Persistent minimal sequences of SARS-CoV-2

Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. In addition, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. Availability and implementation https://github.com/cobilab/eagle. Supplementary information Supplementary data are available at Bioinformatics online.

New Advances Along the Common Coagulation Pathway

Hemostasis is achieved through spatially and temporally regulated thrombin generation following vascular injury. Blood coagulation factor V plays an important role in this process as it has a major impact on thrombin production. FV is a large, heavily glycosylated protein sharing homology and domain organization with FVIII (A1-A2-B-A3-C1-C2). It is an inactive procofactor and must be cleaved by thrombin or other proteases to remove the B-domain to yield activated FV (FVa). FVa is a cofactor for FXa in the prothrombinase complex, the enzyme that activates prothrombin. Given the profound effect FVa has on thrombin formation, FV activation represents an important step in hemostasis. Mechanistic studies have revealed that proteolysis within the FV B-domain serves to remove key autoinhibitory sequences that serve to conceal/block FXa binding site(s). These sequences consist of an evolutionary conserved basic region (BR) in the middle of the B-domain and flanking acidic regions (AR1 and AR2) which define the minimal sequences necessary to maintain FV as a procofactor. Removal of either of these regions results in a molecule that can function in prothrombinase. These sequences are intact and present in plasma FV; however, FV released by activated platelets and FV cleaved by FXa represent active forms FV(a) that lack the BR. Recent work indicates these forms of FV(a) may be regulated by TFPIathrough molecular mimicry. TFPIahas a C-terminal basic tail which shares remarkable homology to the FV BR suggesting TFPIamay be an important regulator at the level of prothrombinase. Remarkably, another form of FV missing the BR, resulting from alternative splicing, has been recently described. The FV-East Texas, FV-Amsterdam, and FV-Atlanta alterations all result in the enhanced production of an alternatively spliced form of FV (FV-short) that has most of the B-domain removed including the BR. While these forms of FV should be constitutively active, studies have shown that FV-short circulates in complex with TFPIa. Further, in each of the clinical cases, TFPIalevels are substantially elevated resulting in a bleeding phenotype. While there are several remaining unanswered questions, the FV(a)-TFPIα interaction as well as the identification of FV-short, has the potential to fundamentally alter our understanding of the regulation of the initiation of coagulation. Disclosures Camire: Bayer: Consultancy; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Spark Therapeutics: Membership on an entity's Board of Directors or advisory committees.

Top-Down Structure Influences Learning of Non-Adjacent Dependencies in an Artificial Language

Due to the hierarchical organization of natural languages, words that are syntactically related are not always linearly adjacent. For example, the subject and verb in the child always runs agree in person and number, although they are not adjacent in the sequences of words. Since such dependencies are indicative of abstact linguistc structure, it is of significant theoretical interest how these relationships are acquired by language learners. Most experiments that investigate non-adjacent dependency (NAD) learning have used artificial languages in which the to-be-learned dependencies are isolated, by presenting the minimal sequences that contain the dependent elements. However, dependencies in natural language are not typically isolated in this way. We report the first demonstration to our knowledge of successful learning of embedded NADs, in which silences do not mark dependency boundaries. Subjects heard passages of English with a predictable structure, interspersed with passages of the artificial language. The English sentences were designed to induce boundaries in the artificial languages. In Experiment 1 & 3 the artificial NADs were contained within the induced boundaries and subjects learned them, whereas in Experiment 2 & 4, the NADs crossed the induced boundaries and subjects did not learn them. We take this as evidence that sentential structure was “carried over” from the English sentences and used to organize the artificial language. This approach provides several new insights into the basic mechanisms of NAD learning in particular and statistical learning in general. © American Psychological Association. This paper is not the copy of record and may not exactly replicate the final, authoritative version of the article. Please do not copy or cite without authors permission. The final article is available via its DOI: 10.1037/xge0000384

Differential Roles of Individual Domains in Selection of Secretion Route of a Streptococcus parasanguinis Serine-Rich Adhesin, Fap1

ABSTRACT Fimbria-associated protein 1 (Fap1) is a high-molecular-mass glycosylated surface adhesin required for fimbria biogenesis and biofilm formation in Streptococcus parasanguinis. The secretion of mature Fap1 is dependent on the presence of SecA2, a protein with some homology to, but with a different role from, SecA. The signals that direct the secretion of Fap1 to the SecA2-dependent secretion pathway rather than the SecA-dependent secretion pathway have not yet been identified. In this study, Fap1 variants containing different domains were expressed in both secA2 wild-type and mutant backgrounds and were tested for their ability to be secreted by the SecA- or SecA2-dependent pathway. The presence or absence of the cell wall anchor domain (residues 2531 to 2570) at the C terminus did not alter the selection of the Fap1 secretion route. The Fap1 signal peptide (residues 1 to 68) was sufficient to support the secretion of a heterologous protein via the SecA-dependent pathway, suggesting that the signal peptide was sufficient for recognition by the SecA-dependent pathway. The minimal sequences of Fap1 required for the SecA2-dependent pathway included the N-terminal signal peptide, nonrepetitive region I (residues 69 to 102), and part of nonrepetitive region II (residues 169 to 342). The two serine-rich repeat regions (residues 103 to 168 and 505 to 2530) were not required for Fap1 secretion. However, they were both involved in the specific inhibition of Fap1 secretion via the SecA-dependent pathway.

Identification of minimal sequences of the Rhopalosiphum padi virus 5′ untranslated region required for internal initiation of protein synthesis in mammalian, plant and insect translation systems

Rhopalosiphum padi virus (RhPV) is a member of the family Dicistroviridae. The genomes of viruses in this family contain two open reading frames, each preceded by distinct internal ribosome entry site (IRES) elements. The RhPV 5′ IRES is functional in mammalian, insect and plant translation systems and can form 48S initiation complexes in vitro with just the mammalian initiation factors eIF2, eIF3 and eIF1. Large regions of the 5′ untranslated region (UTR) can be deleted without affecting initiation-complex formation. The minimal sequences required for directing internal initiation in mammalian (rabbit reticulocyte lysate), plant (wheatgerm extract) and insect (Sf21 cells) translation systems have now been defined. A fragment (nt 426–579) from the 3′ portion of the 5′ UTR can direct translation in each of these translation systems. In addition, a distinct region (nt 300–429) is also active. Thus, unstructured regions within the 5′ UTR seem to be critical for IRES function.

Memory Capacity for Sequences in a Recurrent Network with Biological Constraints

The CA3 region of the hippocampus is a recurrent neural network that is essential for the storage and replay of sequences of patterns that represent behavioral events. Here we present a theoretical framework to calculate a sparsely connected network's capacity to store such sequences. As in CA3, only a limited subset of neurons in the network is active at any one time, pattern retrieval is subject to error, and the resources for plasticity are limited. Our analysis combines an analytical mean field approach, stochastic dynamics, and cellular simulations of a time-discrete McCulloch-Pitts network with binary synapses. To maximize the number of sequences that can be stored in the network, we concurrently optimize the number of active neurons, that is, pattern size, and the firing threshold. We find that for one-step associations (i.e., minimal sequences), the optimal pattern size is inversely proportional to the mean connectivity c, whereas the optimal firing threshold is independent of the connectivity. If the number of synapses per neuron is fixed, the maximum number P of stored sequences in a sufficiently large, nonmodular network is independent of its number N of cells. On the other hand, if the number of synapses scales as the network size to the power of 3/2, the number of sequences P is proportional to N. In other words, sequential memory is scalable. Further-more, we find that there is an optimal ratio r between silent and nonsilent synapses at which the storage capacity α = P/[c (1 +r)N] assumes a maximum. For long sequences, the capacity of sequential memory is about one order of magnitude below the capacity for minimal sequences, but otherwise behaves similar to the case of minimal sequences. In a biologically inspired scenario, the information content per synapse is far below theoretical optimality, suggesting that the brain trades off error tolerance against information content in encoding sequential memories.

Identification of Spliced Gammaherpesvirus 68 LANA and v-Cyclin Transcripts and Analysis of Their Expression In Vivo during Latent Infection

ABSTRACT Regulation of orf73 (LANA) gene expression is critical to the establishment and maintenance of latency following infection by members of the gamma-2 herpesvirus (rhadinovirus) family. Previous studies of murine gammaherpesvirus 68 (γHV68) have demonstrated that loss of LANA function results in a complete failure to establish virus latency in the spleens of laboratory mice. Here we report the characterization of alternatively spliced LANA and v-cyclin (orf72) transcripts encoded by γHV68. Similar to other rhadinoviruses, alternative splicing, coupled with alternative 3′ processing, of a ca. 16-kb transcriptional unit can lead to expression of either LANA or v-cyclin during γHV68 infection. Spliced LANA and v-cyclin transcripts were initially identified from an analysis of the γHV68 latently infected B-cell lymphoma cell line S11E, but were also detected during lytic infection of NIH 3T12 fibroblasts. 5′ Random amplification of cDNA ends (RACE) analyses identified two distinct promoters, p1 and p2, that drive expression of spliced LANA transcripts. Analysis of p1 and p2, using transiently transfected reporter constructs, mapped the minimal sequences required for promoter activity and demonstrated that both promoters are active in the absence of any viral antigens. Analysis of spliced LANA and v-cyclin transcripts in spleens recovered from latently infected mice at days 16 and 42 postinfection revealed that spliced v-cyclin transcripts can only be detected sporadically, suggesting that these may be associated with cells reactivating from latency. In contrast, spliced LANA transcripts were detected in ca. 1 in 4,000 splenocytes harvested at day 16 postinfection. Notably, based on the frequency of viral genome-positive splenocytes at day 16 postinfection (ca. 1 in 200), only 5 to 10% of viral genome-positive splenocytes express LANA. The failure of the majority of infected splenocytes at day 16 postinfection to express LANA may contribute to the contraction in the frequency of latently infected splenocytes as chronic infection is established, due to failure to maintain the viral episome in proliferating B cells.