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Scientific Reports Jun 2024Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within...
Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.
Topics: Animals; Elephants; RNA, Ribosomal, 16S; Bacteria; Microbiota; High-Throughput Nucleotide Sequencing; Respiratory System; Animals, Zoo; Sequence Analysis, DNA; Animals, Wild; Phylogeny
PubMed: 38926469
DOI: 10.1038/s41598-024-65841-4 -
Methods in Molecular Biology (Clifton,... 2024In traditional cell line design pipelines, cost- and time-intensive long-term stability studies must be performed due to random integration of the transgene into the...
In traditional cell line design pipelines, cost- and time-intensive long-term stability studies must be performed due to random integration of the transgene into the genome. By this, integration into epigenetically silenced regions can lead to silencing of the recombinant promoter over time. Site-specific integration into regions with active chromatin structure can overcome this problem and lead to strong and stable gene expression. Here, we describe a detailed protocol to identify integration sites with epigenetically preferable properties by chromatin immunoprecipitation sequencing and use them for stable and strong gene expression by applying CRISPR/Cas9. Furthermore, the examination of the integration sites with focus on Cas9-targeted sequencing with nanopores is described.
Topics: CRISPR-Cas Systems; Humans; Histone Code; Gene Editing; Cell Line; Epigenesis, Genetic; Chromatin Immunoprecipitation Sequencing; Histones; Chromatin
PubMed: 38926282
DOI: 10.1007/978-1-0716-3878-1_14 -
Molecular Biology Reports Jun 2024Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental and genetically heterogeneous disorder, characterized by small cranium size (> - 3 SD...
Molecular genetics, neuroimaging outcomes, and structural analyses of novel and recurrent variants of WDR62 gene in two consanguineous Pakistani families with autosomal recessive primary microcephaly.
BACKGROUND
Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental and genetically heterogeneous disorder, characterized by small cranium size (> - 3 SD below mean) and often results in varying degree of intellectual disability. Thirty genes have been identified for the etiology of this disorder due to its clinical and genetic heterogeneity.
METHODS AND RESULTS
Here, we report two consanguineous Pakistani families affected with MCPH exhibiting mutation in WDR62 gene. The investigation approach involved Next Generation Sequencing (NGS) gene panel sequencing coupled with linkage analysis followed by validation of identified variants through automated Sanger sequencing and Barcode-Tagged (BT) sequencing. The molecular genetic analysis revealed one novel splice site variant (NM_001083961.2(WDR62):c.1372-1del) in Family A and one known exonic variant NM_001083961.2(WDR62):c.3936dup (p.Val1313Argfs*18) in Family B. Magnetic Resonance Imaging (MRI) scans were also employed to gain insights into the structural architecture of affected individuals. Neurological assessments showed the reduced gyral and sulcal patterns along with normal corpus callosum in affected individuals harboring novel variant. In silico assessments of the identified variants were conducted using different tools to confirm the pathogenicity of these variants. Through In silico analyses, both variants were identified as disease causing and protein modeling of exonic variant indicates subtle conformational alterations in prophesied protein structure.
CONCLUSION
This study identifies a novel variant (c.1372-1del) and a recurrent pathogenic variant c.3936dup (p.Val1313Argfs*18) in the WDR62 gene among the Pakistani population, expanding the mutation spectrum for MCPH. These findings emphasize the importance of genetic counseling and awareness to reduce consanguinity and address the burden of this disorder.
Topics: Humans; Microcephaly; Female; Male; Pedigree; Pakistan; Consanguinity; Mutation; Nerve Tissue Proteins; Neuroimaging; Child; Magnetic Resonance Imaging; High-Throughput Nucleotide Sequencing; Child, Preschool; Adolescent; Cell Cycle Proteins
PubMed: 38926176
DOI: 10.1007/s11033-024-09728-7 -
Anticancer Research Jul 2024Diffuse large B-cell lymphoma of the central nervous system (CNS-DLBCL) is an aggressive B-cell lymphoma with clinical and molecular heterogeneity. Primary CNS-DLBCL... (Comparative Study)
Comparative Study
BACKGROUND/AIM
Diffuse large B-cell lymphoma of the central nervous system (CNS-DLBCL) is an aggressive B-cell lymphoma with clinical and molecular heterogeneity. Primary CNS-DLBCL (PCNSL) affects the brain, eyes, leptomeninges, or spinal cord without systemic involvement. Secondary CNS-DLBCL (SCNSL) manifests concurrently with systemic lymphoma or as an isolated CNS relapse with poor prognosis.
MATERIALS AND METHODS
Next-generation sequencing (NGS) was used to identify genomic alterations in 32 PCNSL and 9 SCNSL cases. Single nucleotide variants and copy number variations in addition to the clinicopathologic data and proposed risk predictive values were compared to aid in diagnostic differentiation between the two types of lymphomas.
RESULTS
The MCD genotype, characterized by mutations in MYD88 and CD79B, is the most common alteration in PCNSL and is associated with lower survival rates. The frequency of MYD88 mutation was significantly higher in PCNSL compared to SCNSL (75.0% vs. 33.3%; p=0.042). Recurrent copy number loss of 6p21 occurred in 56.1% of cases, more often in PCNSL (65.6%) than in SCNSL (22.2%) (p=0.028). Diagnostic positive predictive values (PPV) of MYD88 mutation and 6p21 loss for PCNSL were 89% and 91%, respectively. PPV of both alterations was 93% for the diagnosis of PCNSL.
CONCLUSION
MYD88 mutation and 6p21 loss were significantly higher in PCNSL than in SCNSL, and novel risk prediction models based on these distinct genomic profiles can aid in the clinical differentiation of PCNSL and SCNSL.
Topics: Humans; Lymphoma, Large B-Cell, Diffuse; Female; Male; Middle Aged; Central Nervous System Neoplasms; Aged; Adult; Mutation; Myeloid Differentiation Factor 88; DNA Copy Number Variations; High-Throughput Nucleotide Sequencing; Aged, 80 and over; Prognosis; Young Adult; CD79 Antigens
PubMed: 38925823
DOI: 10.21873/anticanres.17107 -
Journal of Applied Microbiology Jun 2024Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice....
AIM
Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay.
METHODS AND RESULTS
The soils were classified into two groups according to the C and clay content. qPCR, T-RFLP, and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots.
CONCLUSIONS
Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
PubMed: 38925647
DOI: 10.1093/jambio/lxae157 -
Clinical and Translational Science Jun 2024Next-generation sequencing (NGS) significantly enhances precision medicine (PM) by offering personalized approaches to diagnosis, treatment, and prevention of unmet... (Review)
Review
Next-generation sequencing (NGS) significantly enhances precision medicine (PM) by offering personalized approaches to diagnosis, treatment, and prevention of unmet medical needs. Little is known about the current situation of PM in Asia. Thus, we aimed to conduct an overview of the progress and gaps in PM in Asia and enrich it with in-depth insight into the possibilities of future PM in Thailand. This scoping review focused on Asian countries starting with non-cancer studies, including rare and undiagnosed diseases (RUDs), non-communicable diseases (NCDs), infectious diseases (IDs), and pharmacogenomics, with a focus on NGS. Subsequent in-depth interviews with experts in Thailand were performed, and a thematic analysis served as the main qualitative methodology. Out of 2898 searched articles, 387 studies were included after the review. Although most of the studies focused on cancer, 89 (23.0%) studies were related to RUDs (17.1%), NCDs (2.8%), IDs (1.8%), and pharmacogenomics (1.3%). Apart from medicine and related sciences, the studies were mostly composed of PM (61.8%), followed by genetics medicine and bioinformatics. Interestingly, 28% of articles were conducted exclusively within the fields of medicine and related sciences, emphasizing interdisciplinary integration. The experts emphasized the need for sustainability-driven political will, nurturing collaboration, reinforcing computational infrastructure, and expanding the bioinformatic workforce. In Asia, developments of NGS have made remarkable progress in PM. Thailand has extended PM beyond cancer and focused on clinical implementation. We summarized the PM challenges, including equity and efficiency targeting, guided research funding, sufficient sample size, integrated collaboration, computational infrastructure, and sufficient trained human resources.
Topics: Humans; Precision Medicine; Thailand; High-Throughput Nucleotide Sequencing; Pharmacogenetics; Interviews as Topic; Neoplasms
PubMed: 38924657
DOI: 10.1111/cts.13868 -
PloS One 2024Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited,...
Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.
Topics: Polymorphism, Single Nucleotide; Piper nigrum; Sri Lanka; Genetic Variation; Genetics, Population; Genetic Markers; High-Throughput Nucleotide Sequencing; Genome, Plant; Principal Component Analysis
PubMed: 38924027
DOI: 10.1371/journal.pone.0305990 -
Proceedings of the National Academy of... Jul 2024Asthma is a widespread airway disorder where GATA3-dependent Type-2 helper T (Th2) cells and group 2 innate lymphoid cells (ILC2s) play vital roles. Asthma-associated...
Asthma is a widespread airway disorder where GATA3-dependent Type-2 helper T (Th2) cells and group 2 innate lymphoid cells (ILC2s) play vital roles. Asthma-associated single nucleotide polymorphisms (SNPs) are enriched in a region located 926-970 kb downstream from GATA3 in the 10p14 (hG900). However, it is unknown how hG900 affects the pathogenesis of allergic airway inflammation. To investigate the roles of the asthma-associated GATA3 enhancer region in experimental allergic airway inflammation, we first examined the correlation between GATA3 expression and the activation of the hG900 region was analyzed by flow cytometry and ChIP-qPCR. We found that The activation of enhancers in the hG900 region was strongly correlated to the levels of GATA3 in human peripheral T cell subsets. We next generated mice lacking the mG900 region (mG900KO mice) were generated by the CRISPR-Cas9 system, and the development and function of helper T cells and ILCs in mG900KO mice were analyzed in steady-state conditions and allergic airway inflammation induced by papain or house dust mite (HDM). The deletion of the mG900 did not affect the development of lymphocytes in steady-state conditions or allergic airway inflammation induced by papain. However, mG900KO mice exhibited reduced allergic inflammation and Th2 differentiation in the HDM-induced allergic airway inflammation. The analysis of the chromatin conformation around by circular chromosome conformation capture coupled to high-throughput sequencing (4C-seq) revealed that the mG900 region interacted with the transcription start site of with an influencing chromatin conformation in Th2 cells. These findings indicate that the mG900 region plays a pivotal role in Th2 differentiation and thus enhances allergic airway inflammation.
Topics: GATA3 Transcription Factor; Animals; Th2 Cells; Mice; Cell Differentiation; Asthma; Enhancer Elements, Genetic; Humans; Mice, Knockout; Inflammation; Hypersensitivity; Polymorphism, Single Nucleotide; Mice, Inbred C57BL
PubMed: 38923989
DOI: 10.1073/pnas.2320727121 -
HLA Jun 2024HLA-B*38:01:01:18 differs from the HLA-B*38:01:01:01 allele by one nucleotide substitution in the 5'UTR.
HLA-B*38:01:01:18 differs from the HLA-B*38:01:01:01 allele by one nucleotide substitution in the 5'UTR.
Topics: Humans; Alleles; High-Throughput Nucleotide Sequencing; HLA-B Antigens; 5' Untranslated Regions; Exons; Histocompatibility Testing; Base Sequence; Polymorphism, Single Nucleotide; Sequence Alignment; Sequence Analysis, DNA
PubMed: 38923829
DOI: 10.1111/tan.15573 -
Current Protocols Jun 2024Fluorescence in situ hybridization (FISH) is a cytogenetic assay that is widely used in both clinical and research settings to validate genetic aberrations. Simple in...
Fluorescence in situ hybridization (FISH) is a cytogenetic assay that is widely used in both clinical and research settings to validate genetic aberrations. Simple in principle, it is based on denaturation and hybridization of a DNA probe and its complementary sequence; however, it is subject to continuous optimization. Here we share how in-house FISH can be optimized using different control tissues to visualize and ultimately validate common and novel genetic abnormalities unearthed by next-generation sequencing (NGS). Seven specific FISH probes were designed and labeled, and conditions for eight tissue types and one patient-derived tumor organoid were optimized. Formalin-fixed paraffin-embedded (FFPE) tissue slides were used for each experiment. Slides were first deparaffinized, then placed in a pretreatment solution followed by a digestion step. In-house FISH probes were then added to the tissue to be denatured and hybridized, and then washed twice. To obtain optimal results, probe concentration, pepsin incubation time, denaturation, and the two post-hybridization washes were optimized for each sample. By modifying the above conditions, all FISH experiments were optimized in separate tissue types to investigate specific genomic alterations in tumors arising in those tissues. Signals were clear and distinct, allowing for visualization of the selected probes. Following this protocol, our lab has quickly optimized 11 directly labeled in-house FISH probes to support genetic aberrations nominated by NGS, including most recent discoveries through whole-genome sequencing analyses. We describe a robust approach of how to advance in-house labeled FISH probes. By following these guidelines, reliable and reproducible FISH results can be obtained to interrogate FFPE slides from benign, tumor tissues, and patient-derived tumor organoid specimens. This is of most relevance in the era of NGS and precision oncology. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Metaphase FISH optimization Support Protocol 1: In-house probe labeling and preparation Support Protocol 2: Metaphase spread preparation Basic Protocol 2: Optimization of FISH on formalin-fixed paraffin-embedded tissue.
Topics: In Situ Hybridization, Fluorescence; Humans; Precision Medicine; Paraffin Embedding; Neoplasms; High-Throughput Nucleotide Sequencing; DNA Probes
PubMed: 38923415
DOI: 10.1002/cpz1.1093