Search Results (10)

This study explores the accuracy and efficiency of multiple sequence alignment (MSA) programs, focusing on Clustal$\Omega$, MAFFT, and MUSCLE in the context of genotyping SARS-CoV-2 for the Saudi population. Our results indicate that MAFFT outperforms the others, making it an ideal choice for large-scale genomic analyses. The comparative performance of MSAs assembled using MergeAlign demonstrates that MAFFT and MUSCLE consistently exhibit higher accuracy than Clustal$\Omega$ in both reference-based and consensus-based approaches. The evaluation of genotyping effectiveness reveals that the addition of a reference sequence, such as the SARS-CoV-2 Wuhan-Hu-1 isolate, does not significantly affect the alignment process, suggesting that using consensus sequences derived from individual MSA alignments may yield comparable genotyping outcomes. Investigating single-nucleotide polymorphisms (SNPs) and mutations highlights distinctive features of MSA programs. Clustal$\Omega$ and MAFFT show similar counts, while MUSCLE displays the highest SNP count. High-frequency SNP analysis identifies MAFFT as the most accurate MSA program, emphasizing its reliability. Comparisons between Saudi and global SARS-CoV-2 populations underscore regional genetic variations. Saudis exhibit consistently higher frequencies of high-frequency SNPs, attributed to genetic similarity within the population. Transmission dynamics analysis reveals a higher frequency of co-mutations in the Saudi dataset, suggesting shared evolutionary patterns. These findings emphasize the importance of considering regional diversity in genetic analyses. Full article

The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study’s isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33–44 °C), low relative humidity (6–14%), and moderate wind speed (16–21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia. Full article

In elaborating and maintaining myelin sheaths on multiple axons/segments, oligodendrocytes distribute translation of some proteins, including myelin basic protein (MBP), to sites of myelin sheath assembly, or MSAS. As mRNAs located at these sites are selectively trapped in myelin vesicles during tissue homogenization, we performed a screen to identify some of these mRNAs. To confirm locations, we used real-time quantitative polymerase chain reaction (RT-qPCR), to measure mRNA levels in myelin (M) and ‘non-myelin’ pellet (P) fractions, and found that five (LPAR1, TRP53INP2, TRAK2, TPPP, and SH3GL3) of thirteen mRNAs were highly enriched in myelin (M/P), suggesting residences in MSAS. Because expression by other cell-types will increase p-values, some MSAS mRNAs might be missed. To identify non-oligodendrocyte expression, we turned to several on-line resources. Although neurons express TRP53INP2, TRAK2 and TPPP mRNAs, these expressions did not invalidate recognitions as MSAS mRNAs. However, neuronal expression likely prevented recognition of KIF1A and MAPK8IP1 mRNAs as MSAS residents and ependymal cell expression likely prevented APOD mRNA assignment to MSAS. Complementary in situ hybridization (ISH) is recommended to confirm residences of mRNAs in MSAS. As both proteins and lipids are synthesized in MSAS, understanding myelination should not only include efforts to identify proteins synthesized in MSAS, but also the lipids. Full article

To drive the synthesis of metallo-supramolecular assemblies (MSAs) and to fully exploit their functional properties, robust computational tools are crucial. The capability to model and to rationalize different parameters that can influence the outcome is mandatory. Here, we report a computational insight on the factors that can determine the relative stability of the supramolecular isomers helicate and mesocate in lanthanide-based quadruple-stranded assemblies. The considered MSAs have the general formula [Ln₂L₄]²⁻ and possess a cavity suitable to allocate guests. The analysis was focused on three different factors: the ligand rigidity and the steric hindrance, the presence of a guest inside the cavity, and the guest dimension. Three different quantum mechanical calculation set-ups (in vacuum, with the solvent, and with the solvent and the dispersion correction) were considered. Comparison between theoretical and experimental outcomes suggests that all calculations correctly estimated the most stable isomer, while the inclusion of the dispersion correction is mandatory to reproduce the geometrical parameters. General guidelines can be drawn: less rigid and less bulky is the ligand and less stable is the helicate, and the presence of a guest can strongly affect the isomerism leading to an inversion of the stability by increasing the guest size when the ligand is flexible. Full article

Since 2020, the COVID-19 pandemic represented an important worldwide burden. Well-structured surveillance by reliable and timely genomic data collection is crucial. In this study, a genomic monitoring analysis of all SARS-CoV-2 positive samples retrieved at the Fondazione Policlinico Universitario Campus Bio-Medico, in Rome, Italy, between December 2021 and June 2022, was performed. Two hundred and seventy-four SARS-CoV-2-positive samples were submitted to viral genomic sequencing by Illumina MiSeqII. Consensus sequences were generated by de novo assembling using the iVar tool and deposited on the GISAID database. Lineage assignment was performed using the Pangolin lineage classification. Sequences were aligned using ViralMSA and maximum-likelihood phylogenetic analysis was performed by IQ-TREE2. TreeTime tool was used to obtain dated trees. Our genomic monitoring revealed that starting from December 2021, all Omicron sub-lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) were circulating, although BA.1 was still the one with the highest prevalence thought time in this early period. Phylogeny revealed that Omicron isolates were scattered throughout the trees, suggesting multiple independent viral introductions following national and international human mobility. This data represents a sort of thermometer of what happened from July 2021 to June 2022 in Italy. Genomic monitoring of the circulating variants should be encouraged considering that SARS-CoV-2 variants or sub-variants emerged stochastically and unexpectedly. Full article

N6-methyladenosine (m⁶A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m⁶A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m⁶A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m⁶A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways. Full article

Sheet metal part manufacture is a precursor to various upstream assembly processes, including the manufacturing of mechanical and body parts of railcars, automobiles, ships, etc., in the transport manufacturing sector. The (re)manufacturing of railcars comprises a multi-tier manufacturing supply chain, mainly supported by local small and medium enterprises (SMEs), where siloed information leads to information disintegration between supplier and manufacturer. Technology spillovers in information technology (IT) and operational technology (OT) are disrupting traditional supply chains, leading to a sustainable digital economy, driven by new innovations and business models in manufacturing. This paper presents application of industrial DevOps by merging industry 4.0 technologies for collaborative and sustainable supply chains. A blockchain-based information system (IS) and a cloud manufacturing (CM) process system were integrated, for a supply chain management (SCM) system for the railcar manufacturer. A systems thinking methodology was used to identify the multi-hierarchical system, and a domain-driven design approach (DDD) was applied to develop the event-driven microservice architecture (MSA). The result is a blockchain-based cloud manufacturing as a service (BCMaaS) SCM system for outsourcing part production for boxed sheet metal parts. In conclusion, the BCMaaS system performs part provenance, traceability, and analytics in real time for improved quality control, inventory management, and audit reliability. Full article

The distinct neuropathological features of the different α-Synucleinopathies, as well as the diversity of the α-Synuclein (α-Syn) intracellular inclusion bodies observed in post mortem brain sections, are thought to reflect the strain diversity characterizing invasive α-Syn amyloids. However, this “one strain, one disease” view is still hypothetical, and to date, a possible disease-specific contribution of non-amyloid factors has not been ruled out. In Multiple System Atrophy (MSA), the buildup of α-Syn inclusions in oligodendrocytes seems to result from the terminal storage of α-Syn amyloid aggregates first pre-assembled in neurons. This assembly occurs at the level of neuronal cytoplasmic inclusions, and even earlier, within neuronal intranuclear inclusions (NIIs). Intriguingly, α-Syn NIIs are never observed in α-Synucleinopathies other than MSA, suggesting that these inclusions originate (i) from the unique molecular properties of the α-Syn fibril strains encountered in this disease, or alternatively, (ii) from other factors specifically dysregulated in MSA and driving the intranuclear fibrillization of α-Syn. We report the isolation and structural characterization of a synthetic human α-Syn fibril strain uniquely capable of seeding α-Syn fibrillization inside the nuclear compartment. In primary mouse cortical neurons, this strain provokes the buildup of NIIs with a remarkable morphology reminiscent of cat’s eye marbles (see video abstract). These α-Syn inclusions form giant patterns made of one, two, or three lentiform beams that span the whole intranuclear volume, pushing apart the chromatin. The input fibrils are no longer detectable inside the NIIs, where they become dominated by the aggregation of endogenous α-Syn. In addition to its phosphorylation at S129, α-Syn forming the NIIs acquires an epitope antibody reactivity profile that indicates its organization into fibrils, and is associated with the classical markers of α-Syn pathology p62 and ubiquitin. NIIs are also observed in vivo after intracerebral injection of the fibril strain in mice. Our data thus show that the ability to seed NIIs is a strain property that is integrally encoded in the fibril supramolecular architecture. Upstream alterations of cellular mechanisms are not required. In contrast to the lentiform TDP-43 NIIs, which are observed in certain frontotemporal dementias and which are conditional upon GRN or VCP mutations, our data support the hypothesis that the presence of α-Syn NIIs in MSA is instead purely amyloid-strain-dependent. Full article

Proteinaceous nanovaccine delivery systems have significantly promoted the development of various high-efficiency vaccines. However, the widely used method of coupling the expression of scaffolds and antigens may result in their structural interference with each other. Monovalent streptavidin (mSA) is a short monomer sequence, which has a strong affinity for biotin. Here, we discuss an orthogonal, modular, and highly versatile self-assembled proteinaceous nanoparticle chassis that facilitates combinations with various antigen cargos by using mSA and biotin to produce nanovaccines. We first improved the yield of these nanoparticles by appending a short sugar chain on their surfaces in a constructed host strain. After confirming the strong ability to induce both Th1- and Th2-mediated immune responses based on the plasma cytokine spectrum from immunized mice, we further verified the binding ability of biotinylated nanoparticles to mSA-antigens. These results demonstrate that our biotinylated nanoparticle chassis could load both protein and polysaccharide antigens containing mSA at a high affinity. Our approach thus offers an attractive technology for combining nanoparticles and antigen cargos to generate various high-performance nanovaccines. In particular, the designed mSA connector (mSA containing glycosylation modification sequences) could couple with polysaccharide antigens, providing a new attractive strategy to prepare nanoscale conjugate vaccines. Full article

Abnormal accumulation of aggregated α-synuclein (α-Syn) is seen in a variety of neurodegenerative diseases, including Parkinson’s disease (PD), multiple system atrophy (MSA), dementia with Lewy body (DLB), Parkinson’s disease dementia (PDD), and even subsets of Alzheimer’s disease (AD) showing Lewy-body-like pathology. These synucleinopathies exhibit differences in their clinical and pathological representations, reminiscent of prion disorders. Emerging evidence suggests that α-Syn self-assembles and polymerizes into conformationally diverse polymorphs in vitro and in vivo, similar to prions. These α-Syn polymorphs arising from the same precursor protein may exhibit strain-specific biochemical properties and the ability to induce distinct pathological phenotypes upon their inoculation in animal models. In this review, we discuss clinical and pathological variability in synucleinopathies and several aspects of α-Syn fibril polymorphism, including the existence of high-resolution molecular structures and brain-derived strains. The current review sheds light on the recent advances in delineating the structure–pathogenic relationship of α-Syn and how diverse α-Syn molecular polymorphs contribute to the existing clinical heterogeneity in synucleinopathies. Full article