National Center For Biotechnology Information Research Articles

The State of Knowledge of CCA Diversity in the Caribbean Coral Reefs

Crustose coralline algae (CCA) are a diverse and ecologically important species found in most of the world’s oceans. The current lack of taxonomic knowledge and relative abundance compromises our ability to predict species diversity numbers and, thus, their ecological roles and impacts on coral reefs. To gather a better understanding of the state of knowledge of crustose coralline algae taxonomy in the Caribbean, 107 different research papers, and other primary and secondary literature were studied; any source with taxonomical information, species identification, or genetic markers for identification was recorded. All Genebank codes were collected and sorted by supposed species marker and then ran through the National Center of Biotechnology Information. The location these genetic markers were gathered from was compared to the natural habitat range of the species, based on the Algaebank habitat description. Of the supposed 83 described species of crustose algae in the Caribbean, based on morphological characteristics, only 24 total were confirmed by DNA markers. This leaves at least 59 species of CCA to be confirmed in the Caribbean Sea with molecular markers. This indicates the importance of DNA barcode survey studies to assess the accurate diversity of this group in the region. With this limited knowledge apparent, it should be seen that a CCAs phylogenetic and taxonomical review must be done. An in-depth assessment should be conducted on CCA collections to identify the Caribbean species correctly and thus know their biodiversity in local habitats.

Total Transanal Endorectal Pull-through Versus Laparoscopic-Assisted Approach in Children with Rectosigmoid Hirschsprung's Disease: A Systematic Review and Meta-Analysis.

Objective: To compare the clinical outcomes between total transanal endorectal pull-through (TTEPT) and laparoscopic-assisted transanal endorectal pull-through (LTEPT) in children with rectosigmoid Hirschsprung's disease. Methods: A retrospective study was conducted to compare patients with rectosigmoid Hirschsprung's disease who underwent TTEPT or LTEPT at Beijing Children's Hospital between January 2016 and June 2021. Clinical details were collected from medical records. Patients' parents completed the Krickenbeck questionnaire to evaluate the long-term bowel function (age >4 years) by telephone. A literature search was conducted by using the National Center for Biotechnology Information (NCBI) PubMed database. We combined data from our data with eligible articles and performed a meta-analysis. Result: From our data, there was no difference in the incidence of postoperative complications or long-term bowel function between the patients undergoing TTEPT and LTEPT. A meta-analysis, including five published articles and our data, was performed with a total of 414 patients (n = 236 with TTEPT and n = 178 with LTEPT). For postoperative complications, there were no significant differences between TTEPT and LTEPT for the incidence of HAEC (odds ratio [OR], 0.90; 95% confidence interval [CI], 0.45-1.80; P = .77) or anastomotic leak (OR, 2.52; 95% CI, 0.40-15.80; P = .32). Regarding bowel function outcomes, the incidence of soiling (OR, 1.77; 95% CI, 0.84-3.71; P = .13) and constipation (OR, 1.20; 95% CI, 0.54-2.64; P = .66) were also similar for the two approaches. Conclusion: There was no significant difference in postoperative complications and bowel functional outcomes in patients with rectosigmoid HD undergoing TTEPT or LTEPT. Levels of Evidence: III.

HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants

Background: Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Objective: Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. Methods: We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. Results: The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. Conclusion: study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments.

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

Association between Mir-17-92 gene promoter polymorphisms and depression in a Chinese population

BackgroundDepression is a common chronic debilitating disease with a heavy social burden. single nucleotide polymorphisms (SNPs) can affect the function of microRNAs (miRNAs), which is in turn associated with neurological diseases. However, the association between SNPs located in the promoter region of miR-17-92 and the risk of depression remains unclear. Therefore, we investigated the association between rs982873, rs9588884 and rs1813389 polymorphisms in the promoter region of miR-17-92 and the incidence of depression in a Chinese population.Methodswe used GWAS (Genome-wide association study) and NCBI (National Center for Biotechnology Information) to screen three SNPs in the miR-17-92 cluster binding sites. A case-control study (including 555 cases and 541 controls) was conducted to investigate the relationship between the SNPs and risk of depression in different regions of China. The gene sequencing ii was used to genotype the collected blood samples.Resultsthe following genotypes were significantly associated with a reduced risk of depression: rs982873 TC (TC vs. TT: OR = 0.72, 95% CI, 0.54–0.96, P = 0.024; TC/CC vs. TT: OR = 0.74, 95% Cl, 0.56–0.96, P = 0.025); CG genotype of rs9588884 (CG vs. CC: OR = 0.74, 95% CI, 0.55–0.98, P = 0.033; CG/GG vs. CC: OR = 0.75, 95% Cl, 0.57–0.98, P = 0.036); and AG genotype of rs1813389 (AG vs. AA: OR = 0.75, 95% CI, 0.57-1.00, P = 0.049; AG/GG vs. AA: OR = 0.76, 95% Cl, 0.59-1.00, P = 0.047). Stratified analysis showed that there was no significant correlation between the three SNPS and variables such as family history of suicidal tendency (P > 0.05).Conclusionsour findings suggest that rs982873, rs9588884, and rs1813389 polymorphisms may be associated with protective factors for depression.

Immune Responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccines: Updated Insights

Background: Using a multidisciplinary approach, this review explores and investigates the relationship between immune responses, effectiveness, and results of various vaccination strategies among a range of demographics. Moreover, this review aims to aid healthcare professionals in understanding the intricacies of immune responses and their implications for future vaccine development.Methodology: In this systematic review, we employed an electronic online database platform including the National Centre for Biotechnology Information (NCBI), the National Institute for Health and Clinical Excellence (NICE), and the World Health Organization (WHO) for evidence-based material, utilizing the keywords throughout this literature review.Results: This review provides a detailed framework regarding immune responses to the COVID- 19 vaccine, based on demographics, age, sex, types of immunity, and immunization strategies. Such research can provide important academic support for the development of not only COVID- 19 vaccines but also other vaccines.Conclusions: Overall, immune responses tended to dwindle a few months after vaccine administration. This is because B cells block SARS-CoV-2 from infecting cells via antibodies and T cells destroy infected cells. The most efficient tool for providing long-lasting protection against SARS-CoV-2 is vaccination. Humans have developed immunity to SARS-CoV-2, particularly antibody-mediated humoral immunity. The development of vaccines across the whole family of coronaviruses that target antibody epitopes (antigenic determinants) prevents the emergence of mutant strains.

EVALUATION OF PROPHAGES AND ANTI MICROBIAL RESISTANCE PROFILE OF BACILLUS SUBTILIS USING IN SILICO APPROACH

The main objective of this study was to identify the prophages and antimicrobial resistance profile of  Bacillus subtilis using computational methods. Prophages are potential therapeutic antimicrobial agents against antibiotic- resistant pathogens. The potential of prophage to induce antimicrobial resistance and increase pathogenicity in bacterial genomes resulted in renewed interest in the identification of prophage sequences and their associated antimicrobial resistant genes in bacterial genomes. Sequences of Bacillus subtilis retrieved from the  sequence raw archive (SRA) of the National Centre for Biotechnology Information was submitted to  bacterial viral bioinformatics resource centre for genome assembly. Prophage sequences were identified using the PHASTER server. The region length, region position and GC percentage of nucleotides of prophage sequences were identified. The antimicrobial resistance gene family, drug class, resistance mechanism and length of reference sequences were identified using the resistance gene identifier protocol of the comprehensive antimicrobial resistance database. It can be concluded that the Bacillus subtilis strain evaluated contained prophage sequences associated with antimicrobial resistance genes, there is, therefore, the need to assess the safety of bacteriophages before they are   utilized as alternative to antibiotics.

Integrating Bulk RNA and Single-Cell Sequencing Data Unveils Efferocytosis Patterns and ceRNA Network in Ischemic Stroke.

Excessive inflammatory response following ischemic stroke (IS) injury is a key factor affecting the functional recovery of patients. The efferocytic clearance of apoptotic cells within ischemic brain tissue is a critical mechanism for mitigating inflammation, presenting a promising avenue for the treatment of ischemic stroke. However, the cellular and molecular mechanisms underlying efferocytosis in the brain after IS and its impact on brain injury and recovery are poorly understood. This study explored the roles of inflammation and efferocytosis in IS with bioinformatics. Three Gene Expression Omnibus Series (GSE) (GSE137482-3m, GSE137482-18m, and GSE30655) were obtained from NCBI (National Center for Biotechnology Information) and GEO (Gene Expression Omnibus). Differentially expressed genes (DEGs) were processed for GSEA (Gene Set Enrichment Analysis), GO (Gene Ontology Functional Enrichment Analysis), and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses. Efferocytosis-related genes were identified from the existing literature, following which the relationship between Differentially Expressed Genes (DEGs) and efferocytosis-related genes was examined. The single-cell dataset GSE174574 was employed to investigate the distinct expression profiles of efferocytosis-related genes. The identified hub genes were verified using the dataset of human brain and peripheral blood sample datasets GSE56267 and GSE122709. The dataset GSE215212 was used to predict competing endogenous RNA (ceRNA) network, and GSE231431 was applied to verify the expression of differential miRNAs. At last, the middle cerebral artery (MCAO) model was established to validate the efferocytosis process and the expression of hub genes. DEGs in two datasets were significantly enriched in pathways involved in inflammatory response and immunoregulation. Based on the least absolute shrinkage and selection operator (LASSO) analyses, we identified hub efferocytosis-related genes (Abca1, C1qc, Ptx3, Irf5, and Pros1) and key transcription factors (Stat5). The scRNA-seq analysis showed that these hub genes were mainly expressed in microglia and macrophages which are the main cells with efferocytosis function in the brain. We then identified miR-125b-5p as a therapeutic target of IS based on the ceRNA network. Finally, we validated the phagocytosis and clearance of dead cells by efferocytosis and the expression of hub gene Abca1 in MCAO mice models.

Molecular identification of the bacterium acute conjunctivitis by the method of sequensing gen 16S rRNA

Conjunctivitis is the most common eye disease, characterized by contextual inflammation, which can be caused by bacteria. The diagnosis of conjunctivitis is established based various factors, including the patients’s medical history, onset of eye symptoms, non-ocular symptoms, previous disease history, family medical history, allergies, and physical examination of the eyes, which may include assessments of visual acuity and vision field. Some cases of conjunctivitis require laboratory examinations to confirm the diagnosis. These may include cytological examination with Giemsa staining, Chlamydia Diagnostic Test, Nucleic acid amplification tests (NAATs) or Polymerase chain reaction (PCR), and microbiological tests. Microbiological examination helps identify the bacteria responsible for conjunctivitis and aids in treatment by prescribing antibiotics to suppress the growth of the infecting bacteria. While identification tests are not routinely performed, researchers often seek to determine the specific type of bacteria causing conjunctivitis infections, which may require several laboratory tests. Bacterial virulence plays a significant role, with genetic mutations potentially leading to severe infections of varying severity. Virulence genes encode proteins that express pathogenic properties. The species responsible for conjunctivitis can be definitively identified definitively through microbiological examination, utilizing methods such as the 16S Ribosomal RNA Sequencing (rRNA) technique, known for its accuracy and speed. This study aims to analyze the results of rRNA sequencing in cases of acute bacterial conjunctivitis caused by 16S rRNA genotyping. The research employed an exploratory metholodolot, with the results analyzed using the The Basic Local Alignment Search Tool (BLAST) tracking program database on the National Center for Biotechnology Information (NCBI) website. The findings revealed that Sphingomonas paucimobilis encoded the 16S rRNA using Universal Primary 27 F and 1492 R, obtained in a sequence size of 1351bp. The isolate demonstrated similarities to Sphingomonas paucimobilis.

Two putative calcium-dependent protein kinases are involved in the regulation of sugarcane defense genes

Sugarcane is a primary sugar crop and an important source of bioenergy. Pathogens are the major factors affecting sugarcane yield and sugar content. However, the mechanisms of sugarcane defense regulation remain largely unknown, and research on prospective genetic targets for modification is scarce. As the main class of calcium sensors, calcium-dependent protein kinases (CDPKs/CPKs) play a crucial role in the immune regulatory network. Using sugarcane genomic data, we identified 229 putative ScCDPKs in primordial specie Saccharum officinarum. Searching the putative CDPKs in sugarcane cultivars from National Center for Biotechnology Information (NCBI), 12 putative ScCDPKs in cultivars were identified. Phylogenetic analysis revealed evolutionary relationships among these CDPKs in sugarcane cultivars and those in S. officinarum, Arabidopsis thaliana, and rice. Truncation mutants of ScCDPKs were introduced into the reporter system and examined for activity in inducing Sugarcane Pathogenesis Related Protein 1 (ScPR1). The results showed that truncated ScCDPK1 and ScCDPK8 induce higher expression of ScPR1 than full-length ScCDPK1 and ScCDPK8. Additionally, transient expression of truncated ScCDPK1 and ScCDPK8 exhibit stronger activity in sugarcane protoplasts for activation of ScPR1 and sugarcane Serine Protease Inhibitor (ScSPI). These results demonstrate that ScCDPK1 and ScCDPK8 possess auto-inhibitory activity. The findings of this study provide a basis for an in-depth study of the sugarcane CDPK gene family and lay the foundation for further genetic improvement.

Sequence Analysis of some species in the genus Amaranthus L. using Ribulose-1.5 - bisphosphate carboxylase/oxygenase (rbcL) genes

Bioinformatics is a novel method to investigate evolutionary relationships and genetic diversity among species. This study assessed the evolutionary patterns and genetic diversity of Amaranthus species using ribulose-1.5-bisphosphate carboxylase/oxygenase (rbcL gene). A total of 20 full FASTA-format rbcL gene sequences for accessions of Amaranthus tricolor, A. dubius, A. cruentus, A. viridis, and A. spinosus from different regions were retrieved from the National Center for Biotechnology Information. Multiple sequence alignment was used to determine genetic variations. A phylogenetic tree was constructed using neighbor-joining clustering method while a distant matrix was created using Tamura-Nei genetic distance model. From position 1 to 22 in nucleotide alignment, only accession KX082771.1 from USA, aligns. The exclusive alignment in this region suggests an exceptionally conserved sequence among species, implying a common genetic origin. However, from position 23 to 50, nine different accessions namely MN192576.1, MN204800.1, EF590496.1, GQ248546.1, OQ737000.1, MG246937.1, MN104855.1, MN104858.1, and MN04859.1 align. The phylogenetic tree representing the evolutionary relationships offers insights into the genetic diversity and relatedness of these species within specific regions. The genetic distance matrix shows that sequences within the same region share relatively high similarity scores, indicating a genetic connection likely influenced by their geographic proximity. However, sequences from different regions, exhibit moderate genetic differences, emphasizing the genetic diversity across geographically distinct regions. The observed genetic diversity and evolutionary relationships among accessions of Amaranthus revealed by rbcL genes highlight the unique genetic features of these species in different regions, and therefore should be explored for their genetic improvement and conservation purposes.

Network pharmacology prediction and experiment validation of anti liver cancer activity of curcumae rhizoma and hedyotis diffusa willd

Objective: This study aims to elucidate anti liver cancer components and potential mechanisms of Curcumae Rhizoma and Hedyotis diffusa Willd (CR-HDW). Methods: Effective components and targets of CR-HDW were identified from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Liver cancer-related genes were collected from GeneCards, Gene-Disease Association (DisGeNET), and National Center for Biotechnology Information (NCBI). Protein-protein interaction networks, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were conducted to analyze the identified genes. Molecular docking was used to simulate binding of the active components and their target proteins. Cell activity assay, Western blot, and Senescence-associated β-galactosidase (SA-β-gal) experiments were conducted to validate core targets identified from molecular docking. Results: Ten active compounds of CR-HDW were identified including quercetin, 3-epioleanic acid and hederagenin. The primary core proteins comprised Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Protein Kinase B（AKT1）, etc. The pathways for Phosphoinositide 3-kinase (PI3K)/ AKT, cellular senescence, Fork head boxO (FOXO) were revealed as important for anti-cancer activity of CR-HDW. Molecular docking demonstrated strong binding between liver cancer target proteins and major active components of CR-HDW. In vitro experiments confirmed that hederagenin and 3-epioleolic acid inhibited HuH-7 cell growth, reduced expression of PI3K, AKT, and mechanistic target of rapamycin (mTOR) proteins. Hederagenin also induced HuH-7 senescence. Conclusion: In summary, our results suggest that the CR-HDW component (Hederagenin, 3-epoxy-olanolic acid) can inhibit the proliferation of HuH-7 cells by decreasing PI3K, AKT, and mTOR. Hederagenin also induced HuH-7 senescence.

Evaluation of Antifungal Effect of Allium jesdianum Bacterial Endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes

: Antimicrobial resistance (AMR) is the ability of microbes to survive and grow in the presence of antimicrobial drugs. Bacterial endophytes, which reside within plants, can promote plant growth and other essential activities. Endophytes have the potential to produce novel and unique products for use in modern medicine, agriculture, and industry. They may hold the key to combating drug-resistant strains by providing new antimicrobial compounds, potentially leading to the development of new medications. In this study, bacterial endophytes of Allium jesdianum were extracted and characterized. The antifungal effect of these endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes was evaluated. Various parts of the plant were used to isolate ten bacterial endophytes to assess their antifungal properties. Universal eubacterial primers were used to amplify a 1500 bp region of the 16S rRNA gene. The resulting partial nucleotide sequences were compared with sequences available from the National Center for Biotechnology Information (NCBI) and EzBioCloud Database. Subsequent comparisons determined their similarity. Each isolated endophyte was cultured with equal amounts of R. stolonifer, Penicillium, Cladosporium, and T. mentagrophytes. This study measured the level of antagonism by assessing the extent of potential interactions. Ten bacterial endophytes, primarily cocci and bacilli, were extracted from different parts of A. jesdianum. The isolates were identified as Staphylococcus warneri AJB1, Staphylococcus succinus AJB2, Pseudomonas thivervalensis AJB3, Bacillus subtilis AJB4, Acinetobacter lwoffii AJB5, and Pantoea brenneri AJB6. AJB1 and AJB3 showed no antagonistic activity. AJB2, AJB5, and AJB6 displayed antagonistic action against R. stolonifer. Only AJB4 showed strong antagonistic activity against Penicillium. Further research is necessary to determine whether these endophytes possess antibiotic activity and can be used for food preservation.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation.

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

The Effect of Honey on Bacteria Isolated from Urinary Tract Infections among Patients Attending Ruhengeri Referral Hospital

Background: Urinary tract infections (UTIs) occur when bacteria enter the urethra from the skin or rectum and infect the bladder, causing symptoms. UTIs are becoming increasingly multidrug-resistant, with some drugs no longer effective in treatment. According to the National Center for Biotechnology Information (NCBI), honey has been shown to have high osmotic pressure and high acidity that prevent the multiplication of bacteria. This study aimed to evaluate the effect of honey on bacteria isolated from urine samples collected from patients with UTI’s attending Ruhengeri Referral Hospital.
 Methodology: Urine samples were collected in sterile containers at Ruhengeri Referral Hospital and transported to the microbiology laboratory at the Ruhengeri Institute of Higher Education (INES Ruhengeri). Two types of honey, raw and processed were used as antimicrobial agents on bacteria isolated from UTIs. Various methods were used to isolate and identify bacterial isolates, including culture on solid medium, gram staining, and biochemical tests.
 Results: The most commonly isolated bacterium was S. aureus (33.3%) which is in the second group of bacteria susceptible to honey, followed by P. aeruginosa (13.8%) and CoNS (13.8%). E. coli, K. pneumonia, and Streptococcus spp. each accounted for 11.2%. The former and the latter were the most susceptible bacteria to natural honey honey (mIZ = 36 ±2.83; ±4.24 mm, respectively), while E. aerogenes was the least isolated bacterium at 5.5% and the least susceptible to honey.
 Conclusion: Honey was showed to exhibit an antimicrobial effect against all bacteria isolated from the UTI, suggesting natural honey as a remedy in controlling urinary tract bacterial infection. Further studies are needed to evaluate its capacity compared to classical antibiotics currently used to treat bacteria in UTIs. The practical way to use honey to get targeted area is also an interested point that need to be investigated.
 Keywords: Urinary tract infection; honey; bacteria.

Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits.

Pseudomonas aeruginosa is a ubiquitous Gram-negative opportunistic pathogen with remarkable phylogenetic and phenotypic variabilities. In this work, we applied classical molecular networking analysis to secondary metabolite profiling data from seven Pseudomonas aeruginosa strains, including five clinical isolates from the lung secretions of people with cystic fibrosis (CF). We provide three vignettes illustrating how secondary metabolite profiling aids in the identification of rare genomics traits in P. aeruginosa. First, we describe the identification of a previously unreported class of acyl putrescines produced by isolate mFLRO1. Secondary analysis of publicly available metabolomics data revealed that acyl putrescines are produced by <5% of P. aeruginosa strains. Second, we show that isolate SH3A does not produce di-rhamnolipids. Whole-genome sequencing and comparative genomics revealed that SH3A cannot produce di-rhamnolipids because its genome belongs to clade 5 of the P. aeruginosa phylogenetic tree. Previous phylogenetic analysis of thousands of P. aeruginosa strains concluded that <1% of publicly available genome sequences contribute to this clade. Last, we show that isolate SH1B does not produce the phenazine pyocyanin or rhamnolipids because it has a one-base insertion frameshift mutation (678insC) in the gene rhlR, which disrupts rhl-driven quorum sensing. Secondary analysis of the tens of thousands of publicly available genomes in the National Center for Biotechnology Information (NCBI) and the Pseudomonas Genome Database revealed that this mutation was present in only four P. aeruginosa genomes. Taken together, this study highlights that secondary metabolite profiling combined with genomic analysis can identify rare genetic traits of P. aeruginosa isolates.IMPORTANCESecondary metabolite profiling of five Pseudomonas aeruginosa isolates from cystic fibrosis sputum captured three traits present in <1%-5% of publicly available data, pointing to how our current library of P. aeruginosa strains may not represent the diversity within this species or the genetic variance that occurs in the CF lung.

First Report of Sweet Potato Virus E(SPVE) Infecting Sweet Potato in China.

Sweet potato (Ipomoea batatas [L.] Lam.) is a versatile crop, cultivated in the subtropical and tropical areas, as food, fodder, and industrial raw material crop. In China, sweet potato has been used as a health-care food in recent years, as it contains a wide range of nutrients and xenobiotic phytochemicals. However, viral diseases are major constraint for the sweet potato yield and quality, especially the seed production and quality. Over 30 species of viruses infect sweet potato worldwide (Clark et al. 2012). More recently, a few new viruses infected sweet potato were identified, such as sweet potato virus E (SPVE), which was reported in Korea(Jo et al. 2020). In May 2022, a sweet potato sample (JSXZ1) with virus-like symptom, such as mosaic and vein clearing were collected from sweet potato germplasm Xuzhou resource nursery, Jiangsu Province, China (N34˚16', E117˚18') (Fig. S1A). To investigate the virus disease, the sample JSXZ1 showing the typical symptoms of disease was prepared for Small-RNA (sRNA) deep-sequencing. The sRNA library was constructed using TruSeq™ Small RNA Sample Prep Kits (Illumina, San Diego, USA) and sequenced using the Illumine Hiseq 2500 platform by LC-Bop Technologies (Hangzhou) CO., LTD. The sample was sequenced to obtain 26, 358, 439 raw reads and 22, 969, 139 clean reads after quality control trimming and analysis. The Velvet 1.0.5 software was used to de novo assemble the clean reads (18 to 28 nt) into larger contigs, which were then compared with the nucleotide sequences in the National Center for Biotechnology Information (NCBI) database using the BLASTn algorithm. Viruses found in the sample were sweet potato latent virus (SPLV), sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), sweet potato badnavirus A (SPBV-A) and sweet potato badnavirus B (SPBV-B). Surprisingly, besides the viruses listed above, 28 contigs matched sequences of SPVE isolate GS (MH388502). To verify the result, total RNA was extracted from the sample JSXZ1 and from other leave samples (JSXZ2-JSXZ5) that contained SPFMV, SPVC, SPLV, SPVG respectively stored in lab using FastPure Universal Plant Total RNA Isolation Kit (Vazyme Biotech Co., LTD, Nanjing, China). cDNA was synthesized using random primer (hexadeoxyribonucleotide mixture; pd(N)6). The cDNA serves as template in PCR using a newly designed primer pairs based on SPVE p1 gene (SPVE-F: 5'- TCACCAAAAAGAATGCTACAAC-3'/SPVE-R: 5'-GAAATCCTCCCACTCTCCATA-3'). An expected ~500-bp PCR fragment was obtained in JSXZ1, while none of the fragment was obtained from JSXZ2-JSXZ5 (Fig. S1B). The PCR fragment was cloned into pMD18-T vector (Takara Bio Inc., Beijing, China) and plasmid DNA from transformed Escherichia coli DH5α cell (n=3) were commercially sequenced by Sangon Biotech (Shanghai) Co., Ltd. The sequences of the three fragment clones we obtained were 100% identical when compared. A BLASTN analysis of the sequences revealed that they are specific to SPVE and shared 98.62% nucleotide identity to SPVE GS isolate (MH388502) and one sequence was submitted to GenBank (Accession number OQ948331). To determine the occurrence of SPVE in infected sweet potato plants, a total of 37 leaves samples with viral symptom collected from Shandong Province (n=6) and Jiangsu Province (n=31) were indexed by RT-PCR as described before. Only 9 (24.3%) out of 37 from Shandong (n=1) and Jiangsu (n=8) were positive to SPVE respectively. In addition, five additional viruses (SPFMV, SPVC, SPVG, SPLV, SPCSV) were detected among these 37 samples and always in a mixed infection of two or more viruses. To our knowledge, this is the first report of SPVE infecting sweet potato in China. Sweet potato is an important crop in China and other countries (Zhang et al. 2023). China is the largest sweet potato producer all over the world. In addition, as sweet potato is produced through the vegetative propagation mode, thus, more attention should be paid to detection and monitoring of occurrence of SPVE in China.

In silico and PCR Screening for a Live Attenuated Salmonella Typhimurium Vaccine Strain.

The application of live attenuated Salmonella Typhimurium vaccines has significantly helped control Salmonella in poultry products. Because the U.S. Department of Agriculture-Food Safety Inspection Service (USDA-FSIS) scores all Salmonella as positive, regardless of serovar, attenuated vaccine strains that are identified at processing contribute negatively toward Salmonella performance standards. This study was designed to determine the incidence of a live attenuated Salmonella serovar Typhimurium vaccine identified in broiler products by FSIS and to develop a PCR assay for screening of isolates. Salmonella Typhimurium short-read sequences from broiler samples uploaded to the National Center for Biotechnology Information (NCBI) Pathogen Detection database by the USDA-FSIS from 2016 to 2022 were downloaded and assembled. These were analyzed using the Basic Local Alignment Search Tool (BLAST) with a sequence unique to field strains, followed by a sequence unique to the vaccine strain. The PCR assays were developed against field and vaccine strains by targeting transposition events in the crp and cya genes and validated by screening Salmonella serovar Typhimurium isolates. Between 2016 and 2022, 1708 Salmonella Typhimurium isolates of chicken origin were found in the NCBI Pathogen Detection database, corresponding to 7.99% of all Salmonella identified. Of these, 104 (5.97%) were identified as the vaccine strain. The PCR assay differentiated field strains from the vaccine strain when applied to isolates and was also able to detect the vaccine strain from DNA isolated from mixed serovar overnight Salmonella enrichment cultures. Live attenuated Salmonella vaccines are a critical preharvest tool for Salmonella control and are widely used in industry. With forthcoming regulations that will likely focus on Salmonella Typhimurium, along with other serovars, there is a need to distinguish between isolates belonging to the vaccine strain and those that are responsible for causing human illness.

Lithium carbonate-induced confusional state in patients with bipolar disorder: identification of case reports and review of the evidence

Objective: Lithium carbonate is a mood stabilizer used in the treatment of bipolar disorder. However, its narrow therapeutic index (normal = 0.6-1.2 mmol/L) predisposes patients to toxic effects. This study aimed to identify case reports and review the evidence on the frequency, mechanism, risk factors and guidelines associated with a lithium-induced confusional state in patients with bipolar disorder. Methods: All Databases from the National Center for Biotechnology Information (NCBI) were used to search for lithium AND “confusional state” AND “case report” published in English between 2015 and 2020. This search engine was also used to search for lithium AND “confusional state” AND frequency OR mechanism OR “risk factor” OR guideline published in English. Results: Case reports showed (1) all patients were treated with lithium for bipolar disorder and hospitalized for a confusional state, (2) most patients took concomitant therapies and recovered after lithium withdrawal, (3) some patients were female and old-aged (65+ years old), and (4) no ethnicities, causality assessments and dose patterns were reported. Other scientific literature showed (1) frequencies of a lithium-induced confusional state varied from very common (&gt;10%) to rare (&lt;0.01%), (2) inhibition of inositol phosphate-phosphatase (IMPase) and glycogen synthase kinase-3 (GSK3) might result in a lithium-induced confusional state, (3) ageing, diseases and concomitant therapies increased the risk of a lithium-induced confusional state, and (4) patients should complete lab tests and diagnostic procedures to monitor and/or prevent a lithium-induced confusional state. Conclusion: Case reports and other scientific literature elucidated the relationship between lithium and a confusional state.

Identification of fibronectin type III domain containing 3B as a potential prognostic and therapeutic target for pancreatic cancer: a preliminary analysis

BackgroundFibronectin type III domain containing 3B (FNDC3B), a member of the fibronectin type III domain-containing protein family, has been indicated in various malignancies. However, the precise role of FNDC3B in the progression of pancreatic cancer (PC) still remains to be elucidated.MethodsIn this study, we integrated data from the National Center for Biotechnology Information, the Cancer Genome Atlas, Genotype-Tissue Expression database, and Gene Expression Omnibus datasets to analyze FNDC3B expression and its association with various clinicopathological parameters. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, along with Gene Set Enrichment Analysis (GSEA), single sample Gene Set Enrichment Analysis (ssGSEA) and estimate analysis were recruited to delve into the biological function and immune infiltration based on FNDC3B expression. Additionally, the prognostic estimation was conducted using Cox analysis and Kaplan–Meier analysis. Subsequently, a nomogram was constructed according to the result of Cox analysis to enhance the prognostic ability of FNDC3B. Finally, the preliminary biological function of FNDC3B in PC cells was explored.ResultsThe study demonstrated a significantly higher expression of FNDC3B in tumor tissues compared to normal pancreatic tissues, and this expression was significantly associated with various clinicopathological parameters. GSEA revealed the involvement of FNDC3B in biological processes and signaling pathways related to integrin signaling pathway and cell adhesion. Additionally, ssGSEA analysis indicated a positive correlation between FNDC3B expression and infiltration of Th2 cells and neutrophils, while showing a negative correlation with plasmacytoid dendritic cells and Th17 cells infiltration. Kaplan–Meier analysis further supported that high FNDC3B expression in PC patients was linked to shorter overall survival, disease-specific survival, and progression-free interval. However, although univariate analysis demonstrated a significant correlation between FNDC3B expression and prognosis in PC patients, this association did not hold true in multivariate analysis. Finally, our findings highlight the crucial role of FNDC3B expression in regulating proliferation, migration, and invasion abilities of PC cells.ConclusionDespite limitations, the findings of this study underscored the potential of FNDC3B as a prognostic biomarker and its pivotal role in driving the progression of PC, particularly in orchestrating immune responses.