Psittacosis, which is also known as parrot fever, is Chlamydia psittaci (C. psittaci) caused infectious disease. The clinical manifestations vary from asymptomatic infection to severe atypical ...pneumonia or even fatal meningitis. Early recognition of psittacosis is difficult because of its nonspecific clinical manifestations. Culture and gene probe techniques for C. psittaci are not available for routine clinical use, which makes the diagnosis difficult too. Although psittacosis has increasingly been recognized and reported in recent years, cure of severe pneumonia complicated with meningitis, with etiologic diagnosis aided by the use of metagenomic next-generation sequencing (mNGS), is still uncommon. So, it is necessary to report and review such potentially fatal case. When clinicians come across a patient with atypical pneumonia accompanied by symptoms of meningitis, psittacosis should be taken into consideration. mNGS is a promising detection method in such condition and is recommended.
Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next‐generation sequencing (NGS) technologies, allowing large‐scale taxonomic ...identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question “Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?” is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.
•Similar structures are found in FRIM1162 and FRIM1441 mitochondrial genomes.•ORF position differences suggest mitochondrial genome rearrangement.•Different intron patterns in Ceratocystis fimbriata ...mitochondrial genomes.•The mitochondrial uniformity gene organisation and key mutations are observed.•FRIM1162 and FRIM1441 are monophyletic C. fimbriata complex group.
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
Yttrium is a heavy rare earth element (REE) that acquires remarkable characteristics when it is in oxide form and doped with other REEs. Owing to these characteristics Y2O3 can be used in the ...manufacture of several products. However, a supply deficit of this mineral is expected in the coming years, contributing to its price fluctuation. Thus, developing an efficient, cost‐effective, and eco‐friendly process to recover Y2O3 from secondary sources has become necessary. In this study, we used phage surface display to screen peptides with high specificity for Y2O3 particles. After three rounds of enrichment, a phage expressing the peptide TRTGCHVPRCNTLS (DM39) from the random pVIII phage peptide library Cys4 was found to bind specifically to Y2O3, being 531.6‐fold more efficient than the wild‐type phage. The phage DM39 contains two arginines in the polar side chains, which may have contributed to the interaction between the mineral targets. Immunofluorescence assays identified that the peptide's affinity was strong for Y2O3 and negligible to LaPO4:Ce3+,Tb3+. The identification of a peptide with high specificity and affinity for Y2O3 provides a potentially new strategic approach to recycle this type of material from secondary sources, especially from electronic scrap.
A potentially new strategic approach to recycling Y2O3 from secondary sources, especially from electronic scrap, was developed in this study. The phage surface display technique was used to screen peptides with high specificity for this material. By using this strategy, the authors identified a phage‐expressing peptide (TRTGCHVPRCNTLS) that presents high specificity and affinity for Y2O3 particles.
Molecular findings in myeloid neoplasms Tran, Tho B.; Siddon, Alexa J.
International journal of laboratory hematology,
August 2023, 2023-Aug, 2023-08-00, 20230801, Letnik:
45, Številka:
4
Journal Article
Recenzirano
Odprti dostop
The proliferation of new molecular technologies in recent years has greatly advanced our knowledge of the genetics that underlie hematologic cancers. Particularly, with the advent and ...wide‐implementation of next‐generation sequencing (NGS), a host of somatic (and some germline) gene mutations have been identified as significant in the classification, prognostication, and treatment of the spectrum of myeloid neoplasms. These driver and disease modifier mutations now play a prominent role in the updated international diagnostic guidelines of acute myeloid leukemia (AML), myelodysplastic syndromes/neoplasms (MDS), and myeloproliferative neoplasms (MPN). As high‐throughput technologies such as NGS increasingly become standard in the genetic evaluation of myeloid disorders, it is critical that clinicians understand the clinical relevance of these mutations in order to further personalize patient care. In this review we discuss some of the most essential somatic and cytogenetic findings.
Three novel HLA‐A*02:06:01:04, ‐DRB1*12:02:01:02, ‐DQB1*03:01:01:07 and five extended HLA‐B*51:01:05, ‐DRB1*12:02:01:01, ‐DRB1*14:01:01, ‐DRB1*14:04:01:01, ‐DRB1*15:04 alleles.
Molecular markers produced by next‐generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain ...prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms (SNPs) with at least the same accuracy as individual‐based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user‐friendly application assessing the accuracy of allele frequency estimation from both pool‐ and individual‐based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site–associated DNA (RAD) sequencing in pool‐ and individual‐based experiments carried out on the same population of the pine processionary moth (Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost‐effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome‐wide patterns of genetic variation for large numbers of individuals in multiple populations.
Aggressive morphologic variants of mantle cell lymphoma (MCL), including blastoid and pleomorphic (B/P‐MCL), are rare and associated with poor clinical outcomes. The genomic landscape of these ...variants remains incompletely explored. In this multi‐institutional study, we describe recurrent mutations and novel genomic copy number alterations (CNAs) in B/P‐MCL, using next generation sequencing and SNP‐array. Chromothripsis, a recently described phenomenon of massive chromosomal rearrangements, was identified in eight of 13 (62%) B/P MCL cases, and a high degree of genomic complexity with frequent copy number gains and losses was also seen. In contrast, a comparative cohort of nine cases of conventional MCL (C‐MCL) showed no chromothripsis and less complexity. Twelve of 13 (92%) B/P‐MCL cases showed loss of CDKN2A/B (6 biallelic and 6 monoallelic losses); while only one C‐MCL showed monoallelic CDKN2A/B loss. In B/P‐MCL, TP53 was the most commonly mutated gene, with mutations present in eight cases (62%), six of which showed concurrent loss of chromosome 17p. Of the eight cases with chromothripsis, six (85%) harbored TP53 mutations. Other recurrent mutations in B/P‐MCL included ATM (7, 53%), CCND1 (5, 38%), NOTCH1 (2, 18%), NOTCH2, and BIRC3 (each in 3, 23%). Here, we describe high genomic instability associated with chromothripsis and a high frequency of CDKN2A/B and TP53 alterations in the aggressive variants of MCL. The nonrandom chromothripsis events observed in B/P‐MCL may be an indicator of clinically aggressive MCL. In addition, frequent CDKN2A deletion and high genomic instability may provide potential targets for alternative treatment.
Primary liver tumours, including benign liver tumours, hepatocellular carcinoma and cholangiocarcinoma, present a multifaceted challenge, necessitating a collaborative approach, as evidenced by the ...role of the multidisciplinary tumour board (MDTB). The approach to managing primary liver tumours gathers specialized teams, including surgeons, radiologists, oncologists, pathologists, hepatologists, and radiation oncologists, to propose individualized treatment plans. The evolving landscape of primary liver cancer treatment introduces complexities, particularly with the expanding array of systemic and locoregional therapies, alongside the potential integration of molecular biology and artificial intelligence (AI) into MDTB in the future. Precision medicine demands collaboration across disciplines, challenging traditional frameworks. The next decade anticipates the convergence of AI, molecular biology, pathology, and advanced imaging, requiring adaptability in MDTB structure to incorporate these cutting-edge technologies. Navigating this evolution also requires a focus on enhancing basic, translational, and clinical research, as well as boosting clinical trials through an upgraded use of MDTBs as hubs for scientific collaboration and raising literacy about AI and new technologies. In this review, we will delineate the current unmet needs in the clinical management of primary liver cancers, discuss our perspective on the future role of MDTBs in primary liver cancers ("next generation" MDTBs), and unravel the potential power and limitations of novel technologies that may shape the multidisciplinary care landscape for primary liver cancers in the coming decade.
Background.
Although genetic profiling of tumors is a potentially powerful tool to predict drug sensitivity and resistance, its routine use has been limited because clinicians are often unfamiliar ...with interpretation and incorporation of the information into practice. We established a Molecular Tumor Board (MTB) to interpret individual patients’ tumor genetic profiles and provide treatment recommendations.
Patients and Methods.
DNA from tumor specimens was sequenced in a Clinical Laboratory Improvement Amendments‐certified laboratory to identify coding mutations in a 50‐gene panel (n = 34) or a 255‐gene panel (n = 1). Cases were evaluated by a multidisciplinary MTB that included pathologists, oncologists, hematologists, basic scientists, and genetic counselors.
Results.
During the first year, 35 cases were evaluated by the MTB, with 32 presented for recommendations on targeted therapies, and 3 referred for potential germline mutations. In 56.3% of cases, MTB recommended treatment with a targeted agent based on evaluation of tumor genetic profile and treatment history. Four patients (12.5%) were subsequently treated with a MTB‐recommended targeted therapy; 3 of the 4 patients remain on therapy, 2 of whom experienced clinical benefit lasting >10 months.
Conclusion.
For the majority of cases evaluated, the MTB was able to provide treatment recommendations based on targetable genetic alterations. The most common reasons that MTB‐recommended therapy was not administered stemmed from patient preferences and genetic profiling at either very early or very late stages of disease; lack of drug access was rarely encountered. Increasing awareness of molecular profiling and targeted therapies by both clinicians and patients will improve acceptance and adherence to treatments that could significantly improve outcomes.
Implications for Practice:
Case evaluation by a multidisciplinary Molecular Tumor Board (MTB) is critical to benefit from individualized genetic data and maximize clinical impact. MTB recommendations shaped treatment options for the majority of cases evaluated. In the few patients treated with MTB‐recommended therapy, disease outcomes were positive and support genetically informed treatment.
A Molecular Tumor Board (MTB) was established to interpret individual patients’ tumor genetic profiles and provide treatment recommendations. For the majority of cases evaluated in its first year, the MTB was able to provide treatment recommendations based on targetable genetic alterations. Increasing awareness of molecular profiling and targeted therapies by both clinicians and patients will improve acceptance and adherence to treatments that could significantly improve outcomes.
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