-
Nucleic Acids Research Jun 2024Kaposi's sarcoma-associated herpesvirus is the etiologic agent of Kaposi's sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led...
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing.
Kaposi's sarcoma-associated herpesvirus is the etiologic agent of Kaposi's sarcoma and two B-cell malignancies. Recent advancements in sequencing technologies have led to high resolution transcriptomes for several human herpesviruses that densely encode genes on both strands. However, for KSHV progress remained limited due to the overall low percentage of KSHV transcripts, even during lytic replication. To address this challenge, we have developed a target enrichment method to increase the KSHV-specific reads for both short- and long-read sequencing platforms. Furthermore, we combined this approach with the Transcriptome Resolution through Integration of Multi-platform Data (TRIMD) pipeline developed previously to annotate transcript structures. TRIMD first builds a scaffold based on long-read sequencing and validates each transcript feature with supporting evidence from Illumina RNA-Seq and deepCAGE sequencing data. Our stringent innovative approach identified 994 unique KSHV transcripts, thus providing the first high-density KSHV lytic transcriptome. We describe a plethora of novel coding and non-coding KSHV transcript isoforms with alternative untranslated regions, splice junctions and open-reading frames, thus providing deeper insights on gene expression regulation of KSHV. Interestingly, as described for Epstein-Barr virus, we identified transcription start sites that augment long-range transcription and may increase the number of latency-associated genes potentially expressed in KS tumors.
PubMed: 38922687
DOI: 10.1093/nar/gkae540 -
Emerging Microbes & Infections Jun 2024Background Hepatitis E virus (HEV) is an important cause of acute hepatitis, however, is highly neglected and largely underreported. This study aimed to describe the...
Background Hepatitis E virus (HEV) is an important cause of acute hepatitis, however, is highly neglected and largely underreported. This study aimed to describe the detailed epidemiology of hepatitis E (HE) through a 10-year surveillance. A community-based active hepatitis surveillance was conducted between November 2007 and October 2017 in 11 townships of Dongtai City in China, involving 355,673 residents. Serum samples were obtained from patients presenting with hepatitis symptoms for more than 3 days. Serum alanine aminotransferase (ALT) levels greater than 2.5 times the upper limit of normal (ULN) were considered acute hepatitis. Samples were subsequently tested for IgG and IgM anti-HEV antibodies, HEV RNA, and hepatitis B surface antigen (HBsAg). The data indicated the incidence of HE fluctuated downward from 2007 to 2017, with an average annual age-standardized incidence of 17.50 per 100,000, exceeding the 10.26 per 100,000 in the National Notifiable Disease Report System (NNDRS). The incidence was notably higher among males (20.95 per 100,000) and individuals aged 50-69 years (37.47 per 100,000). Genotype 4 (HEV-4) was the predominantly circulating genotype during the study period. Furthermore, the study revealed the incidence of hepatitis with HEV and hepatitis B virus (HBV) co-infection was 4.99 per 100,000. Conclusion The active surveillance system identified a higher incidence of HE compared to NNDRS, with a decreased prevalence over a 10-year period. While efforts are still needed to prevent HE in high-risk populations, including individuals with hepatitis B and the elderly.
PubMed: 38922438
DOI: 10.1080/22221751.2024.2373315 -
Advances in Drug and Alcohol Research 2024The Methadone Maintenance Treatment (MMT) program has been proven to be beneficial in reducing illicit opioid use, increasing access to and retention of HIV treatment...
The Methadone Maintenance Treatment (MMT) program has been proven to be beneficial in reducing illicit opioid use, increasing access to and retention of HIV treatment and other therapies, and reducing HIV transmission, and other drug-related morbidities and mortalities. However, determinants of treatment retention and outcomes for opioid-dependent persons accessing MMT in Kenya are limited. We sought to identify factors contributing to poor treatment outcomes among opioid-dependent persons enrolled in the Mombasa MMT program, between 2017 and 2019. We conducted a retrospective records review for opioid-dependent persons receiving Methadone treatment in the Kisauni MAT clinic enrolled during 2017-2019. We defined poor clinical or health-related treatment outcome as any client Lost-To-Follow-Up (LTFU), turned HIV or Viral hepatitis positive, and/or missed two or more antiretroviral therapy (ART) appointments intake during MMT. Variables abstracted from clinical and pharmacological MMT service delivery tools included socio-demographic characteristics, clinical history, risk factors, and MMT outcomes. Data were analyzed using . We calculated Prevalence Odds Ratios (POR) and 95% Confidence Intervals (CI) to identify factors associated with adverse health outcomes. Of the total 443 eligible records, the mean age was 37 years (SD ± 7.2) and males comprised 90.7%. The majority of females clients, 79.1% (34/43), were aged ≤35 years, 7.0% (3/43) had no education, 32.6% (14/43) were employed, 39.5% (17/43) were HIV positive and 18.6% (8/43) were HCV-positive. Overall, adverse treatment outcomes were at 27.5% (122/443), namely: LTFU at 22.8% (101/443), new HIV cases at 1.0% (4/391), HCV at 1.2% (5/405), and Hepatitis B Virus (HBV) at 1.2% (5/411), and 1.1% (5/443) died. Of HIV-infected clients linked to Comprehensive Care Clinic (CCC), 3.6% (2/56) defaulted from ART, and 25% (2/8) had detectable Viral Load of those retested. Lack of formal education (POR: 2.7, 95% CI: 1.3-5.7), unemployment (POR: 2.4, 95% CI: 1.4-4.0), and being a Non-Injector (POR: 1.7, 95% CI: 1.0-2.9) were negatively associated with treatment retention. Females were younger, and more educated with higher HIV and HCV prevalence. Being a Non-injector, unemployment, and lack of formal education may increase the likelihood of poor treatment outcomes among MMT clients. Closer monitoring of MMT clients with these characteristics is recommended with the integration of CCC into MMT services.
PubMed: 38912085
DOI: 10.3389/adar.2024.11791 -
Frontiers in Plant Science 2024Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by...
Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses.
Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (, , , , , and ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as for efficient nitrogen utilization, for salt tolerance, and for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.
PubMed: 38911983
DOI: 10.3389/fpls.2024.1390603 -
Journal of Dairy Science Jun 2024In French dairy goat systems, kids are generally separated from their mother does shortly after birth. The main drivers of this practice are related to health-especially...
In French dairy goat systems, kids are generally separated from their mother does shortly after birth. The main drivers of this practice are related to health-especially the prevention of the Caprine Arthritis Encephalitis Virus (CAEV) transmission-and economics. However, the separation of young ruminants from their does is being increasingly questioned by society and has raised concerns about the satisfaction of their behavioral needs. Some farmers choose to leave their female kids with their does. The aims of this study were to understand their motivations for leaving kids with their does, to describe how kids are reared in this case and how farmers perceive different aspects of the impacts of this practice. Individual semi-structured interviews were carried out with 40 farmers who had implemented the kids-with-does practice for at least one year. Compared with the national database describing the French population of dairy goat farmers, the characteristics of the interviewed farmers differed from those of the general population. They were younger and had done longer studies. Their farms were smaller, mainly with rare breeds and milk was mainly processed on-farm under an organic certification system. They chose to implement this practice for different reasons: ethical considerations, improving integration of kids within the herd, saving time and increasing comfort at work or improving the kids' growth, welfare, and health. The doe-kid rearing contact practices varied greatly between farms, with some kids staying with their does from a period of 45 d to never being separated; furthermore, some kids remained with their does all day, while others remained together part of the day or for a limited time, and daily contact evolved over time. Overall, farmers were satisfied as the benefits quoted were coherent with their motivations to implement this rearing practice. Most have decided to continue the practice, though usually with changes. However, as 40% of them had only 3 years or less of experience of doe-kid rearing, some had not sufficient hindsight into long-term issues such as the transmission of CAEV. It is crucial to tackle challenges associated with this practice, i.e., potentially wild kids, health issues, and economic consequences stemming from a reduction in marketable milk.
PubMed: 38908689
DOI: 10.3168/jds.2023-24600 -
Current Microbiology Jun 2024Viral-like particles (VLPs) represent versatile nanoscale structures mimicking the morphology and antigenic characteristics of viruses, devoid of genetic material,... (Review)
Review
Viral-like particles (VLPs) represent versatile nanoscale structures mimicking the morphology and antigenic characteristics of viruses, devoid of genetic material, making them promising candidates for various biomedical applications. The integration of artificial intelligence (AI) into VLP research has catalyzed significant advancements in understanding, production, and therapeutic applications of these nanostructures. This comprehensive review explores the collaborative utilization of AI tools, computational methodologies, and state-of-the-art technologies within the VLP domain. AI's involvement in bioinformatics facilitates sequencing and structure prediction, unraveling genetic intricacies and three-dimensional configurations of VLPs. Furthermore, AI-enabled drug discovery enables virtual screening, demonstrating promise in identifying compounds to inhibit VLP activity. In VLP production, AI optimizes processes by providing strategies for culture conditions, nutrient concentrations, and growth kinetics. AI's utilization in image analysis and electron microscopy expedites VLP recognition and quantification. Moreover, network analysis of protein-protein interactions through AI tools offers an understanding of VLP interactions. The integration of multi-omics data via AI analytics provides a comprehensive view of VLP behavior. Predictive modeling utilizing machine learning algorithms aids in forecasting VLP stability, guiding optimization efforts. Literature mining facilitated by text mining algorithms assists in summarizing information from the VLP knowledge corpus. Additionally, AI's role in laboratory automation enhances experimental efficiency. Addressing data security concerns, AI ensures the protection of sensitive information in the digital era of VLP research. This review serves as a roadmap, providing insights into AI's current and future applications in VLP research, thereby guiding innovative directions in medicine and beyond.
Topics: Artificial Intelligence; Computational Biology; Vaccines, Virus-Like Particle
PubMed: 38904765
DOI: 10.1007/s00284-024-03750-5 -
F1000Research 2023Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is...
BACKGROUND
Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is poor despite intensive multi-modal therapies with significant toxicity. Novel therapies are desperately needed. The Zika virus (ZIKV) can access the nervous system and there is growing interest in employing ZIKV as a potential therapy against paediatric nervous system tumours, including neuroblastoma.
METHODS
Here, we perform extensive data mining, integration and re-analysis of ZIKV infection datasets to highlight molecular mechanisms that may govern the oncolytic response in neuroblastoma cells. We collate infection data of multiple neuroblastoma cell lines by different ZIKV strains from a body of published literature to inform the susceptibility of neuroblastoma to the ZIKV oncolytic response. Integrating published transcriptomics, interaction proteomics, dependency factor and compound datasets we propose the involvement of multiple host systems during ZIKV infection.
RESULTS
Through data mining of published literature, we observed most paediatric neuroblastoma cell lines to be highly susceptible to ZIKV infection and propose the PRVABC59 ZIKV strain to be the most promising candidate for neuroblastoma oncolytic virotherapy. ZIKV induces TNF signalling, lipid metabolism, the Unfolded Protein Response (UPR), and downregulates cell cycle and DNA replication processes. ZIKV infection is dependent on sterol regulatory element binding protein (SREBP)-regulated lipid metabolism and three protein complexes; V-ATPase, ER Membrane Protein Complex (EMC) and mammalian translocon. We propose ZIKV non-structural protein 4B (NS4B) as a likely mediator of ZIKVs interaction with IRE1-mediated UPR, lipid metabolism and mammalian translocon.
CONCLUSIONS
Our work provides a significant understanding of ZIKV infection in neuroblastoma cells, which will facilitate the progression of ZIKV-based oncolytic virotherapy through pre-clinical research and clinical trials.
Topics: Humans; Neuroblastoma; Oncolytic Virotherapy; Zika Virus; Proteomics; Cell Line, Tumor; Zika Virus Infection; Transcriptome
PubMed: 38903860
DOI: 10.12688/f1000research.132627.3 -
Cytokine Jun 2024Cytokines may related to intrauterine Hepatitis B virus (HBV) transmission. 205 HBsAg(+) pregnant cases and 74 HBsAg(-) women were included. Neonatal blood samples were...
Cytokines may related to intrauterine Hepatitis B virus (HBV) transmission. 205 HBsAg(+) pregnant cases and 74 HBsAg(-) women were included. Neonatal blood samples were taken within 24 h of delivery and before HBV vaccinations. Serological HBV biomarkers and cytokines were detected. 21.9 % of the newborns from HBsAg(+) women were intrauterinally transmitted, including 7.3 % with dominant transmission (DBT) and 14.6 % occult transmission (OBT). HBV DNA load (odd ratio [OR], 1.44; 95 % confidence interval [CI], 1.05-1.98), interferon-γ (IFN-γ) (OR, 1.01; 95 %CI, 1.00-1.02) and toll-like receptor 9 (TLR9) (OR, 1.27; 95 %CI, 1.06-1.52) positively correlated with DBT. Only IFN-γ (OR, 1.01; 95 %CI, 1.00-1.01) positively associated with OBT. According to the generated restricted cubic spline, TLR9 was positively correlates with rise of DBT in a log-shape. It may be possible to develop a nomogram which intercalates these factors to predict intrauterine HBV transmissions. Further research should consider immune processes involved in chorioamnionitis.
PubMed: 38901264
DOI: 10.1016/j.cyto.2024.156670 -
World Journal of Clinical Cases Jun 2024We present a case of an rearranged sarcoma in the left forearm and analyze its clinicopathological and molecular features.
BACKGROUND
We present a case of an rearranged sarcoma in the left forearm and analyze its clinicopathological and molecular features.
CASE SUMMARY
The patient is a 23-year-old woman. Microscopically, the tumor cells were medium-sized round cells arranged in small nests. The cytoplasm was clear, nuclei were relatively uniform, chromatin was dense, nucleoli were visible, and mitotic figures were rare. Immunohistochemically, the tumor cells were positive for Vimentin, INI-1, CD99, NKX2.2, CyclinD1, friend leukaemia virus integration 1, and NKX3.1. Next-generation sequencing revealed the presence of the fusion gene. rearranged sarcomas are rare and can easily be misdiagnosed.
CONCLUSION
Clinical imaging, immunohistochemistry, and molecular pathology should be considered to confirm the diagnosis.
PubMed: 38899283
DOI: 10.12998/wjcc.v12.i16.2887 -
Molecules (Basel, Switzerland) May 2024Within the fields of infectious disease diagnostics, microfluidic-based integrated technology systems have become a vital technology in enhancing the rapidity, accuracy,... (Review)
Review
Within the fields of infectious disease diagnostics, microfluidic-based integrated technology systems have become a vital technology in enhancing the rapidity, accuracy, and portability of pathogen detection. These systems synergize microfluidic techniques with advanced molecular biology methods, including reverse transcription polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR), have been successfully used to identify a diverse array of pathogens, including COVID-19, Ebola, Zika, and dengue fever. This review outlines the advances in pathogen detection, attributing them to the integration of microfluidic technology with traditional molecular biology methods and smartphone- and paper-based diagnostic assays. The cutting-edge diagnostic technologies are of critical importance for disease prevention and epidemic surveillance. Looking ahead, research is expected to focus on increasing detection sensitivity, streamlining testing processes, reducing costs, and enhancing the capability for remote data sharing. These improvements aim to achieve broader coverage and quicker response mechanisms, thereby constructing a more robust defense for global public health security.
Topics: Humans; Nucleic Acid Amplification Techniques; Molecular Diagnostic Techniques; Microfluidics; Communicable Diseases; COVID-19; SARS-CoV-2; Microfluidic Analytical Techniques; Dengue; Zika Virus Infection; Zika Virus
PubMed: 38893293
DOI: 10.3390/molecules29112417