bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Hot-Swappable Genetic Switch: Building an inducible and trackable functional assay for the essential gene MEDIATOR 21
Authors: Watson Isabella J. , Maranas Cassandra , Nemhauser Jennifer L , Leydon Alexander R 
Published: December 2024

AbstractEssential genes, estimated at approximately 20% of theArabidopsisgenome, are broadly expressed and required for reproductive success. They are difficult to study, as interfering with their function leads to premature death. Transcription is one of the essential functions of life, and the multi-protein Mediator complex coordinates the regulation of gene expression at nearly every eukaryotic promoter. In this study, we focused on a core Mediator component called MEDIATOR21 (MED21), which is required for activation of transcription. Our previous work has also shown a role for MED21 in repression of gene expression through its interaction with a corepressor protein. Here, we sought to differentiate the role MED21 plays in activation versus repression using the model plantArabidopsis. As mutations in MED21 lead to embryo lethal phenotypes, we constructed a set of synthetic switches using PhiC31 serine integrases to create an “on-to-off” inducible loss of function MED21 in a non-essential tissue. Our technology, which we call Integrase Erasers, made it possible formed21mutant plants to survive into adulthood by ablating protein expression selectively in lateral root primordia, allowing quantification and characterization ofmed21mutant phenotypes in a post-embryonic context. In addition, we engineered chemical induction of the Integrase Eraser to ablate MED21 expression in whole seedlings at a user-specified timepoint. Finally, we extended this technology to build a hot swappable Integrase Isoform Switch where expression of the integrase toggled cells from expressing wildtype MED21 to expressing MED21 sequence variants. Our analysis of the entire set of new integrase-based tools demonstrates that this is a highly efficient and robust approach to the study of essential genes.
Reanalysis of metabolomics data reveals that microbiota transfer therapy modulates important fecal and plasma metabolite profiles in children with autism spectrum disorders
Authors: Nirmalkar Khemlal , Qureshi Fatir , Kang Dae-Wook , Hahn Juergen , Adams James B. , Krajmalnik-Brown Rosa 
Published: December 2024

AbstractWhile Autism Spectrum Disorder (ASD) is diagnosed through behavioral symptoms and psychometric evaluations, it has also been associated with distinct metabolomic patterns. A previous clinical trial of Microbiome Transfer Therapy (MTT) in children with ASD and gastrointestinal (GI) issues revealed significant differences in plasma metabolomics between children with ASD and their typically developing (TD) counterparts, which diminished after MTT. The objective of this study was to reanalyze the plasma and fecal samples using updated metabolomics libraries at Metabolon, applying a comprehensive panel of statistical methods. This approach aimed to provide deeper insights into ASD-related metabolic differences and the impact of MTT. The reanalysis identified more statistically significant metabolites and highlighted specific metabolites whose relative intensities differed between the ASD and TD groups, as well as metabolites with significant changes in intensity post-MTT. Several plasma metabolites, including sarcosine, iminodiacetate, caproate, and caprylate, initially showed significant differences between the ASD and TD groups but shifted to resemble TD levels after MTT treatment. In fecal samples, p-cresol sulfate and sphingolipids emerged as metabolites with altered intensities following MTT treatment. Multivariate Fisher’s Discriminant Analysis (FDA) with leave-one-out cross-validation revealed that a set of metabolites—including p-cresol sulfate, hydroxyproline, and caprylate—could robustly classify the ASD and TD cohort’s pre-treatment. However, after treatment, the same FDA model could not distinguish the two groups, as the FDA scores became similar to those of the TD cohort. Our findings enhance the understanding of ASD-associated metabolic changes and highlight the potential of MTT to influence these profiles. This underscores the importance of reanalysis using updated databases and robust statistical methods for comparative analysis. Further studies with larger cohorts and placebo-controlled trials are necessary to validate these results and explore the biochemical pathways involved, paving the way for personalized treatment approaches.
Frequent gastrointestinal cancer complications in Japanese patients with coronary syndromes undergoing percutaneous coronary intervention
Authors: Chiba Yasuyuki , Imagawa Shogo , Takahashi Yuki , Kubo Kimitoshi , Otsuka Kenta , Shimazu Kyo , Anzai Teisuke , Yonezawa Kazuya , Kato Mototsugu , Anzai Toshihisa 
Published: December 2024

AbstractBackgroundGastrointestinal bleeding is a major complication of dual antiplatelet therapy (DAPT) in patients undergoing percutaneous coronary intervention (PCI). Malignancy may be detected due to gastrointestinal bleeding, necessitating critical decisions regarding treatment selection and influencing patient prognosis. This study investigated the frequency of gastrointestinal malignancies, associated factors, and prognoses in patients undergoing perioperative PCI through upper and lower gastrointestinal endoscopy.MethodsThis single-center, retrospective, observational study included 501 Japanese patients who underwent initial PCI between January 2019 and January 2023. Of these patients, 393 who underwent perioperative upper and lower gastrointestinal endoscopy were evaluated for the presence of gastrointestinal malignancy.ResultsOf the total patients, 36% presented with acute coronary syndrome (ACS). Gastrointestinal malignancies were identified in 30 patients (8%), including 18 cases of colorectal cancer and eight cases of gastric cancer. No difference in the frequency of malignancies was observed between patients with ACS and chronic coronary syndrome (CCS) (p = 0.7398). Malignancies were significantly more common in patients with positive faecal immunochemical testing (FIT) (p < 0.0001); however, FIT did not detect all malignancies. The 1500-day survival rate for patients with gastrointestinal malignancies was 64%, with no difference in overall survival between treatment modalities.ConclusionsA considerable proportion of Japanese patients undergoing PCI had gastrointestinal malignancies, regardless of whether they had ACS or CCS, and their prognosis was poor. Upper and lower gastrointestinal endoscopic evaluations should be conducted, including for ACS cases, to prevent DAPT-induced gastrointestinal bleeding and improve prognosis.
A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular ASO activity
Authors: Malong Liza , Roskosch Jessica , Hager Carolina , Fortin Jean-Philippe , Schmucki Roland , Callow Marinella G. , Weile Christian , Romeo Valentina , Patsch Christoph , Martin Scott , Costa Mike , Modrusan Zora , Villaseñor Roberto , Koller Erich , Haley Benjamin , Spang Anne , Roudnicky Filip 
Published: December 2024

AbstractAnti-sense oligonucleotides (ASOs) are modified synthetic single-stranded molecules with enhanced stability, activity, and bioavailability. They associate with RNA through sequence complementarity and can reduce or alter mRNA expression upon binding of splice site positions. To target RNA in the nucleus or cytoplasm, ASOs must cross membranes, a poorly understood process. We have performed an unbiased CRISPR/Cas9 knockout screen with a genetic splice reporter to identify genes that can increase or decrease ASOs activity, resulting in the most comprehensive catalog of ASOs-activity modifier genes. Distinct targets were uncovered, including AP1M1 and TBC1D23, linking ASOs activity to transport of cargo between the Golgi and endosomes. AP1M1 absence strongly increased ASO activity by delaying endosome-to-lysosome transportin vitroandin vivo. Prolonged ASOs residence time in the endosomal system may increase the likelihood of ASOs escape from this organelle before they reach lysosomes. This insight into AP1M1 role in ASOs trafficking suggests a way for enhancing the therapeutic efficacy of ASOs by manipulating the endolysosomal pathways.
Modelling oxaliplatin resistance in colorectal cancer reveals aSERPINE1-based gene signature (RESIST-M) and therapeutic strategies for pro-metastatic CMS4 subtype
Authors: Wong Stephen Qi Rong , Das Mohua , Shirgaonkar Niranjan , Tenzin Kenzom , Chua Huiwen , Chee Lin Xuan , Ahpa Sae Yeoh , Murugiah Astley Aruna , Chua Wei Yong , Theardy Madelaine Skolastika , Thangavelu Matan Thangavelu , Chan Jane Vin , Yap Choon Kong , Tan Iain Bee Huat , Tsantoulis Petros , Tejpar Sabine , Loo Jia Min , Dasgupta Ramanuj 
Published: December 2024

AbstractDrug resistance and distant metastases are major contributors to mortality in colorectal cancer (CRC). Here we investigate mechanisms underlying acquired resistance to oxaliplatin, a first-line, standard-of-care CRC treatment. We generated oxaliplatin-resistant CRC tumor cells with clinically relevant dosing regimen, which displayed enhanced metastatic potential. Transcriptomic and phenotypic analyses revealed a critical function for cholesterol biogenesis in modulating TGF-β signaling activity, which in turn regulatesSERPINE1expression, a gene we identified as a key player in promoting drug resistance and metastasis. Additionally, we uncovered aSERPINE1-associated nine-gene expression signature, RESIST-M, that can predict overall and relapse-free survival (RFS) in clinical cohorts and is able to stratify patients into CMS4/iCMS3-fibrotic CRC-subtypes, underscoring its clinical utility. Using mouse tumor models, we provide further evidence that targetingSERPINE1and cholesterol biogenesis can be viable approaches to re-sensitize the resistant pro-metastatic CRC cells to oxaliplatin. This study not only elucidates the molecular underpinnings of drug resistance and metastasis in primary CRC, but also offers prognostic and therapeutic strategies to guide clinical management of the disease.SignificanceThis study reveals critical resources and insights on oxaliplatin resistance and metastasis in CRC via a novel TGF-β cholesterol axis. We generated improved oxaliplatin-resistant models that enabled identification of a prognosticSERPINE1-based gene signature to predict oxaliplatin resistance-induced metastasis in CRC. This gene signature derived from our models showed that the models can mimic CMS-4/iCMS-fibrotic-like metastatic CRC patients. We validated therapeutic candidates targeting CMS-4/iCMS-fibrotic-like metastatic CRC cells which can reverse drug resistance and metastasis.
Assessing the efficacy of therapeutically promising combination of polymyxin B and triclosan against colistin resistantKlebsiella pneumoniae
Authors: Biswas Soumya , Ghosh Soujanya , Patra Saumya Darshana , Mahapatra Pushney , Verma Gaurav , Misra Namrata , Kushwaha Gajraj Singh , Suar Mrutyunjay 
Published: December 2024

AbstractAntimicrobial resistance (AMR) is one of the greatest public health challenges of current time and it is majorly associated with Gram-negative bacterial infections. Among these infections,Klebsiella pneumoniaeis the most notorious bacterial pathogen in the context of AMR. The inefficiency of currently available antibacterial drugs is becoming common in hospitalized patients and clinicians feel hopeless during treatment. Eventually, clinicians explore old regimes such as colistin to treat these multidrug resistance infections, however, unfortunately, the resistance towards these last-resort drugs is also emerging rapidly. In this study, we examined the occurrence of colistin resistance inKlebsiella pneumoniaeconcerning its mechanism of resistance, chronology, and geographical distribution. We found that resistance, towards these last-resort drugs, colistin and polymyxin B, is emerging rapidly with evolving multiple mechanisms of resistance. Although various attempts are being made to find a solution for this crisis, a combination therapy comprising approved antibacterial drugs may be one of the most suitable strategies to fight against AMR in the current time-ticking situation. Therefore, we evaluated the efficacy of a therapeutically viable combination of polymyxin B and triclosan using a set of standard antibacterial assays forin vitropreclinical efficacy. We found that the combination is highly effective in a colistin-resistant clinical strain ofKlebsiella pneumoniaeas triclosan sensitizes the pathogen towards polymyxin B. Furthermore, the results of additional complementary experiments such as time-kill kinetics, biofilm inhibition, frequency of resistance, cell viability, and cytotoxicity assays show very encouraging results for the feasibility and validation of this combination. Finally, we examined the presence of mutations in field isolates ofKlebsiella pneumoniaeFabI enzyme as it has been hypothesized previously that triclosan may cause mutation in its binding target, FabI. Interestingly, we could not detect any mutation in the triclosan binding site of FabI in the genome of field isolates. Altogether, this study provides an overview of the current situation on colistin resistance, a promising solution for colistin resistance comprising a combination of two already being used antibacterial ingredients based onin vitropreclinical efficacy studies.
Salt-induced reduction of hyperswarming motility inBacillus cereusMHS is associated with reduced flagellation, reduced nanotube formation and reduction in expression of quorum sensing regulator
Authors: Bhadani Nirbhay Kumar , Sarmah Hemanta , Prasad Kritika , Gupta Nisha , Sengupta Tapas K 
Published: December 2024

AbstractBacteria have been known to thrive in challenging environmental niches through diverse phenomena. Swarming is one such favourable adaptation that could help bacteria survive extreme conditions. Therefore, targeting swarming is crucial for improving our understanding of bacterial motility and preventing related infections.Bacillus cereus,which causes food poisoning, has been shown to perform swarming, and salts like NaCl can act as a food preservative to control bacterial growth. In order to explore the possible alterations in the swarming ofBacillus cereusin the presence of salt, the present study encompasses the effect of NaCl on the swarming characteristics of a natural bacterial isolate,Bacillus cereusMHS, with a hyperswarming phenotype. Here we report that the presence of an increased amount of NaCl in growth media could induce a reduction in swarming motility and swarming pattern of MHS on Luria agar plates and the observed reduction in swarming was associated with the reduced flagellation and reduction in bacterial nanotube formation. Gene expression studies supported the phenotypic and ultrastructure observations as the expressions ofbflaandymdbgenes, involved in formations of flagella and nanotubes respectively, were found to be reduced in the swarming MHS cells in the presence of increased NaCl in swarm media. It was also observed that the salt-induced reduction in swarming of MHS is associated with the reduced expression of the quorum sensing regulator geneplcR.This study first time reports the bacterial nanotubes in aBacillus cereusstrain and indicates a possible link between the bacterial nanotube formation and hyperswarming phenotype inBacillus cereusMHS.
Conserved protein Seb1 that interacts with RNA polymerase II and RNA is a bona fide transcription elongation factor
Authors: Kuś Krzysztof , Nielsen Soren , Zenkin Nikolay , Vasiljeva Lidia 
Published: December 2024

ABSTRACTMaturation of protein-coding precursor messenger RNA (pre-mRNA) is closely linked to RNA polymerase II (Pol II) transcription. However, the mechanistic understanding of how RNA processing is coordinated with transcription is incomplete. Conserved proteins interacting with the C-terminal domain of the largest catalytic subunits of Pol II and nascent RNA (CID-RRM factors) were demonstrated to play a role in mRNA 3’-end processing and termination of Pol II transcription. Here, we employ a fully reconstituted system to demonstrate that fission yeast CID-RRM factor Seb1 acts as abona fideelongation factorin vitro. Our analyses show that Seb1 exhibits context-dependent regulation of Pol II pausing, capable of either promoting or inhibiting pause site entry. We propose that CID-RRM factors coordinate Pol II transcription and RNA 3’-end processing by modulating the rate of Pol II transcription.
Combined biosynthesis and site-specific incorporation of phenylalanine derivatives from aryl aldehydes or carboxylic acids in engineered bacteria
Authors: Anderson Shelby R. , Spangler Abigail P. , Jones Michaela A. , Dickey Roman M. , Kunjapur Aditya M. 
Published: December 2024

AbstractApplications of genetic code expansion in live cells are widespread and continually emerging, yet they have been limited by their reliance on the supplementation of non-standard amino acids (nsAAs) to cell culturing media. While advances in cell-free biocatalysis are improving nsAA synthesis cost and sustainability, such processes remain reliant on multi-step processes of product isolation followed by supplementation to engineered cells. Here, we report the design of a modular and genetically encoded system that combines the steps of biosynthesis of diverse phenylalanine derivatives, which are the most frequently used family of nsAAs for genetic code expansion, and their site-specific incorporation within target proteins using a single engineered bacterial host. Unlike previous demonstrations in which individual nsAAs were targeted for biosynthesis and site-specific incorporation, our system serves as a platform that exhibits broad substrate specificity towards commercially ubiquitous, achiral building blocks of aryl aldehydes or carboxylic acids. We demonstrate that this modular system enables high fidelity biosynthesis and incorporation of nsAAs for multiple industrially relevant nsAAs, such as the incorporation of 4,4-L-biphenylalanine within proteins after supplementation with biphenylaldehyde and the incorporation of 4-azido-L-phenylalanine within proteins after supplementation with 4-azido-benzoic acid. Finally, we show that the combination of nsAA biosynthesis and incorporation steps can extend the chemical reach of the intrinsic biological containment strategy of synthetic auxotrophy from nsAAs to low-cost and achiral building blocks. We anticipate that our system will aid industrial-scale manufacturing of proteins that contain nsAAs and democratize access to expensive or commercially unavailable chemistries for labs that lack separations or synthesis expertise.
Stochastic Growth Bursts Enable Burden-Free Flagellum Production in a Single Bacterium
Authors: Garcia-Alcala Mayra , Cluzel Philippe 
Published: December 2024

AbstractIt is widely recognized from population-level measurements that increased production of unnecessary proteins leads to reduced bacterial growth rate, with this effect being particularly severe for flagellum synthesis. Here, we track the relationship between instantaneous growth rate variations and the activity of flagellar genes in lineages of single growing cells of E. coli. Surprisingly, we find that when flagellar gene expression is active, it is also coupled with increased growth rate. We determine that this phenomenon arises from growth bursts after divisions, which drive flagellar expression and temporarily alleviate the associated growth burden. Similar effects were observed with constitutive synthetic expression systems suggesting that an out-of-balance growth process may constitute a general strategy for mitigating the cost of expressing biosynthetically demanding genes in the single cell.
Transition route to elastic and elasto-inertial turbulence in polymer channel flows
Authors: Beneitez M. , Page J. , Dubief Y. , Kerswell R. R. 
Published: December 2024

Viscoelastic shear flows support additional chaotic states beyond simple Newtonian turbulence. In vanishing Reynolds number flows, the nonlinearity in the polymer evolution equation alone can sustain inertialess “elastic” turbulence (ET) while “elasto-inertial” turbulence (EIT) appears to rely on an interplay between elasticity and finite-Re effects. Despite their distinct phenomenology and industrial significance, transition routes and possible connections between these states are unknown. We identify here a common Ruelle-Takens transition scenario for both of these chaotic regimes in two-dimensional direct numerical simulations of FENE-P fluids in a straight channel. The primary bifurcation is caused by a recently discovered “polymer diffusive instability” associated with small but nonvanishing polymer stress diffusion which generates a finite-amplitude, small-scale traveling wave localized at the wall. This is found to be unstable to a large-scale secondary instability which grows to modify the whole flow before itself breaking down in a third bifurcation to either ET or EIT. The secondary large-scale instability waves resemble “center” and “wall” modes, respectively—instabilities which have been conjectured to play a role in viscoelastic chaotic dynamics but were previously only thought to exist far from relevant areas of the parameter space.

Published by the American Physical Society
2024
Enhanced Quantum State Transfer via Feedforward Cancellation of Optical Phase Noise
Authors: Maddox Benjamin P. , Mortlock Jonathan M. , Hepworth Tom R. , Raghuram Adarsh P. , Gregory Philip D. , Guttridge Alexander , Cornish Simon L. 
Published: December 2024

Many experimental platforms for quantum science depend on state control via laser fields. Frequently, however, the control fidelity is limited by optical phase noise. This is exacerbated in stabilized laser systems where high-frequency phase noise is an unavoidable consequence of feedback. Here we implement an optical feedforward technique to suppress laser phase noise in the stimulated Raman adiabatic passage state transfer of ultracold RbCs molecules, across 114 THz, from a weakly bound Feshbach state to the rovibrational ground state. By performing over 100 state transfers on single molecules, we measure a significantly enhanced transfer efficiency of 98.7(1)% limited only by available laser intensity.

Published by the American Physical Society
2024