bluuebunny/crossref_metadata_2025_split huggingface dataset:
New evidence for the presence and function of phosphoinositides (PPIs) in the chloroplast
Authors: Sedaghatmehr Mastoureh , Rößler Frieda , Hertle Alexander P. 
Published: September 2024

AbstractEssential proteins involved in thylakoid formation, including chloroplast-localized Sec14-like protein (CPSFL1) and the vesicle-inducing protein in plastids (VIPP1), bind PPIsin vitrowith high affinity. PPIs are a class of phospholipids characterized by a phosphorylated inositol head group. Although PPIs constitute a relatively small proportion of the total phospholipids, they play essential roles in various regulatory processes. The exact subcellular localization of most PPI species in plants is incomplete due to their rapid turnover and low abundance. Currently there is no documented evidence for the presence and function of phosphoinositides (PPIs) in chloroplasts. In our study, we developed genetically encoded biosensors targeted into plastids, enabling the detection of various PPI isoforms (PI3P, PI4P, PI5P, PI(4,5)P2and PI(3,5)P2) within the chloroplasts. We effectively demonstrated the specificity of our PPI biosensors in detection of PPIs, as evidenced by the alterations in PPI biosensor distribution patterns upon co-expression of PPI modifying enzymes (cTP-SAC7,cTP-PTEN, andcTP-dOCRL). Additionally, our research confirmed the capability of the generated PPI biosensors to detect PPIs within the chloroplasts of both tobacco andArabidopsisin a concentration-dependent manner. Furthermore, we unveiled the association and potential interaction of PI3P with VIPP1. We could show that the increased PPI flux within the cell during heat stress affects PPI levels in the chloroplasts, resulting in different distribution patterns of the PPI biosensors. Finally, plants expressing PPI modifierscTP-SAC7,cTP-PTEN, andcTP-dOCRL,in the chloroplast, showed increased sensitivity to drought stress, likely due to impaired PPI signaling.
Dynamics and Determinants of the Gut Mobilome in Early Life
Authors: Fernández-Pato Asier , Sinha Trishla , Garmaeva Sanzhima , Gulyaeva Anastasia , Kuzub Nataliia , Roux Simon , Fu Jingyuan , Kurilshikov Alexander , Zhernakova Alexandra 
Published: September 2024

AbstractAs mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition, we characterized the gut virome and plasmidome in 195 samples from 28 mother–infant dyads delivered by caesarean section. Infant mobilome increased in richness over the first 6 postnatal weeks, demonstrating high individual-specificity and temporal stability, establishing a personal persistent mobilome. Formula-fed infants exhibited greater mobilome richness than breastfed infants, with plasmid composition influenced by antibiotic exposure and birth weight. Plasmids constituted a significant reservoir of antibiotic resistance genes (ARG), with around 5% of infant gut plasmid taxonomic units carrying ARG. Notably, ARG profiles did not differ with antibiotic exposure at birth. We found that mother–infant sharing of viral and plasmid strains primarily occurred after 6 months of age. Overall, our integrative analysis offers novel insights into the dynamics, modulation, origin, and clinical implications of MGE in the developing gut microbiome.
Two-photon driven photoprotection mechanism in echinenone-functionalized Orange Carotenoid Protein
Authors: Niziński Stanisław , Hartmann Elisabeth , Shoeman Robert L. , Wilson Adjélé , Reinstein Jochen , Kirilovsky Diana , Sliwa Michel , Burdziński Gotard , Schlichting Ilme 
Published: September 2024

AbstractOrange carotenoid protein (OCP) is a photoactive protein that mediates photoprotection in cyanobacteria. OCP binds different ketocarotenoid chromophores such as echinenone (ECN), 3’- hydroxyechinenone (hECN) and canthaxanthin (CAN). In the dark, OCP is in an inactive orange form known as OCPO; upon illumination, a red active state is formed, referred to as OCPR, that can interact with the phycobilisome. Large gaps still exist in the mechanistic understanding of the events between photon absorption and formation of the OCPRstate. Recent studies suggested that more than one photon may be absorbed during the photocycle. Using a two-pulse excitation setup with variable time delays we demonstrate that canthaxanthin-functionalized OCPOforms the OCPRsignature after absorption of a single photon. By contrast, OCPOcomplexed with hECN or ECN does not photoconvert to OCPRupon single photon absorption. Instead, OCPRis formed only upon absorption of a second photon, arriving roughly one second after the first one, implying the existence of a metastable light-sensitive OCP1hvintermediate. To the best of our knowledge, a sequential 2-photon absorption mechanism in a single biological photoreceptor chromophore is unique. It results in a non-linear response function with respect to light intensity, effectively generating a threshold switch. In the case of OCP, this prevents down regulation of photosynthesis at low light irradiance.
Outbreak of Western equine encephalitis virus infection associated with neurological disease in horses following a nearly 40-year intermission period in Argentina
Authors: Vissani Maria Aldana , Alamos Florencia , Tordoya Maria Silvia , Minatel Leonardo , Schammas Juan Manuel , Dus Santos María José , Trono Karina , Barrandeguy Maria E. , Balasuriya Udeni B.R. , Carossino Mariano 
Published: September 2024

ABSTRACTWestern equine encephalitis virus (WEEV) is a mosquito-borne arbovirus (genusAlphavirus, familyTogaviridae) that has reemerged in South America in late 2023 causing severe disease in both horses and humans after a nearly 40-year intermission period. We describe the virological, serological, pathological and molecular features of WEEV infection in horses during the 2023- 2024 outbreak in Argentina. WEEV-infected horses developed neurological signs with mild to severe encephalitis associated with minimal to abundant WEEV-infected cells as demonstrated by WEEV-specificin situhybridization. The distribution of viral RNA was multifocal with predominance within neuronal bodies, neuronal processes, and glial cells in the medulla oblongata and thalamic regions. Phylogenetic analysis of partial nsP4 sequences from three viral isolates obtained from three different provinces of Argentina support grouping with other temporally current WEEV strains from Uruguay and Brazil under a recently proposed novel lineage.
Catalytic relevance of quinol anion in biological energy conversion by respiratory complex I
Authors: Zdorevskyi Oleksii , Laukkanen Johannes , Sharma Vivek 
Published: September 2024

AbstractRedox chemistry of quinones is an essential component of life on earth. In the mitochondrial electron transport chain, ubiquinone molecule is reduced to ubiquinol by respiratory complex I to drive the synthesis of ATP. By performing both classical and hybrid QM/MM simulations on high-resolution cryo-EM structures, including quantitative free energy calculations, we show that semiquinone species in complex I is anionic in nature and is trapped in the active site chamber for its subsequent reduction. Two-electron reduction of ubiquinone yields a metastable ubiquinol anion, which is electrostatically pushed by 15-20 Å towards the exit of the ubiquinone binding chamber to drive the proton pump of complex I. As part of the two-electron reduction of ubiquinone, protonic rearrangements take place in the active site in which a highly conserved histidine converts from its one tautomeric state to another. The combined findings provide a detailed and testable mechanistic picture of proton-coupled electron transfer reaction at the active site of complex I in wild-type as well as mutant conditions.
Improved classification of alcohol intake groups in the Intermittent-Access Two-Bottle choice rat model using a latent class linear mixed model
Authors: Angeles-Valdez Diego , López-Castro Alejandra , Rasgado-Toledo Jalil , Naranjo-Albarrán Lizbeth , Garza-Villarreal Eduardo A. 
Published: September 2024

AbstractAlcohol use disorder (AUD) is a major public health problem in which preclinical models allow the study of AUD development, comorbidities and possible new treatments. The intermittent access two-bottle choice (IA2BC) model is a validated preclinical model for studying alcohol intake patterns similar to those present in AUD in human clinical studies. Typically, the mean/median of overall alcohol intake or the last drinking sessions is used as a threshold to divide groups of animals into high or low alcohol consumers. However, it would be more statistically valuable to stratify the groups using the full consumption data from all drinking sessions. In this study, we aimed to evaluate the effectiveness of using the time series data of all drinking sessions to stratify the population into high or low alcohol consumption groups, using a latent class linear mixed model (LCLMM). We compared LCLMM to traditional classification methods: percentiles, k-means clustering, and hierarchical clustering, and used simulations to compare accuracy between methods. Our results demonstrated that LCLMM outperforms other approaches, achieving superior accuracy (0.94) in identifying consumption patterns. By considering the entire trajectory of alcohol intake, LCLMM provides a more robust and nuanced characterization of high and low alcohol consumers. We advocate for the adoption of longitudinal statistical models in substance use disorder research, both in human studies and preclinical investigations, as they hold promise for enhancing population stratification and refining treatment strategies.
Structural proteomics defines a sequential priming mechanism for the progesterone receptor
Authors: Mann Matthew D. , Wang Min , Ferreon Josephine C. , Suess Michael P. , Jain Antrix , Malovannaya Anna , Alvarez Roberto Vera , Pascal Bruce D. , Kumar Raj , Edwards Dean P. , Griffin Patrick R. 
Published: September 2024

AbstractThe progesterone receptor (PR) is a steroid-responsive nuclear receptor with two isoforms: PR-A and PR-B. Disruption of PR-A:PR-B signaling is associated with breast cancer through interactions with oncogenic co-regulatory proteins (CoRs). However, molecular details of isoform-specific PR-CoR interactions remain poorly understood. Using structural mass spectrometry, we investigate the sequential binding mechanism of purified full-length PR and intact CoRs, steroid receptor coactivator 3 (SRC3) and p300, as complexes on target DNA. Our findings reveal selective CoR NR-box binding by PR and unique interaction surfaces between PR and CoRs during complex assembly, providing a structural basis for CoR sequential binding on PR. Antagonist-bound PR showed persistent CoR interactions, challenging the classical model of nuclear receptor activation and repression. Collectively, we offer a peptide-level perspective on the organization of the PR transcriptional complex and infer the mechanisms behind the interactions of these proteins, both in active and inactive conformations.
Target protein identification in live cells and organisms with a non-diffusive proximity tagging system
Authors: Sun Yingjie , Li Changheng , Deng Xiaofei , Li Wenjie , Deng Xiaoyi , Ge Weiqi , Shi Miaoyuan , Guo Ying , Yu Yanxun V , Zhou Hai-Bing , Jin Youngnam N 
Published: September 2024

AbstractIdentifying target proteins for bioactive molecules is essential for understanding their mechanisms, developing improved derivatives, and minimizing off-target effects. Despite advances in target identification (target-ID) technologies, significant challenges remain, impeding drug development. Most target-ID methods use cell lysates, but maintaining an intact cellular context is vital for capturing specific drug-protein interactions, such as those with transient protein complexes and membrane-associated proteins. To address these limitations, we developed POST-IT (Pup-On-target for Small molecule Target Identification Technology), a non-diffusive proximity tagging system for live cells, orthogonal to the eukaryotic system. POST-IT utilizes an engineered fusion of proteasomal accessory factor A (PafA) and HaloTag to transfer Pup to proximal proteins upon directly binding to the small molecule. After significant optimization to eliminate self-pupylation and polypupylation, minimize depupylation, and optimize chemical linkers, POST-IT successfully identified known targets and discovered a new binder, SEPHS2, for dasatinib, and VPS37C as a new target for hydroxychloroquine, enhancing our understanding these drugs’ mechanisms of action. Furthermore, we demonstrated the application of POST-IT in live zebrafish embryos, highlighting its potential for broad biological research and drug development.
Soil bacteria may be the natural reservoirs of drug resistance genes
Authors: Ahmad Salman , Awan Asad Bashir , Irfan Sofia , Haque Abdul 
Published: September 2024

AbstractSoil bacteria are the main source of antibiotics because they produce them naturally to get territorial advantage. We collected deep soil samples and characterized cultivable microbes. We used morphological and cultural characters, biochemical reactions, 16s RNA PCR and DNA sequencing to identify the isolates. The isolates includedPseudomonasspp (12),Shigellaspp (2),E. coli(1),Klebsiella/Citrobacterspp (1),Micrococcus spp(2), unidentifiedBacillusspp.(18),Bacillus paramycoides(3),Paenibacillus lautus(2),Bacillus pacificus(2), andLysinibacillus pakistanensis(1). Out of these 44 isolates, 33 (75%) were multi-drug resistant. Clinically relevant and clinically irrelevant bacteria had similar drug resistance patterns (88.9% and 88.0%, 88.9% and 88.0%, 100 and 96.0%, 61.1% and 92%, 83.3% and 96%, 33.3% and 36%, 55.6% and 68.0%, and 83.3% and 60%) towards Ampicillin, Amoxicillin, Oxacillin, Azithromycin, Streptomycin, Gentamicin, Ceftriaxone and Sulfamethoxazole respectively. The observation that bacteria which cannot colonize humans/animals and therefore cannot enter the horizontal drug resistance gene transfer cycle in clinical settings also have a large and similar arsenal of drug resistance genes, may indicate that they are actually the natural reservoirs. Because they are more dynamic in their ability to survive in different conditions, they provide better fitness for maintenance of these reservoirs.Impact StatementWe think this study has raised interesting questions and further probing at a larger scale and a greater depth will provide new insight that may be very helpful for understanding the phenomenon of spread of drug resistance among bacteria which is one of the paramount challenges for humanity.
Modular photostable fluorescent DNA blocks dissect the effects of pathogenic mutant kinesin on collective transport
Authors: Kita Tomoki , Sugie Ryota , Suzuki Yuki , Niwa Shinsuke 
Published: September 2024

SUMMARYIntracellular transport is driven by teams of various motor proteins. Advances in DNA nanotechnology have enabled the programmable linkage of different types of motor proteins. In this study, we developed a modular, photostable, fluorescence-labeled tiny DNA origami block (FTOB) for extended observation of collective transport by selected motor combinations. The FTOB is designed as a 4-helix bundle (∼8.4 nm) with densely accumulated fluorescent dyes, minimizing blinking and photobleaching. By designing a pair of connector DNAs, FTOBs are heterodimerized following motor protein attachment using the ALFA-tag/nanobody system. Our system examined the impact of a pathogenic mutant kinesin on its collective movement with wild-type kinesin, clearly observing two distinct behaviors: the team’s velocity was generally governed by the slower mutant but occasionally surged to levels comparable to that of a single wild-type motor. Our photostable, robust, modular FTOB system could serve as a versatile tool for precisely dissecting cooperative cargo transport.
Cell-mechanical parameter estimation from 1D cell trajectories using simulation-based inference
Authors: Heyn Johannes C. J. , Atienza Juanatey Miguel , Falcke Martin , Rädler Joachim O. 
Published: September 2024

AbstractTrajectories of motile cells represent a rich source of data that provide insights into the mechanisms of cell migration via mathematical modeling and statistical analysis. However, mechanistic models require cell type dependent parameter estimation, which in case of computational simulation is technically challenging due to the nonlinear and inherently stochastic nature of the models. Here, we employ simulation-based inference (SBI) to estimate cell specific model parameters from cell trajectories based on Bayesian inference. Using automated time-lapse image acquisition and image recognition large sets of 1D single cell trajectories are recorded from cells migrating on microfabricated lanes. A deep neural density estimator is trained via simulated trajectories generated from a previously published mechanical model of cell migration. The trained neural network in turn is used to infer the probability distribution of a limited number of model parameters that correspond to the experimental trajectories. Our results demonstrate the efficacy of SBI in discerning properties specific to non-cancerous breast epithelial cell line MCF-10A and cancerous breast epithelial cell line MDA-MB-231. Moreover, SBI is capable of unveiling the impact of inhibitors Latrunculin A and Y-27632 on the relevant elements in the model without prior knowledge of the effect of inhibitors. The proposed approach of SBI based data analysis combined with a standardized migration platform opens new avenues for the installation of cell motility libraries, including cytoskeleton drug efficacies,and may play a role in the evaluation of refined models.Subject AreasBiological Physics / Interdisciplinary Physics
Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos
Authors: Jaffe Alexander L. , Harrison Kaitlin , Jain Navami , Taylor-Kearney Leah J. , Wang Renée Z. , Prywes Noam , Shih Patrick M. , Young Jodi , Rocap Gabrielle , Dekas Anne E. 
Published: September 2024

AbstractCyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon to biomass. To date, all studied Cyanobacterial lineages encode carbon fixation machinery hinged upon form I rubisco enzymes within a CO2-concentrating carboxysome. Here, we report that the AMZ IB lineage ofProchlorococcusfrom global oxygen deficient zones (ODZs) harbor both form I and form II rubisco enzymes, the latter of which are typically non-carboxysomal and possess biochemical properties tuned towards low oxygen environments. Our analyses reveal that these cyanobacterial form II enzymes are functionalin vitroand were likely acquired via lateral gene transfer from proteobacteria. Global metagenomic read recruitment demonstrates thatProchlorococcuswith form II rubisco are essentially restricted to ODZs in the Eastern Tropical Pacific, suggesting that acquisition may confer an advantage specifically under low-O2conditions. Populations of AMZ IBProchlorococcusexpress both forms of rubiscoin situ, with the highest form II rubisco expression at depths where both oxygen and light are particularly low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for the overall capacity of ODZs to sequester carbon.
3D modeling of thermostable xylanase from Thermotoga naphthophila a member of GH10 family: characterization studies of recombinant xylanase
Authors: Waris Asma , Awan Ali Raza , Wasim Muhammad , Hashmi Abu Seed , Rashid Naeem , Firyal Sehrish , khalid Aisha , Tayyab Muhammad 
Published: September 2024

AbstractThe current study was planned keeping in view the significance, industrial impact and import of xylanase to Pakistan. In this study, a thermostable recombinant xylanase fromThermotoga naphthophilawas produced and characterized. The PCR product (1.1 kb) was purified, ligated in the pTZ57R/T and was used for transformation of DH5α cells. The presence of the gene in the recombinant pTZ57R/T was confirmed by restriction analysis. The gene was sub-cloned in pET21a and expression was examined using BL21 CodonPlus (DE3) cells. The recombinant xylanase was expressed as an intracellular soluble protein. SDS-PAGE demonstrated the purified recombinant xylanase as 37 kDa protein. Xylanase showed its optimal activity at 90°C and pH 7. The enzyme was found thermostable and retained 67% activity after an incubation of 1.5h at 90°C in the presence of Mn2+. The xylanase activity was enhanced in the presence of Triton X-I00 while the presence of SDS, Tween 20 and Tween 80 showed a declined impact on the activity. Kinetics studies showed the VmaxandKmvalues of 2313 μmol/mg/min and 3.3 mg/ml respectively. The 3D structure analysis demonstrated the presence of a conserved active site comprised of two glutamate and substrate accommodate sites comprised of + 1, +2 and -1, -2 xylose binding sites in the structure of xylanase. The ability of this thermostable xylanase to work at a wide range of temperatures and pH makes it a suitable candidate for industrial applications.
Forecasting COVID-19, Influenza and RSV hospitalisations over winter 2023/24 in England
Authors: Mellor Jonathon , Tang Maria L. , Jones Owen ,   Infectious Disease Modelling Team, Ward Thomas , Riley Steven , Deeny Sarah R. 
Published: September 2024

AbstractSeasonal respiratory viruses cause substantial pressure on healthcare systems, particularly over winter. System managers can mitigate the impact on patient care when they anticipate hospital admissions due to these viruses. Hospitalisation forecasts were used widely during the SARS-CoV-2 pandemic. Now, resurgent seasonal respiratory pathogens add complexity to system planning. We describe how a suite of forecasts for respiratory pathogens, embedded in national and regional decision-making structures, were used to mitigate the impact on hospital systems and patient care.We developed forecasting models predicting hospital admissions and bed occupancy two weeks ahead for COVID-19, influenza, and RSV in England over winter 2023/24. Bed occupancy forecasts were informed by the ensemble admissions models. Forecasts were delivered in real-time at multiple scales. The use of sample-based forecasting allowed for effective reconciliation and trend interpretation.Admission forecasts, particularly RSV and influenza, showed high skill at regional levels. Bed occupancy forecasts had well-calibrated coverage, owing to informative admissions forecasts and slower moving trends. National admissions forecasts had mean absolute percentage errors of 27.3%, 30.9% and 15.7% for COVID-19, influenza, and RSV respectively, with corresponding 90% coverages of 0.439, 0.807 and 0.779.These real-time winter infectious disease forecasts produced by the UK Health Security Agency for healthcare system managers played an informative role in mitigating seasonal pressures. The models were delivered regularly and shared widely across the system to key users. This was achieved by producing reliable, fast, and epidemiologically informed ensembles of models. Though, a higher diversity of model approaches could have improved forecast accuracy.