Structural Variations Research Articles

Mechanisms conferring bacterial cell wall variability and adaptivity.

The bacterial cell wall, a sophisticated and dynamic structure predominantly composed of peptidoglycan (PG), plays a pivotal role in bacterial survival and adaptation. Bacteria actively modify their cell walls by editing PG components in response to environmental challenges. Diverse variations in peptide composition, cross-linking patterns, and glycan strand structures empower bacteria to resist antibiotics, evade host immune detection, and adapt to dynamic environments. This review comprehensively summarizes the most common modifications reported to date and their associated adaptive role and further highlights how regulation of PG synthesis and turnover provides resilience to cell lysis.

Tuning of the Electronic Structure and Reactivity of Metal Complexes with Redox‐Active Guanidine Ligands

Redox‐active ligands change more drastically the electronic structure of metal complexes than non‐redox‐active ligands, with consequences on the magnetic and optical properties as well as the (redox) reactivity. In this work, redox‐active guanidine ligands are integrated in cobalt and copper complexes. The variations in the electronic structures of cobalt complexes, in particular the relative energies of the states corresponding to high spin CoII or low‐spin CoIII, in dependence of the redox‐active o‐diguanidine ligand manifest itself in different magnetic properties. Moreover, the electron transfer rates for copper complexes with two redox‐active diguanidino‐benzene ligands (self‐exchange betweeen a monocationic CuI complex and the corresponding dicationic complex) were varied systematically over two orders of magnitude by choice of the redox‐active diguanidine ligand, realizing redox pairs with intermediate or record‐high rates.

In Vivo Raman Spectroscopy of Muscle Is Highly Sensitive for Detection of Healthy Muscle and Highly Specific for Detection of Disease.

Raman spectroscopy of muscle provides a molecular fingerprint to identify the disease. Previous work has demonstrated effectiveness in differentiating between two groups of equal sizes (e.g., healthy vs disease) but imbalanced multiclass scenarios are more common in medicine. We performed in vivo Raman spectroscopy in a total of 151 mice across four different histopathologies (healthy, acute myopathy, chronic myopathy, neurogenic), with variable numbers in each (class "imbalance"). Using hierarchical modeling and synthetic data generation, we demonstrate high sensitivity (94%) for detection of healthy muscle and high specificity (≥97%) for disease. Further, we demonstrate the potential for unique biomarker development by demonstrating variations in the protein structure across different pathologies. The findings demonstrate the potential of Raman spectroscopy to provide accurate disease identification and unique molecular insights.

Exploring the effective implementation of population-based SHM in existing buildings. Part I: Structural condition assessment

Despite major critical progress over the past few decades, condition-based decision-making concerning the immediate occupancy or efficient operation of an existing building continues to face unresolved issues. The key issue is to determine the structural condition and its residual capacity using data-driven-based methods without knowledge of its life cycle since design (ageing, extreme events, etc.). Environmental and operational variations, boundary conditions and a lack of damage-state building data lead to further uncertainties in the actual assessment of the structural capacity and affect the effectiveness of implementing structural health monitoring (SHM) solution. Recently, population-based SHM has been developed to address some of these issues to enable transfer from data collected from a group of nominally identical buildings, and to model missing data for the target building. This study presents the Build’Health™ framework for operational data-driven SHM, considering populations of buildings evaluated under operational conditions. Fifty-five period-height empirical models obtained from methods based on ambient vibrations recorded in nominally identical reinforced concrete buildings were first identified in the literature to define the building population models, along with design features (such as boundary conditions, geometry or material design). The shift in structural condition of the target building is inferred from the nominally identical building population, after adding empirical variability in the resonance period due to temperature, assumed herein to be the main environmental cause of structural variation. This work presents the framework implemented and its application to five target buildings under different monitoring and structural conditions. This manuscript is the first of a two-part article on population-based SHM relative to structural condition assessment (part I) and damage-feature classification (part II) presenting the Build’Health™ concept.

The formation and propagation of human Robertsonian chromosomes.

Robertsonian chromosomes are a type of variant chromosome found commonly in nature. Present in one in 800 humans, these chromosomes can underlie infertility, trisomies, and increased cancer incidence. Recognized cytogenetically for more than a century, their origins have remained mysterious. Recent advances in genomics allowed us to assemble three human Robertsonian chromosomes completely. We identify a common breakpoint and epigenetic changes in centromeres that provide insight into the formation and propagation of common Robertsonian translocations. Further investigation of the assembled genomes of chimpanzee and bonobo highlights the structural features of the human genome that uniquely enable the specific crossover event that creates these chromosomes. Resolving the structure and epigenetic features of human Robertsonian chromosomes at a molecular level paves the way to understanding how chromosomal structural variation occurs more generally, and how chromosomes evolve.

Photoresponse of Ti3C2Tx MXene promotes its adsorptive-reductive removal of Cr(VI) from water

MXenes, such as Ti3C2Tx, demonstrate tremendous potential as heavy metal adsorbents due to their abundant reaction sites, high hydrophilicity, controllable interlayer spacing, and inherent reduction ability. However, their structural dependent pollutant removal performances and the related mechanisms are far less studied. Therefore, the removing abilities of Cr(VI) from water on Ti3C2Tx MXenes with different structures (multilayer (ML-) and delaminated (DL-) Ti3C2Tx) synthesized via several etching techniques were evaluated. Focusing on the most effective ML- and DL-Ti3C2Tx obtained by acid/fluoride salt etching, the impacts of structural variations on the Cr(VI) removal performances were explored. Both ML- and DL-Ti3C2Tx demonstrate outstanding Cr(VI) adsorption and reduction capabilities, achieving equilibrium within 500 min with capacities of 92.7 and 205 mg/g, respectively. The differences in removal mechanisms stemed from the varying adsorption and reduction capacities of two MXenes. ML-Ti3C2Tx, with lower surface area and porosity, had low adsorption capacity but superior reduction ability, efficiently converting most Cr(VI) to Cr(III) (66.8%). Conversely, DL-Ti3C2Tx exhibited better removal efficiency but a lower capacity for reduction (45.7%). Notably, although the partial reduction of DL-Ti3C2Tx to TiO2 results in its limited chemical reduction capacity, Ti3C2Tx might serve as a co-catalyst for TiO2, boosting the photoresponsiveness of DL-Ti3C2Tx or TiO2 through Ti3C2Tx/TiO2 heterojunctions, thereby facilitating photocatalysis to realize the reduction of Cr(VI). Both Ti3C2Tx exhibited both excellent Cr(VI) removal capacity and detoxification capacity, demonstrating their high potential in treating heavy metal pollutants in wastewater.

Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC

The 3D genome prediction in cancer is crucial for uncovering the impact of structural variations (SVs) on tumorigenesis, especially when they are present in noncoding regions. We present InfoHiC, a systemic framework for predicting the 3D cancer genome directly from whole-genome sequencing (WGS). InfoHiC utilizes contig-specific copy number encoding on the SV contig assembly, and performs a contig-to-total Hi-C conversion for the cancer Hi-C prediction from multiple SV contigs. We showed that InfoHiC can predict 3D genome folding from all types of SVs using breast cancer cell line data. We applied it to WGS data of patients with breast cancer and pediatric patients with medulloblastoma, and identified neo topologically associating domains. For breast cancer, we discovered super-enhancer hijacking events associated with oncogenic overexpression and poor survival outcomes. For medulloblastoma, we found SVs in noncoding regions that caused super-enhancer hijacking events of medulloblastoma driver genes (GFI1, GFI1B, and PRDM6). In addition, we provide trained models for cancer Hi-C prediction from WGS at https://github.com/dmcb-gist/InfoHiC, uncovering the impacts of SVs in cancer patients and revealing novel therapeutic targets.

Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism

How phenotypic diversity originates and persists within populations are classic puzzles in evolutionary biology. While balanced polymorphisms segregate within many species, it remains rare for both the genetic basis and the selective forces to be known, leading to an incomplete understanding of many classes of traits under balancing selection. Here, we uncover the genetic architecture of a balanced sexual mimicry polymorphism and identify behavioral mechanisms that may be involved in its maintenance in the swordtail fish Xiphophorus birchmanni. We find that ∼40% of X.birchmanni males develop a "false gravid spot," a melanic pigmentation pattern that mimics the "pregnancy spot" associated with sexual maturity in female live-bearing fish. Using genome-wide association mapping, we detect a single intergenic region associated with variation in the false gravid spot phenotype, which is upstream of kitlga, a melanophore patterning gene. By performing long-read sequencing within and across populations, we identify complex structural rearrangements between alternate alleles at this locus. The false gravid spot haplotype drives increased allele-specific expression of kitlga, which provides a mechanistic explanation for the increased melanophore abundance that causes the spot. By studying social interactions in the laboratory and in nature, we find that males with the false gravid spot experience less aggression; however, they also receive increased attention from other males and are disdained by females. These behavioral interactions may contribute to the maintenance of this phenotypic polymorphism in natural populations. We speculate that structural variants affecting gene regulation may be an underappreciated driver of balanced polymorphisms across diverse species.

Complex genetic variation in nearly complete human genomes.

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps1,2 and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into α-satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference1 significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference3 to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.

Effect of water occurrence in coal reservoirs on the production capacity of coalbed methane by using NMR simulation technology and production capacity simulation

The occurrence of gas and water is a critical factor affecting the production capacity of coalbed methane. Therefore, occurrence and dynamic interaction between gas and water in coal reservoirs need to be studied. T2 spectrum of all the samples were studied by NMR technique at 0, 5, 9, and 28 h of natural evaporation. Then, multifractal model was used to characterize water distribution heterogeneity, and a novel evaluation coefficient was proposed to characterize distribution heterogeneity of water content, the correlation among evaluation coefficient, water distribution heterogeneity and pore structure parameters was analyzed. The results are as follows. In the saturated state, the moisture distribution of three types is heterogeneous. Type A of adsorption pore-developed exhibits strong moisture variation heterogeneity of small pores, in contrast to the uniform moisture variation in large pores. Type B of fracture-developed has the highest coefficient of variation in moisture distribution. The coefficient of variation A1 for moisture content can determine the speed of moisture transport and evaporation in the pore structure. A lower A1 indicates a greater moisture transport volume and faster moisture transport rate over the same time. The coefficient of variation A2 for moisture distribution represents the heterogeneity of moisture content variation in the pore structure. That is, a smaller A2 indicates better heterogeneity in the distribution of moisture content in the pore structure. Numerical simulation indicates the average gas production and the peak gas production time increase and decrease with the initial moisture content (Sgrw) increases, respectively. These findings provide practical guidance for coalbed methane development, especially in optimizing coalbed methane production capacity prediction and improving recovery efficiency.

The influence of G-tract and loop length on the topological variability of putative five and six G-quartet DNA structures in the human genome

Local variation of DNA structure and its dynamic nature play an essential role in the regulation of important biological processes. One of the most prominent noncanonical structures are G-quadruplexes, which form in vivo within guanine-rich regions and have been demonstrated to be involved in the regulation of transcription, translation and telomere maintenance. We provide an analysis of G-quadruplex formation in sequences with five and six guanine residues long G-tracts, which have emerged from the investigation of the gapless human genome and are associated with genes related to cancer and neurodegenerative diseases. We systematically explored the effect of G-tract and loop elongations by means of NMR and CD spectroscopy and polyacrylamide electrophoresis. Despite both types of elongation leading up to structural polymorphism, we successfully determined the topologies of four out of eight examined sequences, one of which contributes to a very scarce selection of currently known intramolecular four G-quartet structures in potassium solutions. We demonstrate that examined sequences are incompatible with five or six G-quartet structures with propeller loops, although the compatibility with other loop types cannot be factored out. Lastly, we propose a novel approach towards specific G-quadruplex targeting that could be implemented in structures with more than four G-quartets.

Analysis of the structure and trend prediction of China's total health expenditure.

In the context of rapid economic and social development, there has been a continuous intensification of population aging, transformation of disease patterns, and wide application of new medical technologies. As a result, health expenditures in various countries have sharply soared. How to utilize limited medical resources to maximize the improvement of health levels has become a hot and challenging issue related to the well-being of all humanity. The relevant indicators of total health expenditure play a crucial role in monitoring and evaluating the fairness of health financing and health security in the region. This study explores the changes in the main expenses that constitute China's total health expenditure and uses indicators related to health expenditure to observe the changes and future development trends of China's health expenditure. Based on this, the utilization of China's health expenditure is monitored to identify possible problems, and thereby targeted suggestions for promoting the development of China's health and wellness cause are put forward. Based on the comparison of previous literature, this paper analyzes the changes and future development trends in China's health expenditure by using the relevant indicators of China's health expenditure through the structural variation analysis method and the gray prediction model. The results show that the scale of government, social, and out-of-pocket health expenditures has continuously expanded, with social health expenditures becoming the main funding source for total health expenditures. The burden of medical expenditures on individuals has been further reduced. In the institutional method of total health expenditures, hospital expenditures account for about 60% of the total and are the main component. The expenditures of health administration and medical insurance management institutions are the main driving force behind the growth of total health expenditures. However, the proportion of health expenditures in China's GDP is relatively low, so more investment is needed in the healthcare sector, and the burden of individual medical expenses also needs to be continuously reduced. In the future, China should further increase its investment in the medical and health sector. Specifically, the government should persist in investing in fundamental medical and health services. Simultaneously, efforts should be made to establish a scientific cost control mechanism for pharmaceuticals and broaden financing channels for healthcare, such as accelerating the development of commercial health insurance.

Why Are Some Pnictogen(III) Pincer Complexes Planar and Others Pyramidal?

Geometrically-constrained pnictogen pincer complexes have emerged in recent years as platforms for unique stoichiometric and catalytic chemical transformations. These complexes feature dynamic conformations ranging from fully planar at the pnictogen centre to distorted-pyramidal geometries, as well as variation between phases. Although the valued reactivity of pnictogen pincer complexes is ascribed to their geometries, there is no unified model to explain the observed conformational outcomes across different ligands and pnictogen centres. Here we propose such a model through computational analysis of more than 1300 structures across 64 complexes (16 ligands and 4 heavy pnictogens), explaining the experimental observations and making new predictions. By looking at signatures of bond stability (bond lengths, Wiberg bond indices) and delocalization (NPA charges, Hirshfeld charges), our framework posits a pnictogen-based σ-bonding effect that favours pyramidalization and exists in competition with a ligand-based π-bonding effect that favours planarity. Variations in structure as a function of pnictogen identity, ligand tethering, electronics, and aromaticity can be reconciled with reference to a balance between these two opposing forces. Careful consideration of the σ/π-bonding effects may aid in the rational design of future pnictogen pincer complexes with predictable geometries and reactivities.

Application of Bioelectrical Impedance Analysis in Weight Management of Children with Spina Bifida.

Children with spina bifida (SB) face an elevated risk of obesity, which necessitates precise methods for assessing body composition to ensure effective weight management. Conventional measures like BMI are inadequate for this population because of variations in growth patterns and skeletal structure. Bioelectrical impedance analysis (BIA) is a method that offers a clearer picture of body composition, yet its use in children with SB remains underexplored. Conducted on 57 children with SB and 28 healthy controls, with a median age of 11 years, this study evaluated anthropometrics, including BMI and BIA-derived metrics. The Hoffer's scale to assess physical activity was applied in SB children. Results showed that while 32% of SB patients were classified as overweight or obese based on BMI, 62% exhibited high body fat percentage via BIA. Fat-free mass, muscle and fat mass, and fat-to-muscle ratio (FMR) differed significantly compared to the reference group. Non-ambulators showed a higher median body fat mass percentage (25.9% vs. 17.8%, p = 0.01) and FMR (0.92 vs. 0.44, p = 0.003) in comparison to the community walkers. In SB children, BIA-measured fat mass is a better obesity indicator than BMI. Non-ambulatory, SB patients with obesity had the highest FMR values, indicating a higher risk for metabolic syndrome.

Impact responses and injury analyses of a three-year-old occupant seating in forward and rearward facing CRSs using different computational models

To investigate the reliability and necessity of utilising a human biomechanical model in automotive safety, the frontal collision simulation test was conducted employing the TUST IBMs 3YO model and the Q3 dummy model. The kinematic and biomechanical injury parameters of the occupants were comparatively analysed. The results indicate consistent trends in acceleration changes between the two computational models. Variations in neck structure resulted in a 25% to 28% difference in the peak values of neck injury parameters. Differences in spine structure and materials made the spine angle change trends of the Q3 model more sensitive to the type of child restraint system (CRS). The human biomechanical model allows for the evaluation of occupant injury risk from multiple perspectives. Therefore, employing an advanced computational model of the human body with higher biofidelity provides a more reliable and effective method for investigating injury mechanisms and developing protective countermeasures for child occupants.

Protective effect of the perchlorophenyl group in organophosphorus chemistry

The homoleptic phosphine with the bulky perchlorophenyl group, (C6Cl5)3P (1), exhibits trigonal pyramidal structure (TPY-3), yet considerably flattened: Σ(C–P–C') = 321.0(1)°. Key steric and electronic properties of this simple organophosphorus species have been estimated by calculation. Attending to its characteristic features, 1 can be rated as a deactivated phosphine, where the less-basic P atom is sterically shielded by the bulky C6Cl5 groups. This marked inertness notwithstanding, it has been possible to obtain (under harsh conditions) derivatives with phosphorus in high oxidation state, namely the phosphine oxide (C6Cl5)3PO (2) and the difluorophosphorane (C6Cl5)3PF2 (3). These four- and five-substituted derivatives respectively exhibit trigonal pyramidal (TPY-4) and trigonal bipyramidal (TBPY-5) structures. The Σ(C–P–C') value steadily increases along the series 1–3, according to the referred structural variation. The P–C bond length is, in turn, invariably maintained at about 185 pm regardless of the different oxidation state, the increasing number of substituents around the P atom and the overall geometry. The hypervalent difluorophosphorane (C6Cl5)3PF2 (3) dissociates one of the axial fluorides in the gas phase giving rise to the fluorophosphonium cation [(C6Cl5)3PF]+, as detected by mass spectrometry. This cation is identified as a Lewis superacid.

A systematical comparation of Cu (II) adsorption behavior and mechanism between biomass fly ash and biogas residue pyrolysis char

Biomass fly ash (BFA) and biogas residues are the main by-products of biomass direct-fired power generation and biogas production. This study compares the Cu(II) adsorption mechanisms of BFA and biogas residue pyrolysis char (BRPC) through systematic tests. BFA exhibited a significantly higher adsorption capacity (75.34 mg/g) than BRPC (42.80 mg/g). The pseudo-first-order kinetic model best described BFA, while the Elovich model was optimal for BRPC. Both materials fit the Freundlich isotherm model. BFA's superior mineral co-precipitation and ion-exchange capacity are due to its rich mineral content, particularly calcium. BRPC benefits from an additional functional group complex adsorption due to its pyrolytic charcoal content. Variations in pore structure of BFA and BRPC did not demonstrate a significant effect on the adsorption. The results of this study provide essential data support for the potential of high-value utilization of BFA and BRPC and the innovative modification of high-performance biomass-based heavy metal adsorbent materials.

Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity of Ilex Species.

The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species.

Mapping fine-scale carbon sequestration benefits and landscape spatial drivers of urban parks using high-resolution UAV data

Urban parks offer dual ecological benefits by increasing carbon sinks and reducing carbon emissions and are considered an important natural strategy for cities to achieve “double carbon” goals. However, rapid, efficient, and accurate quantification of the carbon sequestration benefits of urban parks poses a significant challenge. To address this, we utilized unmanned aerial vehicle (UAV) multispectral data to construct large-area, high-resolution models of urban park carbon sequestration benefits, replacing traditional, time-consuming, and laborious large-scale field surveys. Additionally, we explored the relationship between urban park landscape patterns and the benefits of carbon sequestration. First, we used data from 12 tree species to calculate the carbon storage based on tree species and compared these results with those calculated based on forest type. Second, three prediction models were constructed using multispectral vegetation index only, texture features only, and a combination of both, in conjunction with gradient boosting decision Trees (GBDT), random forest (RF), and backpropagation (BP) neural network to generate carbon sequestration benefit maps for the entire park. These maps allowed us to determine how variations in urban park landscape structures affect carbon stocks. The results show that UAV multispectral imagery provides a fast and accurate method for measuring the carbon sequestration benefits of urban parks and offers an alternative method for generating carbon sequestration benefit maps. This research reveals the benefits of urban park carbon sequestration and explores the spatial patterns within landscapes. The findings are of great significance for guiding the estimation of urban carbon sequestration benefits and achieving carbon neutrality.

Energy prices and the structure of inflation in European Union countries

Abstract Since 2022, in almost every inflation category, a strong divergence in price dynamics among the EU countries has become visible. The first aim of this paper is to assess the impact of changes in energy prices on the differentiation in price dynamics in individual inflation categories in EU countries. The second aim is to isolate those components of inflation that have significantly differentiated the countries in the crisis year of 2022. The research was conducted based on the vector-autoregressive model, the Granger causality test, cluster analysis and analysis of variance. It can be concluded that there is a causal relationship between energy prices and the differentiation in the price growth rate in certain inflation categories. In 2022, the EU member states were divided into two quite distinct clusters. This article adds value to current research by taking into account the level of variation in the inflation structure among EU countries.