bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient degradation of oxidized polyethylene containing ester bonds by cutinase or lipase in aqueous phase
Authors: Kong Demin , Wang Lei , Xia Wei , Shi Meng , Wu Jing 
Published: September 2024

AbstractPolyethylene is a widely used plastic that presents challenges in degrading within natural environments. Therefore, the degradation of polyethylene is of utmost importance. Currently, physical or chemical methods are efficient but more dangerous. Conversely, biological methods are safer but less efficient. Combining the two approaches to create entirely new polyethylene degradation pathways is a viable idea. Based on the previous research, it is an effective method to add ester bonds inside polyethylene and degrade using cutinase or lipase. However, the method only detected a decrease in molecular weight and did not observe a rate of weight loss at the macroscopic level. In this research, rapid degradation of polyethylene is achieved by optimizing catalysis conditions and machine learning. Finally, the maximum weight loss up to 80.51% within 24h and a mild catalysis environment (60-80°C). Furthermore, the method’s versatility was confirmed for cutinase and lipase. Overall, this research has established an effective, efficient, and mild degradation process of polyethylene, significantly contributing to the progress in polyethylene degradation.
Field-testedHaHB11andHaHB4soybean exhibit increased grain number and heat tolerance at the reproductive stage
Authors: Raineri Jesica , Montero Bulacio Enrique , Campi Mabel , Portapila Margarita , Otegui María Elena , Chan Raquel Lía 
Published: September 2024

AbstractSoybean is one of the primary sources of vegetable oil and protein worldwide. However, its yield improvement has lagged behind the other major crops. This study explored the potential of the sunflower transcription factor HaHB11 to enhance soybean yield and heat stress tolerance. We generated transgenic soybean plants expressing HaHB11 and evaluated their performance across four field trials. The HaHB11 plants showed a significant increase in grain number per plant compared to controls, which can be related to an increased number of nodes and pods per plant. Flowering dynamics analysis revealed delayed blooming and an increased number of flowers per node, leading to a higher pod set, particularly between nodes four and six. Principal component analysis across field trials identified temperature as a crucial factor influencing grain number, enhancing the differences exhibited by HaHB11 plants. The pollen from transgenic plants germinated better, and tubes were longer than controls under heat stress. Carbohydrate distribution analyses indicated differential allocation of nutrients, supporting the increased pod and grain set in HaHB11 plants. Additionally, vegetation indices can distinguish HaHB11 plants from controls in several developmental stages. These results indicated that HaHB11 enhances soybean yield under heat stress, becoming a promising technology for soybean improvement.HighlightSoybean transformed with the sunflower geneHaHB11was tested in the field for four campaigns, showing differential allocation of nutrients, increased number of nodes, pods, grains, and heat tolerance.
Burden of Latent Tuberculosis Infection among Healthcare Workers of Primary Health Centres and its Association with Clinical Laboratory Parameters
Authors: Selvavinayagam Sivaprakasam T. , Sankar Ganga , Yong Yean K. , Sankar Sathish , Zhang Ying , Tan Hong Y. , Balakrishnan Pachamuthu , Murugesan Amudhan , Rajeshkumar Manivannan , Frederick Asha , Kumar Masilamani Senthil , PriyaRaj Paulkanraj , Prabhakaran Jesudoss , Sangeetha Pattusamy , Arunpathy Pasupathy , Charu Rajamani , Muruganandam Nagarajan , Sakate Deepak M. , Jayakumar Deepak , Dhandapani Prabu , Rudrapathy Parthiban , Velu Vijayakumar , Emmenegger Marc , Larsson Marie , Shankar Esaki M. , Raju Sivadoss 
Published: September 2024

SummaryObjectivesHealthcare workers (HCWs) are at high risk of latent tuberculosis infection (LTBI) due to their continued occupational exposure. The incidence of LTBI among the HCWs has seldom been investigated. Primary health centres (PHCs) provide effective and affordable medical care largely for the local population. The HCWs of PHCs who are likely to have increased occupational exposure have an increased risk of reactive as well as LTBI, and contribute to overall TB transmission than the general population.MethodsA cross-sectional study (March–April 2024) was carried out to assess the burden of LTBI among the HCWs of PHCs (n=64) across Chennai, India. Blood samples were analyzed for gamma interferon using a QuantiFERON-TB Gold Plus assay. A complete baseline health profile, including complete blood count, blood glucose, liver and renal functions, and ferritin levels was estimated to identify potential biomarkers that are independently associated with LTBI.ResultsThe present study revealed an LTBI prevalence of 25.3% (n=99) among PHC workers. The red cell distribution width was significantly associated with LTBI positivity among different biochemical and haematological parameters analyzed. Factors such as individuals’ age, underlying comorbid conditions (30.3%; n=30), and longer employment duration (28%; n=28) were significantly associated with IGRA positivity. IGRA positivity was significantly associated with decreased RDW-SD in females, overweight, and participants with ‘O’ blood group.ConclusionsThe study reported a high prevalence of LTBI among HCWs of PHCs, which necessitates their periodical screening for the elimination of TB.
Structural Characterization of mRNA Lipid Nanoparticles in the Presence of Intrinsic Drug-free Lipid Nanoparticles
Authors: Chen Xiaoxia , Ye Yongfeng , Li Mengrong , Zuo Taisen , Xie Zhenhua , Ke Yubin , Cheng He , Hong Liang , Liu Zhuo 
Published: September 2024

AbstractLipid nanoparticles (LNPs) have emerged as a versatile platform for mRNA delivery across a range of applications, including disease prevention, cancer immunotherapy, and gene editing. Structural models of mRNA-containing lipid nanoparticles (mRNA-LNPs) have also been proposed based on characterization of samples by using various advanced techniques. Among these, small angle neutron scattering (SANS) has proven essential for elucidating the lipid distribution within mRNA-LNPs, a factor crucial to both their preparation and efficacy. However, recent findings suggest that the mRNA-LNP samples prepared via commercial microfluidic techniques may contain a substantial fraction of drug-free LNPs, casting doubt on the validity of earlier structural models. In this study, we employed contrast variation SANS to characterize both drug-free LNPs and our mRNA-LNP sample, and quantified the proportion of drug-free LNPs present to be ∼30% in our mRNA-LNP sample using nano flow cytometry. By removing the contributions of drug-free LNPs from the SANS data of our mRNA-LNP sample, we were able to precisely characterize the structure of mRNA-LNPs. Consequently, we proposed structural models for both drug-free LNPs and mRNA-LNPs. Notably, our analysis revealed similar lipid distributions and shell thicknesses between the two particle types, while the solvent content in mRNA-LNPs was significantly higher, leading to a larger core size. This work not only offers a method for accurately characterizing the structure of mRNA-LNPs, but also establishes criteria for selecting appropriate analytical techniques based on the structural parameters of interest. Therefore, our findings hold significant implications for the mechanistic understanding and quality control of mRNA-based vaccines.SignificancePrecise structural determination of mRNA-containing lipid nanoparticles (mRNA-LNPs) is vital for mechanistic insights into their preparation, delivery, immunogenicity, and storage, which are critical to the development of mRNA-based vaccines. However, most previous studies overlooked the substantial presence of drug-free LNPs within these samples. Here, we identified that approximately 30% of the nanoparticles in our mRNA-LNP sample were drug-free. By integrating contrast variation small angle neutron scattering (SANS) data from both drug-free LNPs and mRNA-LNPs, we developed structural models for both particle types, and provided a guidance for characterization technique selection based on concerned structural features. Beyond mechanistic insight on structure, our approach offers a robust method for quality assessment and process monitoring in mRNA-based vaccine production.
Measuring 3-dimensional dynamics of membrane in living cell with metal-induced energy transfer imaging/spectroscopy
Authors: Chen Tao , Gallea José Ignacio , Karedla Narain , Wang Dongxia , Enderlein Jörg 
Published: September 2024

AbstractThe dynamics of cellular membranes are crucial for many essential cellular processes. Despite various methods available to study membrane dynamics, simultaneously measuring membrane diffusion and fluctuations within living cell membranes remains challenging. In this study, we developed a method combining metal-induced energy transfer (MIET) with fluorescence correlation spectroscopy (FCS) to accurately measure the three-dimensional (3D) dynamics of membranes, including transverse diffusion and vertical fluctuations. Our approach achieves a spatiotemporal resolution of one nanometer and few microseconds. We demonstrate the efficacy of our technique through experiments on the diffusion and transversal undulations of model membranes. Additionally, we showcase the versatility of MIET-FCS by applying it to various membrane systems within living cells, such as the plasma membrane, endoplasmic reticulum, and nuclear envelope. Our findings provide a powerful tool for investigating complex membrane dynamics in diverse cellular environments, advancing the field of membrane biophysics.
Quantifying evolution of SNPs that affect RNA secondary structure inArabidopsis thalianagenes
Authors: Martin Galen T. , Fiscus Christopher J. , Gaut Brandon S. 
Published: September 2024

ABSTRACTSingle-stranded RNA molecules have the ability to form intramolecular bonds between nucleotides and create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural selection. Here we examined the population genetics of these mutations withinArabidopsis thalianagenes. We began by identifying derived SNPs with the potential to alter secondary structures within coding regions, using a combination of computational prediction and empirical data analysis. We then examined nucleotide diversity and allele frequencies of these “pair-changing mutations” (pcM) in 1,001A. thalianagenomes to infer selective pressures on these sites. The pcM SNPs at synonymous sites had an 8.8% reduction in nucleotide diversity relative to non-pcM SNPs at synonymous sites, and they were found at lower allele frequencies. We used demographic modeling to estimate selection coefficients from the pcM allele frequency spectrum, finding that pcMs had estimated selection coefficients ∼3 to 5x smaller than nonsynonymous mutations. Additionally, we explored associations of pcMs with bioclimatic variables and gene expression. They exist at higher frequencies in higher latitudes and colder environments, with mean annual temperature explaining 51% of the variation in pcM frequency among subpopulations. Alleles containing pcMs had an average reduction of 137.4 normalized counts compared to genes with the ancestral secondary structure (mean expression = 3215.7 normalized counts). Overall, we conclude that structure-altering mutations are subject to intermediate levels of selection.
Evolution of tRNA pool shapes variation in selection on codon usage across the Saccharomycotina subphylum
Authors: Cope Alexander L. , Shah Premal 
Published: September 2024

AbstractAcross the major taxonomical domains, synonymous codons of an amino acid are found to be used in unequal frequencies. This codon usage bias – both in terms of the degree of bias and the identity of codons used – is highly variable, even among closely related species. Within a species, genome-wide codon usage bias reflects a balance between adaptive and non-adaptive microevolutionary processes. Variation in these microevolutionary processes results in across-species variation in codon usage bias. As codon usage bias is tightly linked to important molecular and biophysical processes, it is critical to understand how changes to these processes drive changes to the microevolutionary processes. Here we employ a population genetics model of coding sequence evolution to quantify natural selection and mutation biases on a per-codon basis and estimate gene expression levels across the budding yeasts Saccharomycotina subphylum. We interrogate the impact of variation in molecular mechanisms hypothesized to be driving the microevolution of codon usage. We find that natural selection and mutation biases evolved rapidly over macroevolutionary time, with high variability between closely related species. The majority (324/327) of yeasts exhibited clear signals of translational selection, with selection coefficients being correlated with codon-specific estimates of ribosome waiting times within species. Across species, natural selection on codon usage correlated with changes to ribosome waiting times, indicating that tRNA pool evolution is a major factor driving changes to natural selection on codon usage. We find evidence that changes to tRNA modification expression can contribute to changes in natural selection across species independent of changes to tRNA gene copy number, suggesting tRNA modifications also play a role in shaping natural selection on codon usage. Our work firmly establishes how changes to microevolutionary processes can be driven by changes to molecular mechanisms, ultimately shaping the macroevolutionary variation of a trait.
Abnormal vasculature reduces overlap between drugs and oxygen in a tumour computational model: implications for therapeutic efficacy
Authors: Enjalbert Romain , Köry Jakub , Krüger Timm , Bernabeu Miguel O. 
Published: September 2024

AbstractThe tumour microvasculature is abnormal, and as a consequence oxygen and drug transport to the tumour tissue is impaired. The abnormal microvasculature contributes to tumour tissue hypoxia, as well as to varying drug penetration depth in the tumour. Many anti-cancer treatments require the presence of oxygen to be fully efficacious, however the question of how well oxygen concentration overlaps with drug concentration is not elucidated, which could compromise the therapeutic effect of these drugs. In this work we use a computational model of blood flow and oxygen transport, and develop a model for an oxygen-dependent drug, T-DM1, to study the overlap of oxygen and drug concentration in healthy and tumour tissue, where we assume the tumour tissue to compress blood vessels. Our results show that, due to the compressed vessels present in tumours, areas of sufficient oxygen concentration for a drug to function overlap poorly with areas of sufficient drug concentration, covering 28% of the tumour tissue, compared to 82% in healthy tissue. The reduction in drug and oxygen overlap is due to the altered red blood cell dynamics through the abnormal microvasculature, and indicates that drug transport to tumours should not be considered independently of oxygen transport in cases where the drug requires oxygen to function.
Inter-kingdom signaling by theLegionellaautoinducer LAI-1 involves the antimicrobial guanylate binding protein GBP
Authors: Solger Franziska , Rauch Jonas , Vormittag Simone , Fan Mingzhen , Raykov Lyudmil , Charki Paul , Soldati Thierry , Seibel Jürgen , Hilbi Hubert 
Published: September 2024

AbstractThe causative agent of Legionnaires’ disease,Legionella pneumophila, is an amoebae-resistant environmental bacterium, which replicates intracellularly in a distinct compartment, the “Legionella-containing vacuole” (LCV).L. pneumophilaemploys the α-hydroxyketone compound LAI-1 (Legionellaautoinducer-1) for intra-species and inter-kingdom signaling. LAI-1 promotes intracellular replication and inhibits the migration of mammalian cells andDictyostelium discoideum. In this study, we revealed that LAI-1 and “clickable” azido-LAI-1 derivatives inhibit the migration ofD. discoideumand localize to LCVs. Azido-LAI-1 colocalizes with the LCV markers calnexin, P4C, and AmtA, but not with mitochondrial or lipid droplet markers. Intriguingly, LAI-1 dependent inhibition ofD. discoideummigration involves the single guanylate-binding protein (GBP), a member of the GBP family of large GTPases, which in metazoan organisms promote cell autonomous immunity.D. discoideumlacking GBP (Δgnbp) allows more efficient intracellular replication ofL. pneumophila, without apparently compromising LCV remodeling or integrity, and GBP-GFP localizes to the ER at LCV-ER membrane contact sites (MCS). However, the peri-LCV localization of LAI-1 and GBP is not mutually dependent. Synthetic LAI-1 inhibits the expansion/remodeling of LCVs (but not vacuoles harboring avirulentL. pneumophila) in a GBP-dependent manner. Taken together, the work shows that LAI-1 localizes to LCVs, and LAI-1-dependent inter-kingdom signaling involvesD. discoideumGBP, which localizes to LCV-ER MCS and acts as an antimicrobial factor by restricting the intracellular growth ofL. pneumophila.Author SummarySmall molecule inter-kingdom signaling between pathogens and host cells represents a crucial but only partly understood aspect of microbial virulence. The amoeba-resistant opportunistic pathogenLegionella pneumophilaemploys the compound LAI-1 (Legionellaautoinducer-1) for intra-species and inter-kingdom signaling. In metazoan cells, the conserved and wide-spread family of guanylate-binding protein (GBP) large GTPases usually comprises several distinct paralogues, which are implicated in pathogen detection, inflammation, cell death pathways, and cell autonomous immunity. In the social amoebaDictyostelium discoideum, only a singleGBPgene of unknown function is present. Using approaches from organic chemistry, genetics, cell biology and infection biology, we reveal that GBP is involved in the inhibition ofD. discoideummigration and pathogen vacuole expansion/remodeling by LAI-1 as well as in intracellular growth ofL. pneumophila. This study provides a novel link between small molecule inter-kingdom signaling and GBP-dependent cell autonomous immunity.
Extracellular Ligand-Responsive Translational Regulation of Synthetic mRNAs using Engineered Receptors
Authors: Nakanishi Hideyuki , Itaka Keiji 
Published: September 2024

AbstractmRNA drugs can encode any protein and are regarded as a promising therapeutic modality. In this study, we developed a new mRNA system allowing extracellular ligand-responsive translational regulation. This system consists of three mRNAs, two of which encode components for detecting extracellular ligands, and the other encodes the protein of interest, with a binding motif on 5’UTR for translational regulation. In the presence of ligand biomolecules such as arginine vasopressin (AVP) and prostaglandin E2 (PGE2), the translation level of the protein of interest is upregulated or downregulated in a ligand biomolecule concentration-dependent manner. We showed upregulation of anti-inflammatory signaling in response to an inflammatory mediator, PGE2, demonstrating that this system allowed production of the therapeutic proteins according to the disease site environment. This system will pave the way for the next-generation mRNA drugs that self-adjust their protein production levels in response to fluctuating disease states.Graphical AbstractmRNAs encoding regulatory components (an engineered receptor and a translational regulator) and a target mRNA are co-transfected into mammalian cells. In the absence of the ligand, the target mRNA is translationally repressed by the translational regulator. The ligand induces engineered receptor-mediated degradation of the translational regulator protein, resulting in the translational activation of the target mRNA.
AAV9-mediated targeting of natural antisense transcript as a novel treatment for Dravet Syndrome
Authors: Diaz Juan Antinao , Chilcott Ellie , Almacellas Barbanoj Amanda , Keegan Anna , McTague Amy , Cross J Helen , Schorge Stephanie , Lignani Gabriele , Waddington Simon Nicholas , Karda Rajvinder 
Published: September 2024

AbstractDravet syndrome (DS) is a severe childhood onset developmental and epileptic encephalopathy which leads to life-long disability. Symptoms usually manifest in the first year of life and include prolonged severe seizures, developmental delay and severe intellectual disability. DS patients have an increased mortality rate, including sudden unexpected death in epilepsy (SUDEP). Approximately 90% of patients carry a heterozygous loss-of-function mutation in theSCN1Agene, which encodes a voltage-gated sodium ion channel, NaV1.1. The NaV1.1 channel is expressed in the brain and at a lower level, in the heart. Previous studies have identified a long non-coding RNA (lncRNA) which specifically downregulatesSCN1Agene expression. This natural antisense transcript (NAT) can be modulated by AntagoNATs, small synthetic oligonucleotides developed to inhibit NAT function. In a DS mouse model, AntagoNATs were shown to modulateScn1aexpression by targeting theScn1aNAT, improving seizure frequency after repeated administration. Here, we have developed novel AntagoNATs and incorporated these into a clinically relevant adeno-associated virus serotype 9 (AAV9) gene therapy vector, to test in a DS mouse model (Scn1a+/-) and provide a one-off treatment approach.Eighteen AntagoNATs were testedin vitro; from the best performing candidates, we selected two AntagoNAT sequences (K & H) forin vivotesting as they had the highest homology (90%) to humanSCN1ANAT. We administered both vectors to newbornScn1a+/-mice via intracerebroventricular (ICV) and intravenous (IV) injection to target the brain and heart. AAV9-AntagoNAT-H significantly increased survival, decreased febrile seizures and reduced spontaneous seizure frequency compared to the PBS control group. When administered at P14 by ICV and IV injection, AAV9-AntagoNAT-H increased survival. In this proof-of-concept study, we have demonstrated for the first time the delivery of AntagoNAT technology via an AAV9 vector and thus offering the possibility of a one-time treatment for DS patients.