bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in Relevant Physicochemical Properties Correlate with Synergistic Activity of Antimicrobial Peptides
Authors: Medvedeva Angela , Teimouri Hamid , Kolomeisky Anatoly B. 
Published: June 2023

AbstractWith the urgent need for new medical approaches due to increased bacterial resistance to antibiotics, antimicrobial peptides (AMPs) have been considered as potential treatments for infections. Experiments indicate that combinations of several types of AMPs might be more effective at inhibiting bacterial growth with reduced toxicity and a lower likelihood of inducing bacteria resistance. The molecular mechanisms of AMP-AMP synergistic antimicrobial activity, however, remain not well understood. Here, we present a theoretical approach that allows us to relate the physicochemical properties of AMPs and their antimicrobial cooperativity. A concept of physicochemical similarity is introduced, and it is found that less similar AMPs with respect to certain physicochemical properties lead to greater synergy because of their complementary antibacterial actions. The analysis of correlations between the similarity and the antimicrobial properties allows us to effectively separate synergistic from non-synergistic AMPs pairs. Our theoretical approach can be used for the rational design of more effective AMPs combinations for specific bacterial targets, for clarifying the mechanisms of bacterial elimination, and for a better understanding of cooperativity phenomena in biological systems.Author summaryIt is impossible to imagine modern medicine without antibiotics. But there is a growing problem of increased bacterial resistance to them. These considerations stimulated a search for novel methods to defend against infections. Antimicrobial peptides (AMPs) came out as powerful antibacterial agents. It was also found that combinations of AMPs are even more efficient than individual peptides. The mechanisms of such synergistic activities, however, are not understood. We developed a computational framework that allows us to connect the physicochemical properties of AMPs and their abilities to cooperatively eliminate infections. It is found that less similar peptides might exhibit synergy because of their complementary antibacterial properties. Our theoretical approach might lead to a better rational design of new antimicrobial drugs.
Appropriate sampling and long follow-up are required to rigorously evaluate longevity of humoral memory after vaccination
Authors: Ganusov Vitaly V. 
Published: June 2023

AbstractOne of the goals of vaccination is to induce long-term immunity against the infection and/or disease. However, evaluating the duration of protection following vaccination often requires long-term follow-ups that can conflict with the desire to rapidly publish results. Arunachalam et al. JCI 2023 followed individuals receiving third or fourth dose of mRNA COVID19 vaccines for up to 6 months and in finding that the levels of SARS-CoV2-specific antibodies (Abs) declined with similar rates for the two groups came to the conclusion that additional boosting is unnecessary to prolong immunity to SARS-CoV-2. However, this may be premature conclusion to make. Accordingly, we demonstrate that measuring Ab levels at 3 time points and only for a short (up to 6 month) duration does not allow to accurately and rigorously evaluate the long-term half-life of vaccine-induced Abs. By using the data from a cohort of blood donors followed for several years, we show that after re-vaccination with vaccinia virus (VV), VV-specific Abs decay bi-phasically and even the late decay rate exceeds the true slow loss rate of humoral memory observed years prior to the boosting. We argue that mathematical modeling should be used to better optimize sampling schedules to provide more reliable advice about the duration of humoral immunity after repeated vaccinations.
Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study
Authors: Wang Yuxuan , Selvaraj Margaret Sunitha , Li Xihao , Li Zilin , Holdcraft Jacob A. , Arnett Donna K. , Bis Joshua C. , Blangero John , Boerwinkle Eric , Bowden Donald W. , Cade Brian E. , Carlson Jenna C. , Carson April P. , Chen Yii-Der Ida , Curran Joanne E. , de Vries Paul S. , Dutcher Susan K. , Ellinor Patrick T. , Floyd James S. , Fornage Myriam , Freedman Barry I. , Gabriel Stacey , Germer Soren , Gibbs Richard A. , Guo Xiuqing , He Jiang , Heard-Costa Nancy , Hildalgo Bertha , Hou Lifang , Irvin Marguerite R. , Joehanes Roby , Kaplan Robert C. , Kardia Sharon LR. , Kelly Tanika N. , Kim Ryan , Kooperberg Charles , Kral Brian G. , Levy Daniel , Li Changwei , Liu Chunyu , Lloyd-Jone Don , Loos Ruth JF. , Mahaney Michael C. , Martin Lisa W. , Mathias Rasika A. , Minster Ryan L. , Mitchell Braxton D. , Montasser May E. , Morrison Alanna C. , Murabito Joanne M. , Naseri Take , O’Connell Jeffrey R. , Palmer Nicholette D. , Preuss Michael H. , Psaty Bruce M. , Raffield Laura M. , Rao Dabeeru C. , Redline Susan , Reiner Alexander P. , Rich Stephen S. , Ruepena Muagututi’a Sefuiva , Sheu Wayne H-H. , Smith Jennifer A. , Smith Albert , Tiwari Hemant K. , Tsai Michael Y. , Viaud-Martinez Karine A. , Wang Zhe , Yanek Lisa R. , Zhao Wei ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Rotter Jerome I. , Lin Xihong , Natarajan Pradeep , Peloso Gina M. 
Published: June 2023

AbstractLong non-coding RNAs (lncRNAs) are known to perform important regulatory functions. Large-scale whole genome sequencing (WGS) studies and new statistical methods for variant set tests now provide an opportunity to assess the associations between rare variants in lncRNA genes and complex traits across the genome. In this study, we used high-coverage WGS from 66,329 participants of diverse ancestries with blood lipid levels (LDL-C, HDL-C, TC, and TG) in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program to investigate the role of lncRNAs in lipid variability. We aggregated rare variants for 165,375 lncRNA genes based on their genomic locations and conducted rare variant aggregate association tests using the STAAR (variant-Set Test for Association using Annotation infoRmation) framework. We performed STAAR conditional analysis adjusting for common variants in known lipid GWAS loci and rare coding variants in nearby protein coding genes. Our analyses revealed 83 rare lncRNA variant sets significantly associated with blood lipid levels, all of which were located in known lipid GWAS loci (in a ±500 kb window of a Global Lipids Genetics Consortium index variant). Notably, 61 out of 83 signals (73%) were conditionally independent of common regulatory variations and rare protein coding variations at the same loci. We replicated 34 out of 61 (56%) conditionally independent associations using the independent UK Biobank WGS data. Our results expand the genetic architecture of blood lipids to rare variants in lncRNA, implicating new therapeutic opportunities.
ORBIT forE. coli: Kilobase-scale oligonucleotide recombineering at high throughput and high efficiency
Authors: Saunders Scott H. , Ahmed Ayesha M. 
Published: June 2023

AbstractMicrobiology and synthetic biology depend on reverse genetic approaches to manipulate bacterial genomes; however, existing methods require molecular biology to generate genomic homology, suffer from low efficiency, and are not easily scaled to high throughput applications. To overcome these limitations, we developed a system for creating kilobase-scale genomic modifications that uses DNA oligonucleotides to direct the integration of a non-replicating plasmid. This method, Oligonucleotide Recombineering followed by Bxb-1 Integrase Targeting (ORBIT) was pioneered inMycobacteria, and here we adapt and expand it forE. coli. Our redesigned plasmid toolkit achieved nearly 1000x higher efficiency than λ Red recombination and enabled precise, stable knockouts (<134 kb) and integrations (<11 kb) of various sizes. Additionally, we constructed multi-mutants (double and triple) in a single transformation, using orthogonal attachment sites. At high throughput, we used pools of targeting oligonucleotides to knock out nearly all known transcription factor and small RNA genes, yielding accurate, genome-wide, single mutant libraries. By counting genomic barcodes, we also show ORBIT libraries can scale to thousands of unique members (>30k). This work demonstrates that ORBIT forE. coliis a flexible reverse genetic system that facilitates rapid construction of complex strains and readily scales to create sophisticated mutant libraries.
Enabling AI in Synthetic Biology through Construction File Specification
Authors: Ataii Nassim , Bakshi Sanjyot , Chen Yisheng , Fernandez Michael , Shao Zihang , Scheftel Zachary , Tou Connor , Vega Mia , Wang Yuting , Zhang Hanxiao , Zhao Zexuan , Anderson J. Christopher 
Published: June 2023

AbstractThe Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases ‘Experiment’ objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.
Enteropathway: the metabolic pathway database for the human gut microbiota
Authors: Shiroma Hirotsugu , Darzi Youssef , Terajima Etsuko , Nakagawa Zenichi , Tsuchikura Hirotaka , Tsukuda Naoki , Moriya Yuki , Okuda Shujiro , Goto Susumu , Yamada Takuji 
Published: June 2023

AbstractThe human gut microbiota produces diverse, extensive metabolites which have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3,121 compounds, 3,460 reactions, and 837 modules that were obtained from 835 manually curated scientific literature. Notably, 757 modules of these modules are new entries and cannot be found in any other databases. The database is accessible from a web application (https://enteropathway.org) that offers a metabolic diagram for graphical visualization of metabolic pathways, a customization interface, and an enrichment analysis feature for highlighting enriched modules on the metabolic diagram. Overall, Enteropathway is a comprehensive reference database and a tool for visual and statistical analysis in human gut microbiota studies and was designed to help researchers pinpoint new insights into the complex interplay between microbiota and host metabolism.
The alternative sigma factor RpoD4 pulses at division and links the clock and the cell cycle inSynechococcus elongatus
Authors: Ye Chao , Saez Teresa , Das Arijit K. , Martins Bruno M.C. , Locke James C.W. 
Published: June 2023

AbstractThe cyanobacterial circadian clock is an extensive regulator of gene expression, generating a 24-hour rhythm in the majority of genes inSynechococcus elongatusPCC7942. This raises the question of how the cyanobacterial clock regulates, and receives input from, the diverse cellular processes it controls. Alternative sigma factors, which bind to the core RNA polymerase enzyme and direct the synthesis of specific sets of transcripts, are one mechanism for the clock to set the time of its outputs. In this work, we use single-cell time-lapse microscopy to reveal the transcriptional dynamics of RpoD4, an alternative sigma factor that was previously reported as either arrhythmic or circadian. We find instead that RpoD4 pulses at cell division, dynamics missed by previous bulk averaging. The circadian clock modulates the amplitude of RpoD4 expression pulses, as well as the timing of pulses through its control of division timing. In turn, arpoD4mutation causes a reduction in clock period. Further, arpoD4mutant results in smaller cell size, and increasing expression of RpoD4 results in larger cell sizes in a dose-response manner, allowing tunable control of cell size. Thus, our single-cell analysis has revealed pulsing gene expression dynamics in cyanobacteria, linking the clock, RpoD4 and the cell cycle.
Electron microscopic and crystallographic studies of bacteriophage Sf6 procapsid-like particles assembled from heterologously expressed capsid protein gp5
Authors: Zhao Haiyan , Tang Liang 
Published: June 2023

AbstractMany double-stranded DNA (dsDNA) viruses undergo a capsid maturation process during assembly of infectious virus particles, which involves transformation of a metastable capsid precursor called procapsid into a stable, DNA-filled capsid usually with a larger size and a more angular shape. Sf6 is a tailed dsDNA bacteriophage that infectsShigella flexneri. The phage Sf6 capsid protein gp5 was heterologously expressed and purified. Electron microscopy showed that the gp5 spontaneously assembled into spherical, procapsid-like particles. We also observed tube-like and cone-shaped particles reminiscent of human immunodeficiency virus. The gp5 procapsid-like particles were crystallized and crystals diffracted beyond 4.3 Å resolution. X-ray data at 5.9 Å resolution were collected with a completeness of 31.1% and an overallRmerge of 15.0%. The crystals belong to the space groupC2 with unit cell dimensions of a=973.326 Å, b=568.234 Å, c=565.567 Å, and β=120.540°. Self-rotation function showed the 532 symmetry, confirming formation of icosahedral particles. The particle was situated at the origin of the crystal unit cell with the icosahedral 2-fold axis coinciding with the crystallographicbaxis, and there is a half of the icosahedral particle in the crystallographic asymmetric unit.
Liver-specification of human iPSC-derived endothelial cells transplanted into mouse liver
Authors: Yap Kiryu K. , Schröder Jan , Gerrand Yi-Wen , Kong Anne M. , Fox Adrian M. , Knowles Brett , Banting Simon W. , Elefanty Andrew G. , Stanley Eduoard G. , Yeoh George C. , Lockwood Glen P. , Cogger Victoria C. , Morrison Wayne A. , Polo Jose M. , Mitchell Geraldine M. 
Published: June 2023

ABSTRACTLiver sinusoidal endothelial cells (LSECs) play an important role in liver development, regeneration and pathophysiology, but the differentiation process that generates their unique tissue-specific phenotype is poorly understood and difficult to study as primary cells are only available in limited quantities. To address this, we hypothesised that human induced pluripotent stem cell (hiPSC)-derived endothelial cells (iECs) can produce hiPSC-derived LSECs upon transplantation into the livers ofFah−/−/Rag2−/−/Il2rg−/−mice, and serve as a model to study LSEC specification. Progressive and long-term repopulation of the liver vasculature was observed, as iECs expanded along the sinusoids that run between hepatocytes and increasingly produced human factor VIII, indicating differentiation into LSEC-like cells. To chart the developmental profile associated with LSEC specification, the bulk transcriptome of transplanted cells at time-points between 1 and 12 weeks were compared against primary human adult LSECs, which demonstrated a chronological increase in LSEC markers, LSEC differentiation pathways, and zonation. Bulk transcriptome analysis suggested that the transcription factorsNOTCH1,GATA4, andFOSplay a central role in LSEC specification, interacting with a network of 27 transcription factors. Novel markers associated with this process includeEMCNandCLEC14A. Additionally, single cell transcriptomic analysis demonstrated that transplanted iECs at 4 weeks contain zonal subpopulations with a region-specific phenotype. Collectively, this study confirms that hiPSC can adopt LSEC-like features and provides insight into LSEC specification. This humanised xenograft system can be applied to further interrogate LSEC developmental biology and pathophysiology, bypassing current logistical obstacles associated with primary human LSECs.
Serovar-level Identification of Bacterial Foodborne Pathogens From Full-length 16S rRNA Gene Sequencing
Authors: Grinevich Dmitry , Harden Lyndy , Thakur Siddhartha , Callahan Benjamin J 
Published: June 2023

AbstractThe resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogensEscherichia coliandSalmonella, the primary sub-species classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are therefore of interest for pathogen surveillance. Here we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotypingS. entericaandE. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predictingSalmonellaserotypes onin silicotest data, and identified key pathogenic serovars ofSalmonellaandE. coliin isolate and environmental test samples. Although serotype prediction from 16S sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intra-species variation and direct sequencing from environmental samples could be valuable.
Targeting Ribosome Biogenesis as a Novel Therapeutic Approach to Overcome EMT-related Chemoresistance in Breast Cancer
Authors: Ban Yi , Zou Yue , Liu Yingzhuo , Lee Sharrell B. , Bednarczyk Robert B. , Sheng Jianting , Cao Yuliang , Wong Stephen T. C. , Gao Dingcheng 
Published: June 2023

AbstractEpithelial-to-mesenchymal transition (EMT) contributes significantly to chemotherapy resistance and remains a critical challenge in treating advanced breast cancer. The complexity of EMT, involving redundant pro-EMT signaling pathways and its paradox reversal process, mesenchymal-to-epithelial transition (MET), has hindered the development of effective treatments. In this study, we utilized a Tri-PyMT EMT lineage-tracing model and single-cell RNA sequencing (scRNA-seq) to comprehensively analyze the EMT status of tumor cells. Our findings revealed elevated ribosome biogenesis (RiBi) during the transitioning phases of both EMT and MET processes. RiBi and its subsequent nascent protein synthesis mediated by ERK and mTOR signalings are essential for EMT/MET completion. Importantly, inhibiting excessive RiBi genetically or pharmacologically impaired the EMT/MET capability of tumor cells. Combining RiBi inhibition with chemotherapy drugs synergistically reduced metastatic outgrowth of epithelial and mesenchymal tumor cells under chemotherapies. Our study suggests that targeting the RiBi pathway presents a promising strategy for treating patients with advanced breast cancer.SignificanceThis study uncovers the crucial involvement of ribosome biogenesis (RiBi) in the regulation of epithelial and mesenchymal state oscillations in breast cancer cells, which plays a major role in the development of chemoresistant metastasis. By proposing a novel therapeutic strategy targeting the RiBi pathway, the study offers significant potential to enhance treatment efficacy and outcomes for patients with advanced breast cancer. This approach could help overcome the limitations of current chemotherapy options and address the complex challenges posed by EMT-mediated chemoresistance.
Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies
Authors: Husser Mathieu C. , Pham Nhat P. , Law Chris , Araujo Flavia R. B. , Martin Vincent J.J. , Piekny Alisa 
Published: June 2023

AbstractEndogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.