How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?

Well-annotated gene and genomic sequences serve as a foundation for making inferences in molecular biology and evolution and can directly impact public health. The first SARS-CoV-2 genome was submitted to the GenBank database hosted by the U.S.

Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Lepeletier, 1836 (Hymenoptera, Vespidae).

The Asian hornet, , is an invasive species that has not only expanded its range in Asia but has also invaded European countries, and it incurs significant costs on local apiculture. This phylogeographic study aims to trace the evolutionary trajectory of and its close relatives; it aims to identify features that characterize an invasive species. The last successful invasion of into France occurred in late May, 2002, and into South Korea in early October, 2002, which were estimated by fitting a logistic equation to the number of observations over time.

Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.

Different bacterial species have dramatically different generation times, from 20-30 min in to about two weeks in . The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses of translation, i.

Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA.

The Asian giant hornet, , is an invasive species that could potentially destroy the local honeybee industry in North America. It has been observed to nest in the coastal regions of British Columbia in Canada and Washington State in the USA. What is the source population of the immigrant hornets? The identification of the source population can shed light not only on the route of immigration but also on the similarity between the native habitat and the potential new habitat in the Pacific Northwest.

Characterization of the diversity of type IV secretion system-encoding plasmids in .

The multi-drug resistant pathogen has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution.

Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria.

The dynamic structures and varying functions of intrinsically disordered proteins (IDPs) have made them fascinating subjects in molecular biology. Investigating IDP abundance in different bacterial species is crucial for understanding adaptive strategies in diverse environments. Notably, thermophilic bacteria have lower IDP abundance than mesophiles, and a negative correlation with optimal growth temperature (OGT) has been observed.

Computational Design of Novel Griseofulvin Derivatives Demonstrating Potential Antibacterial Activity: Insights from Molecular Docking and Molecular Dynamics Simulation.

In response to the urgent demand for innovative antibiotics, theoretical investigations have been employed to design novel analogs. Because griseofulvin is a potential antibacterial agent, we have designed novel derivatives of griseofulvin to enhance its antibacterial efficacy and to evaluate their interactions with bacterial targets using in silico analysis. The results of this study reveal that the newly designed derivatives displayed the most robust binding affinities towards PBP2, tyrosine phosphatase, and FtsZ proteins.

Horizontal Gene Transfer and Drug Resistance Involving .

(Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions.

Identification of host receptors for viral entry and beyond: a perspective from the spike of SARS-CoV-2.

Identification of the interaction between the host membrane receptor and viral receptor-binding domain (RBD) represents a crucial step for understanding viral pathophysiology and for developing drugs against pathogenic viruses. While all membrane receptors and carbohydrate chains could potentially be used as receptors for viruses, prioritized searches focus typically on membrane receptors that are known to have been used by the relatives of the pathogenic virus, e.g.

Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time.

Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains.

In Silico Exploration of Microtubule Agent Griseofulvin and Its Derivatives Interactions with Different Human β-Tubulin Isotypes.

Tubulin isotypes are known to regulate microtubule stability and dynamics, as well as to play a role in the development of resistance to microtubule-targeted cancer drugs. Griseofulvin is known to disrupt cell microtubule dynamics and cause cell death in cancer cells through binding to tubulin protein at the taxol site. However, the detailed binding mode involved molecular interactions, and binding affinities with different human β-tubulin isotypes are not well understood.

Clinical characteristics of hypercalcemic crises in a tertiary children's hospital.

Background: Hypercalcemic crisis is considered a critical and fatal endocrine condition. To date, few reports have focused on hypercalcemic crises in children.

Aim: To explore the etiology and identify the clinical characteristics related to hypercalcemic crises in children.

Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori.

Acid-resistance in gastric pathogen Helicobacter pylori requires the coordination of four essential processes to regulate urease activity. Firstly, urease expression above a base level needs to be finely tuned at different ambient pH. Secondly, as nickel is needed to activate urease, nickel homeostasis needs to be maintained by proteins that import and export nickel ions, and sequester, store and release nickel when needed.

Proteins from Thermophilic Often Do Not Fold Correctly in a Mesophilic Expression System Such as .

Majority of protein structure studies use () and other model organisms as expression systems for other species' genes. However, protein folding depends on cellular environment factors, such as chaperone proteins, cytoplasmic pH, temperature, and ionic concentrations. Because of differences in these factors, especially temperature and chaperones, native proteins in organisms such as extremophiles may fold improperly when they are expressed in mesophilic model organisms.

Griseofulvin: An Updated Overview of Old and Current Knowledge.

Griseofulvin is an antifungal polyketide metabolite produced mainly by ascomycetes. Since it was commercially introduced in 1959, griseofulvin has been used in treating dermatophyte infections. This fungistatic has gained increasing interest for multifunctional applications in the last decades due to its potential to disrupt mitosis and cell division in human cancer cells and arrest hepatitis C virus replication.

Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean ( L.).

Common bean ( L.) is a food crop that is an important source of dietary proteins and carbohydrates. Marsh spot is a physiological disorder that diminishes seed quality in beans.

In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19.

Treatment options for Coronavirus Disease 2019 (COVID-19) remain limited, and the option of repurposing approved drugs with promising medicinal properties is of increasing interest in therapeutic approaches to COVID-19. Using computational approaches, we examined griseofulvin and its derivatives against four key anti-SARS-CoV-2 targets: main protease, RdRp, spike protein receptor-binding domain (RBD), and human host angiotensin-converting enzyme 2 (ACE2). Molecular docking analysis revealed that griseofulvin (CID 441140) has the highest docking score (-6.

Effect of prophylactic use of hydrolyzed protein formula on gastrointestinal diseases and physical growth in preterm infants: a Meta analysis.

Objectives: To systematically evaluate the effect of prophylactic use of hydrolyzed protein formula on gastrointestinal diseases and physical development in preterm infants.

Methods: A computerized search was performed in the databases including China National Knowledge Infrastructure, Wanfang Data, Weipu, PubMed, Embase, and the Cochrane Library to identify randomized controlled trials of the effect of prophylactic use of hydrolyzed protein formula on gastrointestinal diseases and physical growth in preterm infants. RevMan 5.

Post-Alignment Adjustment and Its Automation.

Multiple sequence alignment (MSA) is the basis for almost all sequence comparison and molecular phylogenetic inferences. Large-scale genomic analyses are typically associated with automated progressive MSA without subsequent manual adjustment, which itself is often error-prone because of the lack of a consistent and explicit criterion. Here, I outlined several commonly encountered alignment errors that cannot be avoided by progressive MSA for nucleotide, amino acid, and codon sequences.

Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes.

The polyketide griseofulvin is a natural antifungal compound and research in griseofulvin has been key in establishing our current understanding of polyketide biosynthesis. Nevertheless, the griseofulvin gsf biosynthetic gene cluster (BGC) remains poorly understood in most fungal species, including Penicillium griseofulvum where griseofulvin was first isolated. To elucidate essential genes involved in griseofulvin biosynthesis, we performed third-generation sequencing to obtain the genome of P.

Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes.

All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages.

Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines.

The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5'-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination.

Depression of Pyroptosis by Inhibiting Caspase-1 Activation Improves Neurological Outcomes of Kernicterus Model Rats.

Kernicterus is a severe complication of extreme neonatal hyperbilirubinemia. Prolonged exposure to high-level unconjugated bilirubin (UCB) directly damages brain tissue. Neuroinflammation is believed to contribute to UCB-induced neurotoxicity.

Does Require Specific Post-Translational Silencing against Leaky Translation of Hac1up?

encodes a key transcription factor that transmits the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus and regulates downstream UPR genes in . In response to the accumulation of unfolded proteins in the ER, Ire1p oligomers splice pre-mRNA () via a non-conventional process and allow the spliced () to be translated efficiently. However, leaky splicing and translation of may occur in non-UPR cells to induce undesirable UPR.