Individual Sequences Research Articles

An intelligent ubiquitous compression technique for DNA sequencing using Hadoop

To solve the problem of reducing the amount of data storage in the practical application of massive biomedical data and efficiently using existing storage devices and bandwidth resources to store shared data. The proposed model includes both compression modes: the first is a single sequence compression mode designed for the characteristics of a large number of repeated substrings in DNA sequences; the second is a reference-based multi-sequence compression mode designed for the very similar characteristics of DNA sequences of different individuals of the same species. Both types of compression use the Lempel–Ziv–Welch (LZ) compression method, which is quite comparable to one another, to examine the sequence, as well as to study and classify the repetitive data that exists between a single sequence and numerous sequences in the sequence set. The proposed method aims to solve the problem of high pressure caused by single-point processing of large sequence files, effectively reduces redundant information by using the local correlation of data, and effectively uses the computing resources of a cloud platform that is used for biological information processing to support the efficient storage, transmission, and sharing of data.

Phylogenetic study of theileria ovis and theileria lestoquardi in infected sheep and it is associated ticks in mosul city, Iraq

This is a first molecular report investigate the phylogenic analysis of Theileria spp. in sheep and it's infested ticks in Mosul city-Iraq. A total of 185 blood samples were collected from sheep in different areas of Mosul city. A sixty five Ixodid ticks were also collected from different parts of infected animals. The overall prevalence of Theileria spp. was 52.4% (97 out of 185), for Theileria ovis it was 9.7%, Theileria lestoquardi it was 20% and mixed infection it was 22.7% in sheep in Mosul city, based on conventional-PCR and multiplex-PCR techniques. the infestation rat of Ixodid ticks on sheep was 11.8% (22 out of 185) and three species of Ixodid ticks (n=65) were identified and classified: Hyalomma anatolicum anatolicum 37 (56.9%), Rhipicephalus sanguineus 16 (24.6%), Rh. turanicus 12 (18.4%) based on microscopic examination. BLASTn individual sequencing analysis of six sequences of 18S rRNA gene, composing sequences of T. ovis (n=3) (One extracted from sheep blood and two extracted from engorged female ticks), and sequences of T. lestoquardi (n=3) (One extracted from sheep blood and two extracted from engorged female ticks).

Rare ATG7 genetic variants predispose patients to severe fatty liver disease.

Non-alcoholic fatty liver disease (NAFLD) is the leading cause of liver disorders and has a strong heritable component. The aim of this study was to identify new loci that contribute to severe NAFLD by examining rare variants. We performed whole-exome sequencing in individuals with NAFLD and advanced fibrosis or hepatocellular carcinoma (n= 301) and examined the enrichment of likely pathogenic rare variants vs. the general population. This was followed by validation at the gene level. In patients with severe NAFLD, we observed an enrichment of the p.P426L variant (rs143545741 C>T; odds ratio [OR] 5.26, 95% CI 2.1-12.6; p= 0.003) of autophagy-related 7 (ATG7), which we characterized as a loss-of-function, vs. the general population, and an enrichment in rare variants affecting the catalytic domain (OR 13.9; 95% CI 1.9-612; p= 0.002). In the UK Biobank cohort, loss-of-function ATG7 variants increased the risk of cirrhosis and hepatocellular carcinoma (OR 3.30; 95% CI 1.1-7.5 and OR 12.30, 95% CI 2.6-36, respectively; p <0.001 for both). The low-frequency loss-of-function p.V471A variant (rs36117895 T>C) was also associated with severe NAFLD in the clinical cohort (OR 1.7; 95% CI 1.2-2.5; p= 0.003), predisposed to hepatocellular ballooning (p= 0.007) evolving to fibrosis in the Liver biopsy cohort (n= 2,268), and was associated with liver injury in the UK Biobank (aspartate aminotransferase levels, p <0.001), with a larger effect in severely obese individuals in whom it was linked to hepatocellular carcinoma (p= 0.009). ATG7 protein localized to periportal hepatocytes, particularly in the presence of ballooning. In the Liver Transcriptomic cohort (n= 125), ATG7 expression correlated with suppression of the TNFα pathway, which was conversely upregulated in p.V471A carriers. We identified rare and low-frequency ATG7 loss-of-function variants that promote NAFLD progression by impairing autophagy and facilitating ballooning and inflammation. We found that rare mutations in agene called autophagy-related 7 (ATG7) increase the risk of developing severe liver disease in individuals with dysmetabolism. These mutations cause an alteration in protein function and impairment of self-renewal of cellular content, leading to liver damage and inflammation.

Impact of measuring heteroplasmy of a pathogenic mitochondrial DNA variant at the single-cell level in individuals with mitochondrial disease.

Pathogenic mitochondrial DNA heteroplasmy has mainly been assessed with bulk sequencing in individuals with mitochondrial disease. However, the distribution of heteroplasmy at the single-cell level in skin fibroblasts obtained from individuals, together with detailed clinical and biochemical information, remains to be investigated. We used the mitochondrial DNA single-cell assay for the transposase-accessible chromatin sequencing method. Skin fibroblasts were obtained from six individuals with mitochondrial disease and pathogenic m.3243A>G variants of differing severity. Different distributions of heteroplasmy at the single-cell level were identified in skin fibroblasts from all six individuals. Four individuals with different outcomes showed similar averaged heteroplasmy rates with normal mitochondrial respiratory chain enzyme activity, while the distribution of single-cell heteroplasmy patterns differed among the individuals. This study showed different heteroplasmy distribution patterns at the single-cell level in individuals with the m.3243A>G variant, who had a similar averaged heteroplasmy rates with normal mitochondrial respiratory chain enzyme activity. Whether such different heteroplasmy distribution patterns explain the different clinical outcomes should be assessed further in future studies. Measuring heteroplasmy of pathogenic mitochondrial DNA variants at the single-cell level could be important in individuals with mitochondrial disease.

Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

Genome-wide methods offer a powerful approach to detect signatures of drug selection. However, limited availability of suitable reference genomes and the difficulty of obtaining field populations with well-defined, distinct drug treatment histories mean there is little information on the signatures of selection in parasitic nematodes and on how best to detect them. This study addresses these knowledge gaps by using field populations of Haemonchus contortus with well-defined benzimidazole treatment histories, leveraging a recently completed chromosomal-scale reference genome assembly. We generated a panel of 49,393 genomic markers to genotype 20 individual adult worms from each of four H. contortus populations: two from closed sheep flocks with an approximate 20 year history of frequent benzimidazole treatment, and two populations with a history of little or no treatment. Sampling occurred in the same geographical region to limit genetic differentiation and maximise the detection sensitivity. A clear signature of selection was detected on chromosome I, centred on the isotype-1 β-tubulin gene. Two additional, but weaker, signatures of selection were detected; one near the middle of chromosome I spanning 3.75 Mbp and 259 annotated genes, and one on chromosome II spanning a region of 3.3 Mbp and 206 annotated genes, including the isotype-2 β-tubulin locus. We also assessed how sensitivity was impacted by sequencing depth, worm number, and pooled versus individual worm sequence data. This study provides the first known direct genome-wide evidence for any parasitic nematode, that the isotype-1 β-tubulin gene is quantitatively the single most important benzimidazole resistance locus. It also identified two additional genomic regions that likely contain benzimidazole resistance loci of secondary importance. This study provides an experimental framework to maximise the power of genome-wide approaches to detect signatures of selection driven by anthelmintic drug treatments in field populations of parasitic nematodes.

Branding and tracing seaweed: Development of a high-resolution genetic kit to identify the geographic provenance of Alaria esculenta

Global seaweed production increased rapidly in the past 50 years, mostly in Asia. Recently seaweed aquaculture has been attracting more attention worldwide because of its potential as a form of sustainable agriculture that provides food, feed, fertiliser, bio-stimulants and other valuable products. Quality characteristics of seaweeds are species-dependent, influenced by the genetic makeup of the individual, and by the environmental conditions where the seaweeds are grown. Those two factors largely depend on their place of origin. Traceability in terms of geographic provenance would therefore add commercial value to seaweed products . Here we describe the development of a method to identify/certify the place of origin of the blown alga Alaria esculenta . We identified Single Nucleotide Polymorphisms (SNPs) on the nuclear, plastid and mitochondrial genomes by analysing whole-genome sequences of individuals originated from Ireland, Northern Ireland, Faroe Islands, Greenland, Norway and Atlantic Canada. Multi-dimensional scaling (MDS) plots of the nuclear SNPs, but not of the organellar SNPs, showed a clear separation of individual samples by the country of origin. We then identified country-specific nuclear SNPs and designed a set of cleaved amplified polymorphic sequence (CAPS) assays to detect two or three of specific SNPs per country. The SNPs were tested on individuals, including those whose genome sequence had not been determined, and were shown to successfully identify individual's country of origin. This method allows accurate determination of the geographic provenance of Alaria esculenta . This tool could form the base for branding seaweed products with certified origin, and for the development of mass identification kits using metabarcoding . It also has the potential to be used to monitor seaweed farms for invasion of non-native varieties of a seaweed species, and, more broadly, to monitor effects of climate change on the diversity of seaweed populations. • Nuclear SNPs distinguish the geographical location of Alaria esculenta strains. • Organellar SNPs failed to distinguish geographical location of the strains. • Country-specific nuclear SNPs allowed developing CAPS assays. • The method can be deployed for both ecological and industrial applications.

Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination

BackgroundEquid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates.ResultsWhole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination.ConclusionsAnalysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve.

People with chronic wounds cared for at home in Belgium: Prevalence and exploration of care integration needs using health care trajectory analysis

BackgroundLittle is known about the prevalence of people with chronic wounds cared for at home and their care integration needs in Belgium. In high-income countries, chronic wounds are associated with ageing processes, chronic diseases and social and financial vulnerability, resulting in multiple needs. To meet these needs, many health care providers (with nurses figuring prominently) are involved. This can lead to fragmented health care trajectories and the need to strengthen care coordination. ObjectivesThis study aims to estimate the prevalence of people with chronic wounds cared for at home in Belgium. It also seeks to explore their health care trajectories and the risk of fragmentation of care to inform policy makers, care providers and research. DesignCross-sectional. Setting(s)Home care. ParticipantsRoutinely collected data of reimbursed care of 3467 people with a chronic wound cared for at home in 2018. MethodsWe applied a stratification method to our sample based on health care trajectories. First, we constructed individual sequences of care received during the year. Then we summarised the health care events using a K-mers approach. Finally, a multinomial mixture model was used on the previously obtained summary to cluster individuals according to their health care trajectories. Afterwards, other epidemiological, socioeconomic and health care use indicators were calculated for each health care trajectory group.We also estimated the prevalence of people with chronic wounds treated at home. ResultsWe constructed six health care trajectory groups for two age categories (<65 and ≥65 years) showing different intensity of care use and type of care. In some health care trajectory groups, generalist care was found to be predominant. In others, specialist care appeared more prevalent. Depending on the health care trajectory group, a significant proportion of people had multiple care providers involved (mainly nurses, medical specialists and GPs), and many of them also had multiple transitions between care settings.The prevalence of people with chronic wounds treated at home rises significantly with age: 0.3%, 95%CI (0.2%–0.4%) for people aged under 65, 2.5%, 95%CI (2.3%–2.8%) for people aged 65 and over. ConclusionA significant proportion of people with chronic wounds experienced multiple transitions and met many health care providers. This can lead to complex trajectories and risk of fragmentation. Nurses, who are intensively involved in wound care at home, with the appropriate skills, could play a ‘reference’ role to promote continuity of care and better coordination. RegistrationNot registered.

Genetic association-based functional analysis detects HOGA1 as a potential gene involved in fat accumulation.

Although there are a number of discoveries from genome-wide association studies (GWAS) for obesity, it has not been successful in linking GWAS results to biology. We sought to discover causal genes for obesity by conducting functional studies on genes detected from genetic association analysis. Gene-based association analysis of 917 individual exome sequences showed that HOGA1 attains exome-wide significance (p-value < 2.7 × 10–6) for body mass index (BMI). The mRNA expression of HOGA1 is significantly increased in human adipose tissues from obese individuals in the Genotype-Tissue Expression (GTEx) dataset, which supports the genetic association of HOGA1 with BMI. Functional analyses employing cell- and animal model-based approaches were performed to gain insights into the functional relevance of Hoga1 in obesity. Adipogenesis was retarded when Hoga1 was knocked down by siRNA treatment in a mouse 3T3-L1 cell line and a similar inhibitory effect was confirmed in mice with down-regulated Hoga1. Hoga1 antisense oligonucleotide (ASO) treatment reduced body weight, blood lipid level, blood glucose, and adipocyte size in high-fat diet-induced mice. In addition, several lipogenic genes including Srebf1, Scd1, Lp1, and Acaca were down-regulated, while lipolytic genes Cpt1l, Ppara, and Ucp1 were up-regulated. Taken together, HOGA1 is a potential causal gene for obesity as it plays a role in excess body fat development.

Study on dietary intake, risk assessment, and molecular toxicity mechanism of benzo[α]pyrene in college students in China Bashu area.

As an extremely strong polycyclic aromatic hydrocarbon carcinogen, benzo[α]pyrene (BaP) is often produced during food processing at high temperatures. Recently, food safety, as well as toxicity mechanism and risk assessment of BaP, has received extensive attention. We first constructed the database of BaP pollution concentration in Chinese daily food with over 104 data items; collected dietary intake data using online survey; then assessed dietary exposure risk; and finally revealed the possible toxicity mechanism through four comparative molecular dynamics (MD) simulations. The statistical results showed that the concentration of BaP in olive oil was the highest, followed by that in fried meat products. The margins of exposure and incremental lifetime cancer risk both indicated that the dietary exposure to BaP of the participants was generally safe, but there were still some people with certain carcinogenic risks. Specifically, the health risk of the core district population was higher than that of the noncore district in Bashu area, and the female postgraduate group was higher than the male group with bachelor degree or below. From MD trajectories, BaP binding does not affect the global motion of individual nucleic acid sequences, but local weak noncovalent interactions changed greatly; it also weakens molecular interactions of nucleic acid with Bacillus stearothermophilus DNA polymerase I large fragment (BF), and significantly changes the cavity structure of recognition interface. This work not only reveals the possible toxicity mechanism of BaP, but also provides theoretical guidance for the subsequent optimization of food safety standards and reference of rational diet.

DBFE: distribution-based feature extraction from structural variants in whole-genome data.

Whole-genome sequencing has revolutionized biosciences by providing tools for constructing complete DNA sequences of individuals. With entire genomes at hand, scientists can pinpoint DNA fragments responsible for oncogenesis and predict patient responses to cancer treatments. Machine learning plays a paramount role in this process. However, the sheer volume of whole-genome data makes it difficult to encode the characteristics of genomic variants as features for learning algorithms. In this article, we propose three feature extraction methods that facilitate classifier learning from sets of genomic variants. The core contributions of this work include: (i) strategies for determining features using variant length binning, clustering and density estimation; (ii) a programing library for automating distribution-based feature extraction in machine learning pipelines. The proposed methods have been validated on five real-world datasets using four different classification algorithms and a clustering approach. Experiments on genomes of 219 ovarian, 61 lung and 929 breast cancer patients show that the proposed approaches automatically identify genomic biomarkers associated with cancer subtypes and clinical response to oncological treatment. Finally, we show that the extracted features can be used alongside unsupervised learning methods to analyze genomic samples. The source code of the presented algorithms and reproducible experimental scripts are available on Github at https://github.com/MNMdiagnostics/dbfe. Supplementary data are available at Bioinformatics online.

Individual-Level Routinization and Exploration-Exploitation Choice: An Experimental Study

The question of why individuals choose to explore or exploit as their routines accumulate remains largely unexplored in the organizational literature in a strict causal sense. To bridge this gap, we conducted an experimental laboratory study of individual decision-making sequences using a real-effort task and a two-phase procedure involving a training phase and an active phase. The former involved a learning process in which participants used their own skills to solve the same task across eight rounds to simulate the development of individual-level routines. In the active phase, we observed sequential choices to exploit an established routine, explore a new routine, or exploit a new routine. Participants were financially incentivized to abandon an established routine by providing higher performance-related payoffs for exploring unknown task environments. Our findings show that initial conditions related to task environment complexity matter; we found that when individuals are initially exposed to simpler tasks, they were more likely to continue exploiting an established routine. When initially exposed to more complex tasks, they were more likely to explore new and more profitable tasks, and then to continue exploiting the new routines they learned. Interestingly, we find not only that different kinds of performance feedback lead the exploration-exploitation choice, but our results also show how the feedback-choice linkage is contingent upon the task environment, i.e. the context (simple or complex) in which initial routines are formed. These findings contribute to the literature on individual search by demonstrating the important role of routinization and initial conditions in exploration and exploitation behavior.

2021 Bioinformatics and Translational Informatics Best Papers.

To identify and summarize the top bioinformatics and translational informatics papers published in 2021 for the IMIA Yearbook. We performed a broad literature search to retrieve Bioinformatics and Translational Informatics (BTI) papers and coupled this with a series of editorial and peer reviews to identity the top papers in the area. We identified a final candidate list of 15 BTI papers for peer-review; from these candidates, the top three papers were chosen to highlight in this synopsis. These papers expand the integration of multi-omics data with electronic health records and use advanced machine learning approaches to tailor models to individual patients. In addition, our honorable mention paper foreshadows the growing impact of BTI research on precision medicine through the continued development of large clinical consortia. In the top BTI papers this year, we observed several important trends, including the use of deep-learning approaches to analyse diverse data types, the development of integrative and web-accessible bioinformatics pipelines, and a continued focus on the power of individual genome sequencing for precision health.

The value of noncontrast MRI in evaluating breast imaging reporting and data system category 0 lesions on digital mammograms.

BackgroundBenign and malignant diagnosis of nonpalpable breast imaging reporting and data system (BI-RADS) category 0 lesions on digital mammograms (DMs) is very important. We compared the diagnostic performance of non-contrast-enhanced magnetic resonance imaging (MRI) and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) for them. We sought to evaluate BI-RADS category 0 lesions using 3 MRI sequences: short tau inversion recovery (STIR), STIR combined with high b value diffusion-weighted imaging (STIR-DWI), and DCE-MRI.MethodsWe retrospectively reviewed 114 breast DMs rated as nonpalpable BI-RADS category 0 lesions in 112 patients from January 2014 to June 2019. STIR, high b value DWI, and DCE-MRI were performed for all patients. Two breast radiologists read individual sequences (STIR, DWI, DCE-MRI) and pairs of sequences (STIR-DWI) to detect BI-RADS category 0 lesions in DMs. Receiver operating characteristic (ROC) curve analysis was used to assess diagnostic performance according to a best valuable comparator that combined MRI imaging, clinical, and pathological data.ResultsAmong of 114 lesions (the median age of patients was 47 years; the median size of the lesion was 19 mm), 32 (48.5%) malignant lesions were missed by STIR, 9 (13.6%) malignant lesions were missed by STIR-DWI, and 3 (4.5%) malignant lesions were missed by DCE-MRI. The principal finding of our study was that STIR-DWI and DCE-MRI showed higher diagnostic accuracy than did STIR (P<0.01). STIR-DWI showed higher accuracy [area under the curve (AUC) =0.858; sensitivity =87.8%] for BI-RADS category 0 lesions in DMs than did STIR (AUC =0.754; sensitivity =51.5%), while the performance was comparable to that of DCE-MRI (AUC =0.884; sensitivity =95.5%).ConclusionsUsing pairs of sequences (STIR-DWI) is a non-contrast-enhanced MRI technique and had an equal diagnostic performance in distinguishing benign from malignant lesions among nonpalpable BI-RADS category 0 lesions to that of DCE-MRI. As a result, STIR-DWI as having the potential to improve the safety and efficacy in of breast cancer screening, especially in nonpalpable BI-RADS category 0 lesions at in DMs.

The genetic characterization of hemagglutinin (HA), neuraminidase (NA) and polymerase acidic (PA) genes of H3N2 influenza viruses circulated in Guangdong Province of China during 2019-2020.

The evolution of seasonal influenza viruses, which can cause virus antigenic drift to escape human herd immunity, is a significant public health problem. Here, we obtained hemagglutinin (HA), neuraminidase (NA), and polymerase acidic protein (PA) the gene sequences of 84 influenza virus isolates collected in Guangdong Province during the 2019-2020 influenza season. Phylogenetic analyses revealed all these isolates were genetically similar to the viruses of clade 3C2a A1b, specifically those within subclades of A1b 137F (59 cases), A1b 186D (19 cases), and A1b 94N (6 cases). The influenza virus isolates were distinct from the World Health Organization recommended influenza A vaccine virus for the 2019-2020 Northern Hemisphere season (A/Kansas/14/2017; H3N2). Phylogenies inferred from the individual gene segment sequences revealed that one reassortment event occurred among these clades. The genetic variation involved mutations within viral antigenic epitopes and two N-glycosylation site alterations. The novel mutation sites of G202D and D206N in the HA gene, E344K in the NA gene, and K626R in the PA gene which may affect the spread of the virus were observed. We investigated the evolution of these genes and found that the HA and NA genes were under greater pressure than PA gene. Mutations associated with conferring resistance to NA inhibitors or baloxavir acid were not found. Our results suggest that a rapid evolution of the H3N2 influenza virus occurred, thus continuous monitoring is critical for establishing appropriate vaccine formulations or drug delivery for targeting influenza.

PHIP variants associated with Chung-Jansen syndrome disrupt replication fork stability and genome integrity.

Chung–Jansen syndrome (CJS) is a rare, autosomal dominant disorder characterized by developmental delay, intellectual disability/cognitive impairment, behavioral challenges, obesity, and dysmorphic features. CJS is associated with heterozygous variants in PHIP (Pleckstrin-Homology Interacting Protein), a gene that encodes one of several substrate receptors for Cullin4-RING (CRL4) E3 ubiquitin ligase complex. Full-length PHIP, also called DCAF14, was recently identified to function as a replication stress response protein. Herein, we report the identification of two PHIP missense variants identified by exome sequencing in unrelated individuals with CJS. The variants p.D488V and p.E963G occur in different functional elements of DCAF14-WD40 repeat domain and pleckstrin homology-binding region (PBR), respectively. Using DNA fiber assays, we reveal that cells expressing either variant exhibit defective replication fork progression in conditions of replication stress. Furthermore, unlike wild-type DCAF14, both variants fail to accomplish DNA replication after exposure to genotoxic stress indicating a critical role of DCAF14 in protecting stalled replication forks. Thus, we have identified replication defects associated with CJS variants and predict replication-associated genome instability with CJS syndrome.

Characterisation of the blood RNA host response underpinning severity in COVID-19 patients

Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. In this study, for the first time, we show how immunomodulatory treatments commonly administered to COVID-19 patients greatly alter the transcriptome. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response.

Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells

Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effective genetic tools that can be grown without regard for biosafety issues. Whole-genome sequencing of mutant individuals reduces the effort required for mutant screening, thereby increasing their utility. In this study, we sequenced members of a mutant library of Oryza sativa cv. Nipponbare derived from treating single fertilized egg cells with N-methyl-N-nitrosourea (MNU). By whole-genome sequencing 266 M1 plants in this mutant library, we identified a total of 0.66 million induced point mutations. This result represented one mutation in every 146-kb of genome sequence in the 373 Mb assembled rice genome. These point mutations were uniformly distributed throughout the rice genome, and over 70,000 point mutations were located within coding sequences. Although this mutant library was a small population, nonsynonymous mutations were found in nearly 61% of all annotated rice genes, and 8.6% (3248 genes) had point mutations with large effects on gene function, such as gaining a stop codon or losing a start codon. WGS showed MNU-mutagenesis using rice fertilized egg cells induces mutations efficiently and is suitable for constructing mutant libraries for an in silico mutant screening system. Expanding this mutant library and its database will provide a useful in silico screening tool that facilitates functional genomics studies with a special emphasis on rice.

Molecular systematics and biogeographic insights of the Calomys callosus complex (Rodentia, Cricetidae)

AbstractThe genus Calomys includes several species that have very similar external morphologies, which often leads to confusing field identification and has resulted in conflictive taxonomic histories. One of its clades involves large‐sized body forms, known as the Calomys callosus complex. In a previous study, a biogeographic hypothesis was proposed to explain a south‐to‐north colonisation of South America by species of this complex. However, other studies which not included all members of the complex' members and that used different molecular markers, did not support that biogeographic hypothesis. Here we explore the relationships among C. callosus sensu stricto (s.s.), C. fecundus, C. callidus, C. venustus, C. tocantinsi and Calomys sp. using two mitochondrial genes (Cyt‐b and Control Region) and two nuclear genes (Rhp3 and i7FGB) data. We also applied several gene trees and species delimitation methods to elucidate the taxonomy, distribution and evolutionary relationships among the analysed species. By including sequences of individuals from Argentina, Brazil, Bolivia and Paraguay, we reconstructed the possible ancestral biogeographic origin of the complex. Two main clades were recovered: the western showed the relationships (C. venustus [C. fecundus–Calomys sp.]), while the eastern (C. callidus [C. callosus s.s.–C. tocantinsi]). These results support the original biogeographic hypothesis and suggest the following scenario: in the west, from the Espinal ecoregion, first the Tucumane–Bolivian Yungas and later, the Beni savanna would have been colonised. In the east, from the Espinal, first the Chaco and later the Cerrado ecoregions may have been occupied.

SLITRK2 variants associated with neurodevelopmental disorders impair excitatory synaptic function and cognition in mice

SLITRK2 is a single-pass transmembrane protein expressed at postsynaptic neurons that regulates neurite outgrowth and excitatory synapse maintenance. In the present study, we report on rare variants (one nonsense and six missense variants) in SLITRK2 on the X chromosome identified by exome sequencing in individuals with neurodevelopmental disorders. Functional studies showed that some variants displayed impaired membrane transport and impaired excitatory synapse-promoting effects. Strikingly, these variations abolished the ability of SLITRK2 wild-type to reduce the levels of the receptor tyrosine kinase TrkB in neurons. Moreover, Slitrk2 conditional knockout mice exhibited impaired long-term memory and abnormal gait, recapitulating a subset of clinical features of patients with SLITRK2 variants. Furthermore, impaired excitatory synapse maintenance induced by hippocampal CA1-specific cKO of Slitrk2 caused abnormalities in spatial reference memory. Collectively, these data suggest that SLITRK2 is involved in X-linked neurodevelopmental disorders that are caused by perturbation of diverse facets of SLITRK2 function.