The Novel Sequence Distance Measuring Algorithm Based on Optimal Transport and Cross-Attention Mechanism

In this paper, we propose a novel sequence distance measuring algorithm based on optimal transport (OT) and cross-attention mechanism. Given a source sequence and a target sequence, we first calculate the ground distance between each pair of source and target terms of the two sequences. The ground distance is calculated over the subsequences around the two terms. We firstly pay attention from each the source terms to each target terms with attention weights, so that we have a representative source subsequence vector regarding each term in the target subsequence. Then, we pay attention from each representative vector of the term of the target subsequence to the entire source subsequence. In this way, we construct the cross-attention weights and use them to calculate the pairwise ground distances. With the ground distances, we derive the OT distance between the two sequences and train the attention parameters and ground distance metric parameters together. The training process is conducted with training triplets of sequences, where each triplet is composed of an anchor sequence, a must-link sequence, and a cannot-link sequence. The corresponding hinge loss function of each triplet is minimized, and we develop an iterative algorithm to solve the optimal transport problem and the attention/ground distance metric parameters in an alternate way. The experiments over sequence similarity search benchmark datasets, including text, video, and rice smut protein sequence data, are conducted. The experimental results show the algorithm is effective.

Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19: Protection of mice after a single immunization

Vaccines of outstanding efficiency, safety, and public acceptance are needed to halt the current SARS-CoV-2 pandemic. Concerns include potential side effects caused by the antigen itself and safety of viral DNA and RNA delivery vectors. The large SARS-CoV-2 spike (S) protein is the main target of current COVID-19 vaccine candidates but can induce non-neutralizing antibodies, which might cause vaccination-induced complications or enhancement of COVID-19 disease. Besides, encoding of a functional S in replication-competent virus vector vaccines may result in the emergence of viruses with altered or expanded tropism. Here, we have developed a safe single round rhabdovirus replicon vaccine platform for enhanced presentation of the S receptor-binding domain (RBD). Structure-guided design was employed to build a chimeric minispike comprising the globular RBD linked to a transmembrane stem-anchor sequence derived from rabies virus (RABV) glycoprotein (G). Vesicular stomatitis virus (VSV) and RABV replicons encoding the minispike not only allowed expression of the antigen at the cell surface but also incorporation into the envelope of secreted non-infectious particles, thus combining classic vector-driven antigen expression and particulate virus-like particle (VLP) presentation. A single dose of a prototype replicon vaccine complemented with VSV G, VSVΔG-minispike-eGFP (G), stimulated high titers of SARS-CoV-2 neutralizing antibodies in mice, equivalent to those found in COVID-19 patients, and protected transgenic K18-hACE2 mice from COVID-19-like disease. Homologous boost immunization further enhanced virus neutralizing activity. The results demonstrate that non-spreading rhabdovirus RNA replicons expressing minispike proteins represent effective and safe alternatives to vaccination approaches using replication-competent viruses and/or the entire S antigen.

Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19

SummaryThe large SARS-CoV-2 spike (S) protein is the main target of current COVID-19 vaccine candidates but can induce non-neutralizing antibodies, which may cause vaccination-induced complications or enhancement of COVID-19 disease. Besides, encoding of a functional S in replication-competent virus vector vaccines may result in the emergence of viruses with altered or expanded tropism. Here, we have developed a safe single round rhabdovirus replicon vaccine platform for enhanced presentation of the S receptor-binding domain (RBD). Structure-guided design was employed to build a chimeric minispike comprising the globular RBD linked to a transmembrane stem-anchor sequence derived from rabies virus (RABV) glycoprotein (G). Vesicular stomatitis virus (VSV) and RABV replicons encoding the minispike not only allowed expression of the antigen at the cell surface but also incorporation into the envelope of secreted non-infectious particles, thus combining classic vector-driven antigen expression and particulate virus-like particle (VLP) presentation. A single dose of a prototype replicon vaccine, VSVΔG-minispike-eGFP (G), stimulated high titers of SARS-CoV-2 neutralizing antibodies in mice, equivalent to those found in COVID-19 patients. Boost immunization with the identical replicon further enhanced neutralizing activity. These results demonstrate that rhabdovirus minispike replicons represent effective and safe alternatives to vaccination approaches using replication-competent viruses and/or the entire S antigen.HighlightsSARS-CoV-2 S RBD antigen is preferred over entire S to preclude potential disease enhancing antibodiesconstruction of a chimeric rhabdovirus minispike protein presenting RBD in native conformationconstruction of single round VSV and rabies virus replicon vaccinespresentation of minispike antigen on cells and on noninfectious VLPsstrong induction of SARS-CoV-2 neutralizing antibodies by the VSV replicon/VLP system in vaccinated mice

DENV2 Pseudoviral Particles with Unprocessed Capsid Protein Are Assembled and Infectious

Proteolytic processing of flavivirus polyprotein is a uniquely controlled process. To date, the sequential cleavage of the capsid anchor sequence at the junction of C-PrM has been considered essential for the production of flaviviruses. In this study, we used two experimental approaches to show the effect of unprocessed capsid on the production and infectivity of dengue virus 2 (DENV2) pseudoviral particles. The results showed that (1) both mature and unprocessed capsids of DENV2 were equally efficient in the viral RNA packaging and also in the assembly of infective particles; (2) DENV2 variants, in which the viral and host mediated cleavage of Ca peptide were independent, produced significantly higher levels of infective particles. Overall, this study demonstrated that unlike other flaviviruses, DENV2 capsid does not require a cleavable Ca sequence, and the sequential cleavage is not an obligatory requirement for the morphogenesis of infective pseudoviral particles.

Reorientation of the first signal-anchor sequence during potassium channel biogenesis at the Sec61 complex

The Sec61 translocon provides an unexpectedly flexible and dynamic environment within which transmembrane regions of nascent polypeptides can be completely reoriented during the biosynthesis of multiple-spanning membrane proteins.