Structural Differences Research Articles

A chromosome-level genome of mango exclusively from long-read sequence data.

Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.

Phylogenetic position and genetic features of HIV-1 in CNS

Background. Due to the wide coverage with antiretroviral therapy, the life expectancy of HIV infected people has significantly increased. Against the background of a decrease in mortality from HIV infection, HIV-associated neurocognitive disorders, which develop even during effective treatment, are of high importance. The overall prevalence of this pathology among HIV-infected people reaches 42.6%.
 The objective of the study was to research the genetic features and phylogenetic position of HIV-1 persisting in the central nervous system.
 Materials and methods. The clinical study group consisted of 38 patients with severe neurocognitive disorders against the background of HIV infection in stage 4B. The viral load of HIV-1 in blood plasma and cerebrospinal fluid (CSF) was measured using the "AmpliSens HIV Monitor-FRT" reagents kit. Sanger sequencing was performed using the AmpliSens HIV-Resist-Seq assay kit on an Applied Biosystems 3500 analyzer. Phylogenetic analysis of the pol gene fragments of HIV-1 strains (the site encoding the viral protease and part of the reverse transcriptase) was carried out using maximum likelihood method with the GTR+G nucleotide substitution model. Comparisons of the tertiary structure of viral proteins were performed according to three-dimensional models of the protease and p51 and p66 reverse transcriptase subunits obtained by homologous reconstruction using the SWISS-MODEL tools.
 Results. The viral load in the sample of patients with severe CNS lesions in blood plasma was 6.27 times higher than in CSF and amounted to 4.67 and 3.87 lg copies/ml respectively by median (p = 0,004).
 Phylogenetic analysis with the use of all available HIV-1 genomes from GenBank, which differed from the studied ones by less than 5% showed close genetic relations of viruses circulating in Chelyabinsk region, apart from strains circulating in Russian Federation, with viruses circulating in neighboring countries, in most abundance — from Ukraine and Kyrgyzstan, slightly less — from Belarus, Tajikistan, Kazakhstan and Armenia and also with strains from certain foreign countries: Poland and Germany. Phylogenetic analysis of 38 HIV-1 genomes revealed significant genetic distances between HIV isolates from blood plasma and CSF in 5 patients, 4 of whom were PWID, which may indicate an event of superinfection.
 The amount of independent amino acid substitutions in protease in isolates from blood plasma ranged from 1 to 3, in isolates from CSF — from 1 to 2. An amount of such substitutions in a fragment of reverse transcriptase in isolates from blood plasma ranged from 1 to 6, while in isolates from CSF, it ranged from 1 to 7. HIV isolates from blood plasma and CSF from 5 patients had differences in the tertiary structure of HIV-1 reverse transcriptase p51 subunit in amino acid positions 16–20 and 210–235. Isolates from 3 other patients differed in the tertiary structure only in amino acid positons 210–235. Isolates from 3 patients differed in the structure of HIV-1 RT p66 subunit in a non-nucleoside reverse transcriptase inhibitor binding pocket (NNRTI) region. Fixed differences in the tertiary structure of p51 subunit required at minimum only 1 amino acid substitution to emerge. Alterations in the tertiary structure of p66 subunit required at least 3 amino acid substitutions.
 Conclusion. Microevolution of HIV-1 proceeds in parallel within the same patient, in different compartments, which is reflected in the accumulation of amino acid substitutions different from another compartment in the conserved pol gene. There is a weak correlation between the viral load level in plasma and in CSF. The genetic heterogeneity of HIV strains from patients of the Chelyabinsk region indicates a high frequency of reintroduction of HIV infection in the region from other countries. Differences in the tertiary structure of HIV-1 reverse transcriptase between blood plasma and CSF isolates are regularly fixed in certain domens, which also confirms the presence of parallel HIV microevolution during virus persistence in tissues separated by the blood-brain barrier which allows a better understanding of the fixation trends of individual amino acid substitutions during HIV-induced damage to central nervous system.

Evolution and Influencing Factors of Spatial Correlation Network of Construction Carbon Emission in China from the Perspective of Whole Life Cycle

Based on the whole life cycle perspective, the carbon emissions of the provincial construction industry in China from 2011 to 2019 were calculated from the production, construction, operation, and demolition stages of building materials. A spatial correlation network matrix of the carbon emissions in the construction industry was constructed by using the modified gravity model, and the structural characteristics of the correlation network were described by introducing social network analysis. Through the quadratic assignment program, the spatial correlation matrix of carbon emissions in the construction industry and its influencing factors were regressed and analyzed. The conclusions were as follows:① the spatial correlation network of carbon emissions in China's construction industry clearly existed. The network density and network correlation numbers were gradually rising, and the network tightness and stability were gradually improving. ② Shanghai, Tianjin, Beijing, and Jiangsu had a higher degree centrality and closeness centrality, which are the core and dominant positions of the spatial correlation network of carbon emissions in the construction industry. Zhejiang replaced Shanghai in the top four from 2013 to 2018, and the betweenness centrality of each province had unbalanced characteristics. ③ Beijing, Tianjin, Jiangsu, Inner Mongolia, Shanghai, and Shandong were "net beneficiaries" blocks, receiving the carbon emissions from other regions. Four provinces, Guangdong, Chongqing, Fujian, and Shandong, belonged to the "broker" sector, achieving a dynamic balance between the production and consumption sides of building carbon emissions. The remaining 20 provinces played a "net spillovers" role, actively sending carbon emissions from the construction industry to other provinces. The correlation between blocks was much greater than the correlation relationship within the blocks. ④ Industrial structure, urban population, spatial adjacency, consumption level, and construction industry process structure had a significant influence on the spatial correlation of carbon emissions in the construction industry. The greater the inter-provincial differences in industrial structure, urban population, spatial adjacency, and consumption level, the greater the similarity of inter-provincial construction industry process structure, and the stronger the spatial correlation and spatial spillover of the construction industry carbon emissions. Finally, according to the evolution characteristics and influencing factors of the spatial correlation network of building carbon emissions, relevant countermeasures and suggestions were provided for the collaborative carbon reduction development of the construction industry region.

Leveraging Crystallization Pathway to Control Structure in Hf0.5Zr0.5O2 Nanoparticles

Hf0.5Zr0.5O2‐based materials have garnered significant attention for applications requiring ferroelectricity at the nanoscale. This behavior arises due to the stabilization of metastable phases at room temperature. However, the synthesis of phase pure Hf0.5Zr0.5O2 remains a challenging problem in both thin films and nanoparticles. Herein, the crystallization of Hf0.5Zr0.5O2 nanoparticles from an as‐synthesized amorphous phase is studied. By tailoring the aggregate nature of the intermediate amorphous nanoparticles via different drying processes, the crystallization pathway can be altered, resulting in significant differences in crystal structure, crystallite size, and crystallite morphology after calcination. X‐ray diffraction (XRD) and Rietveld refinement show the dominant crystallographic phase changes from a monoclinic structure to a cubic structure for samples with decreased aggregation. Samples prepared via freeze drying exhibit the most aggregation control and correspond with the observation of single‐crystalline particle aggregates and branching structures attributed to a crystallization by particle attachment mechanism. Herein, differing crystallization pathways lead to unique crystal morphologies that stabilize the traditionally high‐temperature phases of Hf0.5Zr0.5O2‐based materials that are necessary for functional applications.

High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9.

The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.

Evolution game model and simulation of enterprise R&D cooperative innovation network under network externalities

ABSTRACT Multi-agent cooperation, pooling innovative resources, helps to develop key technologies and major projects in enterprises. However, the multi-agent cooperation of enterprises makes the cooperative relationship unstable, and behaviours such as moral hazard, spillover of technology or information are more likely to occur, thereby increasing the risk of enterprises. In this research an enterprise R&D cooperative evolutionary game model is built to investigate the influence of Network externalities on enterprise R&D cooperation in innovation networks. Furthermore, the evolution of innovative network structure of game results is simulated by means of computer technology so that the effects of network externalities on corporation degree, agglomeration and network structure are analyzed. The results show that Network externalities led to a decrease of cooperated partners, a decline in cooperation degree and agglomeration of enterprises, and a shrinking enterprise R&D cooperation tendency. The influence of network externalities shows significant structural differences in the three types of enterprise networks: the degree of enterprise cooperation and agglomeration fluctuates greatly in the scale-free network, but slightly in the small-world network and the random network.

Similarity Network Analysis of the Adaptive Immune Response in the Proximal Airway.

Recent immunologic study of the adaptive immune repertoire in the subglottic airway demonstrated high-frequency T cell clones that do not overlap between individuals. However, the anatomic distribution and antigenic target of the T cell repertoire in the proximal airway mucosa remain unresolved. Single-cell RNA sequencing of matched scar and unaffected mucosa from idiopathic subglottic stenosis patients (iSGS, n = 32) was performed and compared with airway mucosa from healthy controls (n = 10). T cell receptor (TCR) sequences were interrogated via similarity network analysis to explore antigenic targets using the published algorithm: Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH2). The mucosal T cell repertoire in healthy control airways consisted of highly expressed T cell clones conserved across anatomic subsites (trachea, bronchi, bronchioles, and lung). In iSGS, high-frequency clones were equally represented in both scar and adjacent non-scar tissue. Significant differences in repertoire structure between iSGS scar and unaffected mucosa was observed, driven by unique low-frequency clones. GLIPH2 results suggest low-frequency clones share targets between multiple iSGS patients. Healthy airway mucosa has a highly conserved T cell repertoire across multiple anatomic subsites. Similarly, iSGS patients have highly expressed T cell clones present in both scar and unaffected mucosa. iSGS airway scar possesses an abundance of less highly expanded clones with predicted antigen targets shared between patients. Interrogation of these shared motifs suggests abundant adaptive immunity to viral targets in iSGS airway scar. These results provide insight into disease pathogenesis and illuminate new treatment strategies in iSGS. NA Laryngoscope, 134:3245-3252, 2024.

Functional Conservation of the Small GTPase Rho5/Rac1-A Tale of Yeast and Men.

Small GTPases are molecular switches that participate in many essential cellular processes. Amongst them, human Rac1 was first described for its role in regulating actin cytoskeleton dynamics and cell migration, with a close relation to carcinogenesis. More recently, the role of Rac1 in regulating the production of reactive oxygen species (ROS), both as a subunit of NADPH oxidase complexes and through its association with mitochondrial functions, has drawn attention. Malfunctions in this context affect cellular plasticity and apoptosis, related to neurodegenerative diseases and diabetes. Some of these features of Rac1 are conserved in its yeast homologue Rho5. Here, we review the structural and functional similarities and differences between these two evolutionary distant proteins and propose yeast as a useful model and a device for high-throughput screens for specific drugs.

The effects of habitat and climate on tick abundance and diversity on a game reserve in the Limpopo Province, South Africa

ABSTRACT The livelihoods of local farmers and game ranchers in Africa – and the communities these businesses support – are threatened by tick-borne diseases that kill and weaken livestock. Understanding the local ecology of ticks may inform cost-effective and sustainable techniques for controlling tick populations. Our objective was to describe differences in tick abundance, species richness, and community structure in three different habitats from June-July 2022 on a game reserve in the Limpopo Province of South Africa. Ticks were sampled using the drag method, in 54 30 m × 5 m transects evenly distributed across bushveld, long grass, and short grass habitats. Total tick abundance and species richness were significantly greater in long grass than in bushveld and short grass. Although there were no significant differences among the habitats in Simpson’s diversity, the composition of the communities did vary significantly, with the relative abundances of Rhipicephalus appendiculatus and R. evertsi evertsi peaking in long grass, Amblyomma hebraeum peaking in bushveld, and R. decoloratus peaking in short grass. Differences in habitat suitability for ticks and habitat use by ungulate hosts may explain the significant effect of habitat on tick abundance, species richness, and community structure.

Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice.

Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism.

Unraveling Convolution Neural Networks: A Topological Exploration of Kernel Evolution

Convolutional Neural Networks (CNNs) have become essential in deep learning applications, especially in computer vision, yet their complex internal mechanisms pose significant challenges to interpretability, crucial for ethical applications. Addressing this, our paper explores CNNs by examining their topological changes throughout the learning process, specifically employing persistent homology, a core method within Topological Data Analysis (TDA), to observe the dynamic evolution of their structure. This approach allows us to identify consistent patterns in the topological features of CNN kernels, particularly through shifts in Betti curves, which is a key concept in TDA. Our analysis of these Betti curves, initially focusing on the zeroth and first Betti numbers (respectively referred to as Betti-0 and Betti-1, which denote the number of connected components and loops), reveals insights into the learning dynamics of CNNs and potentially indicates the effectiveness of the learning process. We also discover notable differences in topological structures when CNNs are trained on grayscale versus color datasets, indicating the need for more extensive parameter space adjustments in color image processing. This study not only enhances the understanding of the intricate workings of CNNs but also contributes to bridging the gap between their complex operations and practical, interpretable applications.

Direct and Indirect Factors Affecting the Forced Swim Test to Investigate the Level of Depression in Rodents

Context: The forced swim test (FST) is employed to examine depression and depressive-like behaviors in rodents, such as mice and rats. In this test, increased periods of immobility and decreased swimming by the animal indicate heightened despair and depression-like behaviors. Evidence Acquisition: This review discusses the impacts of the animals' race, gender, age, and weight and environmental factors like light, noise, and smell on the FST. Results: Our review reveals that racial differences in rats and mice can influence their behavior. Differences in the nervous system structure and sex hormones related to gender are also significant. Additionally, animals that are very young or old, and those that are either very overweight or underweight, are unsuitable for the FST. Environmental factors such as light, noise, and smell were identified as confounding factors that could influence the outcomes and compromise the study's reliability. Conclusions: It is essential to consider these factors and enhance the conditions and environment to carry out a standardized test. Furthermore, by acquiring more detailed information about these factors and minimizing or eliminating their effects, studies can yield more reliable results.

Long‐term differences in population structure, body size and distribution patterns of amphipods and isopods in wetlands with declining hydroperiods

Abstract In many regions, climatic drying is shortening hydroperiods and freshwater biodiversity is declining. Aquatic species that lack a desiccation‐resistant life stage are predicted to have the least ability to persist in drying climates, yet such species may occur in intermittent waterbodies. We examined the distribution of two crustacean species that lack desiccation‐resistant life stages: the isopod Paramphisopus palustris and amphipod Chiltoniidae sp.nov., before and after the commencement of severe climatic drying in Swan Coastal Plain wetlands, south‐western Australia. Historical distribution data for these species were obtained from studies of the same set of wetlands in 1989–1990. We determined whether population or body size differed between hydrological regimes (perennial, semi‐perennial, seasonal) between 1989–1990 and 2018–2019 for both species. Amphipods, isopods and environmental variables were sampled from 42 wetlands in 2018–2019. Thirty‐three wetlands (22 perennial, 11 seasonal) persisted with the same hydrological regime in both time periods and eight wetlands that were perennial in 1989–1990 had shifted to a drier hydrological regime (four became semi‐perennial, four became seasonal) by 2018–2019. Drying wetland hydrological regimes did not correspond to more limited spatial distributions for either species. Hydrological regime had no effect on amphipod counts, although abundances were lower in 2018–2019 than 1989–1990. In 2018–2019, male amphipods were larger than females in seasonal wetlands, but sexes were the same size in perennial wetlands and females were larger than males in semi‐perennial wetlands. Furthermore, amphipods of both sexes were considerably smaller in semi‐perennial than seasonal or perennial wetlands. Isopod distributions differed between the two sampling periods, with populations primarily lost from wetlands that remained perennial. This unexpected result was likely caused by prolonged periods of high summer–autumn water temperatures and stratification in shallow perennial wetlands that caused anoxia in bottom waters and made surface waters excessively hot for isopods. By contrast, drying seasonal wetlands seemingly offered suitable habitat in summer–autumn. Mean isopod head and body length did not differ between hydrological regimes or sexes, but became smaller between 1989–1990 and 2018–2019 (15 mm average body length in 1989 vs. 8.3 mm in 2018–2019; 17 mm maximum size in 1989–1990 vs. 13.2 mm in 2018–2019). The absence of population losses associated with drying hydrological regimes indicates that the current level of drying is within the tolerance range of both species. However, increased temperatures may be causing body size (and possibly fecundity) to decline for isopods. As global warming continues to shorten wetland hydroperiods in many regions, numerous species will struggle to complete their life cycles, leading to extirpation. Our findings suggest that climate change may also cause conditions in perennial wetlands to exceed the tolerances of species that lack desiccation resistance traits. This emphasises the need to better understand both environmental and habitat changes along the drying trajectory in wetlands and the fundamental life‐history and physiological traits that enable the survival of aquatic invertebrates that lack desiccation resistance. This includes not only species responses to drying, but also responses to other stressors (e.g., prolonged stratification) caused by global warming.

Molecule aging induced by electron attacking

Here we propose a new concept of “molecule aging”: with some special treatment, a molecule could be “aged” by losing some unknown tiny particles or pieces from atoms in the molecule. Such “aging” or loss of unknown tiny particles does not change apparently its molecular structure or chemical composition, but some physicochemical properties could be changed irreversibly. We further confirm such “molecule aging” via a long-term electron attacking to age water (H2O) molecules. The IR spectra show no structural difference between the fresh water and the aged one, while the NMR spectra show that the electron attacking can decrease the size of water clusters. Such facts indicate that the electron attacking indeed can “affect” the structure of water molecule slightly but without damaging to its basic molecule frame. Further exploration reveals that the hydrogen evolution reaction (HER) activity of the aged water molecule is lower than the fresh water on the same Pt/C electrocatalyst. The density functional theory calculations indicate that the shortened O–H bond in H2O indeed can present lower HER activity, so the observed size decrease of water clusters from NMR probably could be attributed to the shortening of O–H bond in water molecules. Such results indicate significantly that the molecule aging can produce materials with new functions for new possible applications.

Let's not use it! A dynamic no-use zone between the home ranges of two spider monkey groups.

It is common that neighboring groups of the same species use some of the same areas, resulting in home-range overlap. Areas between the home ranges of neighboring groups not used by either group (no-use zone or NUZ) are rarely reported. Here, we report the existence of a NUZ between the home ranges of two Geoffroy's spider monkey groups, and examine its spatial changes over time and the ecological and behavioral underpinnings of such phenomenon. Although its size and location changed between 2017 and 2022, the NUZ was always present. We did not find any differences in the vegetation structure and composition between the NUZ and the ranging areas and in the monkeys' activity patterns between areas adjacent to the NUZ and the other parts of the ranging areas. The number of monkey vocalizations was lower and subgroup size was smaller (although the number of males did not differ) in areas adjacent to the NUZ than in the other parts of the ranging areas. Both changes possibly reflect the tendency to conceal their presence to the neighboring group. Our findings contribute to the understanding of primate space use and highlight the need to focus on the areas delimiting home ranges.

Exploring the Effects of Robertsonian Translocation 1/29 (Rob (1;29)) on Genetic Diversity in Minor Breeds of Spanish Berrenda Cattle via Genome-Wide Analysis.

Most of the previous studies on the genetic variability in Spanish "Berrenda" breeds have been carried out using DNA microsatellites. The present work aimed to estimate the genetic diversity, population structure, and potential genetic differences among individuals of both Berrenda breeds and groups based on the presence of the Robertsonian chromosomal translocation, rob (1;29). A total of 373 samples from animals belonging to the two breeds, including 169 cases diagnosed as rob (1;29)-positive, were genotyped using an SNP50K chip. The genetic diversity at the breed level did not show significant differences, but it was significantly lower in those subpopulations containing the rob (1;29). Runs of homozygosity identified a region of homozygosity on chromosome 6, where the KIT (KIT proto-oncogene, receptor tyrosine kinase) gene, which determines the typical spotted coat pattern in both breeds, is located. The four subpopulations considered showed minor genetic differences. The regions of the genome that most determined the differences between the breeds were observed on chromosomes 4, 6, 18, and 22. The presence of this Robertsonian translocation did not result in sub-structuring within each of the breeds considered. To improve the reproductive performance of Berrenda breeds, it would be necessary to implement strategies considering the involvement of potential breeding stock carrying rob (1;29).

Evaluating the photodynamic efficacy of nebulized curcumin-loaded liposomes prepared by thin-film hydration and dual centrifugation: In vitro and in ovo studies

Lung cancer, one of the most common causes of high mortality worldwide, still lacks appropriate and convenient treatment options. Photodynamic therapy (PDT) has shown promising results against cancer, especially in recent years. However, pulmonary drug delivery of the predominantly hydrophobic photosensitizers still represents a significant obstacle. Nebulizing DPPC/Cholesterol liposomes loaded with the photosensitizer curcumin via a vibrating mesh nebulizer might overcome current restrictions. In this study, the liposomes were prepared by conventional thin-film hydration and two other methods based on dual centrifugation. The liposomes' physicochemical properties were determined before and after nebulization, showing that liposomes do not undergo any changes. However, morphological characterization of the differently prepared liposomes revealed structural differences between the methods in terms of lamellarity. Internalization of curcumin in lung adenocarcinoma (A549) cells was visualized and quantified. The generation of reactive oxygen species because of the photoreaction was also proven. The photodynamic efficacy of the liposomal formulations was tested against A549 cells. They revealed different phototoxic responses at different radiant exposures. Furthermore, the photodynamic efficacy was investigated after nebulizing curcumin-loaded liposomes onto xenografted tumors on the CAM, followed by irradiation, and evaluated using positron emission tomography/computed tomography and histological analysis. A decrease in tumor metabolism could be observed. Based on the efficacy of curcumin-loaded liposomes in 2D and 3D models, liposomes, especially with prior film formation, can be considered a promising approach for PDT against lung cancer.

Preclinical characterisation of gallium-68 labeled ferrichrome siderophore stereoisomers for PET imaging applications

BackgroundSiderophores are small iron-binding molecules produced by microorganisms to facilitate iron acquisition from the environment. Radiolabelled siderophores offer a promising solution for infection imaging, as they can specifically target the pathophysiological mechanisms of pathogens. Gallium-68 can replace the iron in siderophores, enabling molecular imaging with positron emission tomography (PET). Stereospecific interactions play a crucial role in the recognition of receptors, transporters, and iron utilisation. Furthermore, these interactions have an impact on the host environment, affecting pharmacokinetics and biodistribution. This study examines the influence of siderophore stereoisomerism on imaging properties, with a focus on ferrirubin (FR) and ferrirhodin (FRH), two cis–trans isomeric siderophores of the ferrichrome type.ResultsTested siderophores were labelled with gallium-68 with high radiochemical purity. The resulting complexes differed in their in vitro characteristics. [68Ga]Ga-FRH showed less hydrophilic properties and higher protein binding values than [68Ga]Ga-FR. The stability studies confirmed the high radiochemical stability of both [68Ga]Ga-siderophores in all examined media. Both siderophores were found to be taken up by S. aureus, K. pneumoniae and P. aeruginosa with similar efficacy. The biodistribution tested in normal mice showed rapid renal clearance with low blood pool retention and fast clearance from examined organs for [68Ga]Ga-FR, whereas [68Ga]Ga-FRH showed moderate retention in blood, resulting in slower pharmacokinetics. PET/CT imaging of mice injected with [68Ga]Ga-FR and [68Ga]Ga-FRH confirmed findings from ex vivo biodistribution studies. In a mouse model of S. aureus myositis, both radiolabeled siderophores showed radiotracer accumulation at the site of infection.ConclusionsThe 68Ga-complexes of stereoisomers ferrirubin and ferrirhodin revealed different pharmacokinetic profiles. In vitro uptake was not affected by isomerism. Both compounds had uptake with the same bacterial culture with similar efficacy. PET/CT imaging showed that the [68Ga]Ga-complexes accumulate at the site of S. aureus infection, highlighting the potential of [68Ga]Ga-FR as a promising tool for infection imaging. In contrast, retention of the radioactivity in the blood was observed for [68Ga]Ga-FRH. In conclusion, the stereoisomerism of potential radiotracers should be considered, as even minor structural differences can influence their pharmacokinetics and, consequently, the results of PET imaging.

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity. We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules. Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.

Influence of temperature on ‘Rojo Brillante’ persimmon drying. Quality characteristics and drying kinetics

A physico-chemical characterization and drying kinetics study was performed for whole ‘Rojo Brillante’ persimmon subjected to hot-air drying at 35 ᵒC, 40 ᵒC and 45 ᵒC. Fruit was dried until a moisture content of 30 g water/100 g product, which is required to be considered dried persimmon. This moisture value was obtained after 12, 8 and 7 d when the drying process was applied at 35 ᵒC, 40 ᵒC and 45 ᵒC, respectively. All the drying treatments caused flesh structure changes, shrinkage and secondary epidermis formation. The final product's quality characteristics especially the texture, strongly depended on drying temperature. The fruit dried at 35 ᵒC exhibited a gelatinous internal texture and a thin secondary epidermis, similarly to that obtained during a natural drying process. The drying treatment at 40 ᵒC resulted in fruit having more rubbery flesh. However, the fruit dried at 45 ᵒC had a corky texture, with a very thick secondary epidermis that resulted in excessively tough fruit for commercialization purposes. The differences in flesh structure were revealed in the microstructural study by Cryo-FESEM. In all cases, soluble tannins content lowered to non-astringency values. Hot-air drying technology proved to be a good alternative to valorize discarded ‘Rojo Brillante’ persimmon.