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Type I interferon (IFN-I) plays an important role in the innate immune response through inducing IFN-I-stimulated genes (ISGs). However, how alternative splicing (AS) events, especially over time, affect their function remains poorly understood. We generated an annotation (113,843 transcripts) for IFN-I-stimulated human B cells called isoISG using high-accuracy long-read sequencing data from PacBio Sequel II/IIe. Transcript isoform profiling using isoISG revealed that isoform switching occurred in the early response to IFN-I so that ISGs would gain functional domains (e.g., C4B) or higher protein production (e.g., IRF3). Conversely, isoforms lacking functional domains increased during the late phase of IFN-I response, mainly due to intron retention events. This suggests that isoform switching both triggers and terminates IFN-I responses at the translation and protein levels. Furthermore, genetic variants influencing the isoform ratio of ISGs were associated with immunological and infectious diseases. AS has essential roles in regulating innate immune response and associated diseases.

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Hepatitis B virus (HBV) can be transmitted within a family, but an interspousal transmission in elderly cases is rare and the change of viral quasispecies during the event is unclear. We experienced two acute hepatitis B males (AH1 and AH2, 67 and 71 years old, respectively) whose HBV was transmitted from their wives with chronic HBV infection (CH1 and CH2, 67 and 66 years old, respectively). To clarify the characteristics of HBV quasispecies in such cases, we performed long-read deep sequencing of HBV preS1/preS2/S domain using samples from the 2 couples. HBV full-genome sequences determined with direct sequencing showed that the HBV sequences belonged to subgenotype B1. AH1 was 98.0-99.2 % identical to CH1, and AH2 was 98.5-99.5 % identical to CH2, whereas the identity between AH1 and AH2 was 96.9 %. The long-read deep sequencing of amplicons including preS1/preS2/S domains with PacBio Sequel IIe showed the numbers of nucleotides with >5 % substitution frequencies in AH1, AH2, CH1 and CH2 were 0 (0 %), 4 (0.31 %), 39 (3.06 %) and 28 (2.20 %), respectively, indicating that CH1 and CH2 were more heterogeneous than AH1 and AH2. From a phylogenetic analysis based on the deep sequencing, minor CH1/CH2 clones that were close to AH1/AH2 clones were considered to be substantially distinct from the major populations in CH1/CH2. The major population formed during chronic infection under the immune pressure might not be suitable to establish new infection and this might be one of the reasons why the transmission had not occurred for a long time after marriage.

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BACKGROUND: Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter. RESULTS: Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring. CONCLUSIONS: Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs.

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(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.

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Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.

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BACKGROUND: The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions. RESULTS: This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols. CONCLUSION: This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.

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Introduction Acute encephalitis syndrome (AES) in pediatric patients can lead to a range of disabilities, affecting various aspects of their daily lives. The disease is caused by a diverse group of pathogens including viruses, bacteria, fungi, and protozoans. While significant progress has been made in combating the acute phase of the disease, the lingering effects on the physical, cognitive, and emotional well-being of survivors have yet to be comprehensively explored. The present retrospective study was conducted to investigate disabilities including neurological squeals and functional impairment challenges faced by AES survivors as they navigate life with disabilities. Methods We conducted a comprehensive retrospective analysis of medical records of pediatric patients diagnosed with AES and evaluated their follow-up visits at regular intervals during the study period. The Liverpool scoring system and clinical examinations were utilized to assess the presence and severity of disabilities in the patients. Results A total of 134 pediatric AES patients were included in the study; among them, 56% were males, and 44% were females. The mean age of the participants was 4.8 ± 3.1 years, and the mean number of days of hospitalization was 27.8 ± 30.8. Only 9.7% of the patients were found to be Japanese encephalitis (JE)-positive, and 87.5% of the participants were found to have disabilities in some or the other domain of the Liverpool Outcome Score (LOS). There were statistically significant correlations between the age of the patients and the LOS at follow-up. Post-recovery disabilities were more severe among patients who required a prolonged duration of hospitalization. Conclusion A considerable proportion of AES survivors are left with disabilities. Causes other than Japanese encephalitis are now more frequent in AES. The need for prolonged hospitalization is related to more severe disabilities. The early identification of disabilities through the Liverpool scoring system and clinical examination can aid in implementing appropriate intervention strategies.

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Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4-67.6 megabases genomes in 178-204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.

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INTRODUCTION: Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), and SJS/TEN overlap syndrome are rare severe hypersensitivity reactions that lead to epithelial sloughing. Studies investigating the chronic multisystem effects of these syndromes and assessing patients in terms of quality of life (QOL), depression, and anxiety in the pediatric population are limited. In this study, we aimed to investigate the long-term effects of these diseases from a multisystem perspective. METHOD: Sixteen pediatric patients diagnosed with SJS, TEN, and SJS/TEN overlap syndrome were evaluated between September 2020 and March 2021. Physical and eye examinations were performed. To evaluate QOL and psychological status, Children's Dermatology Life Quality Index (CDLQI), Screen for Child Anxiety-Related Emotional Disorders (SCARED), and Children's Depression Inventory (CDI) were conducted. The patients' general characteristics, symptoms, and examination findings at their first admission were retrospectively obtained from the hospital's electronic records. RESULTS: Nineteen percent of the patients were female (n = 3). There were 7 patients (44%) with the diagnosis of SJS, 5 patients (31%) with TEN, and 4 patients (25%) with SJS/TEN overlap. The median follow-up time of the subjects was 6.5 years. The most common sequelae in the chronic period were skin changes (n = 13, 81%). Hyperpigmentation was the most common skin change (n = 9, 56%). In the last evaluation, 9 cases had eye involvement. In two cases, eye examination was normal in the acute phase, while ocular involvement was present in the chronic period. In 4 (50%) patients, there was height and/or weight percentile loss. Three patients' SCARED scores and 2 patients' CDI scores were high. According to the CDLQI survey, SJS, TEN, or SJS/TEN overlap syndrome had a small to moderate effect on the QOL in the 43% (n = 6) of the patients. The ANA values of 3 patients (60%) were positive at the follow-up and negative at the first admission. CONCLUSION: SJS, TEN, and SJS/TEN overlap syndrome may cause sequelae even after a long time of the onset of the disease. Patients' QOL and psychological status can be affected negatively. Ocular symptoms may develop in the follow-up, even without involvement in the acute period. Patients with SJS, TEN, and SJS/TEN overlap syndrome should be followed up in the chronic period and approached multidisciplinary.

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During the past decade, the characterization of microbial community in soil of contaminated sites was primarily done by high-throughput short-read amplicon sequencing. However, due to the similarity of 16S rRNA and ITS genes amplicon sequences, the short-read approach often limits the microbial composition analysis at the species level. Here, we simultaneously performed full-length and short-read amplicon sequencing to clarify the community composition and ecological status of different microbial taxa in contaminated soil from a high-resolution perspective. We found that (1) full-length 16S rRNA gene sequencing gave better resolution for bacterial identification at all levels, while there were no significant differences between the two sequencing platforms for fungal identification in some samples. (2) Abundant taxa were vital for microbial co-occurrences network constructed by both full-length and short-read sequencing data, and abundant fungal species such as Mortierella alpine, Fusarium solani, Mrakia frigida, and Chaetomium homopilatum served as the keystone species. (3) Heavy metal correlated with the microbial community significantly, and bacterial community and its abundant taxa were assembled by deterministic process, while the other taxa were dominated by stochastic process. These findings contribute to the understanding of the ecological mechanisms and microbial interactions in site soil ecosystems and demonstrate that full-length sequencing has the potential to provide more details of microbial community.

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The Pectobacterium pathogens cause soft rot and blackleg diseases on many plants and crops, including potatoes. Here, we first report a high-quality genome assembly and announcement of the P. polaris strain QK413-1, which causes blackleg disease in potatoes in China. The QK413-1 genome was sequenced and assembled using the PacBio Sequel II and Illumina sequencing platform. The assembled genome has a total size of 5,005,507 bp with a GC content of 51.81%, encoding 4,782 open reading frames, including 639 virulence genes, 273 drug resistance genes, and 416 secreted proteins. The QK413-1 genome sequence provides a valuable resource for the control of potato blackleg and research into its mechanism.

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Retinitis pigmentosa (RP) is a group of inherited retinal diseases characterized by the progressive degeneration of rod then cone photoreceptors. Most of the known mutations that cause RP reside in the protein-coding portions of DNA; however, a growing number of pathogenic mutations have been identified within the non-coding portions. This chapter details a brief method for the detection of structural variants throughout the genome for the identification of novel mutations and to ultimately provide patients with a precise molecular diagnosis.

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Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.

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La espina bífida, o mielodisplasia, es una anomalía de origen multifactorial congénita que se presenta con mayor frecuencia durante el desarrollo embrionario. Se produce por el cierre parcial de los pliegues neurales conjuntamente con una fusión defectuosa de los arcos vertebrales. Su clínica es variable e incluye una serie de manifestaciones como expresión del compromiso neurológico. El diagnóstico se basa en la presencia de las manifestaciones clínicas ayudado de estudios imagenológicos. La corrección quirúrgica del defecto es la conducta terapéutica que se preconiza como adecuada. Se presenta el caso de una paciente de 34 años de edad con mielomeningocele no corregido en edad infantil que se presenta con complicaciones infecciosas y secuelas neurológicas. Se administró esquema de antibioticoterapia con varios antibióticos de amplio espectro, y se decidió intervenir quirúrgicamente, con lo que se logró el cierre del orificio comunicante de la región espinal con el exterior. Además, se reconstruyó la zona aledaña al mielomeningocele para evitar posible sepsis del Sistema Nervioso Central. La paciente tuvo una evolución favorable y fue dada de alta hospitalaria a los 7 días posteriores a la intervención quirúrgica sin secuelas neurológicas(AU)

Spine bifida, or myelodysplasia, is a multifactorial congenital anomaly that occurs most frequently during embryonic development. It is produced by the partial closure of the neural folds together with a defective fusion of the vertebral arches. Its clinic is variable and includes a series of manifestations as an expression of neurological compromise. The diagnosis is based on the presence of clinical manifestations, aided by imaging studies. Surgical correction of the defect is the therapeutic conduct that is recommended as adequate. This report presents the case of a 34-year-old patient with uncorrected myelomeningocele in childhood who presented with infectious and neurological sequelae complications(AU)

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Carbon monoxide (CO) poisoning is a serious health problem. The main pathophysiological mechanism of acute CO poisoning is hypoxia due to the formation of carboxyhemoglobin (COHb). Delayed neuropsychiatric sequel (DNPS) occurs following an interval of several days to several weeks post-CO exposure and can present in many different manifestations, ranging from behavioral and mood disorders to encephalopathy and seizures and cause long-term neuropsychiatric sequel. The pathogenesis of DNPS following CO poisoning is a complex one that encompasses hypoxia-induced encephalopathy as well as inflammation, direct cellular changes and damage. The incidence varies and treatment is debated. We display a case of a previously healthy 13-year-old boy suffering from DNPS, presenting with seizures and encephalopathy and later developing optic nerve damage. Increased awareness to this condition might help diagnose future patients and aid in the understanding of the pathogenesis and treatment options for this poorly understood condition.

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Las secuelas de quemadura en la región tóraco-mamaria producidas en la niñez pueden causar cicatrices patológicas y retracciones debido a su difícil cicatrización. Su reconstrucción es parte fundamental del tratamiento para mejorar la estética corporal, el bienestar psicosocial y la calidad de vida en estos pacientes. Presentamos el caso clínico de una mujer de 42 años con secuela por placa cicatricial en hipocondrio izquierdo y glándula mamaria derecha con retracción, producida en la infancia por quemadura por fuego directo, resuelta con colgajo de abdominoplastia inversa que permitió buena cobertura, eliminación de defecto y formación de surco inframario con aumento de volumen del polo inferior de la mama y resultados estéticos satisfactorios. (AU)

Burn sequels in the thorax and mammary region produced in childhood can cause pathological scars and retractions due to difficult scaring. Reconstruction is a fundamental part of treatment to improve body aesthe- tics, psychosocial aspects and quality of life in patients. We present a case report of a 42 year-old woman with scarring plaque in left hypochondria and right mammary gland with retraction, produced in childhood by burning with direct fire, solved with reverse abdominoplasty flap which allowed good coverage, elimination of the defect and creation of the inframary groove with increased volu- me of the lower pole of the breast and satisfactory aesthetic results. (AU)

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The influx of maternal oral microbes is considered to play an important role in the acquisition and development of infant oral microbiota. In this study, we examined tongue swab samples from 448 mother-infant pairs at 4-month checkups. The bacterial composition of each sample was determined using PacBio single-molecule long-read sequencing of the full-length 16S rRNA gene and the amplicon sequence variant (ASV) approach. Although the infant oral microbiota was distinctly different from the mother oral microbiota, ASVs shared with their biological mother accounted for a median relative abundance of 9.7% (range of 0.0 to 99.3%), which was significantly higher than that of ASVs shared with unrelated mothers. This shared abundance was strongly associated with the feeding method of infants rather than their delivery mode or antibiotic exposure, and formula-fed infants had higher shared abundance than exclusively breastfed infants. Our study presents strain-level evidence for mother-to-infant transmission of oral bacteria and suggests that colonization of maternal oral bacteria is higher in formula-fed infants. IMPORTANCE Acquisition of oral bacteria during infancy can affect the subsequent formation of stable oral microbiota. This study focused on the mother-to-infant transmission of oral bacteria, a major acquisition route of infant oral microbiota, and demonstrated that most infants acquired oral bacteria from their biological mother even at the single-nucleotide level. Our results also indicated that the occupancies of maternal oral bacteria in infant oral microbiota were associated with the feeding methods of infants. These data could increase understanding of the early development of oral microbiota in infants and its potential associations with oral microbiota-related diseases.

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Gray mold (Botrytis elliptica) causes a deleterious fungal disease that decreases the ornamental value and yield of lilies. Lilium oriental hybrid 'Sorbonne' is a variety that is resistant to gray mold. Understanding the mechanism of resistance against B. elliptica infection in 'Sorbonne' can provide a basis for the genetic improvement in lily plants. In this study, a PacBio Sequel II system was used to sequence the full-length transcriptome of Lilium 'Sorbonne' after inoculation with B. elliptica. A total of 46.64 Gb subreads and 19,102 isoforms with an average length of 1598 bp were obtained. A prediction analysis revealed 263 lncRNAs, and 805 transcription factors, 4478 simple sequence repeats, and 17,752 coding sequences were identified. Pathogenesis-related proteins (PR), which may play important roles in resistance against B. elliptica infection, were identified based on the full-length transcriptome data and previously obtained second-generation transcriptome data. Nine non-redundant potential LhSorPR proteins were identified and assigned to two groups that were composed of two LhSorPR4 and seven LhSorPR10 proteins based on their genetic relatedness. The real-time quantitative reverse transcription PCR (qRT-PCR) results showed that the patterns of expression of nine differentially expressed PR genes under B. elliptica stress were basically consistent with the results of transcriptome sequencing. The pattern of expression of LhSorPR4s and LhSorPR10s genes in different tissues was analyzed, and the expression of each gene varied. Furthermore, we verified the function of LhSorPR4-2 gene in Lilium. The expression of LhSorPR4-2 was induced by phytohormones such as methyl jasmonate, salicylic acid, and ethephon. Moreover, the promoter region of LhSorPR4-2 was characterized by several functional domains associated with phytohormones and stress response. The overexpression of LhSorPR4-2 gene in 'Sorbonne' increased the resistance of the lily plant to B. elliptica and correlated with high chitinase activity. This study provides a full-length transcript database and functionally analyzed the resistance of PR gene to B. elliptica in Lilium, thereby introducing the candidate gene LhSorPR4-2 to breed resistance in Lilium.

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