Individual Sequences Research Articles

Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination.

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.

Population Genomics of Nonrecessive Resistance to Bt Toxin Cry1Ac in Helicoverpa armigera From Northern China.

Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis (Bt) have provided control of some key pests since 1996. However, the evolution of resistance by pests reduces the benefits of Bt crops. Resistance to Bt crops that is not recessively inherited is especially challenging to manage. Here we analyzed nonrecessive resistance to Bt toxin Cry1Ac in eight field populations of Helicoverpa armigera sampled in 2018 from northern China, where this global pest has been exposed to Cry1Ac in Bt cotton since 1997. Bioassays revealed 7.5% of field-derived larvae were resistant to Cry1Ac of which 87% had at least one allele conferring nonrecessive resistance. To analyze this nonrecessive resistance, we developed and applied a variant of a genomic mapping approach called quantitative trait locus (QTL)-seq. This analysis identified a region on chromosome 10 associated with nonrecessive resistance to Cry1Ac in all 21 backcross families derived from field-collected moths. Individual sequencing revealed that all 21 field-collected resistant grandparents of the backcross families had a previously identified dominant point mutation in the tetraspanin gene HaTSPAN1 that occurs in the region of chromosome 10 identified by QTL-seq. QTL-seq also revealed a region on chromosome 26 associated with nonrecessive resistance in at most 14% of the backcross families. Overall, the results imply the point mutation in HaTSPAN1 is the primary genetic basis of nonrecessive resistance to Cry1Ac in field populations of H. armigera from northern China. Moreover, because nonrecessive resistance is predominant, tracking the frequency of this point mutation could facilitate resistance monitoring in the region.

A review of HLA matching to improve clinical outcome in bone marrow transplants and the role of haplotyping in unrelated donor transplants

When the first allogeneic bone marrow transplants in humans was attempted, little was known of the major histocompatibility complex (HLA) and its role in ensuring success of the graft. Therefore, many of the early attempts resulted in failure. During the 1970s just a small number of alleles were detected serologically and the mixed lymphocyte reaction (MLR) served as a surrogate for class II matching, the DR series of alleles not being formally serologically defined until 1978. Nevertheless, selection of nuclear family members who were two HLA haplotype matched became possible using serology and the MLR and transplant successes were reported. The breakthrough in technology was undoubtedly the introduction of DNA techniques, particularly DNA sequencing. This enabled fully matched unrelated individuals to be found as potential bone marrow donors. Genetic phasing or haplotyping of unrelated donors who are found on bone marrow registries has remained elusive until recently. The development of individual chromosome sequencing will permit haplotype matching in the absence of family studies and will expedite studies aimed at identifying other genes which are important matching factors. AIM: The aim of this review is to outline the technological advances that have been made in HLA genotyping over the last 50 years. The progress from serology to DNA sequence as part of the matching algorithm is one of the reasons clinical results have improved so much during this period. This review outlines the DNA techniques that have been utilised for this purpose, concluding with a discussion of the value of haplotype matching in unrelated donor transplants, where the donor has been sourced from a bone marrow registry. Haplotype matching represents one of the last remaining hurdles to be overcome in unrelated donor bone marrow transplants.

Evaluation of frequency, severity, and independent risk factors for recurrence of disease activity after fingolimod discontinuation in a large real-world cohort of patients with multiple sclerosis.

Clinical and radiological signs of recurring disease activity (RDA) have been described in patients with multiple sclerosis (pwMS) after discontinuation of fingolimod (FGL). To describe frequency, severity and potential risk factors for RDA after FGL discontinuation in a large real-world cohort of pwMS. Post-FGL RDA was defined as evidence of clinical and/or radiological activity within 6 months after FGL discontinuation. Relapses with Expanded Disability Status Scale increase ⩾2 points and/or magnetic resonance imaging (MRI) activity with at least five cerebral gadolinium-enhancing lesions and/or ⩾6 cerebral new T2 lesions were defined as severe recurring disease activity (sRDA). Using a multivariate logistic model, we explored the influence of age, disease duration, sex, clinical, and MRI activity under FGL on the occurrence of RDA. We identified 110 pwMS who discontinued FGL. Thirty-seven (33.6%) developed post-FGL RDA and 13 (11.8%) also fulfilled criteria for sRDA. Younger age at diagnosis [odds ratio (OR) = 1.10, p < 0.01], shorter disease duration (OR = 1.17, p < 0.01), and MRI activity under FGL (OR = 2.92, p = 0.046) were independent risk factors for the occurrence of post-FGL RDA. Individual risk assessment and optimal treatment sequencing can help to minimize the risk of post-FGL RDA. Early switch to highly effective disease-modifying therapy might reduce occurrence of post-FGL RDA.

Model-Free Undetectable Attacks on Linear Systems Using LWE-Based Encryption

We show that the homomorphic property, a desired property in encrypted control, can lead to failure in the cyber defense of a dynamical control system from undetectable attacks, even though individual signal sequences remain unknown to the attacker. We consider an encryption method based on the Learning with Errors (LWE) problem and demonstrate how model-free undetectable attacks on linear systems over integers can be computed from sampled inputs and outputs that are encrypted. Previous work has shown that computing such attacks is possible on nonencrypted systems. Applying this earlier work to our scenario, with minor modifications, typically amplifies the error in encrypted messages unless a short vector problem is solved. Given that an attacker obtains a short vector, we derive the probability that the attack is detected and show how it explicitly depends on the encryption parameters. Finally, we simulate an attack obtained by our method on an encrypted linear system over integers and conduct an analysis of the probability that the attack will be detected.

Visualizing Population Structures by Multidimensional Scaling of Smoothed PCA-Transformed Data

Population structure can be revealed using Single Nucleotide Polymorphisms (SNPs) which are genetic variations found in the DNA sequences of individuals. Due to the large number of SNPs, visualization of SNP data is often achieved through dimensionality reduction. Although Principal Component Analysis (PCA) has been extensively used for SNP data visualization, some other dimensionality reduction methods have been shown to be more successful in revealing complex population structures. Nevertheless, these techniques often suffer from reduced ability to preserve the global structure in the SNP data, namely the relative genetic distance between subpopulations, or from high computational cost. In this work, a method which uses Multidimensional Scaling (MDS) of smoothed PCA-transformed data (MSSPD) is proposed. MSSPD successfully reveals population structures in 2D maps, while being more effective than other techniques in preserving the global structure. In terms of computational efficiency, MSSPD is comparable to the fastest SNP visualization methods.

Formamide-Free Genomic In Situ Hybridization (ff-GISH).

Fluorescence in situ hybridization allows for the mapping of various sequence types in the genomes and is thus widely used in structural, functional, and evolutionary studies. One particular type of in situ hybridization that specifically allows to map whole parental genomes in diploid and polyploid hybrids is genomic in situ hybridization (GISH). The efficiency of GISH, i.e., the specificity of hybridization of genomic DNA probes to the parental subgenomes in hybrids depends, among others, on the age of the polyploids and the similarity of the parental genomes, specifically their repetitive DNA fractions. Typically, high levels of overall repeat similarity between the parental genomes result in lower efficiency of GISH. Here, we present the formamide-free GISH (ff-GISH) protocol that can be applied to diploid and polyploid hybrids of both monocots and dicots. ff-GISH allows higher efficiency of the labeling of the putative parental genomes compared to the standard GISH protocol and allows discrimination of parental chromosome sets that share up to 80-90% repeat similarity. This modified method is nontoxic, is simple, and lends itself to modifications. It can also be used for standard FISH and mapping of individual sequence types in chromosomes/genomes.

Oxygen Consumption and Heart Rate Responses in Different Vinyasa Yoga Sequences.

Yoga is widely practiced for its numerous health benefits, and it can also increase energy expenditure. Vinyasa yoga, a system of hatha yoga, meets criteria for moderate-intensity physical activity. It is unclear whether the individual sequences produce different oxygen consumption (VO2) and heart rate responses. The purpose of the present study was therefore to evaluate potential differences in VO2 and heart rate responses across sequences of a 60-minute vinyasa session. Participants included 40 healthy male (n = 20) and female (n = 20) adults (age 30.9 ± 8.8 y) with self-reported yoga experience. The sequence implemented was based on Baron Baptiste's Journey into Power sequence. This vinyasa yoga practice included several sequences: integration, sun salutation, crescent lunges, balancing, standing, back bending, and restorative. VO2 (mL/kg/min) was measured by portable indirect calorimetry and expressed as metabolic equivalents (MET). Heart rate was measured using a Polar HR monitor and presented as a percentage of age-predicted maximal heart rate (APMHR). METs and APMHR differed significantly across sequences (each p < 0.001). METs for the integration, sun-salutation, crescent-lunges, balancing, standing, back-bending, and restorative sequences were significantly different from one another (p < 0.001); balancing and back-bending sequences, however, were similar. During the integration and restorative sequences, APMHR was similar (p = 1.00) and significantly lower compared to sun-salutation, crescent-lunge, balancing, standing, and back-bending sequences (each p < 0.001). METs and APMHR differed significantly across sequences of a vinyasa yoga practice. These data could inform an individualized yoga series based on current fitness levels to maintain or improve cardiorespiratory fitness.

Защитное действие вакцинации против кори, краснухи и паротита в отношении COVID-19

Based on the results of studies, it has been shown that vaccination against measles, mumps rubella (MMR) can prevent mortality and severe forms of COVID-19 in vulnerable groups of the population. It was found that the high level of vaccination coverage against MMR was inversely correlated with the mortality rate from COVID-19 – the higher the vaccination rate against MMR, the lower the number of mortality from COVID-19 and severe forms. The effect of MMR immunization on the incidence of COVID-19 is explained by correspondence between COVID-19 virus proteins and MMR viruses. The results of studies conducted in various countries and have shown that the effect of protection against COVID-19 is based on the homology of individual sequences of SARS-CoV-2 coronavirus proteins with MMR viruses. The similarity of the SARS-COV-2 virus with the MMR viruses allows the MMR vaccine to be used for mass use for non-specific protection against COVID-19. In order to increase the effectiveness of vaccination against MMR in people with impaired health, the use of immunomodulatory drugs is recommended. This approach not only increases specific immunity against vaccinated infections, but also enhances nonspecific protection against COVID-19. Key words: SARS-CoV-2 virus, live vaccines, COVID-19 disease, immunization, measles, rubella, mumps

Evolution and emergence of mosquito-borne viruses of medical importance: towards a routine metagenomic surveillance approach

Abstract During the last two decades, the world has witnessed the emergence and re-emergence of arthropod-borne viruses, better known as arboviruses. The close contact between sylvatic, rural and peri-urban vector species and humans has been mainly determined by the environment-modifying human activity. The resulting interactions have led to multiple dead-end host infections and have allowed sylvatic arboviruses to eventually adapt to new vectors and hosts, contributing to the establishment of urban transmission cycles of some viruses with enormous epidemiologic impact. The metagenomic next-generation sequencing (NGS) approach has allowed obtaining unbiased sequence information of millions of DNA and RNA molecules from clinical and environmental samples. Robust bioinformatics tools have enabled the assembly of individual sequence reads into contigs and scaffolds partially or completely representing the genomes of the microorganisms and viruses being present in biological samples of clinical relevance. In this review, we describe the different ecological scenarios for the emergence of viral diseases, the virus adaptation process required for the establishment of a new transmission cycle and the usefulness of NGS and computational methods for the discovery and routine genomic surveillance of mosquito-borne viruses in their ecosystems.

The 2000HIV study: Design, multi-omics methods and participant characteristics.

Even during long-term combination antiretroviral therapy (cART), people living with HIV (PLHIV) have a dysregulated immune system, characterized by persistent immune activation, accelerated immune ageing and increased risk of non-AIDS comorbidities. A multi-omics approach is applied to a large cohort of PLHIV to understand pathways underlying these dysregulations in order to identify new biomarkers and novel genetically validated therapeutic drugs targets. The 2000HIV study is a prospective longitudinal cohort study of PLHIV on cART. In addition, untreated HIV spontaneous controllers were recruited. In-depth multi-omics characterization will be performed, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and metagenomics, functional immunological assays and extensive immunophenotyping. Furthermore, the latent viral reservoir will be assessed through cell associated HIV-1 RNA and DNA, and full-length individual proviral sequencing on a subset. Clinical measurements include an ECG, carotid intima-media thickness and plaque measurement, hepatic steatosis and fibrosis measurement as well as psychological symptoms and recreational drug questionnaires. Additionally, considering the developing pandemic, COVID-19 history and vaccination was recorded. Participants return for a two-year follow-up visit. The 2000HIV study consists of a discovery and validation cohort collected at separate sites to immediately validate any finding in an independent cohort. Overall, 1895 PLHIV from four sites were included for analysis, 1559 in the discovery and 336 in the validation cohort. The study population was representative of a Western European HIV population, including 288 (15.2%) cis-women, 463 (24.4%) non-whites, and 1360 (71.8%) MSM (Men who have Sex with Men). Extreme phenotypes included 114 spontaneous controllers, 81 rapid progressors and 162 immunological non-responders. According to the Framingham score 321 (16.9%) had a cardiovascular risk of >20% in the next 10 years. COVID-19 infection was documented in 234 (12.3%) participants and 474 (25.0%) individuals had received a COVID-19 vaccine. The 2000HIV study established a cohort of 1895 PLHIV that employs multi-omics to discover new biological pathways and biomarkers to unravel non-AIDS comorbidities, extreme phenotypes and the latent viral reservoir that impact the health of PLHIV. The ultimate goal is to contribute to a more personalized approach to the best standard of care and a potential cure for PLHIV.

Descriptive text to the Geological map of Denmark, 1:50 000, Møn 1511 I, 1511 IV and 1512 II

Descriptive text to the Geological map of Denmark, 1:50 000, Møn 1511 I, 1511 IV and 1512 II

DNA Droplets: Intelligent, Dynamic Fluid.

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Secure genotype imputation using homomorphic encryption

Genotype imputation estimates missing genotypes from the haplotype or genotype reference panel in individual genetic sequences, which boosts the potential of genome-wide association and is essential in genetic data analysis. However, the genetic sequences involve people’s privacy, confirming an individual’s identification and even disease information. This work proposes a secure genotype imputation model, which uses a linear regression model and the homomorphic encryption scheme over ciphertext to impute missing genotypes. The inference model is trained with float plaintext parameters, which are round into integers to avoid high complexity homomorphic evaluation on float number operations without bootstrapping operations. Even though the rounding parameters in the inference model are not the same as those in the trained model, We find that it will no effect on the outcome of the homomorphic prediction. Thus, a high-efficiency genotype imputation inference model over the ciphertext is obtained while keeping the high-security level. The simulation results indicate that the accuracy of the secure inference model is almost the same as the original model trained on float parameters. The secure inference model’s accuracy is 98.6% for a single genotype.

PP 1.43 – 00206 Evaluating integrated HIV-1 quasispecies using Near Full Length sequencing in ART-suppressed individuals in the Drexel CARES Cohort

PP 1.43 – 00206 Evaluating integrated HIV-1 quasispecies using Near Full Length sequencing in ART-suppressed individuals in the Drexel CARES Cohort

The complete mitochondrial genome of Tuta absoluta (Lepidoptera: Gelechiidae) and genetic variation in two newly invaded populations in China

• The size of mitogenome sequences in T. absoluta varied among individuals from different geographical locations. • The differences in the lengths of intergenic spacer were contributed to the size difference of mitogenomes among different populations. • cox2 , atp6 , nad1 and nad5 genes were sensitive mitochondrial gene markers for population genetics in T. absoluta . Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is a devastating invasive pest worldwide, causing severe damage to tomatoes. Recently, it has been recorded in the northwestern and southwestern parts of China. Here, the mitogenomes and genetic variation of two newly invaded T. absoluta populations in Xinjiang and Yunnan, were determined. The results showed that the complete mitogenome size of T. absoluta is 15298 bp for the individual from Xinjiang and 15296 bp for the individual from Yunnan, which were both longer than the reported mitogenome from Spain (15290 bp). The mitogenome sequences of individuals collected from three locations showed high levels of sequence similarity, except for 8 polymorphic sites, which were in genes cox2 (1 site), cox3 (2 sites), cob (1 site) , atp6 (1 site), nad1 (2 sites) and nad5 (1 site). Tuta absoluta mitogenomes share many features with other 6 Gelechiidae mitogenomes, except for several differences in the start and stop codons of protein-coding genes and the length of intergenic spacers. Seven partial mitochondrial genes ( cox1 , cox2 , cox3 , atp6 , cob , nad1 , and nad5 ) were used for genetic variation analysis, and significant population differentiation was found between the two populations based on cox2 , atp6 , nad1 , and nad5 . The complete mitogenomes and sensitive mitochondrial gene markers reported here provide useful data for further population genetics study of this pest.

Dietary and management factors influence the equine gastric microbiome.

The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors. 57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease. Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collection of glandular mucosal pinch biopsies. 16S rRNA amplicon sequencing was used for microbiome analysis. Similarity and diversity indices and sequence read counts of individual taxa were compared between diet and management factors. Differences were detected in association with offering hay, type of hay, sweet feed, turnout, and stalling. Offering hay and stalling showed differences in similarity indices, whereas hay type, sweet feed, and turnout showed differences in similarity and diversity indices. Offering hay, hay type, and sweet feed were also associated with differences in individual sequence read counts. This study provides preliminary characterization of the complex relationship between the glandular gastric microbiome and diet/management factors. The ideal microbiome to promote a healthy glandular gastric environment remains unknown.

DACSR: Decoupled-Aggregated End-to-End Calibrated Sequential Recommendation

Sequential recommendations have made great strides in accurately predicting the future behavior of users. However, seeking accuracy alone may bring side effects such as unfair and overspecialized recommendation results. In this work, we focus on the calibrated recommendations for sequential recommendation, which is connected to both fairness and diversity. On the one hand, it aims to provide fairer recommendations whose preference distributions are consistent with users’ historical behaviors. On the other hand, it can improve the diversity of recommendations to a certain degree. But existing methods for calibration have mainly relied on the post-processing on the candidate lists, which require more computation time in generating recommendations. In addition, they fail to establish the relationship between accuracy and calibration, leading to the limitation of accuracy. To handle these problems, we propose an end-to-end framework to provide both accurate and calibrated recommendations for sequential recommendation. We design an objective function to calibrate the interests between recommendation lists and historical behaviors. We also provide distribution modification approaches to improve the diversity and mitigate the effect of imbalanced interests. In addition, we design a decoupled-aggregated model to improve the recommendation. The framework assigns two objectives to two individual sequence encoders, and aggregates the outputs by extracting useful information. Experiments on benchmark datasets validate the effectiveness of our proposed model.

Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls: Retrospective evaluation of UK Biobank array data.

The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly genotyped on the UK Biobank Axiom array and via whole exome sequencing. However, in a study using the exome sequencing results of the first 50k individuals as reference (truth), it was observed that the positive predictive value (PPV) decreased along with the number of heterozygous array calls per variant. We developed a novel addition to the genotyping algorithm, Rare Heterozygous Adjusted (RHA), to significantly improve PPV in variants with minor allele frequency below 0.01%. The improvement in PPV was roughly equal when comparing to the exome sequencing of 50k individuals, or to the more recent ~200k individuals. Sensitivity was higher in the 200k data. The improved calling algorithm, along with enhanced quality control of array probesets, significantly improved the positive predictive value and the sensitivity of array data, making it suitable for the detection of ultra-rare variants.

Development of a deep learning method for improving diagnostic accuracy for uterine sarcoma cases

Uterine sarcomas have very poor prognoses and are sometimes difficult to distinguish from uterine leiomyomas on preoperative examinations. Herein, we investigated whether deep neural network (DNN) models can improve the accuracy of preoperative MRI-based diagnosis in patients with uterine sarcomas. Fifteen sequences of MRI for patients (uterine sarcoma group: n = 63; uterine leiomyoma: n = 200) were used to train the models. Six radiologists (three specialists, three practitioners) interpreted the same images for validation. The most important individual sequences for diagnosis were axial T2-weighted imaging (T2WI), sagittal T2WI, and diffusion-weighted imaging. These sequences also represented the most accurate combination (accuracy: 91.3%), achieving diagnostic ability comparable to that of specialists (accuracy: 88.3%) and superior to that of practitioners (accuracy: 80.1%). Moreover, radiologists’ diagnostic accuracy improved when provided with DNN results (specialists: 89.6%; practitioners: 92.3%). Our DNN models are valuable to improve diagnostic accuracy, especially in filling the gap of clinical skills between interpreters. This method can be a universal model for the use of deep learning in the diagnostic imaging of rare tumors.