Search bioRxiv⌕ Search

Biology subjects

Hsu, C.-M.

Publications and source records attributed to Hsu, C.-M..

3 recordsLinked to original sources

Distinct subcellular localizations of DUF1218 proteins in Marchantia polymorpha and Nicotiana benthamiana reveal two different plasmodesmata-targeting mechanisms

Plasmodesmata are membrane-lined channels connecting plant cells to facilitate intercellular transport of molecules. Although many plasmodesmata-localized proteins have evolved throughout plant evolution, whether they use a conserved targeting system remains unclear. In the bryophyte Marchantia polymorpha, we identified two DUF1218-domain proteins homologous to the Arabidopsis plasmodesmata-localized AtTVA. When ectopically expressed, MpDUF1218-1 localized to plasmodesmata in both Nicotiana benthamiana and M. polymorpha, whereas MpDUF1218-2 formed cytoplasmic puncta in both species. Unexpectedly, AtTVA formed cytoplasmic puncta rather than localizing to plasmodesmata in M. polymorpha. Domain-swap analyses revealed that the first helix of MpDUF1218-1 is crucial for plasmodesmata localization in N. benthamiana, while the first two helices are required in M. polymorpha. In contrast, the second and third helices of AtTVA contribute to its plasmodesmata localization in N. benthamiana. Further domain dissection indicated that other regions of MpDUF1218-1 also contribute to accurate targeting by regulating its distribution among the ER, cytoplasmic puncta, and plasma membrane. Together, our findings suggest that MpDUF1218-1 is targeted by a mechanism shared between the two species, whereas AtTVA relies on a distinct mechanism present in N. benthamiana but absent in M. polymorpha, suggesting the emergence of alternative plasmodesmata-targeting pathways during land plant evolution.

plant biology↗

The potential SARS-CoV-2 entry inhibitor

Outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan and has rapidly spread to almost all parts of world. In coronaviruses, the receptor binding domain (RBD) in the distal part of S1 subunit of SARS-CoV-2 spike protein can directly bind to angiotensin converting enzyme 2 (ACE2). RBD promote viral entry into the host cells and is an important therapeutic target. In this study, we discovered that theaflavin showed the lower idock score (idock score: -7.95 kcal/mol). To confirm the result, we discovered that theaflavin showed FullFitness score of -991.21 kcal/mol and estimated {Delta}G of -8.53 kcal/mol for the most favorable interaction with contact area of SARS-CoV-2 RBD by SwissDock service. Regarding contact modes, hydrophobic interactions contribute significantly in binding and additional hydrogen bonds were formed between theaflavin and Arg454, Phe456, Asn460, Cys480, Gln493, Asn501 and Val503 of SARS-CoV-2 RBD, near the direct contact area with ACE2. Our results suggest that theaflavin could be the candidate of SARS-CoV-2 entry inhibitor for further study.

bioinformatics↗

variant2literature: full text literature search for genetic variants

MotivationWhole genome sequencing (WGS) by next-generation sequencing produces millions of variants for an individual. The retrieval of biomedical literature for such a large number of genetic variants remains challenging, because in many cases the variants are only present in tables as images, or in the supplementary documents of which the file formats are diverse.\n\nResultsThe proposed tool named variant2literature from the TaiGenomics (Toolkits for AI genomics) resolves the problem by incorporating text recognition with image processing. In addition to the adoption of advanced image-based text retrieval, the recall rate of finding the literature containing the variants of interest is further improved by employing the skill of variant normalization. Different variant presentations are transformed into chromosome coordinates (standard VCF format) such that false negatives can be largely avoided. variant2literature is available in two ways. First, a web-based interface is provided to search all the literature in PMC Open Access Subset. Second, the command-line executable can be downloaded such that the users are free to search all the files in a specified directory locally.\n\nAvailabilityhttp://variant2literature.taigenomics.com/\n\nContactchienyuchen@ntu.edu.tw

genetics↗