Severe Acute Respiratory syndrome 2 (SARS-CoV-2) is a respiratory virus responsible for coronavirus disease 19 (COVID-19) and the still ongoing and unprecedented global pandemic. The key viral ...protein for cell infection is the spike glycoprotein, a surface-exposed fusion protein that both recognizes and mediates entry into host cells. Within the spike glycoprotein, a fatty acid binding pocket (FABP) was confirmed, with the crystallization of linoleic acid (LA) occupying a well-defined site. Importantly, when the pocket is occupied by a fatty acid, an inactive conformation is stabilized, and cell recognition is hindered. In this review, we discuss ligands reported so far for this site, correlating their activity predicted through in silico studies with antispike experimental activity, assessed by either binding assays or cell-infection assays. LA was the first confirmed ligand, cocrystallized in a cryo-EM structure of the spike protein, resulting in increased stability of the inactive conformation of the spike protein. The next identified ligand, lifitegrast, was also experimentally confirmed as a ligand with antiviral activity, suggesting the potential for diverse chemical scaffolds to bind this site. Finally, SPC-14 was also confirmed as a ligand, although no inhibition assays were performed. In this review, we identified 20 studies describing small-molecule compounds predicted to bind the pocket in in silico studies and with confirmed binding or in vitro activity, either inhibitory activity against the spike-ACE2 interaction or antiviral activity in cell-based assays. When considering all ligands confirmed with in vitro assays, a good overall occupation of the pocket should be complemented with the ability to make direct interactions, both hydrophilic and hydrophobic, with key amino acid residues defining the pocket surface. Among the active compounds, long flexible carbon chains are recurrent, with retinoids capable of binding the FABP, although bulkier systems are also capable of affecting viral fitness. Compounds able to bind this site with high affinity have the potential to stabilize the inactive conformation of the SARS-CoV-2 spike protein and therefore reduce the virus’s ability to infect new cells. Since this pocket is conserved in highly pathogenic human coronaviruses, including MERS-CoV and SARS-CoV, this effect could be exploited for the development of new antiviral agents, with broad-spectrum anticoronavirus activity.
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IJS, KILJ, NUK, PNG, UL, UM
Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by synovial joint inflammation and cartilage and bone tissue destruction. Although there exist some treatment strategies for ...RA, they are not completely safe and effective. Therefore, it is important to develop and test new drugs for RA that specifically target inflamed/swollen joints and simultaneously attenuate other possible damages to healthy tissues. Nanotechnology can be a good alternative to consider when envisioning precise medication for treating RA. Through the use of nanoparticles, it is possible to increase bioavailability and bioactivity of therapeutics and enable selective targeting to damaged joints. Herein, recent studies using nanoparticles for the treatment of RA, namely with liposomes, polymeric nanoparticles, dendrimers, and metallic nanoparticles, have been reviewed. These therapeutic strategies have shown great promise in improving the treatment over that by traditional drugs. The results of these studies confirm that feasibility of the use of nanoparticles is mainly due to their biocompatibility, low toxicity, controlled release, and selective drug delivery to inflamed tissues in animal RA models. Therefore, it is possible to claim that nanotechnology will, in the near future, play a crucial role in advanced treatments and patient-specific therapies for human diseases such as RA.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Gene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication events throughout evolution, resulting in multiple copies of ...an ancestral gene. Over time, these copies can acquire mutations and structural variations, resulting in members that may vary in size, motif ordering and sequence. Multigene families have been described in a broad range of organisms, from single-celled bacteria to complex multicellular organisms, and have been linked to an array of phenomena, such as host-pathogen interactions, immune evasion and embryonic development. Despite the importance of gene families, few approaches have been developed for estimating and graphically visualizing their diversity patterns and expression profiles in genome-wide studies. Here, we introduce an R package named dgfr, which estimates and enables the visualization of sequence divergence within gene families, as well as the visualization of secondary data such as gene expression. The package takes as input a multi-fasta file containing the coding sequences (CDS) or amino acid sequences from a multigene family, performs a pairwise alignment among all sequences, and estimates their distance, which is subjected to dimension reduction, optimal cluster determination, and gene assignment to each cluster. The result is a dataset that allows for the visualization of sequence divergence and expression within the gene family, an approximation of the number of clusters present in the family. dgfr provides a way to estimate and study the diversity of gene families, as well as visualize the dispersion and secondary profile of the sequences. The dgfr package is available at https://github.com/lailaviana/dgfr under the GPL-3 license.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Addressing the challenges of quiescence and post-treatment relapse is of utmost importance in the microbiology field. This study shows that Leishmania infantum and L. donovani parasites rapidly enter ...into quiescence after an estimated 2-3 divisions in both human and mouse bone marrow stem cells. Interestingly, this behavior is not observed in macrophages, which are the primary host cells of the Leishmania parasite. Transcriptional comparison of the quiescent and non-quiescent metabolic states confirmed the overall decrease of gene expression as a hallmark of quiescence. Quiescent amastigotes display a reduced size and signs of a rapid evolutionary adaptation response with genetic alterations. Our study provides further evidence that this quiescent state significantly enhances resistance to treatment. Moreover, transitioning through quiescence is highly compatible with sand fly transmission and increases the potential of parasites to infect cells. Collectively, this work identified stem cells in the bone marrow as a niche where Leishmania quiescence occurs, with important implications for antiparasitic treatment and acquisition of virulence traits.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•Introduction of a novel semi-analytical solution for ultrasonic fatigue specimens.•The method is simpler and faster for iterative modelling of ultrasonic specimens.•The method is demonstrated with ...both uniaxial and multiaxial ultrasonic specimens.•The results showed that this method can predict the induced stress amplitude.•Optimisation algorithms will benefit from the fast computation for specimen design.
Ultrasonic fatigue specimens require rigorous design. The entire machine and specimen setup must vibrate in resonance at high frequencies, with the desired mode shapes that produce the intended stresses. The connection between parts must be considered too as they should allow for the desired mode shape to vibrate in free-free conditions. Most published research uses an analytical method that works only for uniaxial tension–compression or pure torsion specimens. This limits the range of experiments. In this paper, a semi-analytical formulation that can model more complex ultrasonic specimen geometries for a variety of stress states is proposed, namely multiaxial tension–torsion. Comparing numerical simulations with the analytical method show a good correlation between results. This work can help other researchers to design and conduct more varied and efficient ultrasonic fatigue experiments.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The effective osteogenic commitment of human bone marrow mesenchymal stem cells (hBMSCs) is critical for bone regenerative therapies. Extracellular vesicles (EVs) derived from hBMSCs have a ...regenerative potential that has been increasingly recognized. Herein, the osteoinductive potential of osteogenically induced hBMSC-EVs was examined. hBMSCs secreted negatively charged nanosized vesicles (∼35 nm) with EV-related surface markers. The yield of EVs over 7 days was dependent on an osteogenic stimulus (standard chemical cocktail or RUNX2 cationic-lipid transfection). These EVs were used to sequentially stimulate homotypic uncommitted cells during 7 days, matching the seeding density of EV parent cells, culture time, and stimuli. Osteogenically committed hBMSC-EVs induced an osteogenic phenotype characterized by marked early induction of BMP2, SP7, SPP1, BGLAP/IBSP, and alkaline phosphatase. Both EV groups outperformed the currently used osteoinductive strategies. These data show that naturally secreted EVs can guide the osteogenic commitment of hBMSCs in the absence of other chemical or genetic osteoinductors.
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•hBMSC-EV secretion during culture is osteogenic stimulus dependent•Osteogenically induced hBMSC-EVs are early osteoinductors•Osteogenically induced hBMSC-EVs outperform currently used osteoinductive strategies
In this article, Neves and colleagues show that hBMSCs secrete populations of nanosized EVs during the osteogenic commitment induced either by standard osteogenic medium or by Runx-2 transfection. Furthermore, the EVs obtained during both hBMSC osteogenic induction methods carry potent signals that are efficient in driving the osteogenic lineage progression of homotypic cells.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In today's volatile, uncertain, and complex business environments, manufacturing companies must not only adapt to market demands but also minimize the time between problem occurrence and resolution. ...The implementation of lean manufacturing systems has been crucial in this regard. However, traditional approaches have shown notable inefficiencies that can be effectively addressed through digitalization. By embracing digital solutions, manufacturing companies can ensure efficient continuous improvement, driving performance to higher levels. This study aims to find a digital solution for a specific company that faces daily challenges associated with low visibility into production. An investigation revealed that the Lean tools used by the company were outdated, directly affecting the generated information and consequently, decision-making. The integration of a Manufacturing Execution System into the factory's dynamics was the solution found. In this context, a step-by-step methodology is proposed to guide the implementation. As a result, a prototype of the system was designed. The validation of the system by end-users demonstrates the success of the proposed methodology.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Ultrasound showing an anechoic collection with interspersed echogenic foci (blue arrows ‐ gas bubbles) proximal to the hyperechoic bone flap (red asterisk; post‐decompressive craniectomy). Serratia ...marcescens was isolated from the collected fluid. Bedside ultrasound can be a reliable and effective tool to aid in the diagnosis of bone flap infections.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Clostridioides
(
Clostridium
)
difficile
infection (CDI) is an evolving global healthcare problem, and owing to the diverse and dynamic molecular epidemiology of
C
.
difficile
, new strains continue ...to emerge. In Brazil, only two cases of CDI due to the so called hypervirulent PCR ribotype (RT) 027 belonging to clade 2 have ever been reported, whereas incidence of CDI due to another “hypervirulent” RT078 (clade 5) has not yet been reported. In contrast, novel clade 2 strains have been identified in different hospitals. To better understand the epidemiology of CDIs in Brazil, this study aimed to genotypically and phenotypically characterize three novel Brazilian clade 2 strains (RT883, 884, and 885) isolated from patients with confirmed CDI. In addition, to better understand the circulating RTs, a two-year sampling was conducted in patients from the same hospital and in several domestic and wild animal species. The three strains examined showed lower production of A/B toxins than the control RT027, although two of these strains harbored a truncated
tcdC
gene. All strains showed swimming motility similar to that of RT027, while RT883 showed higher spore production than the reference strain. In the
in vivo
hamster model, the lethality of all strains was found to be similar to that of RT027. Both cgMLST and cgMLSA analyses revealed a high genetic similarity among the three-novel clade 2 isolates. In the two-year survey in animals and humans, RT883, 884, and 885 were not detected; however, three new RTs (RT988, RT989, and RT990) were isolated, two of which were genetically related to the three previously reported clade 2 strains. RT106 and RT126 were most frequently detected in humans (47.9%) and animals (57.9%), respectively. Furthermore, RT027 and RT078 were not detected in humans. The results of this study suggest that these novel clade 2 strains have virulence potential and that new strains from clade 2 continue to emerge in our setting, indicating the need for long-term local surveillance.
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