Search Results (33)

Single-stranded DNA (ssDNA) viruses are a diverse group of pathogens with broad host range, including bacteria, archaea, protists, fungi, plants, invertebrates, and vertebrates. Their small compact genomes have evolved to encode multiple proteins. This review focuses on the structure and functional diversity of the icosahedral capsids across the ssDNA viruses. To date, X-ray crystallography and cryo-electron microscopy structural studies have provided detailed capsid architectures for 8 of the 35 ssDNA virus families, illustrating variations in assembly mechanisms, symmetry, and structural adaptations of the capsid. However, common features include the conserved jelly-roll motif of the capsid protein and strategies for genome packaging, also showing evolutionary convergence. The ever-increasing availability of genomic sequences of ssDNA viruses and predictive protein modeling programs, such as using AlphaFold, allows for the extension of structural insights to the less-characterized families. Therefore, this review is a comparative analysis of the icosahedral ssDNA virus families and how the capsid proteins are arranged with different tessellations to form icosahedral spheres. It summarizes the current knowledge, emphasizing gaps in the structural characterization of the ssDNA capsidome, and it underscores the importance of continued exploration to understand the molecular underpinnings of capsid function and evolution. These insights have implications for virology, molecular biology, and therapeutic applications. Full article

We report the results of our computations of the spectral polynomials and spectra of a number of graphs possessing automorphism symmetries beyond cubic and icosahedral symmetries. The spectral (characteristic) polynomials are computed in fully expanded forms. The coefficients of these polynomials contain a wealth of combinatorial information that finds a number of applications in many areas including nanomaterials, genetic networks, dynamic stereochemistry, chirality, and so forth. This study focuses on a number of symmetric and semi-symmetric graphs with automorphism groups of high order. In particular, Heawood, Coxeter, Pappus, Möbius–Kantor, Tutte–Coxeter, Desargues, Meringer, Dyck, n-octahedra, n-cubes, icosahedral fullerenes such as C₈₀(I_h), golden supergiant C₂₄₀(I_h), Archimedean (I_h), and generalized Petersen graphs up to 720 vertices, among others, have been studied. The spectral polynomials are computed in fully expanded forms as opposed to factored forms. Several applications of these polynomials are briefly discussed. Full article

A novel vibriophage vB_VpaM_XM1 (XM1) was described in the present study. Morphological analysis revealed that phage XM1 had Myovirus morphology, with an oblate icosahedral head and a long contractile tail. The genome size of XM1 is 46,056 bp, with a G + C content of 42.51%, encoding 69 open reading frames (ORFs). Moreover, XM1 showed a narrow host range, only lysing Vibrio xuii LMG 21346 (T) JL2919, Vibrio parahaemolyticus 1.1997, and V. parahaemolyticus MCCC 1H00029 among the tested bacteria. One-step growth curves showed that XM1 has a 20-min latent period and a burst size of 398 plaque-forming units (PFU)/cell. In addition, XM1 exhibited broad pH, thermal, and salinity stability, as well as strong lytic activity, even at a multiplicity of infection (MOI) of 0.001. Multiple genome comparisons and phylogenetic analyses showed that phage XM1 is grouped in a clade with three other phages, including Vibrio phages Rostov 7, X29, and phi 2, and is distinct from all known viral families that have ratified by the standard genomic analysis of the International Committee on Taxonomy of Viruses (ICTV). Therefore, the above four phages might represent a new viral family, tentatively named Weiviridae. The broad physiological adaptability of phage XM1 and its high lytic activity and host specificity indicated that this novel phage is a good candidate for being used as a therapeutic bioagent against infections caused by certain V. parahaemolyticus strains. Full article

This paper is part of a series that describes the Fibonacci icosagrid quasicrystal (FIG) and its relation to the $E_8$ root lattice. The FIG was originally constructed to represent the intersection points of an icosahedrally symmetric collection of planar grids in three dimensions, with the grid spacing of each following a Fibonacci chain. It was found to be closely related to a five-fold compound of 3D sections taken from the 4D Elser–Sloane quasicrystal (ESQC), which is derived via a cut-and-project process from $E_8$. More recently, a direct cut-and-project from $E_8$ has been found which yields the FIG (presented in another paper of this series). The present paper focuses not on the full quasicrystal, but on the relationship between the root polytope of $E_8$ (Gosset’s $4_{21}$ polytope) and the core polyhedron generated in the FIG, a compound of 20 tetrahedra referred to simply as a 20-Group. In particular, the $H_3$ symmetry of the FIG can be seen as a five-fold or “golden” composition of tetrahedral symmetry (referring to the characteristic appearance of the golden ratio). This is shown to mirror a connection between tetrahedral and five-fold symmetries present in the $4_{21}$. Indeed, the rotations that connect tetrahedra contained within the $4_{21}$ are shown to induce, in a certain natural way, the tetrahedron orientations in the 20-Group. Full article

Dengue virus is an enveloped virus with an icosahedral assembly of envelope proteins (E). The E proteins are arranged as a head-to-tail homodimer, and domain III (EDIII) is placed at the edge of the dimer, converging to a pentamer interface. For a structure-based approach, cholera toxin B (CTB) was harnessed as a structural scaffold for the five-fold symmetry of EDIII. Pivoted by an RNA-mediated chaperone for the protein folding and assembly, CTB-EDIII of dengue serotype 1 (DV1) was successfully produced as soluble pentamers in an E. coli host with a high yield of about 28 mg/L. Immunization of mice with CTB-DV1EDIII elicited increased levels of neutralizing antibodies against infectious viruses compared to the control group immunized with DV1EDIII without CTB fusion. IgG isotype switching into a balanced Th1/Th2 response was also observed, probably triggered by the intrinsic adjuvant activity of CTB. Confirming the immune-enhancing potential of CTB in stabilizing the pentamer assembly of EDIII, this study introduces a low-cost bacterial production platform designed to augment the soluble production of subunit vaccine candidates, particularly those targeting flaviviruses. Full article

The symmetries of a Riemann surface $\mathsf{\Sigma }\setminus \left\{a_i\right\}$ with n punctures $a_i$ are encoded in its fundamental group ${\pi }_1\left(\mathsf{\Sigma }\right)$. Further structure may be described through representations (homomorphisms) of ${\pi }_1$ over a Lie group G as globalized by the character variety $\mathcal{C}=\mathrm{Hom}({\pi }_1,G)/G$. Guided by our previous work in the context of topological quantum computing (TQC) and genetics, we specialize on the four-punctured Riemann sphere $\mathsf{\Sigma }=S_2^{\left(4\right)}$ and the ‘space-time-spin’ group $G=S{L}_2\left(\mathbb{C}\right)$. In such a situation, $\mathcal{C}$ possesses remarkable properties: (i) a representation is described by a three-dimensional cubic surface $V_{a,b,c,d}(x,y,z)$ with three variables and four parameters; (ii) the automorphisms of the surface satisfy the dynamical (non-linear and transcendental) Painlevé VI equation (or $P_{VI}$); and (iii) there exists a finite set of 1 (Cayley–Picard)+3 (continuous platonic)+45 (icosahedral) solutions of $P_{VI}$. In this paper, we feature the parametric representation of some solutions of $P_{VI}$: (a) solutions corresponding to algebraic surfaces such as the Klein quartic and (b) icosahedral solutions. Applications to the character variety of finitely generated groups $f_p$ encountered in TQC or DNA/RNA sequences are proposed. Full article

The topological partition theory states that icosahedral group affine extensions (fullerenes symmetry) are the most effective way to energetically optimize the surface covering. In recent decades, potential applications of fullerene symmetry have emerged in the major fields of biology, like enzyme inhibition and antiviral therapy. This research suggests a novel perspective to interpret the underlying spatial organization of cell populations in tissues from the polyhedral graph theory. We adopted this theoretical framework to study HUVEC cell in vitro angiogenesis assays on Matrigel. This work underscores the importance of extracellular ${\mathrm{C}\mathrm{a}}^{2+}$ gradients, both from conditioned BJ and pretreated HUVEC cells, in angiogenesis fullerene-rule spatial minimization. Full article

Hepatitis B virus (HBV) is the primary contributor to severe liver ailments, encompassing conditions such as cirrhosis and hepatocellular carcinoma. Globally, 257 million people are affected by HBV annually and 887,000 deaths are attributed to it, representing a substantial health burden. Regrettably, none of the existing therapies for chronic hepatitis B (CHB) have achieved satisfactory clinical cure rates. This issue stems from the existence of covalently closed circular DNA (cccDNA), which is difficult to eliminate from the nucleus of infected hepatocytes. HBV genetic material is composed of partially double-stranded DNA that forms complexes with viral polymerase inside an icosahedral capsid composed of a dimeric core protein. The HBV core protein, consisting of 183 to 185 amino acids, plays integral roles in multiple essential functions within the HBV replication process. In this review, we describe the effects of sulfamoyl-based carboxamide capsid assembly modulators (CAMs) on capsid assembly, which can suppress HBV replication and disrupt the production of new cccDNA. We present research on classical, first-generation sulfamoyl benzocarboxamide CAMs, elucidating their structural composition and antiviral efficacy. Additionally, we explore newly identified sulfamoyl-based CAMs, including sulfamoyl bicyclic carboxamides, sulfamoyl aromatic heterocyclic carboxamides, sulfamoyl aliphatic heterocyclic carboxamides, cyclic sulfonamides, and non-carboxamide sulfomoyl-based CAMs. We believe that certain molecules derived from sulfamoyl groups have the potential to be developed into essential components of a well-suited combination therapy, ultimately yielding superior clinical efficacy outcomes in the future. Full article

We have developed a highly efficient computation method based on density functional theory (DFT) within a set of fully symmetrized basis functions for the C₆₀ buckyball, which possesses the icosahedral ($I_h$) point-group symmetry with 120 symmetry operations. We demonstrate that our approach is much more efficient than the conventional approach based on three-dimensional plane waves. When applied to the calculation of optical transitions, our method is more than one order of magnitude faster than the existing DFT package with a conventional plane-wave basis. This makes it very convenient for modeling optical and transport properties of quantum devices related to buckyball crystals. The method introduced here can be easily extended to other fullerene-like materials. Full article

A worldwide ecological issue, cyanobacterial blooms in marine and freshwater have caused enormous losses in both the economy and the environment. Virulent cyanophages—specifically, infecting and lysing cyanobacteria—are key ecological factors involved in limiting the overall extent of the population development of cyanobacteria. Over the past three decades, reports have mainly focused on marine Prochlorococcus and Synechococcus cyanophages, while information on freshwater cyanophages remained largely unknown. In this study, a novel freshwater cyanophage, named Lbo240-yong1, was isolated via the double-layer agar plate method using Leptolyngbya boryana FACHB-240 as a host. Transmission electron microscopy observation illustrated the icosahedral head (50 ± 5 nm in diameter) and short tail (20 ± 5 nm in length) of Lbo240-yong1. Experimental infection against 37 cyanobacterial strains revealed that host-strain-specific Lbo240-yong1 could only lyse FACHB-240. The complete genome of Lbo240-yong1 is a double-stranded DNA of 39,740 bp with a G+C content of 51.99%, and it harbors 44 predicted open reading frames (ORFs). A Lbo240-yong1 ORF shared the highest identity with a gene of a filamentous cyanobacterium, hinting at a gene exchange between the cyanophage and cyanobacteria. A BLASTn search illustrated that Lbo240-yong1 had the highest sequence similarity with the Phormidium cyanophage Pf-WMP4 (89.67% identity, 84% query coverage). In the proteomic tree based on genome-wide sequence similarities, Lbo240-yong1, three Phormidium cyanophages (Pf-WMP4, Pf-WMP3, and PP), one Anabaena phage (A-4L), and one unclassified Arthronema cyanophage (Aa-TR020) formed a monophyletic group that was more deeply diverging than several other families. Pf-WMP4 is the only member of the independent genus Wumpquatrovirus that belongs to the Caudovircetes class. Pf-WMP3 and PP formed the independent genus Wumptrevirus. Anabaena phage A-4L is the only member of the independent Kozyakovvirus genus. The six cyanopodoviruses share similar gene arrangements. Eight core genes were found in them. We propose, here, to set up a new taxonomic family comprising the six freshwater cyanopodoviruses infecting filamentous cyanobacteria. This study enriched the field’s knowledge of freshwater cyanophages. Full article

The inadequate therapeutic opportunities associated with carbapenem-resistant Pseudomonas aeruginosa (CRPA) clinical isolates impose a search for innovative strategies. Therefore, our study aimed to characterize and evaluate two locally isolated phages formulated in a hydrogel, both in vitro and in vivo, against CRPA clinical isolates. The two phages were characterized by genomic, microscopic, phenotypic characterization, genomic analysis, in vitro and in vivo analysis in a Pseudomonas aeruginosa-infected skin thermal injury rat model. The two siphoviruses belong to class Caudovirectes and were named vB_Pae_SMP1 and vB_Pae_SMP5. Each phage had an icosahedral head of 60 ± 5 nm and a flexible, non-contractile tail of 170 ± 5 nm long, while vB_Pae_SMP5 had an additional base plate containing a 35 nm fiber observed at the end of the tail. The hydrogel was prepared by mixing 5% w/v carboxymethylcellulose (CMC) into the CRPA propagated phage lysate containing phage titer 10⁸ PFU/mL, pH of 7.7, and a spreadability coefficient of 25. The groups were treated with either Phage vB_Pae_SMP1, vB_Pae_SMP5, or a two-phage cocktail hydrogel cellular subepidermal granulation tissues with abundant records of fibroblastic activity and mixed inflammatory cell infiltrates and showed 17.2%, 25.8%, and 22.2% records of dermal mature collagen fibers, respectively. In conclusion, phage vB_Pae_SMP1 or vB_Pae_SMP5, or the two-phage cocktails formulated as hydrogels, were able to manage the infection of CRPA in burn wounds, and promoted healing at the injury site, as evidenced by the histopathological examination, as well as a decrease in animal mortality rate. Therefore, these phage formulae can be considered promising for clinical investigation in humans for the management of CRPA-associated skin infections. Full article

Rotavirus (RV) is a non–enveloped icosahedral virus with an 11–segment double–stranded RNA genome, belonging to the family of rotaviruses. RV is one of the pathogens causing diarrhea in infants and young animals, and it induces the production of type I interferons (IFNs), which can trigger antiviral function by inducing the production of interferon–stimulated genes (ISGs). Although IFITM3, an ISG localizing to late endosomes, can limit many viral infections, whether or not it restricts the infection of RV is still unknown. Therefore, we attempted to determine whether IFITM3 also restricts RV infection by using over–expression and knockout cell strains. It was found that IFITM3–expressing cell strains were less susceptible to RV infection, as the replication of RV in over–expressing cells was significantly less than in control group cells. Correspondingly, IFITM3–knockout cells were significantly susceptible compared to the normal cells. Furthermore, the IFN–induced antiviral effect was significantly attenuated in the absence of IFITM3, and IFITM3 delayed RV escape from endosomes in the presence of IFITM3, suggesting that endogenous IFITM3 is of great importance in type I IFN–mediated antiviral responses and may restrict infection by affecting the function of the late endosomal compartment. In conclusion, these data provide the first evidence that IFITM3 limits RV infection in vitro and delays RV escape from late endosomes into the cytoplasm. Full article

Ruthenium, palladium and platinum fall within the group of noble metals that are widely used in catalysis, especially for the electrocatalytic production of hydrogen. The dominant phase of the bulk Ru metal is hexagonal close-packed (hcp), which has been studied extensively. However, significantly less attention has been paid to the face-centred cubic (fcc) phases, which have been observed in nanoparticles. In this study, we have carried out density functional theory calculations with long-range dispersion corrections [DFT-D2, DFT-D3 and DFT-D3-(BJ)] to investigate the lattice parameters, surface energies and work functions of the (001), (011) and (111) surfaces of Ru, Pd and Pt in the fcc phase. When investigating the surface properties of the three metals, we observed that the DFT-D2 method generally underestimated the lattice parameters by up to 2.2% for Pt and 2.8% for Ru. The surface energies followed the observed trend (111) < (001) < (011) for both Ru and Pd with all three methods, which is comparable to experimental data. For Pt the same trend was observed with DFT-D2 and DFT-D3(BJ), but it deviated to Pt (111) < Pt (011) < Pt (001) for the DFT-D3 method. DFT-D2 overestimated the surface energies for all three Miller Indexes by 82%, 73%, and 60%, when compared to experimental values. The best correlation for the surface energies was obtained with the DFT-D3 and DFT-D3(BJ) methods, both of which have deviate by less than 15% deviation for all surfaces with respect to experiment. The work function followed the trend of Φ (111) < Φ (001) < Φ (011) for all three metals and calculated by all three methods. Five different types of Ru, Pd and Pt nanoparticles were considered, including icosahedral, decahedral, cuboctahedral, cubic and spherical particles of different sizes. The bulk, surface and nanoparticle calculations showed that the DFT-D2 method for Pt overestimated the exchange-correlation, leading to higher energy values that can be contributed erroneously to a more stable structure. The calculations showed that as soon as the surface-to-bulk ratio > 1, the energy per atom resembles bulk energy values. Full article

The alloys based on Ti-Zr are considered an excellent candidate for hydrogen storage applications. In this communication, we report the results of Fe substitution for Ni in the well-known Ti₄₅Zr₃₈Ni₁₇ compound. The parent and related compounds can be obtained as amorphous powders, transforming into the quasicrystalline phase (i-phase) after annealing. The amorphous Ti₄₅Zr₃₈Fe₁₇ phase is transformed into the icosahedral quasicrystalline state, and it is a quasi-continuous process. The i-phase is well-developed close to 500 °C. At higher temperatures, the quasicrystal structure transforms into the other phase: the w-phase (an approximant to the crystalline phase) and another crystal phase with a small addition of the FeZr₃ and the Fe₂(ZrTi)₃. The amorphous Ti₄₅Zr₃₈Fe₁₇ phases can be hydrogenated while maintaining the amorphous nature, which constitutes another very fascinating research field for our group. The investigated alloy shows a good capacity for gaseous H₂ at level 2.54 wt.% at elevated temperatures. The ferromagnetic signal of the amorphous TiZrFe comes from magnetic nanocrystallites in the amorphous matrix. After heating, the magnetic signal significantly decreases due to the lack of long-range magnetic ordering in the i-phase of the Ti₄₅Zr₃₈Fe₁₇ alloy. Full article

Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models. Full article