Bennett Keiryn L. , Indiveri Cesare , Nowikovsky Karin 
Published: November 2021

AbstractMitochondrial Ca2+ ions are crucial regulators of bioenergetics, cell death pathways and cytosolic Ca2+ homeostasis. Mitochondrial Ca2+ content strictly depends on Ca2+ transporters. In recent decades, the major players responsible for mitochondrial Ca2+ uptake and release have been identified, except the mitochondrial Ca2+/H+ exchanger (CHE). Originally identified as the mitochondrial K+/H+ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identified MICS1, the only mitochondrial member of the TMBIM family. Applying cell-based and cell-free biochemical assays, here we demonstrate that MICS1 is responsible for the Na+- and permeability transition pore-independent mitochondrial Ca2+ release and identify MICS1 as the long-sought mitochondrial CHE. This finding provides the final piece of the puzzle of mitochondrial Ca2+ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca2+ exchange.
Cells use molecular working memory to navigate in changing chemoattractant fields
Authors: Nandan Akhilesh , Das Abhishek , Lott Robert , Koseska Aneta 
Published: November 2021

AbstractIn order to migrate over large distances, cells within tissues and organisms rely on sensing local gradient cues. These cues however are multifarious, irregular or conflicting, changing both in time and space. Here we find that single cells utilize a molecular mechanism akin to a working memory, to generate persistent directional migration when signals are disrupted by temporally memorizing their position, while still remaining adaptive to spatial and temporal changes of the signal source. Using dynamical systems theory, we derive that these information processing capabilities are inherent for protein networks whose dynamics is maintained away from steady state through organization at criticality. We demonstrate experimentally using the Epidermal growth factor receptor (EGFR) signaling network, that the memory is maintained in the prolonged receptor’s activity via a slow-escaping remnant, a dynamical ”ghost” of the attractor of the polarized signaling state, that further results in memory in migration. As this state is metastable, it also enables continuous adaptation of the migration direction when the signals vary in space and time. We therefore show that cells implement real-time computations without stable-states to navigate in changing chemoattractant fields by memorizing position of disrupted signals while maintaining sensitivity to novel chemical cues.
Physiological and molecular mechanism of tolerance of two maize genotypes under multiple abiotic stresses
Authors: Rafique Suphia 
Published: November 2021

AbstractAbiotic stresses are the major threat to crops regardless of their nature, duration, and frequency, their occurrence either singly, and or combination is deleterious for the plant growth and development. Maize is most important crop largely grown in tropical region in summer rainy season, often face a stress combination of drought and waterlogging. We previously showed under multiple stresses up-regulated leaf proteins of maize plants were involved to enhance the tolerance mechanism of tolerant genotype. Whereas, in susceptible genotypes up-regulated proteins ameliorate to survive the stressful condition. Further to understand the response of roots proteome under multiple stresses was determined using the 2DE technique. The results of the root proteome show the up-regulated proteins of CML49 genotype (tolerant) are involved in enhancing the N content, cell wall remodeling, and acclimatization during the stresses. Up-regulated proteins of CML100 genotype (sensitive) are stressed marker of roots primary and secondary metabolism. However, the root proteome of both genotypes correlates with the leaf proteome (previous). Therefore, the present study and our previous results provide comprehensive insight into the molecular mechanisms of tolerance in multiple abiotic stresses of maize plants.
Nucleolar-based Dux repression is essential for 2-cell stage exit
Authors: Xie Sheila Q. , Leeke Bryony J. , Whidling Chad , Wagner Ryan T. , Garcia-Llagostera Ferran , Chammas Paul , Cheung Nathan T-F. , Dormann Dirk , McManus Michael T. , Percharde Michelle 
Published: November 2021

AbstractUpon fertilisation, the mammalian embryo must switch from dependence on maternal transcripts to transcribing its own genome, and in mice involves the transient upregulation of MERVL transposons and MERVL-driven genes at the 2-cell stage. The mechanisms and requirement for MERVL and 2-cell (2C) gene upregulation are poorly understood. Moreover, this MERVL-driven transcriptional program must be rapidly shut off to allow 2C exit and developmental progression. Here, we report that robust ribosomal RNA (rRNA) synthesis and nucleolar maturation are essential for exit from the 2C state. 2C-like cells and 2C embryos show similar immature nucleoli with altered structure and reduced rRNA output. We reveal that nucleolar disruption via blocking Pol I activity or preventing nucleolar phase separation enhances conversion to a 2C-like state in embryonic stem cells (ESCs) by detachment of the MERVL activator Dux from the nucleolar surface. In embryos, nucleolar disruption prevents proper Dux silencing and leads to 2-4 cell arrest. Our findings reveal an intriguing link between rRNA synthesis, nucleolar maturation and gene repression during early development.
Self-organization of kinetochore-fibers in human mitotic spindles
Authors: Conway William , Kiewisz Robert , Fabig Gunar , Kelleher Colm P. , Wu Hai-Yin , Anjur-Dietrich Maya , Müller-Reichert Thomas , Needleman Daniel 
Published: November 2021

ABSTRACTDuring eukaryotic cell division, chromosomes are linked to microtubules (MTs) in the spindle by a macromolecular complex called the kinetochore. The bound kinetochore microtubules (KMTs) are crucial to ensuring accurate chromosome segregation. Recent electron tomography reconstructions (Kiewisz et al. 2021) captured the positions and configurations of every MT in human mitotic spindles, revealing that many KMTs in these spindles do not reach the pole. Here, we investigate the processes that give rise to this distribution of KMTs using a combination of analysis of the electron tomography reconstructions, photoconversion experiments, quantitative polarized light microscopy, and biophysical modeling. Our results indicate that in metaphase, KMTs grow away from the kinetochores along well-defined trajectories, continually decreasing in speed as they approach the poles. The locations of KMT minus ends, and the turnover and movements of tubulin in KMTs, are consistent with models in which KMTs predominately nucleate de novo at kinetochores and are inconsistent with substantial numbers of non-KMTs being recruited to the kinetochore in metaphase. Taken together, this work leads to a mathematical model of the self-organization of kinetochore-fibers in human mitotic spindles.
METTL3 promotes homologous recombination repair and modulates chemotherapeutic response by regulating the EGF/Rad51 axis
Authors: Li Enjie , Xia Mingyue , Du Yu , Long Kaili , Ji Feng , Pan Feiyan , He Lingfeng , Hu Zhigang , Guo Zhigang 
Published: November 2021

AbstractMETTL3 and N6-methyladenosine (m6A) are involved in many types of biological and pathological processes, including DNA repair. However, the function and mechanism of METTL3 in DNA repair and chemotherapeutic response remain largely unknown. In present study, we identified that METTL3 participates in the regulation of homologous recombination repair (HR), which further influences chemotherapeutic response in breast cancer (BC) cells. Knockdown of METTL3 sensitized BC cells to Adriamycin (ADR) treatment and increased accumulation of DNA damage. Mechanically, we demonstrated that inhibition of METTL3 impaired HR efficiency and increased ADR-induced DNA damage by regulating m6A modification of EGF/RAD51 axis. METTL3 promoted EGF expression through m6A modification, which further upregulated RAD51 expression, resulting in enhanced HR activity. We further demonstrated that the m6A “reader,” YTHDC1, bound to the m6A modified EGF transcript and promoted EGF synthesis, which enhanced HR and cell survival during ADR treatment. Our findings reveal a pivotal mechanism of METTL3-mediated HR and chemotherapeutic drug response, which may contribute to cancer therapy.