Linear Sequence Research Articles

Molecular evolution of the mammalian kinetochore complex.

Mammalian centromeres are satellite-rich chromatin domains that serve as sites for kinetochore complex assembly. Centromeres are highly variable in sequence and satellite organization across species, but the processes that govern the co-evolutionary dynamics between rapidly evolving centromeres and their associated kinetochore proteins remain poorly understood. Here, we pursue a course of phylogenetic analyses to investigate the molecular evolution of the complete kinetochore complex across primate and rodent species with divergent centromere repeat sequences and features. We show that many protein components of the core centromere associated network (CCAN) harbor signals of adaptive evolution, consistent with their intimate association with centromere satellite DNA and roles in the stability and recruitment of additional kinetochore proteins. Surprisingly, CCAN and outer kinetochore proteins exhibit comparable rates of adaptive divergence, suggesting that changes in centromere DNA can ripple across the kinetochore to drive adaptive protein evolution within distant domains of the complex. Our work further identifies kinetochore proteins subject to lineage-specific adaptive evolution, including rapidly evolving proteins in species with centromere satellites characterized by higher-order repeat structure and lacking CENP-B boxes. Thus, features of centromeric chromatin beyond the linear DNA sequence may drive selection on kinetochore proteins. Overall, our work spotlights adaptively evolving proteins with diverse centromere-associated functions, including centromere chromatin structure, kinetochore protein assembly, kinetochore-microtubule association, cohesion maintenance, and DNA damage response pathways. These adaptively evolving kinetochore protein candidates present compelling opportunities for future functional investigations exploring how their concerted changes with centromere DNA ensure the maintenance of genome stability.

A nonlinear Filbert-like matrix with three free parameters: From linearity to nonlinearity

Abstract Filbert and Lilbert matrices are defined by terms of linear Fibonacci-like sequences. By considering terms of such linear recurrences and additional free parameters, we define a nonlinear variant of these matrices via ratios of q-forms of terms of Fibonacci-like sequences whose indices are in nonlinear forms. We derive explicit formulae for the matrices L and U come from LU-decomposition, their inverses, inverse of the main matrices and their determinants.

Protecting Group-Free Total Synthesis of (-)-Boscartin H.

Herein, we report the first protecting group-free total synthesis of (-)-boscartin H, which features a 5-12-5-fused tricyclic structure. The key steps, which include a diastereoselective THF-ring-forming/aldol reaction sequence and ring-closing metathesis, afforded high stereoselectivity with (-)-boscartin H obtained in 3.6% overall yield using a 11-step long linear sequence. In addition, X-ray crystallography clearly confirmed the stereochemistry of boscartin H.

On multiplicative dependent vectors with coordinates from certain higher order recurrences

In this paper, we prove that there are finitely many multiplicative dependent vectors with coordinates from non-degenerate linear recurrence sequences [Formula: see text] of a fixed order [Formula: see text] These sequences satisfy the recurrence relation [Formula: see text] with initials [Formula: see text]. Here, the coefficients of the recurrence relation are positive integers satisfying [Formula: see text] or [Formula: see text] In both these conditions, [Formula: see text]

LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here, we report linear amplification-based bisulfite sequencing (LABS), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.

Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases.

Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics.

On Robustness for the Skolem, Positivity and Ultimate Positivity Problems

The Skolem problem is a long-standing open problem in linear dynamical systems: can a linear recurrence sequence (LRS) ever reach 0 from a given initial configuration? Similarly, the positivity problem asks whether the LRS stays positive from an initial configuration. Deciding Skolem (or positivity) has been open for half a century: the best known decidability results are for LRS with special properties (e.g., low order recurrences). But these problems are easier for "uninitialized" variants, where the initial configuration is not fixed but can vary arbitrarily: checking if there is an initial configuration from which the LRS stays positive can be decided in polynomial time (Tiwari in 2004, Braverman in 2006). In this paper, we consider problems that lie between the initialized and uninitialized variants. More precisely, we ask if 0 (resp. negative numbers) can be avoided from every initial configuration in a neighborhood of a given initial configuration. This can be considered as a robust variant of the Skolem (resp. positivity) problem. We show that these problems lie at the frontier of decidability: if the neighbourhood is given as part of the input, then robust Skolem and robust positivity are Diophantine hard, i.e., solving either would entail major breakthroughs in Diophantine approximations, as happens for (non-robust) positivity. However, if one asks whether such a neighbourhood exists, then the problems turn out to be decidable with PSPACE complexity. Our techniques also allow us to tackle robustness for ultimate positivity, which asks whether there is a bound on the number of steps after which the LRS remains positive. There are two variants depending on whether we ask for a "uniform" bound on this number of steps. For the non-uniform variant, when the neighbourhood is open, the problem turns out to be tractable, even when the neighbourhood is given as input.

DEAttentionDTA: protein-ligand binding affinity prediction based on dynamic embedding and self-attention.

Predicting protein-ligand binding affinity is crucial in new drug discovery and development. However, most existing models rely on acquiring 3D structures of elusive proteins. Combining amino acid sequences with ligand sequences and better highlighting active sites are also significant challenges. We propose an innovative neural network model called DEAttentionDTA, based on dynamic word embeddings and a self-attention mechanism, for predicting protein-ligand binding affinity. DEAttentionDTA takes the 1D sequence information of proteins as input, including the global sequence features of amino acids, local features of the active pocket site, and linear representation information of the ligand molecule in the SMILE format. These three linear sequences are fed into a dynamic word-embedding layer based on a 1D convolutional neural network for embedding encoding and are correlated through a self-attention mechanism. The output affinity prediction values are generated using a linear layer. We compared DEAttentionDTA with various mainstream tools and achieved significantly superior results on the same dataset. We then assessed the performance of this model in the p38 protein family. The resource codes are available at https://github.com/whatamazing1/DEAttentionDTA.

How to Implement Authentic Scenario-Based Training

When used in the UK, scenarios are commonly positioned at the end of a linear training sequence where they are often used to test skills after the isolated practice of those skills has been completed. In contrast to the above view, authentic SBT is an approach based on concepts, tactics, and strategies, rather than skill. The focus is on introducing increasingly complex ‘whole’ scenarios (i.e., radio-call to event resolution) as training progresses. SBT has been shown to improve officer performance under pressure when high-fidelity (i.e., realistic) scenarios are used in this way in integrated de-escalation and use-of-force training. The challenges to implement authentic SBT are significant. When used in inappropriate ways, SBT will struggle to gain acceptance. However, when practice is premised on authentic SBT, it can be an important catalyst for changes to training.

Early research on anther-smut disease: A fuller view of science?

The anther-smut host-pathogen system has provided extensive insights into the evolutionary ecology of disease resistance, transmission modes, host shifts, pathogen specialization, and disease evolution in metapopulations. It also has led to unexpected insights into sex ratio distorters, sex chromosome evolution, and transposable elements in fungi. In addition, anther-smut disease played a major role in Linnaeus' germ theory and the correspondence on parasitic castration between Darwin and Becker, one of the first female botanists. Here, we explicitly highlight some of the realities in the process of science, using an unusual autobiographical approach to describe how we came to collaborate on this system in the 1980s. Using perspectives from our different career stages, we present a surprising narrative that could not be deduced from merely reading the published papers. While our work was grounded in previous ecological and evolutionary theory, it was the product as much of empirical failures and intellectual roadblocks, as the result of a progressive scientific method. Our experiences illustrate not only the "human dimension of science" but more importantly show that linear sequences of hypothesis testing do not necessarily lead to new study systems and new ideas. We suggest there is a need to re-evaluate the scientific method in ecology and evolution, especially where the challenge is to engage in a productive dialog between natural history and theory.

Global seroprevalence of neutralizing antibodies against adeno-associated virus serotypes used for human gene therapies

Adeno-associated virus (AAV) vectors are promising gene therapy candidates, but pre-existing anti-AAV neutralizing antibodies (NAbs) pose a significant challenge to successful gene delivery. Knowledge of NAb seroprevalence remains limited and inconsistent. We measured activity of NAbs against six clinically relevant AAV serotypes across 10 countries in adults (n= 502) and children (n= 50) using a highly sensitive transduction inhibition assay. NAb prevalence was generally highest for AAV1 and lowest for AAV5. There was considerable variability across countriesand geographical regions. NAb prevalence increased with age and was higher in females, participants of Asian ethnicity, and participants in cancer trials. Co-prevalence was most frequently observed between AAV1 and AAV6 and less frequently between AAV5 and other AAVs. Machine learning analyses revealed a unique clustering of AAVs that differed from previous phylogenetic classifications. These results offer insights into the biological relationships between the immunogenicity of AAVs in humans beyond that observed previously using standard clades, which are based on linear capsid sequences. Our findings may inform improved vector design and facilitate the development of AAV vector-mediated clinical gene therapies.

The ring of finite algebraic numbers and its application to the law of decomposition of primes

In this paper, we develop an explicit method to express finite algebraic numbers (in particular, certain idempotents among them) in terms of linear recurrent sequences, and give applications to the characterization of the splitting primes in a given finite Galois extension over the rational field.

Chemoenzymatic Synthesis of N,N,N‐Trimethyl‐D‐Glucosamine Chitotriomycin and Its Analogues

Comprehensive SummaryN,N,N‐Trimethyl‐D‐glucosamine (TMG)‐chitotriomycin, a naturally occurring chitin related oligosaccharide, is a specific β‐N‐acetylhexosaminidases (HexNAcases) inhibitor for insects and fungi. Although TMG‐chitoriomycin holds great promise as a novel class insecticide and fungicide, the limited accessibility of TMG‐chitotriomycin prevents its further biological evaluation. We report herein a simple and eco‐friendly chemoenzymatic approach for the efficient synthesis of TMG‐chitotriomycin and its analogues. In this strategy, the readily available chitosan was enzymatically hydrolyzed and chemically N‐acetylated to afford the chitooligosaccharides ranging from disaccharide to hexasaccharide. These chitooligosaccharides were selectively deacetylated by two different chitin deacetylases followed by chemical N‐trimethylation to obtain the desired TMG‐chitotriomycin and a total of 13 TMG‐chitotriomycin analogues in the longest linear sequence of 4 steps in over 12% total yields.

High-throughput nanopore DNA sequencing of large insert fosmid clones directly from bacterial colonies.

Fosmids and cosmids are vectors frequently used in functional metagenomic studies. With a large insert capacity (around 30 kb) they can encode dozens of cloned genes or in some cases, entire biochemical pathways. Fosmids with cloned inserts can be transferred to heterologous hosts and propagated to enable screening for new enzymes and metabolites. After screening, fosmids from clones with an activity of interest must be de novo sequenced, a critical step toward the identification of the gene(s) of interest. In this work, we present a new approach for rapid and high-throughput fosmid sequencing directly from Escherichia coli colonies without liquid culturing or fosmid purification. Our sample preparation involves fosmid amplification with phi29 polymerase and then direct nanopore sequencing using the Oxford Nanopore Technologies system. We also present a bioinformatics pipeline termed "phiXXer" that facilitates both de novo read assembly and vector trimming to generate a linear sequence of the fosmid insert. Finally, we demonstrate the accurate sequencing of 96 fosmids in a single run and validate the method using two fosmid libraries that contain cloned large insert (~30-40 kb) genomic or metagenomic DNA.IMPORTANCELarge-insert clone (fosmids or cosmids) sequencing is challenging and arguably the most limiting step of functional metagenomic screening workflows. Our study establishes a new method for high-throughput nanopore sequencing of fosmid clones directly from lysed Escherichia coli cells. It also describes a companion bioinformatic pipeline that enables de novo assembly of fosmid DNA insert sequences. The devised method widens the potential of functional metagenomic screening by providing a simple, high-throughput approach to fosmid clone sequencing that dramatically speeds the pace of discovery.

POSoligo software for in vitro gene synthesis

Oligonucleotide synthesis is vital for molecular experiments. Bioinformatics has been employed to create various algorithmic tools for the in vitro synthesis of nucleotides. The main approach to synthesizing long-chain DNA molecules involves linking short-chain oligonucleotides through ligase chain reaction (LCR) and polymerase chain reaction (PCR). Short-chain DNA molecules have low mutation rates, while LCR requires complementary interfaces at both ends of the two nucleic acid molecules or may alter the conformation of the nucleotide chain, leading to termination of amplification. Therefore, molecular melting temperature, length, and specificity must be considered during experimental design. POSoligo is a specialized offline tool for nucleotide fragment synthesis. It optimizes the oligonucleotide length and specificity based on input single-stranded DNA, producing multiple contiguous long strands (COS) and short patch strands (POS) with complementary ends. This process ensures free 5′- and 3′-ends during oligonucleotide synthesis, preventing secondary structure formation and ensuring specific binding between COS and POS without relying on stabilizing the complementary strands based on Tm values. POSoligo was used to synthesize the linear RBD sequence of SARS-CoV-2 using only one DNA strand, several POSs for LCR ligation, and two pairs of primers for PCR amplification in a time- and cost-effective manner.

Approximation properties of the univariate and bivariate Bernstein-Stancu operators of max-product kind

This paper presents the nonlinear maximum product type of univariate and bivariate Bernstein–Stancu operators and uses new definitions to investigate the approximation properties. The order of approximation obtained with the nonlinear maximum product type of operator sequences would be better than the degree of approximation of the known linear operator sequences.

Total Synthesis of the Conjugation-Ready Tetrasaccharide Repeating Unit of Shewanella japonica Type Strain KMM 3299T.

Here we report the first total synthesis of the conjugation-ready tetrasaccharide repeating unit of Shewanella japonica type strain KMM 3299T. The presence of rare deoxyamino sugars and installation of three consecutive 1,2-cis glycosidic linkages makes the synthesis formidable. The challenging late-stage oxidation was overcome by using a galacturonate donor. The total synthesis was completed via a longest linear sequence of 22 steps in an overall yield of 3.5% starting from d-mannose.

Flexible and Convergent Enantioselective Total Synthesis of (R)-Juglanaloids A and B: Two Phthalide Spiro Alkaloids with Potential Alzheimer's Disease Inhibitory Activity.

Juglanaloids A and B are recently isolated natural products characterized by an unprecedented spiro bicyclic isobenzofuranone-tetrahydrobenzazepinone framework and a promising antiamyloid activity. Here reported is a straightforward convergent total synthesis of these natural products, which were obtained in high enantiomeric purity (94% and >99% ee for juglanaloids A and B, respectively) through an eight-step longest linear sequence, based on an efficient and reliable enantioselective phase-transfer-catalyzed alkylation step. Considering the interesting biological activity of juglanaloids, this convenient, highly enantioselective, flexible, and predictable synthetic strategy promises to be a powerful tool for accessing potentially bioactive spiro bicyclic phthalide-tetrahydrobenzazepinone derivatives.

A study of extractive summarization of long documents incorporating local topic and hierarchical information

In recent years, the transformer-based language models have achieved remarkable success in the field of extractive text summarization. However, there are still some limitations in this kind of research. First, the transformer language model usually regards the text as a linear sequence, ignoring the inherent hierarchical structure information of the text. Second, for long text data, traditional extractive models often focus on global topic information, which poses challenges in how they capturing and integrating local contextual information within topic segments. To address these issues, we propose a long text extractive summarization model that employs a local topic information extraction module and a text hierarchical extraction module to capture the local topic information and document's hierarchical structure information of the original text. Our approach enhances the ability to determine whether a sentence belongs to the summary. In this experiment, ROUGE score is used as the experimental evaluation index, and evaluates the model on three large public datasets. Through experimental validation, the model demonstrates superior performance in terms of ROUGE-1, ROUGE-2, and ROUGE-L scores compared to current mainstream summarization models, affirming the effectiveness of incorporating local topic information and document hierarchical structure into the model.

CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes

RNA sequencing (RNA-seq) technology has become one of the standard tools for studying biological mechanisms at the transcriptome level. Advances in RNA-seq technology have led to the development of numerous publicly available tools for RNA-seq data analysis. Most of these tools target linear genome sequences despite the necessity of studying organisms with circular genome sequences. For example, studying the infection mechanisms of viroids which comprise 246–401 nucleotides circular RNAs and target plants may prevent tremendous economic and agricultural damage. Unfortunately, using the available tools to construct workflows for the analysis of circular genome sequences is difficult, especially for non-bioinformaticians. To overcome this limitation, we present CircSeqAlignTk, an easy-to-use and richly documented R package. CircSeqAlignTk offers both command line and graphical user interfaces for end-to-end RNA-seq data analysis, spanning alignment to the visualisation of circular genome sequences, via a series of functions. Moreover, it includes a feature to generate synthetic sequencing data that mirrors real RNA-seq data from biological experiments. CircSeqAlignTk not only provides an easy-to-use analysis interface for novice users but also allows developers to evaluate the performance of alignment tools and new workflows.