Strong Sequence Research Articles

Spontaneous transmembrane pore formation by short-chain synthetic peptide

Amphiphilic β-peptides, which are synthetically designed short-chain helical foldamers of β-amino acids, are established potent biomimetic alternatives of natural antimicrobial peptides. An intriguing question is how the distinct molecular architecture of these short-chain and rigid synthetic peptides translates to its potent membrane-disruption ability. Here, we address this question via a combination of all-atom and coarse-grained molecular dynamics simulations of the interaction of mixed phospholipid bilayer with an antimicrobial 10-residue globally amphiphilic helical β-peptide at a wide range of concentrations. The simulation demonstrates that multiple copies of this synthetic peptide, initially placed in aqueous solution, readily self-assemble and adsorb at membrane interface. Subsequently, beyond a threshold peptide/lipid ratio, the surface-adsorbed oligomeric aggregate moves inside the membrane and spontaneously forms stable water-filled transmembrane pores via a cooperative mechanism. The defects induced by these pores lead to the dislocation of interfacial lipid headgroups, membrane thinning, and substantial water leakage inside the hydrophobic core of the membrane. A molecular analysis reveals that despite having a short architecture, these synthetic peptides, once inside the membrane, would stretch themselves toward the distal leaflet in favor of potential contact with polar headgroups and interfacial water layer. The pore formed in coarse-grained simulation was found to be resilient upon structural refinement. Interestingly, the pore-inducing ability was found to be elusive in a non-globally amphiphilic sequence isomer of the same β-peptide, indicating strong sequence dependence. Taken together, this work puts forward key perspectives of membrane activity of minimally designed synthetic biomimetic oligomers relative to the natural antimicrobial peptides.

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica).

Potyvirids (the family Potyviridae) are the largest family of plant RNA viruses. Two novel potyvirid viruses, Striga-associated poty-like virus 1 (SaPlV1) and Striga-associated poty-like virus 2 (SaPlV2), were identified from the transcriptome data of purple witchweed (Striga hermonthica). SaPlV1 was most closely related to bellflower veinal mottle virus (BVMoV), the only member of the genus Bevemovirus, and then to macluraviruses (the genus Macluravirus). The SaPlV1 genome encodes a 2462-amino acid (aa) polyprotein that may be cleaved into nine mature peptides. The cleavage sites of SaPlV1, BVMoV, and macluravirus polyproteins shared strong sequence similarities. SaPlV2 was most closely related to celery latent virus, the sole species of the genus Celavirus, which is the most divergent potyvirid genus. The SaPlV2 polyprotein contained 3329 aa and it may be cleaved into at least seven or eight mature peptides. Phylogenetic analysis suggested that SaPlV1 and SaPlV2 may be novel species of the genera Bevemovirus and Celavirus, respectively. The genome sequences of SaPlV1 and SaPlV2 are useful resources for studying the genome evolution of potyvirids. Keywords: Striga-associated poty-like virus 1; Striga-associated poty-like virus 2; Potyviridae; Beve- movirus; Celavirus; purple witchweed; Striga hermonthica.

Structural stability of spiral beams and fine structure of an energy flow

The problem of structural stability of wave systems with great numbers of degrees of freedom directly concerns the issue of redistribution of energy fluxes in structured vortex beams that ensure their stability under propagating and focusing. A special place in this variety is occupied by spiral vortex beams capable of mapping complex figures, letters and even words. Spiral beams contain an infinite set of Laguerre-Gauss beams with a strong sequence of topological charges and radial numbers, their amplitudes and phases are tightly matched. Therefore, the problem of structural stability plays a special role for their applications. Using a combination of theory and computer simulation, supported by experiment, we ana-lyzed the structure of critical points in energy flows for two main types of spiral beams: triangular beams with zero radial number and triangular beams with complex framing of their faces with both quantum numbers. Structural stability is provided by triads of critical points, both inside and outside the triangle, which direct the light flux along the triangular generatrix and hold the framing when rotating the beam. The experiment showed that a simple triangular spiral beam turns out to be stable even with small alignment inaccuracies, whereas a complex triangular beam with a fram-ing requires careful alignment

Consistency of the frequency polygon estimators of density mode for strongly mixing processes

We consider a simple estimator of the density mode using the frequency polygon estimate. We investigate strong consistency of the estimator for strong mixing sequence of real variables under mild assumptions. We study the almost sure rate of convergence and we show that the estimator can achieve optimal almost sure rates of convergence for appropriate choices of the bin widths. The asymptotic normality of the simple estimator is given and a simulation study is performed. Our asymptotic results are obtained without any differentiability condition assumed on the density around the mode.

Autophosphorylation of the CK1 Kinase Domain Regulates Enzyme Activity and Substrate Specificity

CK1 enzymes are conserved, acidophilic serine/threonine kinases with a variety of critical cellular functions; misregulation of CK1 contributes to cancer, neurodegenerative diseases, and sleep phase disorders. Despite this, little is known about how CK1 activity is controlled. CK1 kinases have highly similar catalytic domains, plus a conserved extension to that kinase domain that is important for enzyme stability and activity. In contrast to the catalytic domains, the C-terminal tails of CK1 family members diverge in sequence and length; however, they all appear to serve as substrates of autophosphorylation. The autophosphorylated tails are proposed to inhibit kinase activity by acting as pseudosubstrates. In addition to C-terminal autophosphorylation, autophosphorylation of the CK1Σ kinase domain has been detected, but its effect on CK1 activity and cellular function has never been explored. Here, we addressed the role of kinase domain autophosphorylation in human CK1δ and CK1Σ, as well as Hhp1 and Hhp2, their homologues in Schizosaccharomyces pombe. In each case, we found that autophosphorylation of a conserved threonine residue in the kinase domain inhibited enzyme activity. This site resides in the mobile L-EF loop proximal to the active site, distinct from the well-characterized T-loop autophosphorylation that occurs in other kinase families. We propose that phosphorylation on the L-EF loop inhibits substrate docking with the kinase domain by shielding the positively charged substrate binding pocket. Consistent with this hypothesis, yeast and human enzymes with phosphoablating mutations at this site were hyperactive in vitro. In vivo, mutation of this site protected yeast cells from heat shock, indicating a change in the phosphorylation of substrates in the stress response pathway. To determine whether other pathways may also be rewired by this mutation, we utilized quantitative phosphoproteomics to probe the substrateomes of wildtype and mutant Hhp1 and Hhp2. We found that ablating autophosphorylation in the kinase domain significantly changed the substrate profiles of these enzymes, suggesting that this regulatory mechanism influences substrate specificity in addition to catalytic activity. Due to the strong sequence conservation of this autophosphorylation site and the functional importance of the L-EF loop, which is unique to the CK1 family of kinases, this mechanism is likely to regulate the majority of CK1 enzymes in vivo. We predict that kinase domain autophosphorylation works in conjunction with other mechanisms, such as C-terminal autophosphorylation, to ultimately determine the extent to which different substrates are phosphorylated in different cellular contexts.

Sequence Conservation and Structural Modeling of an Arginyl‐tRNA Transferase 1 (ATE1)

Arginyl-tRNATransferase 1 (ATE1) is a eukaryotic enzyme that arginylates cellular proteins, is an essential regulator of eukaryotic homeostasis via its involvement in the N-degron pathway, and regulates essential physiological processes such as embryogenesis, aging, cell migration, muscle contraction, and stress. Despite its importance, the structure, mechanism of action, and regulation of ATE1 has yet to be elucidated. The objective of this work is to model the three-dimensional fold of an ATE1, and to determine essential conserved residues that are involved in substrate recognition and enzymatic arginylation. In this study, we have modeled the structure of Saccharomyces cerevisiae ATE1 (ScATE1) and identified a putative location of the GCN5-related N-acetyl transferase (GNAT) fold, which is structurally conserved amongst amino-acid transferases. Additionally, we have performed a large-scale sequence alignment across eukaryotic ATE1s to map conserved residues onto our three-dimensional model. Notably, we have identified a highly-conserved His residue that would be consistent with the recognition of a negatively charged substrate and is located in a structural homologous site in bacterial amino-acid transferases. We hypothesize that this highly conserved (>90%) His residue is essential for substrate recognition, and site-directed mutagenesis is underway to verify this hypothesis. These results provide the first structural insights into the enzyme active site and mechanism of substrate recognition for ScATE1, and the strong sequence conservation suggest a common mode of action across eukaryotic homologs.

MBOVPG45_0375 Encodes an IgG-Binding Protein and MBOVPG45_0376 Encodes an IgG-Cleaving Protein in Mycoplasma bovis.

Mycoplasma bovis is a significant bacterial pathogen which is able to persist in cattle and cause chronic diseases. This phenomenon may relate to M. bovis evading the immune system of the host. Immunoglobulin-binding proteins are widely distributed in a variety of pathogenic bacteria, including some Mycoplasma species. These proteins are considered to help the bacteria evade the immune response of the host. Here we found M. bovis strain PG45 can bind to IgG from several animals. MBOVPG45_0375 encodes a putative membrane protein, has strong amino acid sequence similarity with Immunoglobulin G-binding protein in Mycoplasma mycoides subsp. capri. Hence, we constructed recombinant MBOVPG45_0375 (r0375) in the Escherichia coli expression system and demonstrated that r0375 can bind to IgG non-immunologically rather than specific binding similar to interaction of antigen and antibody. Moreover, r0375 can bind to the Fab fragment of IgG. Also, the binding of r0375 and IgG inhibits the formation of antigen-antibody union. Furthermore, MBOVPG45_0376 encodes an IgG-cleaving protein of M. bovis strain PG45. Nevertheless, r0375 binding to IgG is required for the cleavage activity of recombinant 0376 (r0376). The activity of r0376 is also affected by incubation time and temperature. In addition, we found both MBOVPG45_0375 and MBOVPG45_0376 are membrane proteins of M. bovis strain PG45. These results about MBOVPG45_0375 as an IgG-binding protein and MBOVPG45_0376 as an IgG-cleaving protein offer a new insight into the interaction between M. bovis and its host.

Sequence-dependent nucleosome formation in trinucleotide repeats evaluated by in vivo chemical mapping

Trinucleotide repeat sequences (TRSs), consisting of 10 unique classes of repeats in DNA, are members of microsatellites and abundantly and non-randomly distributed in many eukaryotic genomes. The lengths of TRSs are mutable, and the expansions of several TRSs are implicated in hereditary neurological diseases. However, the underlying causes of the biased distribution and the dynamic properties of TRSs in the genome remain elusive. Here, we examined the effects of TRSs on nucleosome formation in vivo by histone H4–S47C site-directed chemical cleavages, using well-defined yeast minichromosomes in which each of the ten TRS classes resided in the central region of a positioned nucleosome. We showed that (AAT)12 and (ACT)12 act as strong nucleosome-promoting sequences, while (AGG)12 and (CCG)12 act as nucleosome-excluding sequences in vivo. The local histone binding affinity scores support the idea that nucleosome formation in TRSs, except for (AGG)12, is mainly determined by the affinity for the histone octamers. Overall, our study presents a framework for understanding the nucleosome-forming abilities of TRSs.

Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs.

Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.

Simple method of selecting totalistic rules for pseudorandom number generator based on nonuniform cellular automaton

This paper is devoted to selecting rules for one-dimensional (1D) totalistic cellular automaton (TCA). These rules are used for the generation of pseudorandom sequences, which could be useful in cryptography. The power of pseudorandom number generator (PRNG) based on nonuniform TCA can be improved using not only one rule but a large set of rules. For this purpose, each subset of rules should be analyzed with its assignation to cellular automaton (CA) cells should be analyzed. We examine each of the subsets of totalistic rules, consisting of rules with neighborhood radius equal to 1 and 2. The entropy of bitstreams generated by the nonuniform TCA points out the best set of rules appropriate for the TCA-based generator. The paper also presents the method of simple selection of CA rules based on a cryptographic criterion known as a balance. The proposed method selects a maximal size of the set of available CA rules for a given neighborhood radius and suitable for PRNG. The method guarantees to avoid conflicting assignments of rules resulting in the creation of unwanted stable bit sequences, and provides high-quality pseudorandom sequences. This technique is used to verify the subsets of rules selected experimentally. Verified rules are proposed for 1D TCA-based PRNG as a new subset of best nonuniform TCA rules. New picked, examined, and verified subset of rules could be used in TCA-based PRNG and provide cryptographically strong bit sequences and huge keyspace.

Composition and distribution of fish environmental DNA in an Adirondack watershed.

BackgroundEnvironmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration.MethodsWe characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments.ResultsWe found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.

Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2?

A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.

LncEvo: automated identification and conservation study of long noncoding RNAs

BackgroundLong noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are assumed to not encode proteins. Although a growing body of evidence indicates that the vast majority of lncRNAs are potentially nonfunctional, hundreds of them have already been revealed to perform essential gene regulatory functions or to be linked to a number of cellular processes, including those associated with the etiology of human diseases. To better understand the biology of lncRNAs, it is essential to perform a more in-depth study of their evolution. In contrast to protein-encoding transcripts, however, they do not show the strong sequence conservation that usually results from purifying selection; therefore, software that is typically used to resolve the evolutionary relationships of protein-encoding genes and transcripts is not applicable to the study of lncRNAs.ResultsTo tackle this issue, we developed lncEvo, a computational pipeline that consists of three modules: (1) transcriptome assembly from RNA-Seq data, (2) prediction of lncRNAs, and (3) conservation study—a genome-wide comparison of lncRNA transcriptomes between two species of interest, including search for orthologs. Importantly, one can choose to apply lncEvo solely for transcriptome assembly or lncRNA prediction, without calling the conservation-related part.ConclusionslncEvo is an all-in-one tool built with the Nextflow framework, utilizing state-of-the-art software and algorithms with customizable trade-offs between speed and sensitivity, ease of use and built-in reporting functionalities. The source code of the pipeline is freely available for academic and nonacademic use under the MIT license at https://gitlab.com/spirit678/lncrna_conservation_nf.

Insights into the planktonic to sessile transition in a marine biofilm-forming Pseudoalteromonas isolate using comparative proteomic analysis

Bacterial biofilms play an important role in marine biofouling. The formation of a biofilm starts when marine bacterial cells transition from a planktonic to an attached state. However, the molecular mechanisms involved in this transition are poorly understood. Here, 51 strains of marine bacteria were isolated from natural biofilms growing on submerged artificial surfaces (glass slides, epoxy panels, and bridge pillars) and evaluated for their biofilm-forming capacity. Eleven strains formed relatively strong biofilms and 16S rRNA gene sequence analysis indicated that they belonged to the genera Leisingera, Roseobacter, Pseudoalteromonas, Alteromonas, Tenacibaculum, Vibrio, Chryseobacterium, Aquimarina, and Acinetobacter. Strain Pseudoalteromonas sp. W-7 showed efficient and rapid attachment and was therefore chosen for further study. An iTRAQ-based comparative proteomic analysis of planktonic and attached strain W-7 cells was carried out. A total of 3468 proteins were identified, of which 163 showed significant differential expression (120 down-regulated and 43 up-regulated in attached cells relative to planktonic cells). KEGG (Kyoto encyclopedia of genes and genomes) analysis indicated that pyruvate metabolism, carbon fixation, and carbon metabolism were significantly affected in attached cells. Up-regulated proteins such as UTP-glucose-1-phosphate uridylyltransferase, acetyltransferase component of pyruvate dehydrogenase complex, OmpA-like protein, and acetyl-coenzyme A synthetase may be important during initial adhesion. Our findings provide a deeper understanding of the planktonic to sessile transition of marine fouling bacteria.

Topographic effects observed at Amatrice hill during the 2016–2017 Central Italy seismic sequence

The estimate of seismic site effects by experimental approaches is based on different assumptions aimed at simplifying the complex actual site conditions and related uncertainties. However, the reliability of the results can increase if the experimental data is focused on quite strong seismic sequences and the on-site acquisition of a large number of signals is deemed strategic for the assessment of the expected phenomena. Based on these considerations, the ground motion at the Red Zone sector of Amatrice hill, violently struck by the 2016–2017 Central Italy seismic sequence, was analyzed via an observational approach. A large set of weak motions (moment magnitudeMw 2.5–3.9) was analyzed in this study by means of standard (SSR) and horizontal to vertical (HVSR) spectral ratio techniques. The results from the experimental analysis of the site effects by using weak motion and noise signals show a significant amplification at the top of Amatrice hill with a remarkable polarization of the motion and changes in spectral shapes according to the topographic setting of the relief.

High PGL productivity in Bacillus subtilis by optimizing the SD sequence

Alkaline polygalacturonate lyase (PGL, EC 4.2.2.2) can catalyze the cleavage of a-1, 4-glycosidic bonds of polygalacturonate by a trans-elimination reaction and generate an unsaturated oligogalacturonates. As the critical enzyme of many environmental friendly processes, alkaline PGL has been widely used in many fields including paper, textile and beverage industries. At present, Bacillus subtilis is an ideal strain for producing PGL, but the yield is too low for industrial production. In this study, the effect of different SD sequences on the production of PGL was comparatively investigated, and the strong SD sequence (AGAGAACAAGGAGGG G) directed efficient PGL secretory expression and increased PGL yield to 264.5 U·mL-1 with a high productivity. As a result, the PGL yield in B. subtilis was effecively increased and laid the solid foundation for PGL industrial production.

Activity-dependent conformational transitions of the insulin receptor–related receptor

The insulin receptor (IR), insulin-like growth factor 1 receptor (IGF-1R), and insulin receptor-related receptor (IRR) form a mini family of predimerized receptor-like tyrosine kinases. IR and IGF-1R bind to their peptide agonists triggering metabolic and cell growth responses. In contrast, IRR, despite sharing with them a strong sequence homology, has no peptide-like agonist but can be activated by mildly alkaline media. The spatial structure and activation mechanisms of IRR have not been established yet. The present work represents the first account of a structural analysis of a predimerized receptor-like tyrosine kinase by high-resolution atomic force microscopy in their basal and activated forms. Our data suggest that in neutral media, inactive IRR has two conformations, where one is symmetrical and highly similar to the inactive Λ/U-shape of IR and IGF-1R ectodomains, whereas the second is drop-like and asymmetrical resembling the IRR ectodomain in solution. We did not observe complexes of IRR intracellular catalytic domains of the inactive receptor forms. At pH 9.0, we detected two presumably active IRR conformations, Γ-shaped and T-shaped. Both of conformations demonstrated formation of the complex of their intracellular catalytic domains responsible for autophosphorylation. The existence of two active IRR forms correlates well with the previously described positive cooperativity of the IRR activation. In conclusion, our data provide structural insights into the molecular mechanisms of alkali-induced IRR activation under mild native conditions that could be valuable for interpretation of results of IR and IGF-IR structural studies.

Tracing the Emotional Roadmap of Depressive Users on Social Media Through Sequential Pattern Mining

Depression is one of the most growing health disorders, generating social and economic problems. The affective computing models focus on analyzing unique user posts, not observing temporal behavior patterns, which are essential to track changes and the evolution of emotional behavior and user context, that involves the persistent analysis of feelings and characteristics over time. This article proposes the TROAD framework for longitudinal recognition of sequential patterns from depressive users on social media. The framework identifies the best interval to analyze every user activity, extracts emotional and contextual features from user data, and models the features into time windows to recognize sequential patterns from depressive user behavior. The main characteristics of the users found in the top-10 rules are negative emotions: violence, pain, shame, depression, sadness, and silence. We obtained strong sequence patterns with a minimum of 70% of support, 81% of confidence, and 69% regarding sequential confidence, considering periods of silence between users' posts. Without considering silent periods, the rules showed 70%, 86%, and 38% of support, confidence, and sequential confidence. TROAD computational approach is a promising tool for clinical specialists in human behavior.

Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology.

Peptide nucleic acids (PNAs) are getting prodigious interest currently in the biomedical and diagnostic field as an extremely powerful tool because of their potentiality to hybridize with natural nucleic acids. Although PNA has strong affinity and sequence specificity to DNA/RNA, there is a considerable ongoing effort to further enhance their special chemical and biological properties for potential application in numerous fields, notably in the field of therapeutics. The toolbox for backbone modified PNAs synthesis has been extended substantially in recent decades, providing a more efficient synthesis of peptides with numerous scaffolds and modifications. This paper reviews the various strategies that have been developed so far for the modification of the PNA backbone, challenging the search for new PNA systems with improved chemical and physical properties lacking in the original aegPNA backbone. The various practical issues and limitations of different PNA systems are also summarized. The focus of this review is on the evolution of PNA by its backbone modification to improve the cellular uptake, sequence specificity, and compatibility of PNA to bind to DNA/RNA. Finally, an insight was also gained into major applications of backbone modified PNAs for the development of biosensors.

Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures.

Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 31 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients. Clonal expansion of the B cell population is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 1,254 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls or individuals following seasonal influenza vaccination. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralizing antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA, and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand patient responses.