Multiple Assembly Research Articles

Deciphering Gorilla gorilla gorilla immunoglobulin loci in multiple genome assemblies and enrichment of IMGT resources.

Through the analysis of immunoglobulin genes at the IGH, IGK, and IGL loci from four Gorilla gorilla gorilla genome assemblies, IMGT® provides an in-depth overview of these loci and their individual variations in a species closely related to humans. The similarity between gorilla and human IG gene organization allowed the assignment of gorilla IG gene names based on their human counterparts. This study revealed significant findings, including variability in the IGH locus, the presence of known and new copy number variations (CNVs), and the accurate estimation of IGHG genes. The IGK locus displayed remarkable homogeneity and lacked the gene duplication seen in humans, while the IGL locus showed a previously unconfirmed CNV in the J-C cluster. The curated data from these analyses, available on the IMGT website, enhance our understanding of gorilla immunogenetics and provide valuable insights into primate evolution.

Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome.

A complete telomere-to-telomere (T2T) genome has been a longstanding goal in the field of genomic research. By integrating high-coverage and precise long-read sequencing data using multiple assembly strategies, we present here the first T2T gap-free genome assembly of Ganoderma leucocontextum strain GL72, a Tibetan medicinal mushroom. The T2T genome, with a size of 46.69 Mb, consists 13 complete nuclear chromosomes and typical telomeric repeats (CCCTAA)n were detected at both ends of 13 chromosomes. The high mapping rate, uniform genome coverage, a complete BUSCOs of 99.7%, and base accuracy exceeding 99.999% indicate that this assembly represents the highest level of completeness and quality. Regions characterized by distinct structural attributes, including highest Hi-C interaction intensity, high repeat content, decreased gene density, low GC content, and minimal or no transcription levels across all chromosomes may represent potential centromeres. Sequence analysis revealed the first Copia centromeric retrotransposon in macro-fungi genome. Phylogenomic analysis identified that G. leucocontextum and G. tsugae diverged from the other Ganoderma species approximately 9.8-17.9 MYA. The prediction of secondary metabolic clusters confirmed the capability of this fungus to produce a substantial quantity of metabolites. This T2T gap-free genome will contribute to the genomic 'dark matter' elucidation and server as a great reference for genetics, genomics, and evolutionary studies of G. leucocontextum.

System reliability and sensitivity analysis for extendible support structures with multiple assembly failure modes

The extendible support structure (ESS) is the indispensable ingredient of space antennas, and its assembly reliability is of significant importance for the work performance of the latter. Specifically, pointing accuracy of the panels is critical to the electromagnetic performance of the space antenna and angular error of the locking joints directly determines whether the joint can be successfully locked so as to maintain the structural configuration of the ESS. Thus, this paper proposes a novel analytical approach to system reliability and sensitivity analysis for the ESS considering pointing accuracy and angular errors. At first, the failure mechanism of the ESS due to pointing deviation and angular error is comprehensively analyzed. On this basis, system reliability with those multiple failure modes for the ESS is mathematically defined. To solve this problem, the structural error model of the ESS considering manufacturing errors, assembly deviations and part deformations is first established so that the limit-state functions characterizing the pointing deviation and angular errors are accordingly formulated. Then, a novel framework based on expectation propagation is explored for system reliability and sensitivity analysis with multiple failure modes, of which the notable merit is that it is analytical. Based on this novel expectation-propagation-based framework, the systematic assembly reliability of the ESS is conducted in a closed-form manner. Finally, case studies and practical experiments are conducted to validate the effectiveness of the proposed method. The results demonstrate that it can provide an accurate and efficient system reliability and sensitivity analysis for the ESS.

Topology optimization of modular structures with multiple assemblies and applications to airborne shelves

This work is devoted to the aeronautical application of topology optimization for modular structures with multiple assemblies that consist of repeated standard modules and optional reinforcements. These kinds of structures are widely used owing to their transportability, reconfigurability, low manufacturing and service costs. In this work, the design of airborne shelves with modular structures characterized by the standard module configuration is formulated for the first time as a topology optimization problem of multiple assemblies and multiple load cases subjected to the volume constraint. It is shown that the weighted compliance design of multiple assemblies is a compromising solution compared to the optimization result of each individual assembly of standard modules. Meanwhile, the performance of optimized airborne shelves with the modular structures can effectively be ameliorated with the help of reinforcements.

Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms.

A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.

Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages

How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.

MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq.

Single-cell DNA template strand sequencing (Strand-seq) allows a range of various genomic analysis including chromosome length haplotype phasing and structural variation (SV) calling in individual cells. Here, we present MosaiCatcher v2, a standardized workflow and reference framework for single-cell SV detection using Strand-seq. This framework introduces a range of functionalities, including: an automated upstream Quality Control (QC) and assembly sub-workflow that relies on multiple genome assemblies and incorporates a multistep normalization module, integration of the single-cell nucleosome occupancy and genetic variation analysis SV functional characterization and of the ArbiGent SV genotyping modules, platform portability, as well as a user-friendly and shareable web report. These new features of MosaiCatcher v2 enable reproducible computational processing of Strand-seq data, which are increasingly used in human genetics and single-cell genomics, toward production environments. MosaiCatcher v2 is compatible with both container and conda environments, ensuring reproducibility and robustness and positioning the framework as a cornerstone in computational processing of Strand-seq data. MosaiCatcher v2 is a standardized workflow, implemented using the Snakemake workflow management system. The pipeline is available on GitHub: https://github.com/friendsofstrandseq/mosaicatcher-pipeline/ and on the snakemake-workflow-catalog: https://snakemake.github.io/snakemake-workflow-catalog/?usage=friendsofstrandseq/mosaicatcher-pipeline. Strand-seq example input data used in the publication can be found in the Data availability statement. Additionally, a lightweight dataset for test purposes can be found on the GitHub repository.

Surface-Plasmon-Polaritons for Reversible Assembly of Gold Nanoparticles, In Situ Nanogap Tuning, and SERS.

A transportable reversible assembly of gold nanoparticles (AuNPs) in an aqueous environment addresses the need for in situ surafce-enhanced Raman spectroscopy (SERS) hotspot creation for biological applications. Usually, light-directed AuNP assembly methods use higher laser powers and surfactants and are, hence, unsuitable for biological applications. Here, surface plasmon polaritons-assisted dynamic assembly of AuNPs are demonstrated at laser power density as low as 100nWµm-2 . The AuNP assembly with multiple controllable hotspots is generated in an Au-water interface for solution-based SERS measurements. The major advantage of the method is that the interparticle nanogap is tunable to achieve analyte and AuNP-specific optimum SERS enhancement. The SERS intensity is reproducible on multiple reassembly cycles and assembly attempts, proving repeatability in the produced nanogap pattern. The assembly experiments reveal the influence of AuNP surface charge and the resulting polarizability on the SPP forces. The developed system and method can detect sulforhodamine 101(SR101) dye molecules at concentrations as low as 10-10 m. Further, the SERS measurements on double-stranded DNA suggest that the molecules are oriented in a fashion to expose adenosine to the enhanced field, leading to its dominance in the recorded spectra.

Cellulose nanofibril matrix drives the dynamic formation of spheroids.

Multicellular spheroids, which mimic the natural organ counterparts, allow the prospect of drug screening and regenerative medicine. However, their application is hampered by low processing efficiency or limited scale. This study introduces an efficient method to drive rapid multicellular spheroid formation by a cellulose nanofibril matrix. This matrix enables the facilitated growth of spheroids (within 48 h) through multiple cell assembly into size-controllable aggregates with well-organized physiological microstructure. The efficiency, dimension, and conformation of the as-formed spheroids depend on the concentration of extracellular nanofibrils, the number of assembled cells, and the heterogeneity of cell types. The above strategy allows the robust formation mechanism of compacted tumoroids and hepatocyte spheroids.

A strategy for human safety monitoring in high-temperature environments by 3D-printed heat-resistant TENG sensors

Flexible wearable devices based on triboelectric nanogenerators (TENGs) can be used to track many parameters around the human body, including signals from motions, gestures, and contacts, to perform a variety of tasks. However, it is still a challenge to achieve wide working temperature and multi-parameter body motion sensing with TENG sensors. To address that, this work reports a facile 3D printing-based strategy for preparing functionalized heat-resistant TENG sensors. In detail, a printable heat-resistant ink and multiple 3D printing-based assembly methods are proposed. The as-fabricated ink, which could maintain up to 200 ℃, then serves as multiple components in the TENG sensors through patterning. Functionalized TENG sensors and human–machine interfaces are printed and subsequently networked on a human body to sense comprehensive motion information. The results indicate six typical motions can be recognized with 94.85% accuracy based on neural network algorithms. A simple digital twin for motion capture and trace tracking in virtual space is furthermore implemented. Combining the proposed TENG sensors with virtual reality (VR) platforms opens up a new road for human safety monitoring in high-temperature environments.

Phase-amplitude coupling of Go/Nogo task-related neuronal oscillation decreases for humans with insufficient sleep.

Phase-amplitude coupling (PAC) across frequency might be associated with the long-range synchronization of brain networks, facilitating the spatiotemporal integration of multiple cell assemblies for information transmission during inhibitory control. However, sleep problems may affect these cortical information transmissions based on cross-frequency PAC, especially when humans work in environments of social isolation. This study aimed to evaluate changes in the theta-beta/gamma PAC of task-related electroencephalography (EEG) for humans with insufficient sleep. Here, we monitored the EEG signals of 60 healthy volunteers and 18 soldiers in the normal environment, performing a Go/Nogo task. Soldiers also participated in the same test in isolated cabins. These measures demonstrated theta-beta PACs between the frontal and central-parietal, and robust theta-gamma PACs between the frontal and occipital cortex. Unfortunately, these PACs significantly decreased when humans experienced insufficient sleep, which was positively correlated with the behavioral performance of inhibitory control. The evaluation of theta-beta/gamma PAC of Go/Nogo task-related EEG is necessary to help understand the different influences of sleep problems in humans.

Efficient microwave absorbing performance of Ni/carbon nanotubes assembled coronal hollow clusters

The development of wide-band microwave absorbing materials based on carbonaceous fillers remains a great challenge. In this study, carbon nanotubes (CNT) assembled coronal hollow clusters with efficient microwave absorbing performance have been obtained through successive hydrothermal and calcination process. Microstructural analysis reveals the distinct features of multiple assembly structures in the fabricated materials. The electromagnetic responses of Ni/CNT assembled clusters were examined across a frequency range of 2–18 GHz. Results demonstrate that the microwave frequency dispersion of electromagnetic parameters and reflection loss of Ni/CNT clusters are strongly influenced by weight loading. Multi-absorbing peaks with reflection loss better than − 40 dB could be achieved, while the equivalent absorbing band for RL< −10 dB covers 3.2–18 GHz, which account for 92.5% of the whole evaluated frequency range, and 62.5% for condition of RL< −20 dB. Furthermore, intrinsic attenuation beyond thickness derived semi-wavelength resonant absorption makes a major contribution to this superior performance. The underlying mechanism of dielectric response was investigated through Cole-Cole analysis and finite element simulation. ‘Micro-dipoles’ relaxation and hopping relaxation originated from defects within CNT and barrier between CNT, while the high magnetic dissipation capability of Ni nanoparticles make a major contribution to overall absorbing performance. All these are beneficial to regulation and optimization of microwave absorption performance of novel Ni/ CNT functionalized multistage architecture.

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as "pan-conserved segment tags" (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.

A new MIP approach for balancing and scheduling of mixed model assembly lines with alternative precedence relations

ABSTRACT In this paper, a new mixed integer programming (MIP) formulation is developed for balancing and scheduling of mixed model assembly lines with disjunctive precedence constraints among assembly tasks. To represent alternative precedence relations, AND/OR assembly graph was adopted. In case of alternative precedence relations, for each product multiple assembly plans exist, which can be represented by a set of alternative precedence subgraphs and only one of such subgraphs should be selected for each product. As the number of subgraphs exponentially increases with the number of disjunctive relations among the tasks, the computational complexity of simultaneous balancing and scheduling along with the assembly subgraph selection increases with the number of alternative precedence relations. Unlike the other MIP approaches known from the literature, the new model does not need the alternative assembly subgraphs to be to explicitly enumerated as input data and then used for indexing the variables. Instead, a new disjunctive precedence selection and task assignment variable and new constraints are introduced to optimally choose one relation for each subset of alternative precedence relations. The optimal solutions for computational examples of balancing and scheduling problems illustrate a superior performance of the new modelling approach.

Multi-functionalized Metallo-Supramolecular Spoked Wheels: Their Emission-Tunable Hierarchically Assembled System with Dye Molecules.

Supramolecular architectures with multiple emissive units are especially appealing due to their desired properties, such as artificial light harvesting and white-light emission. But fully achieving multi-wavelength photoluminescence in a single supramolecular architecture remains a challenge. In this paper, functionalized supramolecular architectures containing twelve metal centers and six pyrene moieties were nearly quantitatively synthesized by multi-component self-assembly and fully characterized by 1D and 2D nuclear magnetic resonance, dynamic light scattering, electrospray ionization mass spectrometry, traveling-wave ion mobility mass spectrometry, and transmission electron microscopy. Moreover, the hierarchical nano-assemblies were prepared by introducing anionic dyes to the positively charged self-assembled framework, which contained three luminescence centers, namely, pyrene, tpy-Cd coordination parts, and Sulforhodamine B anions. Such a hierarchically assembled system displayed tunable emission by taking full advantage of aggregation-induced emission enhancement, aggregation-caused quenching, and fluorescence resonance energy transfer effects and showed the diverse emission colors. This research provides a new insight for constructing multiple emissive metallo-supramolecular assemblies.

A supramolecular assembly strategy for hydrophilic drug delivery towards synergistic cancer treatment.

To improve the drug loading, tumor targeting, and delivery simplicity of hydrophilic drugs, we propose a supramolecular assembly strategy that potentially benefits a wide range of hydrophilic drug delivery. Firstly, we choose a hydrophilic drug (tirapazamine) as a model drug to directly co-assemble with chlorin e6 (Ce6) at different molar ratios, and systematically evaluate the resultant Ce6-tirapazamine nanoparticles (CT NPs) in aspects of size distribution, polydispersity, morphology, optical properties and molecular dynamics simulation. Based on the assembling facts between Ce6 and tirapazamine, we summarize a plausible rule of the supramolecular assembly for hydrophilic drugs. To validate our findings, more drugs with increasing hydrophilicity, such as temozolomide, gemcitabine hydrochloride and 5-azacytidine, successfully co-assemble with Ce6 into nanostructures by following similar assembling behaviors, demonstrating that our assembling rule may guide a wide range of hydrophilic drug delivery. Next, the combination of Ce6 and tirapazamine was chosen as the representative to investigate the anti-tumor activities of the supramolecular assemblies. CT NPs showed synergistic anti-tumor efficacy, increased tumor accumulation and significant tumor progression and metastasis inhibition in tumor-bearing mice. We anticipate that the supramolecular assembly mechanism will provide broad guidance for developing easy-to-make but functional nanomedicines. STATEMENT OF SIGNIFICANCE: Although thousands of nanomedicines have been developed, only a few have been approved for clinical use. The manufacturing complexity significantly hinders the "bench-to-bed" translation of nanomedicines. Hence, we need to rethink how to conduct research on translational nanomedicines by avoiding more and more complex chemistry and complicated nanostructures. Here, we summarize a plausible rule according to multiple supramolecular assembly pairs and propose a supramolecular assembly strategy that can improve the drug loading, tumor targeting, and manufacturing simplicity of nanomedicine for hydrophilic drugs. The supramolecular assembly strategy would guide a broader range of drug delivery to provide a new paradigm for developing easy-to-make but multifunctional nanoformulations for synergistic cancer treatment.

An intelligent DNA nanomachine for amplified MicroRNA imaging and MicroRNA-Guided efficient gene silencing

The DNA nanomachines as excellent synthetic biological tools have been widely used for the sensitive detection of intracellular microRNA (miRNA) and DNAzyme-involved gene silencing. However, intelligent DNA nanomachines which have the ability to sense intracellular specific biomolecules and respond to external information in complex environments still remain challenging. Herein, we develop a miRNA-responsive DNAzyme cascaded catalytic (MDCC) nanomachine to perform multilayer cascade reactions, enabling the amplified intracellular miRNA imaging and miRNA-guided efficient gene silencing. The intelligent MDCC nanomachine is designed based on multiple DNAzyme subunit-encoded catalyzed hairpin assembly (CHA) reactants sustained by the pH-responsive Zeolitic imidazolate framework-8 (ZIF-8) nanoparticles. After cellular uptake, the MDCC nanomachine degrades in acidic endosome and releases three hairpin DNA reactants and Zn2+, and the latter can act as an effective cofactor for DNAzyme. In the presence of miRNA-21, a catalytic hairpin assembly (CHA) reaction is triggered, which produces a large number of Y-shaped fluorescent DNA constructs containing three DNAzyme modules for gene silencing. The construction of Y-shaped DNA modified with multisite fluorescence and the circular reaction realizes ultrasensitive miRNA-21 imaging of cancer cells. Moreover, miRNA-guided gene silencing inhibits the cancer cell proliferation through the DNAzyme-specific recognition and cleavage of target EGR-1 (Early Growth Response-1) mRNA, which is one key tumor-involved mRNA. The strategy may provide a promising platform for highly sensitive determination of biomolecules and accurate gene therapy of cancer cells.

Gap-free genome assembly of anadromous Coilia nasus

The Chinese tapertail anchovy, Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information of C. nasus were hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome of C. nasus by incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination of de novo prediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes for C. nasus will provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.

A multi-scale map of protein assemblies in the DNA damage response.

The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).

Inferring Historical Introgression with Deep Learning.

Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample sizes, restricted phylogenetic topologies, or hypothesis testing. To overcome these difficulties, we developed a deep learning-based approach, named ERICA, for inferring genome-wide evolutionary relationships and local introgressed regions from sequence data. ERICA accepts sequence alignments of both population genomic data and multiple genome assemblies, and efficiently identifies discordant genealogy patterns and exchanged regions across genomes when compared with other methods. We further tested ERICA using real population genomic data from Heliconius butterflies that have undergone adaptive radiation and frequent hybridization. Finally, we applied ERICA to characterize hybridization and introgression in wild and cultivated rice, revealing the important role of introgression in rice domestication and adaptation. Taken together, our findings demonstrate that ERICA provides an effective method for teasing apart evolutionary relationships using whole genome data, which can ultimately facilitate evolutionary studies on hybridization and introgression.