Nanopore sequencing for detecting reciprocal translocation carrier status in preimplantation genetic testing

HiSIF-DTA: A Hierarchical Semantic Information Fusion Framework for Drug-Target Affinity Prediction

Accurately identifying drug-target affinity (DTA) plays a significant role in promoting drug discovery and has attracted increasing attention in recent years. Exploring appropriate protein representation methods and increasing the abundance of protein information is critical in enhancing the accuracy of DTA prediction. Recently, numerous deep learning-based models have been proposed to utilize the sequential or structural features of target proteins. However, these models capture only the low-order semantics that exist in a single protein, while the high-order semantics abundant in biological networks are largely ignored. In this article, we propose HiSIF-DTA-a hierarchical semantic information fusion framework for DTA prediction. In this framework, a hierarchical protein graph is constructed that includes not only contact maps as low-order structural semantics but also protein-protein interaction (PPI) networks as high-order functional semantics. Particularly, two distinct hierarchical fusion strategies (i.e., Top-down and Bottom-Up) are designed to integrate the different protein semantics, therefore contributing to a richer protein representation. Comprehensive experimental results demonstrate that HiSIF-DTA outperforms current state -of-the-art methods for prediction on the benchmark datasets of the DTA task. Further validation on binary tasks and visualization analysis demonstrates the generalization and interpretation abilities of the proposed method.

A relative-independent haplotype derivation method applied for noninvasive prenatal testing for chromosomal rearrangements in a pregnant carrier

This study aimed to perform noninvasive prenatal testing for structural chromosomal rearrangements (NIPT-SR) for a female pregnant proband carrying a t(4;8) balanced translocation, whose husband exhibited a normal karyotype. NIPT-SR could accurately detect transmission status of structural rearrangements in fetus through Hidden Markov Model (HMM) analysis, which requires the construction of parental haplotypes. To address the challenge of lacking genetic information from other family members of this proband, we developed a novel strategy to infer the fetal inheritance of structural variants by integrating Oxford Nanopore Technologies (ONT) with the NIPT-SR approach. Long-read sequencing was performed on the proband to directly detect the translocation and nearby single nucleotide polymorphisms (SNPs), and to link the structural variants with phased haplotypes. NIPT-SR method was used to infer the fetal inheritance of the constructed haplotypes and to evaluate the potential presence of unbalanced translocation in the fetus. Noninvasive prenatal testing (NIPT) was performed at 12 weeks of gestation, followed by copy number variation sequencing (CNV-seq) and karyotype analysis after birth respectively to confirm the accuracy of NIPT-SR results. Using nanopore sequencing, we identified the precise locations of the breakpoint junctions and successfully established the SNP-based haplotypes that were linked to the breakpoints on chr4 and chr8, without the need for retrieving genetic information of other family members. Haplotype-based analysis of cell-free DNA (cfDNA) indicated that the fetus inherited the normal haplotypes, which was consistent with the NIPT results and confirmed by the postnatal CNV-seq and karyotype analysis. In conclusion, the NIPT-SR method coupled with ONT platform could be used to perform NIPT-SR for those who carries balanced translocation circumventing the need for other family members as reference, providing an important supplement to birth defects prevention.

Revisiting the potential of natural antimicrobial peptides against emerging respiratory viral disease: a review

This review assesses the antiviral capabilities of antimicrobial peptides (AMPs) against SARS-CoV-2 and other respiratory viruses, focussing on their therapeutic potential. AMPs, derived from natural sources, exhibit promising antiviral properties by disrupting viral membranes, inhibiting viral entry, and modulating host immune responses. Preclinical studies demonstrate that peptides such as defensins, cathelicidins, and lactoferrin can effectively reduce SARS-CoV-2 replication and inhibit viral spread. In addition, AMPs have shown potential in enhancing the host's antiviral immunity. Despite these promising outcomes, several challenges require assessments before transforming into clinical translation. Several issues related to peptide stability, cytotoxicity, and efficient delivery systems pose significant limitations to their therapeutic application. Recent advancements in peptide engineering, nanotechnology-based delivery systems, and peptide conjugation strategies have improved AMPs stability and bioavailability; however, further optimization is essential. Moreover, whilst AMPs are safe, their effects on host cells and tissues need a thorough investigation to minimise potential adverse reactions. This review concludes that whilst AMPs present a promising route for antiviral therapies, particularly in targeting SARS-CoV-2, extensive clinical trials and additional studies are required to overcome current limitations. Future research should focus on developing more stable, less toxic AMPs formulations with enhanced delivery mechanisms, aiming to integrate AMPs into viable therapeutic options for respiratory viral diseases, including COVID-19 and other emerging infections.

Subtle translocation does not affect euploid blastocyst rate or pregnancy outcomes during preimplantation genetic testing

RESEARCH QUESTION

Do chromosomal translocation segment size and proportion affect embryo euploidy and pregnancy outcomes during preimplantation genetic testing (PGT) cycles in subtle translocation carriers?

DESIGN

Retrospective cohort study including 207 couples with reciprocal translocation who underwent 232 PGT for structural rearrangements cycles; euploid blastocysts were selected for transfer. A total of 119 couples completed 155 warming transfer cycles, and 58 cycles resulted in clinical pregnancy. According to the size of the translocation segment (threshold 10 Mb), couples were divided into subtle translocation group 1 (translocation segment on either chromosome was <10 Mb) and control group 1 (translocation segments on both chromosomes were ≥10 Mb). Couples were divided into subtle translocation group 2 (proportion on either chromosome segment was <5% relative to the whole chromosome) and control group 2 (proportions on both chromosome segments were ≥5% relative to the whole chromosome). Rates of euploid blastocysts and clinical outcomes were analysed.

RESULTS

No significant differences were found in the rates of euploid blastocysts, (37.11% versus 36.08%; P = 0.817) and clinical pregnancy (32.56% versus 39.28%; P = 0.438) compared with subtle translocation group 1 and control group 1, respectively. Similarly, no significant differences were found in the rates of euploid blastocysts (35.00% versus 36.75%; P = 0.572) and clinical pregnancy (34.28% versus 38.33%; P = 0.663) compared with subtle translocation group 2 and control group 2.

CONCLUSIONS

The size and proportion of a translocation segment did not significantly affect the rate of euploid blastocysts or pregnancy outcomes during PGT cycles for couples with chromosomal translocations.

Aspergillus, Penicillium, and Talaromyces (Eurotiales) in Brazilian caves, with the description of four new species

The study of the Brazilian cave mycobiota has revealed a rich but highly diverse assemblage of fungi, with Aspergillus, Penicillium, and Talaromyces being the most frequently reported genera. The present study investigated the airborne fungi and fungi obtained from the bodies of bats, guano, and the soil/sediment from the caves Urubu (in the Atlantic Forest) and Furna Feia (in the Caatinga dryland forest) in the Northeast region of Brazil. Fungal strains were identified based on morphological features and multilocus phylogenetic analyses of ITS, beta-tubulin (BenA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) sequences. A total of 86 isolates were obtained, representing Aspergillus (34), Penicillium (20), Talaromyces (2), and 30 isolates belonging to other genera that will be reported on elsewhere. These isolates were identified as 18 Aspergillus, nine Penicillium, and one Talaromyces species. Eight of the species identified are reported for the first time from a cave environment. Four species showed unique morphological features and phylogenetic relationships, and are newly described. These include two new species of Aspergillus (A. alvaroi sp. nov. and A. guanovespertilionum sp. nov.), one of Penicillium (P. cecavii sp. nov.), and one of Talaromyces (T. potiguarorum sp. nov.). Our study increases the awareness and known richness of the Brazilian and global fungal diversity found in caves. Citation: Lima JMS, Barbosa RN, Bento DM, Barbier E, Bernard E, Bezerra JDP, Souza-Motta CM (2024). Aspergillus, Penicillium, and Talaromyces (Eurotiales) in Brazilian caves, with the description of four new species. Fungal Systematics and Evolution 14: 89-107. doi: 10.3114/fuse.2024.14.06.

Assembly and comparative analysis of the multichromosomal mitochondrial genome of globally endangered seagrass Halophila beccarii

BACKGROUND

Halophila beccarii is one of the oldest two generations of seagrass plants and one of the 10 species of seagrass currently at risk of extinction worldwide. Therefore, how to effectively protect the H. beccarii resources from extinction is a huge challenge. Molecular biology research can provide a scientific basis for species conservation. So far, there has been no detailed analysis of the mitochondrial genome of the genus Halophila.

RESULTS

The mitochondrial genome of H. beccarii was assembled into 28 circular chromosomes, ranging in length from 41,738 bp to 104,744 bp, with a total length of 1,964,072 bp and a GC content of 46.71%. It contains 39 genes, including 26 protein coding genes, 10 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 850 dispersed repeats, 1,205 simple repeats, 61 tandem repeats, and 120 RNA editing sites. Analysis of codon usage indicates that codons ending in A/U are preferred. Gene migration between the mitochondrial genome and the chloroplast genome was observed through homologous fragment detection. In addition, Ka/Ks analysis showed that most protein coding genes in the mitochondrial genome experienced negative selection, while only the nad3 gene experienced potential positive selection in most Alismatales. Nucleotide polymorphism analysis revealed variations in each gene, with rpl10 being the most significant. In addition, comparative analysis shows that the GC content is conserved, but there are significant differences in the size and structure of mitochondrial genomes among different species of Alismatales. The phylogenetic analysis based on the mitochondrial genome reflects the exact evolutionary and taxonomic status of H. beccarii.

CONCLUSION

In this study, we sequenced and annotated the mitochondrial genome of H. beccarii, and compared it with the mitochondrial genomes of other plants in Alismatales. Our findings enrich the mitogenome database of seagrass plants and highlight the potential for mitochondrial genes to help decipher plant evolutionary history.

Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing

High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.

Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant

BACKGROUND

Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported.

RESULTS

The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense.

CONCLUSIONS

In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

Analysis of Preimplantation and Clinical Outcomes of Two Cases by Oxford Nanopore Sequencing

It is challenging to distinguish embryos with a balanced translocation karyotype from a normal karyotype by existing conventional genetic testing methods. However, in germ-cell gamete generation, chromosome exchange and separation through cell meiosis form a different proportion of unbalanced gametes. Adverse birth events may occur, such as repeated miscarriages and fetal birth defects. In this study, the exact breakpoints of structural variation (SV) from two balanced translocation carrier families by using Nanopore long reads sequencing technology were obtained, and haplotype analysis and Sanger verified the accuracy of the detection results, confirming the application value of the Nanopore sequencing technology in the detection of balanced translocation before embryo implantation. Nanopore long-read sequencing was performed to find the precise breakpoint of chromosome-balanced translocation carriers. The breakpoints were subsequently verified by designing primers across the breakpoints and Sanger sequencing. Haplotype linkage analysis of SNPs which can be linked by a read block of families around the breakpoint regions was followed. After frozen (-thawed) embryo transfer (FET), prenatal cytogenetic analysis of amniotic fluid cells confirmed the predicted karyotypes from the transferred embryos. The presence of breakpoints was detected in three embryos of patient 1. No breakpoints were detected in either embryo of patient 2. One balanced translocated embryo from patient 1 and one normal euploid embryo from patient 2 were transplanted back into the patients, and amniotic fluid cells were analyzed for the karyotype of fetuses. The results were entirely consistent with the fetal karyotype. And through late follow-up, both patients successfully had a live birth fetus. The breakpoint location of the balanced chromosome translocation can be accurately found by Nanopore sequencing. The haplotype of carriers can be successfully constructed by Nanopore and sanger sequencing confirmed that the results were accurate. This is very advantageous for preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) detection in the families without proband.

Preimplantation genetic testing: A remarkable history of pioneering, technical challenges, innovations, and ethical considerations

Preimplantation genetic testing (PGT) has emerged as a powerful companion to assisted reproduction technologies. The origins and history of PGT are reviewed here, along with descriptions of advances in molecular assays and sampling methods, their capabilities, and their applications in preventing genetic diseases and enhancing pregnancy outcomes. Additionally, the potential for increasing accuracy and genome coverage is considered, as well as some of the emerging ethical and legislative considerations related to the expanding capabilities of PGT.

Resolving complex structural variants via nanopore sequencing

The recent development of high-throughput sequencing platforms provided impressive insights into the field of human genetics and contributed to considering structural variants (SVs) as the hallmark of genome instability, leading to the establishment of several pathologic conditions, including neoplasia and neurodegenerative and cognitive disorders. While SV detection is addressed by next-generation sequencing (NGS) technologies, the introduction of more recent long-read sequencing technologies have already been proven to be invaluable in overcoming the inaccuracy and limitations of NGS technologies when applied to resolve wide and structurally complex SVs due to the short length (100-500 bp) of the sequencing read utilized. Among the long-read sequencing technologies, Oxford Nanopore Technologies developed a sequencing platform based on a protein nanopore that allows the sequencing of "native" long DNA molecules of virtually unlimited length (typical range 1-100 Kb). In this review, we focus on the bioinformatics methods that improve the identification and genotyping of known and novel SVs to investigate human pathological conditions, discussing the possibility of introducing nanopore sequencing technology into routine diagnostics.

Not the second fiddle: α cell development, identity, and function in health and diabetes

Historic and emerging studies provide evidence for the deterioration of pancreatic α cell function and identity in diabetes mellitus. Increased access to human tissue and the availability of more sophisticated molecular technologies have identified key insights into how α cell function and identity are preserved in healthy conditions and how they become dysfunctional in response to stress. These studies have revealed evidence of impaired glucagon secretion, shifts in α cell electrophysiology, changes in α cell mass, dysregulation of α cell transcription, and α-to-β cell conversion prior to and during diabetes. In this review, we outline the current state of research on α cell identity in health and disease. Evidence in model organisms and humans suggests that in addition to β cell dysfunction, diabetes is associated with a fundamental dysregulation of α cell identity. Importantly, epigenetic studies have revealed that α cells retain more poised and open chromatin at key cell-specific and diabetes-dysregulated genes, supporting the model that the inherent epigenetic plasticity of α cells makes them susceptible to the transcriptional changes that potentiate the loss of identity and function seen in diabetes. Thus, additional research into the maintenance of α cell identity and function is critical to fully understanding diabetes. Furthermore, these studies suggest α cells could represent an alternative source of new β cells for diabetes treatment.