Deletion Of Element Research Articles

Towards targeted engineering of promoters via deletion of repressive cis-regulatory elements.

Towards targeted engineering of promoters via deletion of repressive cis-regulatory elements.

FEM, DEM and FDEM applications on impact fracture of glass and laminated glass – a review

Structural glass components are prevalently used in engineering. Due to the brittle nature, glass or laminated glass may fracture during an impact action, and the subsequent flying fragments may spread over a wide range, resulting in human injuries and asset losses. In this article, the authors aimed at providing a comprehensive review concerning the numerical applications on the impact fracture of glass and laminated glass, giving emphasis to the literatures published in the last two decades. Relevant numerical applications employing the finite element method (including element deletion method, extended finite element method and some other continuum-based approaches), discrete element method and combined finite-discrete element method were reviewed in-depth, and features of the simulations were summarised. Discussions on the impact fracture characteristics from different computational approaches were performed. Insights into the accuracy, efficiency, ease of implementation and range of applicability were also provided. This review is meant for the rapid and beneficial understanding towards the impact fracture mechanism of glass and laminated glass.

The role and the determination of the LuxI protein binding targets in the formation of biogenic amines in Hafnia alvei H4

Hafnia alvei is a spoilage microorganism that possesses the LuxI/LuxR-type quorum sensing (QS) system. Biogenic amines (BAs) are important in food spoilage and safety, yet the role of QS in BA formation remains poorly understood. This study investigated the ability of H. alvei H4 to produce BAs in fish flesh and decarboxylase culture media. The findings showed that H. alvei H4 produced substantial amounts of putrescine and cadaverine in turbot flesh, with its enhanced amine-producing capacity potentially leading to the eventual deterioration of the fish. Furthermore, the deletion of the QS element—AHL synthase gene luxI—affected the concentrations of both BAs. Based on these observations, the present study conducted multifaceted experiments, including phenotypic assessments and analyses of gene expression, to explore the role of luxI and to identify its specific binding targets. The results indicated that putrescine formation in H. alvei H4 primarily occurred via the arginine deiminase (ADI) pathway, with luxI playing a positive role in the conversion of arginine to ornithine and subsequently to putrescine. The reduction in putrescine content observed in a luxI mutant (ΔluxI) was attributed to the direct binding of the LuxI protein to the promoters of the argF and speC genes, which code for ornithine carbamoyltransferase and ornithine decarboxylase, respectively. The findings of this study provided the basis to understand the influence of QS on BA production in H. alvei, by specifically demonstrating the involvement of the luxI gene on putrescine and cadaverine production.

Effects of Surface Crack Shape on Fracture Behavior of Oil Pipelines Based on the MMC Criterion.

This study employs a hybrid numerical-experimental calibration method based on phenomena to determine the fracture parameters of the Modified Mohr-Coulomb (MMC) model. Using a self-developed VUMAT subroutine and the element deletion technique, the fracture process of a wide plate pipeline is thoroughly analyzed. This study investigates the impact of various crack shapes on the fracture response under tensile loading and the influence of surface crack size on the initiation location of a wide plate. These results demonstrate the calibrated MMC fracture model's accurate prediction of the toughness fracture behavior of X80 pipeline steel. Under equal area conditions of the dangerous section, circular cracks exhibit lower bearing capacity compared to elliptical cracks. Elliptical cracks predominantly propagate in the thickness direction, whereas circular cracks show nearly uniform growth in all directions. Furthermore, when the crack depth is less than half of the wall thickness, the damage accumulation value at the midpoint of the crack front is maximized; conversely, when the crack front is closer to the internal measurement point of the wide plate, the damage accumulation value is maximized.

Fracture predictions in impact three-point bending test of European beech

Hardwood has become widespread in European forests. The strongest factor is climate change and damage to conifers by the bark beetle. The effort to study hardwoods grows with increasing volume of applications. Therefore, European beech wood was investigated under two impact loads in two material directions, resulting in four unique combinations supplemented by the measurement of the friction coefficient. Then, it was computationally simulated to reproduce the cracking, while the material model reflected the orthotropic behaviour in elasticity, plasticity and failure. The model was coded using the user subroutine in Abaqus to initiate and propagate the crack using the element deletion. The resulting reaction forces were in good agreement with those from the experiments. Cracking was numerically simulated in three of four cases as experimentally observed, however, upon larger deflections. Therefore, the model is applicable for further investigations.

Structural variants linked to Alzheimer's Disease and other common age-related clinical and neuropathologic traits.

Advances have led to a greater understanding of the genetics of Alzheimer's Disease (AD). However, the gap between the predicted and observed genetic heritability estimates when using single nucleotide polymorphisms (SNPs) and small indel data remains. Large genomic rearrangements, known as structural variants (SVs), have the potential to account for this missing genetic heritability. By leveraging data from two ongoing cohort studies of aging and dementia, the Religious Orders Study and Rush Memory and Aging Project (ROS/MAP), we performed genome-wide association analysis testing around 20,000 common SVs from 1,088 participants with whole genome sequencing (WGS) data. A range of Alzheimer's Disease and Related Disorders (AD/ADRD) clinical and pathologic traits were examined. Given the limited sample size, no genome-wide significant association was found, but we mapped SVs across 81 AD risk loci and discovered 22 SVs in linkage disequilibrium (LD) with GWAS lead variants and directly associated with AD/ADRD phenotypes (nominal P < 0.05). The strongest association was a deletion of an Alu element in the 3'UTR of the TMEM106B gene. This SV was in high LD with the respective AD GWAS locus and was associated with multiple AD/ADRD phenotypes, including tangle density, TDP-43, and cognitive resilience. The deletion of this element was also linked to lower TMEM106B protein abundance. We also found a 22 kb deletion associated with depression in ROSMAP and bearing similar association patterns as AD GWAS SNPs at the IQCK locus. In addition, genome-wide scans allowed the identification of 7 SVs, with no LD with SNPs and nominally associated with AD/ADRD traits. This result suggests potentially new ADRD risk loci not discoverable using SNP data. Among these findings, we highlight a 5.6 kb duplication of coding regions of the gene C1orf186 at chromosome 1 associated with indices of cognitive impairment, decline, and resilience. While further replication in independent datasets is needed to validate these findings, our results support the potential roles of common structural variations in the pathogenesis of AD/ADRD.

Quantum Physics, Digital Computers, and Life from a Holistic Perspective

Quantum physics is a linear theory, so it is somewhat puzzling that it can underlie very complex systems such as digital computers and life. This paper investigates how this is possible. Physically, such complex systems are necessarily modular hierarchical structures, with a number of key features. Firstly, they cannot be described by a single wave function: only local wave functions can exist, rather than a single wave function for a living cell, a cat, or a brain. Secondly, the quantum to classical transition is characterised by contextual wave-function collapse shaped by macroscopic elements that can be described classically. Thirdly, downward causation occurs in the physical hierarchy in two key ways: by the downward influence of time dependent constraints, and by creation, modification, or deletion of lower level elements. Fourthly, there are also logical modular hierarchical structures supported by the physical ones, such as algorithms and computer programs, They are able to support arbitrary logical operations, which can influence physical outcomes as in computer aided design and 3-d printing. Finally, complex systems are necessarily open systems, with heat baths playing a key role in their dynamics and providing local arrows of time that agree with the cosmological direction of time that is established by the evolution of the universe.

Role of intermolecular potential in adhesive wear behaviors for elastic-plastic spherical microcontacts

This paper aims to investigate the effects of intermolecular potential on adhesive wear behaviors of microcontacts between a rigid flat and an elastic-plastic sphere, using a Finite Element (FE) model. In this model, a separation-dependent adhesive pressure, governed by the Lennard-Jones (LJ) potential, is applied to the surfaces of both the rigid flat and the sphere under combined normal loading and tangential displacement. To assess material damage, the Johnson–Cook (JC) failure and fracture energy criteria are utilized, allowing for element deletion upon reaching the damage threshold. The role of intermolecular potential in the adhesive wear behaviors of spherical microcontacts is evaluated, focusing on wear volume, wear rate, wear morphology and fracture propagation mode under various dimensionless normal loads and adhesive energies. Two fracture propagation modes, namely bidirectional-like and unidirectional-like modes, dependent on normal load and adhesive energy, have been identified. The transition from mild to severe wear regime is found to be closely related to the fracture propagation mode. Additionally, an interesting observation is that relatively high adhesive energy could result in decreased wear volume and wear rate under certain normal loads, which can be attributed to the change in fracture propagation mode caused by the adhesive pressure.

Comprehensive investigation on modelling of low-velocity impact damage response of composite laminates − Experimental correlation and assessment

Low velocity impact (LVI) experiments are performed to provide correlations with the simulation results based on numerical modeling of the intralaminar matrix damage and interlaminar delamination damage of composite laminates. The good agreement between the numerical simulation and experimental results provided validation of the numerical modeling approach. The validated numerical modeling is then used in the parametrical assessment of the influence of material properties and model- related parameters on the global LVI deformation responses and the evolution characteristics of the intralaminar and interlaminar damage. It is observed that the element deletion method is not suitable to resolve the element distortion problem induced by the progressive damage. The numerical convergence problem caused by element distortion can be resolved with appropriate selection of threshold value of the critical damage parameter without element deletion. The parametrical numerical investigations showed that the variations of material properties and parameters related to interlaminar damage exhibited significant influence on the LVI global deformation responses and progressive damage evolutions. Meanwhile, insignificant influence of the material properties related to the intralaminar damage was observed for the normal variations within material scatters.

Metabolic Profile of the Genome-Reduced Bacillus subtilis Strain IIG-Bs-27-39: An Attractive Chassis for Recombinant Protein Production.

The Gram-positive bacterium Bacillus subtilis is extensively used in the industry for the secretory production of proteins with commercial value. To further improve its performance, this microbe has been the subject of extensive genome engineering efforts, especially the removal of large genomic regions that are dispensable or even counterproductive. Here, we present the genome-reduced B. subtilis strain IIG-Bs-27-39, which was obtained through systematic deletion of mobile genetic elements, as well as genes for extracellular proteases, sporulation, flagella formation, and antibiotic production. Different from previously characterized genome-reduced B. subtilis strains, the IIG-Bs-27-39 strain was still able to grow on minimal media. We used this feature to benchmark strain IIG-Bs-27-39 against its parental strain 168 with respect to heterologous protein production and metabolic parameters during bioreactor cultivation. The IIG-Bs-27-39 strain presented superior secretion of difficult-to-produce staphylococcal antigens, as well as higher specific growth rates and biomass yields. At the metabolic level, changes in byproduct formation and internal amino acid pools were observed, whereas energetic parameters such as the ATP yield, ATP/ADP levels, and adenylate energy charge were comparable between the two strains. Intriguingly, we observed a significant increase in the total cellular NADPH level during all tested conditions and increases in the NAD+ and NADP(H) pools during protein production. This indicates that the IIG-Bs-27-39 strain has more energy available for anabolic processes and protein production, thereby providing a link between strain physiology and production performance. On this basis, we conclude that the genome-reduced strain IIG-Bs-27-39 represents an attractive chassis for future biotechnological applications.

Stream-aware indexing for distributed inequality join processing

Inequality join is an operator to join data on inequality conditions and it is a fundamental building block for applications. While methods and optimizations exist for efficient inequality join in batch processing, little attention has been given to its streaming version, particularly to large-scale data-intensive applications that run on Distributed Stream Processing Systems (DSPSs). Designing an inequality join in streaming and distributed settings is not an easy task: (i) indexes have to be employed to efficiently support inequality-based comparisons, but the continuous stream of data imposes continuous insertions, updates, and deletions of elements in the indexes—hence a huge overhead for the DSPSs; (ii) oftentimes real data is skewed, which makes indexing even more challenging.To address these challenges, we propose the Stream-Aware inequality join (STA), an indexing method that can reduce redundancy and index update overhead. STA builds a separate in-memory index structure for hotkeys, i.e., the most frequently used keys, which are automatically identified with an efficient data sketch. On the other hand, the cold keys are treated using a linked set of index structures. In this way, STA avoids many superfluous index updates for frequent items. Finally, we implement four state-of-the-art inequality join solutions for a widely employed DSPS (Apache Storm) and compare their performance with STA on four real-world data sets and a synthetic one. The results of our experimental evaluation reveal that our stream-aware approach outperforms existing solutions.

Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing

CRISPR-Cas greatly facilitated the integration of exogenous sequences into specific loci. However, knockin generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Here, we describe SEED/Harvest, a method to generate knockins in Drosophila, based on CRISPR-Cas and the single-strand annealing (SSA) repair pathway. In SEED (from "scarless editing by element deletion"), a switchable cassette is first integrated into the target locus. In a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knockin generation of both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatiotemporal control of protein labeling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knockins, we developed a genetic toolbox by functionalizing the ALFA nanobody.

The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts.

Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.

Mild phenotypes in patients with different deletions in the 3' enhancer region of SHOX.

Haploinsufficiency of the short stature homeobox-containing (SHOX) gene leads to a phenotypic spectrum ranging from Leri-Weill dyschondrosteosis (LWD) to SHOX-deficient short stature. SHOX nullizygosity leads to Langer mesomelic dysplasia. Pathogenic variants can include whole or partial gene deletions or duplications, point mutations within the coding sequence, and deletions of upstream and downstream regulatory elements. Here we report two families: a non-consanguineous family with a deletion downstream of SHOX, in which the homozygous proband presented with isolated Madelung deformity, without LWD or short stature, as well as a 9-year-old girl with Madelung deformities, mesomelia, a dominant family history of Madelung deformity and a heterozygous deletion of the CNE9 region in the 3' downstream region of SHOX. These case reports provide additional information on the effects of 3' downstream deletions of SHOX, by demonstrating the limited phenotype associated with the recurrent 47.5 kb deletion in a homozygous state and the CNE9 deletion in a heterozygous state.

Comparison of simplified bone-screw interface models in materially nonlinear μFE simulations

Micro finite-element (μFE) simulations serve as a crucial research tool to assist laboratory experiments in the biomechanical assessment of screw anchorage in bone. However, accurately modelling the interface between bone and screw threads at the microscale poses a significant challenge. Currently, the gold-standard approach involves employing computationally intensive physical contact models to simulate this interface. This study compared nonlinear μFE predictions of deformations, whole-construct stiffness, maximum force and damage patterns of three different computationally efficient simplified interface approaches to the general contact interface in Abaqus Explicit, which was defined as gold-standard and reference model. The μCT images (resolution: 32.8 μm) of two human radii with varying bone volume fractions were utilized and a screw was virtually inserted up to 50% and 100% of the volar-dorsal cortex distance. Materially nonlinear μFE models were generated and loaded in tension, compression and shear. In a first step, the common simplification of using a fully-bonded interface was compared to the general contact interface, revealing overestimations of whole-construct stiffness (19% on average) and maximum force (26% on average), along with inaccurate damage pattern replications. To enhance predictions, two additional simplified interface models were compared: tensionally strained element deletion (TED) and a novel modification of TED (TED-M). TED deletes interface elements strained in tension based on a linear-elastic simulation before the actual simulation. TED-M extends the remaining contact interface of TED by incorporating neighboring elements to the contact area. Both TED and TED-M reduced the errors in whole-construct stiffness and maximum force and improved the replication of the damage distributions in comparison to the fully-bonded approach. TED was better in predicting whole-construct stiffness (average error of 1%), while TED-M showed lowest errors in maximum force (1% on average). In conclusion, both TED and TED-M offer computationally efficient alternatives to physical contact modelling, although the fully-bonded interface may deliver sufficiently accurate predictions for many applications.

Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice.

Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.

A finite element model for predicting impact-induced damage to a skin simulant

A finite element model was developed for assessing the efficacy of rugby body padding in reducing the risk of sustaining cuts and abrasions. The model was developed to predict the onset of damage to a soft tissue simulant from concentrated impact loading (i.e., stud impact) and compared against a corresponding experiment. The damage modelling techniques involved defining an element deletion criterion, whereby those on the surface of the surrogate were deleted if their maximum principal stress reached a predefined value. Candidate maximum principal stress values for element deletion criteria were identified independently from puncture test simulations on the soft tissue simulant. Experimental impacts with a stud were carried out at three energies (2, 4 and 6 J), at three angular orientations (0°, 15° and 30°) and compared to corresponding simulations. Suitable maximum principal stress values for element deletion criteria settings were first identified for the 4 J impact, selecting the candidates that best matched the experimental results. The same element deletion settings were then applied in simulations at 2 and 6 J and the validity of the model was further assessed (difference < 15% for the force at tear and < 30% for time to tear). The damage modelling techniques presented here could be applied to other skin simulants to assess the onset of skin injuries and the ability of padding to prevent them.

Analyzing imbalance of short tandem repeats for pancreatic cancer detection.

e16359 Background: Short tandem repeats (STRs), alternatively known as microsatellites, encompass repeat units of 1 to 6 base pairs (bp) in the genome and function as regulators of gene expression, impacting plasticity and complex traits. STRs are prone to hypermutation with alterations correlated to pathogenicity in multiple Mendelian and acquired disorders. STR variant classes include insertions, mobile element insertions (MEIs), deletions, and multi-allelic copy number variants (mCNVs). These can lead to repeat expansions, allelic imbalance (AI), and microsatellite instability (MSI) observed in diseases such as Huntington's disease, hereditary ataxia, and multiple cancers. In pancreatic cancer, AI and associated loss-of-heterozygosity (LOH) at tumor suppressor loci flanked by hypervariable STR regions correspond to a pathogenic phenotype with a risk of aggressive disease. Consequently, it is critical to develop accurate and robust methods to precisely identify and genotype pancreatic samples with varying specimen quality in a clinical setting to aid in diagnosis. Methods: Capillary electrophoresis (CE) and Sanger sequencing have been used to analyze STRs. The availability of newer tools such as 2nd generation short-read (NGS) and 3rd generation long-read (TGS) sequencers could allow for high throughput scaling, however, informatics challenges associated with analyzing repetitive regions remain. Here we developed amplification and enrichment methods for targeted analysis for detection by CE, NGS and TGS. Results: Amplification and enrichment strategies for detecting 17 short tandem repeat regions that play a role in pancreatic carcinogenesis were developed. Methods were optimized for detecting STR alterations in cell-free nucleic acids isolated from endoscope-guided pancreatic fine needle aspirate biopsies. Furthermore, informatics tools were developed to analyze short-read and long-read sequencing data to accurately analyze repeat regions. Conclusions: Here we compared 3 platforms (CE, NGS, and TGS) and found that CE remains the gold standard for analyzing AI/LOH with data comparable to long-read TGS, while short-read NGS is not always amenable to accurate analysis dependent on the region of interest. Additionally, we found that artifacts of amplification persist, irrespective of the 3 platforms analyzed.

Pseudo-static topology optimization using the evolutionary-type method for reinforced concrete shear walls

For improved ductility in seismic-design reinforced concrete shear walls, a methodology referred to as pseudo-static topology optimization is incorporated to guide the design process. This approach involves a stepwise elimination of elements from the initial structural configuration, under specified conditions such as reciprocating loads, displacement constraints and volume limitations. The primary objective of this optimization is to maximize the structural capacity for energy dissipation. This is achieved by creating a sensitivity analysis based on variations in cumulative plastic strain energy resulting from element deletions. The final optimized topologies exhibit bar structures with exceptional capacity for energy dissipation. These optimized configurations evolve with changes in height–width ratios and axial compression ratios, shifting from structures with uniform energy dissipation to those with a two-level distribution. Furthermore, the orientation of the main bars changes from folded bars on both sides to inclined straight bars, depending on the specific conditions.

A 44-Nucleotide Region in the Chikungunya Virus 3' UTR Dictates Viral Fitness in Disparate Host Cells.

We previously reported that deletion of a 44-nucleotide element in the 3' untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic fibroblasts in a manner independent of the type I interferon response, the same mutation decreases viral fitness in C6/36 mosquito cells. Further, the fitness advantage conferred by the UTR deletion in mammalian cells is maintained in vivo in a mouse model of CHIKV dissemination. Finally, SHAPE-MaP analysis of the CHIKV 3' UTR revealed this 44-nucleotide element forms a distinctive two-stem-loop structure that is ablated in the mutant 3' UTR without altering additional 3' UTR RNA secondary structures.