Position In Sequence Research Articles

Analysis of the crystal structure of a parallel three-stranded coiled coil.

Here, we present the crystal structure of the synthetic peptide KE1, which contains four K-coil heptads separated in the middle by the QFLMLMF heptad. The structure determination reveals the presence of a canonical parallel three stranded coiled coil. The geometric characteristics of this structure are compared with other coiled coils with the same topology. Furthermore, for this topology, the analysis of the propensity of the single amino acid to occupy a specific position in the heptad sequence is reported. A number of viral proteins use specialized coiled coil tail needles to inject their genetic material into the host cells. The simplicity and regularity of the coiled coil arrangement made it an attractive system for de novo design of key molecules in drug delivery systems, vaccines, and therapeutics.

Tracking of dynamic gesture fingertips position in video sequence

Tracking of dynamic gesture fingertips position in video sequence

Elucidating Quadruplication Event of PHO1 Gene: A Key Regulator of Plant Phosphate Translocation in Brassica rapa

In response to Pi deprivation, phosphate 1 (PHO1) is a significant regulator at trans-eQTL hotspots in Brassica rapa. Brassica rapa short-read sequencing data analysis revealed four PHO1 paralog genes, PHO1_A, PHO1_B, PHO1_C, and PHO1_D, placed in tandem with very high sequence similarity. However, based on short-read genomic sequence data, only three transcripts are accessible. Five bacterial artificial chromosomes (BACs) can be sequenced using a long-read sequencer, which improves de novo assembly and identifies structural variants. The PHO1 gene’s quadruplicating tandem positions in the genomic sequence were confirmed by an analysis of long-read data. Transcript analysis identified only three groups of PHO1 paralogs (ortholog AT1G14040 in Arabidopsis), i.e., PHO1_A, PHO1_B, and PHO1_D, expressed in B. rapa leaf tissues under Pi deficiency. PHO1_A, with transcript ID XM_009150437.2, has five different splice variants found. These splice variants’ truncated proteins demonstrated PHO1_A’s function in P control as opposed to protein encoding.

Multi-Quantitative Assessment of AS-OCTA Complemented AS-OCT for Monitoring Filtering Bleb Function After Trabeculectomy.

The purpose of this study was to explore a quantitative grading system of the filtering bleb combined anterior segment optical coherence tomography angiography (AS-OCTA) vascular features and optical coherence tomography (OCT) morphological features. One hundred three eyes of 103 patients diagnosed with primary open-angle glaucoma and undergone trabeculectomy over 6 months were divided into success and failure groups according to postoperative intraocular pressure (IOP) level. Vessel density (VD) and vessel diameter index (VDI) were examined by AS-OCTA. Bleb's morphology, including bleb height (BH), and microcyst-structure (MCS) were detected by AS-OCT. Multi-vascular model score (MVMS) was calculated by comprehensive factor analysis, and the comprehensive grading system (MVMS-MCS-BH) was analyzed by linear regression. The efficiency our method was verified by receiver operating characteristic (ROC) analysis. The VD and VDI were higher in the failure group and closely related to post-trabeculectomy IOP (all P = 0.000). The MVMS was mostly consisted of VD in all regions, and VDIs of nasal, central, and temporal positions in sequence. MVMS ≥0, BH <1.33, and non-MCS were significantly associated with IOP increasing (coefficient = -3.23, -3.69, and 8.10, all P = 0.000). MVMS-BH-MCS got a higher area under curve (AUC), sensitivity, and specificity (0.92, 100%, and 80.30%) than the slit-lamp method (0.62, 72.20%, and 46.43%, respectively). The quantitative vascular characteristics detected by AS-OCTA were significant for the bleb monitor. The MVMS-BH-MCS grading system had achieved outstanding accuracy in reflecting the surgical results. The multi-vascular biomarker and comprehensive evaluation combined vascular and morphological parameters yield useful information on surgical outcomes, and help ophthalmologists to monitor patients effectively.

A Practical Survey on Faster and Lighter Transformers

Recurrent neural networks are effective models to process sequences. However, they are unable to learn long-term dependencies because of their inherent sequential nature. As a solution, Vaswani et al. introduced the Transformer, a model solely based on the attention mechanism that is able to relate any two positions of the input sequence, hence modelling arbitrary long dependencies. The Transformer has improved the state-of-the-art across numerous sequence modelling tasks. However, its effectiveness comes at the expense of a quadratic computational and memory complexity with respect to the sequence length, hindering its adoption. Fortunately, the deep learning community has always been interested in improving the models’ efficiency, leading to a plethora of solutions such as parameter sharing, pruning, mixed-precision, and knowledge distillation. Recently, researchers have directly addressed the Transformer’s limitation by designing lower-complexity alternatives such as the Longformer, Reformer, Linformer, and Performer. However, due to the wide range of solutions, it has become challenging for researchers and practitioners to determine which methods to apply in practice to meet the desired tradeoff between capacity, computation, and memory. This survey addresses this issue by investigating popular approaches to make Transformers faster and lighter and by providing a comprehensive explanation of the methods’ strengths, limitations, and underlying assumptions.

All-optical matching structure for multi-order modulation formats

With the development and popularity of the Internet, network security has become a popular topic. The traditional solution for screening the security of network information is to convert the signal transmitted in the optical fiber into an electrical signal through an optical conversion. Then we perform symbol matching within the electronic firewall to determine whether the signal is a risk. However, due to the limitation of carrier recovery time in the semiconductor, the photoelectric converter cannot handle signals with too high rate, and it also causes a large power consumption. To improve the efficiency and scalability of signal matching, we propose an all-optical matching structure. This structure can identify the position of the target sequence in the input data sequence in the all-optical environment, and the structure is suitable for any amplitude and phase modulation format. The matching result of each bit of the target sequence and input data sequence is obtained by phase delay and interference. Then the matching result of each bit of the target sequence and input data sequence is integrated by logic AND gate, regenerator, and delay line. Finally, the matching result between the whole target sequence and the input data sequence is obtained. This structure can avoid photoelectric transformation and processes the signal directly at the optical domain, which greatly reduces the consumption of time and energy. We use VPItransmissionMaker software to simulate and verify the structure. The length of the input signal during the simulation is 8 bits, the length of the target signal is 4 bits, and the transmission rate of the signal is 100 GBaud. We simulated the binary phase shift keying (BPSK), quadrature phase shift keying (QPSK), 8-phase shift keying (8PSK), and 16 quadrature amplitude modulation (16QAM) modulation formats and analyzed the noise performance of the system. The results show that the structure can achieve all-optical matching of high-speed optical signals in BPSK, QPSK, 8PSK, and 16QAM modulation formats and has good anti-noise performance.

Trouble développemental de la coordination et schéma corporel : l’entraînement du couplage perception-action en intervention psychomotrice

HypothesisDevelopmental coordination disorder (DCD) is explained by a defect of the perception-action coupling (PAC) prior to the intentional motor disorder, thus disrupting internal representations including the body schema. The study postulated that training the PAC through motor dissociation exercises would help children with DCD to implicitly develop their body schema (i.e., a function-oriented intervention with a bottom-up approach), observable through motor skills, spatial functions and self-perception. MethodA remote intervention was proposed to 13 children, aged 7 to 10 years, with DCD. Twice a week, for eight weeks, they watched video sessions each composed of an exercise of adaptation of the temporal adjustment of a motor pattern, an exercise of succession of segmental positions or of combination of distinct simultaneous movements, and an exercise of stabilization of an object on oneself during a postural sequence. ResultsThe practice of motor dissociations in the exercises allowed the children to significantly improve their motor skills (e.g., balance, jumping, coordination, manual speed and precision), spatial functions (e.g., mental rotation and visuo-constructive praxis) and self-perception (e.g., perceived physical appearance) with effect sizes ranging from moderate to high: min.: d=0.549 and P=0.048; max.: d=0.883 and P=0.001. ConclusionThe results suggest that PAC training refines sensorimotor representations with transfer effects on motor skills, spatial functions and self-perception. Future studies should confirm this interpretation. In summary, the study shows the effectiveness of a remote intervention in rehabilitation, validates the bottom-up approach, and underlines the importance of supporting children with DCD in the development of their body schema.

CovET: A covariation-evolutionary trace method that identifies protein structure–function modules

Measuring the relative effect that any two sequence positions have on each other may improve protein design or help better interpret coding variants. Current approaches use statistics and machine learning but rarely consider phylogenetic divergences which, as shown by Evolutionary Trace studies, provide insight into the functional impact of sequence perturbations. Here, we reframe covariation analyses in the Evolutionary Trace framework to measure the relative tolerance to perturbation of each residue pair during evolution. This approach (CovET) systematically accounts for phylogenetic divergences: at each divergence event, we penalize covariation patterns that belie evolutionary coupling. We find that while CovET approximates the performance of existing methods to predict individual structural contacts, it performs significantly better at finding structural clusters of coupled residues and ligand binding sites. For example, CovET found more functionally critical residues when we examined the RNA recognition motif and WW domains. It correlates better with large-scale epistasis screen data. In the dopamine D2 receptor, top CovET residue pairs recovered accurately the allosteric activation pathway characterized for Class A G protein-coupled receptors. These data suggest that CovET ranks highest the sequence position pairs that play critical functional roles through epistatic and allosteric interactions in evolutionarily relevant structure-function motifs. CovET complements current methods and may shed light on fundamental molecular mechanisms of protein structure and function.

EE171 Time to Diagnosis and Cost Effectiveness of Whole Exome Sequencing (WES) Position in the Diagnostic Pathways of Patients with Suspected Rare Genetic Disease

Patients with rare genetic diseases (RGD) experience a lengthy diagnostic odyssey, involving complex diagnostic testing pathways. Compared to standard genetic tests, whole exome sequencing (WES) has a higher diagnostic yield and has potential to decrease time to diagnosis which is important for patients with suspected RGD and their families. We estimated time-to-diagnosis and cost-effectiveness of WES at different points in the diagnostic pathway.

CNN–LSTM Neural Network for Identification of Pre-Cooked Pasta Products in Different Physical States Using Infrared Spectroscopy

Infrared (IR) spectroscopy is nondestructive, fast, and straightforward. Recently, a growing number of pasta companies have been using IR spectroscopy combined with chemometrics to quickly determine sample parameters. However, fewer models have used deep learning models to classify cooked wheat food products and even fewer have used deep learning models to classify Italian pasta. To solve these problems, an improved CNN–LSTM neural network is proposed to identify pasta in different physical states (frozen vs. thawed) using IR spectroscopy. A one-dimensional convolutional neural network (1D-CNN) and long short-term memory (LSTM) were constructed to extract the local abstraction and sequence position information from the spectra, respectively. The results showed that the accuracy of the CNN–LSTM model reached 100% after using principal component analysis (PCA) on the Italian pasta spectral data in the thawed state and 99.44% after using PCA on the Italian pasta spectral data in the frozen form, verifying that the method has high analytical accuracy and generalization. Therefore, the CNN–LSTM neural network combined with IR spectroscopy helps to identify different pasta products.

Trimer stability of Helicobacter pylori HtrA is regulated by a natural mutation in the protease domain

The human pathogen Helicobacter pylori is a major risk factor for gastric disease development. Serine protease HtrA is an important bacterial virulence factor that cleaves the cell junction proteins occludin, claudin-8 and E-cadherin, which causes gastric tissue damage. Using casein zymography, we discovered that HtrA trimer stability varies in clinical H. pylori strains. Subsequent sequence analyses revealed that HtrA trimer stability correlated with the presence of leucine or serine residue at position 171. The importance of these amino acids in determining trimer stability was confirmed by leucine-to-serine swapping experiments using isogenic H. pylori mutant strains as well as recombinant HtrA proteins. In addition, this sequence position displays a high sequence variability among various bacterial species, but generally exhibits a preference for hydrophilic amino acids. This natural L/S171 polymorphism in H. pylori may affect the protease activity of HtrA during infection, which could be of clinical importance and may determine gastric disease development.

Combinatorial gene therapy for epilepsy: Gene sequence positioning and AAV serotype influence expression and inhibitory effect on seizures.

Gene therapy with AAV vectors carrying genes for neuropeptide Y and its receptor Y2 has been shown to inhibit seizures in multiple animal models of epilepsy. It is however unknown how the AAV serotype or the sequence order of these two transgenes in the expression cassette affects the actual parenchymal gene expression levels and the seizure-suppressant efficacy. To address these questions, we compared three viral vector serotypes (AAV1, AAV2 and AAV8) and two transgene sequence orders (NPY-IRES-Y2 and Y2-IRES-NPY) in a rat model of acutely induced seizures. Wistar male rats were injected bilaterally with viral vectors and 3 weeks later acute seizures were induced by a subcutaneous injection of kainate. The latency until 1st motor seizure, time spent in motor seizure and latency to status epilepticus were measured to evaluate the seizure-suppressing efficacy of these vectors compared to an empty cassette control vector. Based on the results, the effect of the AAV1-NPY-IRES-Y2 vector was further investigated by in vitro electrophysiology, and its ability to achieve transgene overexpression in resected human hippocampal tissue was evaluated. The AAV1-NPY-IRES-Y2 proved to be better to any other serotype or gene sequence considering both transgene expression and ability to suppress induced seizures in rats. The vector also demonstrated transgene-induced decrease of glutamate release from excitatory neuron terminals and significantly increased both NPY and Y2 expression in resected human hippocampal tissue from patients with drug-resistant temporal lobe epilepsy. These results validate the feasibility of NPY/Y2 receptor gene therapy as a therapeutic opportunity in focal epilepsies.

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

Posttranslational modifications of proteins play essential roles in defining and regulating the functions of the proteins they decorate, making identification of these modifications critical to understanding biology and disease. Methods for enriching and analyzing a wide variety of biological and chemical modifications of proteins have been developed using mass spectrometry-based proteomics, largely relying on traditional database search methods to identify the resulting mass spectra of modified peptides. These database search methods treat modifications as static attachments of a mass to particular position in the peptide sequence, but many modifications undergo fragmentation in tandem mass spectrometry experiments alongside, or instead of, the peptide backbone. While this fragmentation can confound traditional search methods, it also offers unique opportunities for improved searches that incorporate modification-specific fragment ions. Here, we present a new labile mode in the MSFragger search engine that provides the flexibility to tailor modification-centric searches to the fragmentation observed. We show that labile mode can dramatically improve spectrum identification rates of phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides. Each of these modifications presents distinct fragmentation characteristics, showcasing the flexibility of MSFragger labile mode to improve search for a wide variety of biological and chemical modifications.

Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel NaV1.7

Gain-of-function mutations in voltage-gated sodium channel NaV1.7 cause severe inherited pain syndromes, including inherited erythromelalgia (IEM). The structural basis of these disease mutations, however, remains elusive. Here, we focused on three mutations that all substitute threonine residues in the alpha-helical S4-S5 intracellular linker that connects the voltage sensor to the pore: NaV1.7/I234T, NaV1.7/I848T, and NaV1.7/S241T in order of their positions in the amino acid sequence within the S4-S5 linkers. Introduction of these IEM mutations into the ancestral bacterial sodium channel NaVAb recapitulated the pathogenic gain-of-function of these mutants by inducing a negative shift in the voltage dependence of activation and slowing the kinetics of inactivation. Remarkably, our structural analysis reveals a common mechanism of action among the three mutations, in which the mutant threonine residues create new hydrogen bonds between the S4-S5 linker and the pore-lining S5 or S6 segment in the pore module. Because the S4-S5 linkers couple voltage sensor movements to pore opening, these newly formed hydrogen bonds would stabilize the activated state substantially and thereby promote the 8 to 18 mV negative shift in the voltage dependence of activation that is characteristic of the NaV1.7 IEM mutants. Our results provide key structural insights into how IEM mutations in the S4-S5 linkers may cause hyperexcitability of NaV1.7 and lead to severe pain in this debilitating disease.

Genetic diversity and bioinformatic analysis in the L1 gene of HPV genotypes 31, 33, and 58 circulating in women with normal cervical cytology

BackgroundHPV-31, -33, and -58, along with HPV-45 and -52, account for almost 11% of HPV-associated cancers. Our previous studies showed that after HPV-16 and -51, HPV-58 was common and HPV-31 was as frequent as HPV-18 among Iranian women with normal cytology. Hence, in this study, we aimed to investigate the intra-type variations in L1 genes of HPV-58, -31, and -33 to find the predominant lineages circulating in women with normal cytology.MethodsComplete coding sequencing of the L1 gene was amplified and nucleotide and amino acid sequences were compared to those of the references. The selective pressure on L1 protein and whether the variations of the L1 genes embed in L1 loops, or N-glycosylated sites were also investigated.ResultsB1, A, and A1 (sub)lineages were common in the HPV-58, -33, and -31 samples, respectively. Ninety nucleotide mutations were observed. Twenty nine nucleotide changes corresponded to nonsynonymous substitutions in which seventeen mutations were located in L1 loops. Only one codon position in HPV-58 sequences was found as the positive selection. No difference was observed in N-glycosylation sites between reference and understudied amino acid sequences.ConclusionIn the current study, we reported, for the first time, the (sub) lineages, amino acid, and genetic diversity in the L1 gene of circulating HPV-58, -33, and -31, in women with normal cytology, in Iran. Such studies can not only have epidemiological values, but also aid to set vaccination programs.

Ranking parameters driving siring success during sperm competition in the North African houbara bustard

Sperm competition is a powerful force driving the evolution of ejaculate and sperm traits. However, the outcome of sperm competition depends on many traits that extend beyond ejaculate quality. Here, we study male North African houbara bustards (Chlamydotis undulata undulata) competing for egg fertilization, after artificial insemination, with the aim to rank the importance of 14 parameters as drivers of siring success. Using a machine learning approach, we show that traits independent of male quality (i.e., insemination order, delay between insemination and egg laying) are the most important predictors of siring success. Traits describing intrinsic male quality (i.e., number of sperm in the ejaculate, mass motility index) are also positively associated with siring success, but their contribution to explaining the outcome of sperm competition is much lower than for insemination order. Overall, this analysis shows that males mating at the last position in the mating sequence have the best chance to win the competition for egg fertilization. This raises the question of the importance of female behavior as determinant of mating order.

Colorimetric Detection of S1 Nuclease Activity using a Hairpin DNA with Split G-Quadruplex

Hairpin DNA containing split G-quadruplex at its terminus displayed tagging position-dependent horseradish peroxidase activity. In general, the hairpin DNA coupled with one GGG repeat at its 5’-terminus and three GGG repeats at its 3′-terminus demonstrated strong catalytic activity, while slight activity was observed after exchanging the position of split G-quadruplex sequence. Inspired by these observations, a novel colorimetric biosensor for nuclease activity assay was developed by selecting S1 nuclease as the model. Specifically, S1 nuclease cleaves the split G-quadruplex into mono- or oligonucleotide fragments, thereby suppressing the catalytic activity, accompanied by a color change from blue to colorless. Under optimum conditions, S1 nuclease was determined with a linear range from 1.60 to 17.6 U/mL and a detection limit of 1.458 U/mL. The constructed method was simple and did not require complex sequence design, expensive instrumentation, and probe labeling. Most importantly, this work facilitates a better understanding of the catalytic mechanism of the DNAzyme and provides an example of the practical application of G-quadruplex-based DNAzyme.

The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios

Photosynthesis is the predominant biochemical process of carbon dioxide assimilation in the biosphere. To reduce carbon dioxide into organic compounds, photosynthetic organisms have one or two distinct photochemical reaction centre complexes with which they capture solar energy and generate ATP and reducing power. The core polypeptides of the photosynthetic reaction centres show low homologies but share overlapping structural folds, overall architecture, similar functional properties and highly conserved positions in protein sequences suggesting a common ancestry. However, the other biochemical components of photosynthetic apparatus appear to be a mosaic resulting from different evolutionary trajectories. The current proposal focusses on the nature and biosynthetic pathways of some organic redox cofactors that participate in the photosynthetic systems: quinones, chlorophyll and heme rings and their attached isoprenoid side chains, as well as on the coupled proton motive forces and associated carbon fixation pathways. This perspective highlights clues about the involvement of the phosphorus and sulphur chemistries that would have shaped the different types of photosynthetic systems.

Activation of Human CD8+ T Cells with Nitroso Dapsone-Modified HLA-B*13:01-Binding Peptides.

Previous studies have shown that cysteine-reactive drug metabolites bind covalently with protein to activate patient T cells. However, the nature of the antigenic determinants that interact with HLA and whether T cell stimulatory peptides contain the bound drug metabolite has not been defined. Because susceptibility to dapsone hypersensitivity is associated with the expression of HLA-B*13:01, we have designed and synthesized nitroso dapsone-modified, HLA-B*13:01 binding peptides and explored their immunogenicity using T cells from hypersensitive human patients. Cysteine-containing 9-mer peptides with high binding affinity to HLA-B*13:01 were designed (AQDCEAAAL [Pep1], AQDACEAAL [Pep2], and AQDAEACAL [Pep3]), and the cysteine residue was modified with nitroso dapsone. CD8+ T cell clones were generated and characterized in terms of phenotype, function, and cross-reactivity. Autologous APCs and C1R cells expressing HLA-B*13:01 were used to determine HLA restriction. Mass spectrometry confirmed that nitroso dapsone-peptides were modified at the appropriate site and were free of soluble dapsone and nitroso dapsone. APC HLA-B*13:01-restricted nitroso dapsone-modified Pep1- (n = 124) and Pep3-responsive (n = 48) CD8+ clones were generated. Clones proliferated and secreted effector molecules with graded concentrations of nitroso dapsone-modified Pep1 or Pep3. They also displayed reactivity against soluble nitroso dapsone, which forms adducts in situ, but not with the unmodified peptide or dapsone. Cross-reactivity was observed between nitroso dapsone-modified peptides with cysteine residues in different positions in the peptide sequence. These data characterize a drug metabolite hapten CD8+ T cell response in an HLA risk allele-restricted form of drug hypersensitivity and provide a framework for structural analysis of hapten HLA binding interactions.

Universal Stress Proteins: From Gene to Function

Universal stress proteins (USPs) exist across a wide range of species and are vital for survival under stressful conditions. Due to the increasingly harsh global environmental conditions, it is increasingly important to study the role of USPs in achieving stress tolerance. This review discusses the role of USPs in organisms from three aspects: (1) organisms generally have multiple USP genes that play specific roles at different developmental periods of the organism, and, due to their ubiquity, USPs can be used as an important indicator to study species evolution; (2) a comparison of the structures of USPs reveals that they generally bind ATP or its analogs at similar sequence positions, which may underlie the regulatory role of USPs; and (3) the functions of USPs in species are diverse, and are generally directly related to the stress tolerance. In microorganisms, USPs are associated with cell membrane formation, whereas in plants they may act as protein chaperones or RNA chaperones to help plants withstand stress at the molecular level and may also interact with other proteins to regulate normal plant activities. This review will provide directions for future research, focusing on USPs to provide clues for the development of stress-tolerant crop varieties and for the generation of novel green pesticide formulations in agriculture, and to better understand the evolution of drug resistance in pathogenic microorganisms in medicine.