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1.
Biol Res ; 57(1): 59, 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-39223638

ABSTRACT

BACKGROUND: Tumour dormancy, a resistance mechanism employed by cancer cells, is a significant challenge in cancer treatment, contributing to minimal residual disease (MRD) and potential relapse. Despite its clinical importance, the mechanisms underlying tumour dormancy and MRD remain unclear. In this study, we employed two syngeneic murine models of myeloid leukemia and melanoma to investigate the genetic, epigenetic, transcriptomic and protein signatures associated with tumour dormancy. We used a multiomics approach to elucidate the molecular mechanisms driving MRD and identify potential therapeutic targets. RESULTS: We conducted an in-depth omics analysis encompassing whole-exome sequencing (WES), copy number variation (CNV) analysis, chromatin immunoprecipitation followed by sequencing (ChIP-seq), transcriptome and proteome investigations. WES analysis revealed a modest overlap of gene mutations between melanoma and leukemia dormancy models, with a significant number of mutated genes found exclusively in dormant cells. These exclusive genetic signatures suggest selective pressure during MRD, potentially conferring resistance to the microenvironment or therapies. CNV, histone marks and transcriptomic gene expression signatures combined with Gene Ontology (GO) enrichment analysis highlighted the potential functional roles of the mutated genes, providing insights into the pathways associated with MRD. In addition, we compared "murine MRD genes" profiles to the corresponding human disease through public datasets and highlighted common features according to disease progression. Proteomic analysis combined with multi-omics genetic investigations, revealed a dysregulated proteins signature in dormant cells with minimal genetic mechanism involvement. Pathway enrichment analysis revealed the metabolic, differentiation and cytoskeletal remodeling processes involved in MRD. Finally, we identified 11 common proteins differentially expressed in dormant cells from both pathologies. CONCLUSIONS: Our study underscores the complexity of tumour dormancy, implicating both genetic and nongenetic factors. By comparing genomic, transcriptomic, proteomic, and epigenomic datasets, our study provides a comprehensive understanding of the molecular landscape of minimal residual disease. These results provide a robust foundation for forthcoming investigations and offer potential avenues for the advancement of targeted MRD therapies in leukemia and melanoma patients, emphasizing the importance of considering both genetic and nongenetic factors in treatment strategies.


Subject(s)
Disease Models, Animal , Melanoma , Neoplasm, Residual , Animals , Melanoma/genetics , Melanoma/pathology , Mice , Leukemia/genetics , Leukemia/pathology , DNA Copy Number Variations , Exome Sequencing , Mice, Inbred C57BL , Proteomics , Transcriptome , Gene Expression Profiling , Multiomics
2.
Micromachines (Basel) ; 15(7)2024 Jul 22.
Article in English | MEDLINE | ID: mdl-39064443

ABSTRACT

Microfluidic separators play a pivotal role in the biomedical and chemical industries by enabling precise fluid manipulations. Traditional fabrication of these devices typically requires costly cleanroom facilities, which limits their broader application. This study introduces a novel microfluidic device that leverages the passive Zweifach-Fung principle to overcome these financial barriers. Through Lagrangian computational simulations, we optimized an eleven-channel Zweifach-Fung configuration that achieved a perfect 100% recall rate for particles following a specified normal distribution. Experimental evaluations determined 2 mL/h as the optimal total flow rate (TFR), under which the device showcased exceptional performance enhancements in precision and recall for micrometer-sized particles, achieving an overall accuracy of 94% ± 3%. Fabricated using a cost-effective, non-cleanroom method, this approach represents a significant shift from conventional practices, dramatically reducing production costs while maintaining high operational efficacy. The cost of each chip is less than USD 0.90 cents and the manufacturing process takes only 15 min. The development of this device not only makes microfluidic technology more accessible but also sets a new standard for future advancements in the field.

3.
Article in English | MEDLINE | ID: mdl-39007523

ABSTRACT

Solid tumors represent the most common type of cancer in humans and are classified into sarcomas, lymphomas, and carcinomas based on the originating cells. Among these, carcinomas, which arise from epithelial and glandular cells lining the body's tissues, are the most prevalent. Around the world, a significant increase in the incidence of solid tumors is observed during recent years. In this context, efforts to discover more effective cancer treatments have led to a deeper understanding of the tumor microenvironment (TME) and its components. Currently, the interactions between cancer cells and elements of the TME are being intensely investigated. Remarkable progress in research is noted, largely owing to the development of advanced in vitro models, such as tumor-on-a-chip models that assist in understanding and ultimately discovering new effective treatments for a specific type of cancer. The purpose of this article is to provide a review of the TME and cancer cell components, along with the advances on tumor-on-a-chip models designed to mimic tumors, offering a perspective on the current state of the art. Recent studies using this kind of microdevices that reproduce the TME have allowed a better understanding of the cancer and its treatments. Nevertheless, current applications of this technology present some limitations that must be overcome to achieve a broad application by researchers looking for a deeper knowledge of cancer and new strategies to improve current therapies.

4.
Biofabrication ; 16(4)2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38866003

ABSTRACT

Tumor-on-chips (ToCs) are useful platforms for studying the physiology of tumors and evaluating the efficacy and toxicity of anti-cancer drugs. However, the design and fabrication of a ToC system is not a trivial venture. We introduce a user-friendly, flexible, 3D-printed microfluidic device that can be used to culture cancer cells or cancer-derived spheroids embedded in hydrogels under well-controlled environments. The system consists of two lateral flow compartments (left and right sides), each with two inlets and two outlets to deliver cell culture media as continuous liquid streams. The central compartment was designed to host a hydrogel in which cells and microtissues can be confined and cultured. We performed tracer experiments with colored inks and 40 kDa fluorescein isothiocyanate dextran to characterize the transport/mixing performances of the system. We also cultured homotypic (MCF7) and heterotypic (MCF7-BJ) spheroids embedded in gelatin methacryloyl hydrogels to illustrate the use of this microfluidic device in sustaining long-term micro-tissue culture experiments. We further demonstrated the use of this platform in anticancer drug testing by continuous perfusion of doxorubicin, a commonly used anti-cancer drug for breast cancer. In these experiments, we evaluated drug transport, viability, glucose consumption, cell death (apoptosis), and cytotoxicity. In summary, we introduce a robust and friendly ToC system capable of recapitulating relevant aspects of the tumor microenvironment for the study of cancer physiology, anti-cancer drug transport, efficacy, and safety. We anticipate that this flexible 3D-printed microfluidic device may facilitate cancer research and the development and screening of strategies for personalized medicine.


Subject(s)
Antineoplastic Agents , Breast Neoplasms , Printing, Three-Dimensional , Spheroids, Cellular , Humans , Spheroids, Cellular/drug effects , Spheroids, Cellular/pathology , Spheroids, Cellular/metabolism , Breast Neoplasms/drug therapy , Breast Neoplasms/pathology , Breast Neoplasms/metabolism , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Female , MCF-7 Cells , Hydrogels/chemistry , Lab-On-A-Chip Devices , Cell Line, Tumor , Drug Screening Assays, Antitumor , Dextrans/chemistry , Gelatin/chemistry , Doxorubicin/pharmacology , Doxorubicin/chemistry , Cell Survival/drug effects , Methacrylates
5.
Toxicol In Vitro ; 98: 105849, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38772494

ABSTRACT

Concerns over Bisphenol A (BPA) and its substitute, Bisphenol S (BPS), have led to innovative exploration due to potential adverse health effects. BPS, replacing BPA in some regions to avoid toxic impacts, remains insufficiently studied. Besides this, the organ-on-a-chip technology emerges as a transformative solution in drug discovery and chemiclas toxicity testing, minimizing costs and aligning with ethical standards by reducing reliance on animal models, by integrating diverse tissues and dynamic cell environments enhances precision in predicting organ function. Here, we employ a 3-organ-on-a-chip microfluidic device with skin, intestine, and liver cultures to assess the effects of BPA and BPS via topical and oral administration. Our evaluation focused on gene markers associated with carcinogenicity, systemic toxicity, and endocrine disruption. BPA exhibited expected absorption profiles, causing liver injury and genetic modulation in related pathways. BPS, a safer alternative, induced adverse effects on gene expression, particularly in topical absorption, with distinct absorption patterns. Our findings underscore the urgency of addressing BPA and BPS toxicity concerns, highlighting the crucial role of organ-on-a-chip technology in understanding associated health risks. The study promotes the organ-on-a-chip methodology as a valuable tool for safe drug development and disease treatments, offering a novel liver toxicity screening alternative to traditional animal tests. This contributes to advancing comprehension of the biological effects of these compounds, fostering improved safety assessments in human health.


Subject(s)
Benzhydryl Compounds , Lab-On-A-Chip Devices , Liver , Phenols , Skin , Sulfones , Phenols/toxicity , Benzhydryl Compounds/toxicity , Liver/drug effects , Liver/metabolism , Sulfones/toxicity , Animals , Skin/drug effects , Skin/metabolism , Humans , Intestines/drug effects , Endocrine Disruptors/toxicity , Toxicity Tests/methods , Microphysiological Systems
6.
Micromachines (Basel) ; 15(5)2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38793150

ABSTRACT

Managing Multi-Processor Systems-on-Chip (MPSoCs) is becoming increasingly complex as demands for advanced capabilities rise. This complexity is due to the involvement of more processing elements and resources, leading to a higher degree of heterogeneity throughout the system. Over time, management schemes have evolved from simple to autonomous systems with continuous control and monitoring of various parameters such as power distribution, thermal events, fault tolerance, and system security. Autonomous management integrates self-awareness into the system, making it aware of its environment, behavior, and objectives. Self-Aware Cyber-Physical Systems-on-Chip (SA-CPSoCs) have emerged as a concept to achieve highly autonomous management. Communication infrastructure is also vital to SoCs, and Software-Defined Networks-on-Chip (SDNoCs) can serve as a base structure for self-aware systems-on-chip. This paper presents a survey of the evolution of MPSoC management over the last two decades, categorizing research works according to their objectives and improvements. It also discusses the characteristics and properties of SA-CPSoCs and explains why SDNoCs are crucial for these systems.

7.
Methods Mol Biol ; 2801: 125-134, 2024.
Article in English | MEDLINE | ID: mdl-38578418

ABSTRACT

Connexins (Cxs) are transmembrane proteins which form hemichannels and gap junction channels at the plasma membrane. These channels allow the exchange of ions and molecules between the intra- and extracellular space and between cytoplasm of adjacent cells, respectively. The channel function of Cx assemblies has been extensively studied; however, "noncanonical" functions have emerged in the last few decades and have capture the attentions of many researchers, including the role of some Cxs as gene modulators or transcription factors. In this chapter, we describe a protocol to study the interaction of Cx46 with DNA in HeLa cells. These methods can facilitate understanding the role of Cxs in physiological processes and pathological mechanisms, including, for example, the contribution of Cx46 in maintaining stemness of glioma cancer stem cells.


Subject(s)
Connexins , Ion Channels , Humans , Connexins/genetics , Connexins/metabolism , HeLa Cells , Gap Junctions/metabolism , DNA/genetics
8.
Plant J ; 118(6): 1832-1847, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38461471

ABSTRACT

Juncus is the largest genus of Juncaceae and was considered holocentric for a long time. Recent findings, however, indicated that 11 species from different clades of the genus have monocentric chromosomes. Thus, the Juncus centromere organization and evolution need to be reassessed. We aimed to investigate the major repetitive DNA sequences of two accessions of Juncus effusus and its centromeric structure by employing whole-genome analyses, fluorescent in situ hybridization, CENH3 immunodetection, and chromatin immunoprecipitation sequencing. We showed that the repetitive fraction of the small J. effusus genome (~270 Mbp/1C) is mainly composed of Class I and Class II transposable elements (TEs) and satellite DNAs. Three identified satellite DNA families were mainly (peri)centromeric, with two being associated with the centromeric protein CENH3, but not strictly centromeric. Two types of centromere organization were discerned in J. effusus: type 1 was characterized by a single CENH3 domain enriched with JefSAT1-155 or JefSAT2-180, whereas type 2 showed multiple CENH3 domains interrupted by other satellites, TEs or genes. Furthermore, while type 1 centromeres showed a higher degree of satellite identity along the array, type 2 centromeres had less homogenized arrays along the multiple CENH3 domains per chromosome. Although the analyses confirmed the monocentric organization of J. effusus chromosomes, our data indicate a more dynamic arrangement of J. effusus centromeres than observed for other plant species, suggesting it may constitute a transient state between mono- and holocentricity.


Subject(s)
Centromere , Chromosomes, Plant , DNA, Satellite , In Situ Hybridization, Fluorescence , Centromere/genetics , Chromosomes, Plant/genetics , DNA, Satellite/genetics , Genome, Plant/genetics , DNA Transposable Elements/genetics , DNA, Plant/genetics , Repetitive Sequences, Nucleic Acid/genetics , Plant Proteins/genetics , Plant Proteins/metabolism
9.
Anal Chim Acta ; 1299: 342429, 2024 Apr 22.
Article in English | MEDLINE | ID: mdl-38499426

ABSTRACT

3D printing has revolutionized the manufacturing process of microanalytical devices by enabling the automated production of customized objects. This technology promises to become a fundamental tool, accelerating investigations in critical areas of health, food, and environmental sciences. This microfabrication technology can be easily disseminated among users to produce further and provide analytical data to an interconnected network towards the Internet of Things, as 3D printers enable automated, reproducible, low-cost, and easy fabrication of microanalytical devices in a single step. New functional materials are being investigated for one-step fabrication of highly complex 3D printed parts using photocurable resins. However, they are not yet widely used to fabricate microfluidic devices. This is likely the critical step towards easy and automated fabrication of sophisticated, complex, and functional 3D-printed microchips. Accordingly, this review covers recent advances in the development of 3D-printed microfluidic devices for point-of-care (POC) or bioanalytical applications such as nucleic acid amplification assays, immunoassays, cell and biomarker analysis and organs-on-a-chip. Finally, we discuss the future implications of this technology and highlight the challenges in researching and developing appropriate materials and manufacturing techniques to enable the production of 3D-printed microfluidic analytical devices in a single step.


Subject(s)
Microtechnology , Printing, Three-Dimensional , Point-of-Care Systems , Lab-On-A-Chip Devices
10.
Methods Mol Biol ; 2781: 105-117, 2024.
Article in English | MEDLINE | ID: mdl-38502447

ABSTRACT

Modeling human pregnancy is challenging as two subjects, the mother and fetus, must be evaluated in tandem. To understand pregnancy, parturition, and adverse pregnancy outcomes, the two feto-maternal interfaces (FMi) that form during gestation (i.e., the placenta and fetal membrane) need to be investigated to understand their biological roles, and organ dysfunction can lead to adverse outcomes. Adverse pregnancy outcomes such as preterm rupture of the membranes, spontaneous preterm birth, preeclampsia, intra-uterine growth restriction, and gestational diabetes rates are on the rise worldwide, highlighting the need for future studies and a better understanding of molecular and cellular pathways that contribute to disease onset. Current in vivo animal models nor in vitro cell culture systems can answer these questions as they do not model the function or structure of human FMis. Utilizing microfabrication and soft-lithography techniques, microfluidic organ-on-chip (OOC) devices have been adapted by many fields to model the anatomy and biological function of complex organs and organ systems within small in vitro platforms.These techniques have been adapted to recreate the fetal membrane FMi (FMi-OOC) using immortalized cells and collagen derived from patient samples. The FMi-OOC is a four-cell culture chamber, concentric circle system, that contains both fetal (amniochorion) and maternal (decidua) cellular layers and has been validated to model physiological and pathological states of pregnancy (i.e., ascending infection, systemic oxidative stress, and maternal toxicant exposure). This platform is fully compatible with various analytical methods such as microscopy and biochemical analysis. This protocol will outline this device's fabrication, cell loading, and utility to model ascending infection-related adverse pregnancy outcomes.


Subject(s)
Premature Birth , Infant, Newborn , Pregnancy , Female , Animals , Humans , Placenta/metabolism , Extraembryonic Membranes/metabolism , Cell Line , Technology
11.
BMC Bioinformatics ; 25(1): 128, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38528492

ABSTRACT

BACKGROUND: Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect for ensuring not only the accuracy but also the efficiency of the analytical process. This is particularly useful in scenarios involving large data volumes, such as those generated by the ChIP-seq protocol. Against this backdrop, we introduce BIOMAPP::CHIP, a tool specifically designed to optimize the discovery of biological motifs in large data volumes. RESULTS: We conducted a comprehensive set of comparative tests with state-of-the-art algorithms. Our analyses revealed that BIOMAPP::CHIP outperforms existing approaches in various metrics, excelling both in terms of performance and accuracy. The tests demonstrated a higher detection rate of significant motifs and also greater agility in the execution of the algorithm. Furthermore, the SMT component played a vital role in the system's efficiency, proving to be both agile and accurate in kmer counting, which in turn improved the overall efficacy of our tool. CONCLUSION: BIOMAPP::CHIP represent real advancements in the discovery of biological motifs, particularly in large data volume scenarios, offering a relevant alternative for the analysis of ChIP-seq data and have the potential to boost future research in the field. This software can be found at the following address: (https://github.com/jadermcg/biomapp-chip).


Subject(s)
Algorithms , Software , Sequence Analysis, DNA/methods , Chromatin Immunoprecipitation/methods , Binding Sites , Nucleotide Motifs
12.
Orthod Craniofac Res ; 2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38372469

ABSTRACT

OBJECTIVE: To evaluate the efficacy of microchips and 3D microsensors in the measurement of orthodontic forces. METHODS: Through September 2023, comprehensive searches were conducted on PubMed/MEDLINE, SCOPUS and SCIELO without restrictions. RESULTS: After removing duplicate entries and applying the eligibility criteria, 23 studies were included for analysis. All the studies were conducted in vitro, and slightly more than half of them were centred on evaluating orthodontic forces exerted by aligners. Eight utilized microchips as measurement tools, while the remaining studies made use of 3D microsensors for their assessments. In the context of fixed appliances, key findings included a high level of agreement in 3-dimensional orthodontic force detection between simulation results and actual applied forces. Incorporating critical force-moment combinations during smart bracket calibration reduced measurement errors for most components. Translational tooth movement revealed a moment-to-force ratio, aligning with the bracket's centre of resistance. The primary findings in relation to aligners revealed several significant factors affecting the forces exerted by them. Notably, the foil thickness and staging were found to have a considerable impact on these forces, with optimal force transmission occurring at a layer height of 150 µm. Furthermore, the type of material used in 3D-printing aligners influenced the force levels, with attachments proving effective in generating extrusive forces. Deliberate adjustments in aligner thickness were observed to alter the forces and moments generated. CONCLUSIONS: Microchips and 3D sensors provide precise and quantitative measurements of orthodontic forces in in vitro studies, enabling accurate monitoring and control of tooth movement.

13.
Biofabrication ; 16(2)2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38408383

ABSTRACT

'On-a-chip' technology advances the development of physiologically relevant organ-mimicking architecture by integrating human cells into three-dimensional microfluidic devices. This method also establishes discrete functional units, faciliting focused research on specific organ components. In this study, we detail the development and assessment of a convoluted renal proximal tubule-on-a-chip (PT-on-a-chip). This platform involves co-culturing Renal Proximal Tubule Epithelial Cells (RPTEC) and Human Umbilical Vein Endothelial Cells (HUVEC) within a polydimethylsiloxane microfluidic device, crafted through a combination of 3D printing and molding techniques. Our PT-on-a-chip significantly reduced high glucose level, exhibited albumin uptake, and simulated tubulopathy induced by amphotericin B. Remarkably, the RPTEC:HUVEC co-culture exhibited efficient cell adhesion within 30 min on microchannels functionalized with plasma, 3-aminopropyltriethoxysilane, and type-I collagen. This approach significantly reduced the required incubation time for medium perfusion. In comparison, alternative methods such as plasma and plasma plus polyvinyl alcohol were only effective in promoting cell attachment to flat surfaces. The PT-on-a-chip holds great promise as a valuable tool for assessing the nephrotoxic potential of new drug candidates, enhancing our understanding of drug interactions with co-cultured renal cells, and reducing the need for animal experimentation, promoting the safe and ethical development of new pharmaceuticals.


Subject(s)
Epithelial Cells , Kidney Tubules, Proximal , Animals , Humans , Human Umbilical Vein Endothelial Cells , Coculture Techniques , Kidney Tubules, Proximal/metabolism , Lab-On-A-Chip Devices
14.
Electrophoresis ; 45(1-2): 69-100, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37259641

ABSTRACT

Proteins are important molecules involved in an immensely large number of biological processes. Being capable of manipulating proteins is critical for developing reliable and affordable techniques to analyze and/or detect them. Such techniques would enable the production of therapeutic agents for the treatment of diseases or other biotechnological applications (e.g., bioreactors or biocatalysis). Microfluidic technology represents a potential solution to protein manipulation challenges because of the diverse phenomena that can be exploited to achieve micro- and nanoparticle manipulation. In this review, we discuss recent contributions made in the field of protein manipulation in microfluidic systems using different physicochemical principles and techniques, some of which are miniaturized versions of already established macro-scale techniques.


Subject(s)
Microfluidic Analytical Techniques , Nanoparticles , Microfluidics/methods , Microfluidic Analytical Techniques/methods , Nanoparticles/chemistry , Lab-On-A-Chip Devices
16.
HardwareX ; 16: e00493, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38045919

ABSTRACT

Although microparticles are frequently used in chemistry and biology, their effectiveness largely depends on the homogeneity of their particle size distribution. Microfluidic devices to separate and purify particles based on their size have been developed, but many require expensive cleanroom manufacturing processes. A cost-effective, passive microfluidic separator is presented, capable of efficiently sorting and purifying particles spanning the size range of 15 µm to 40 µm. Fabricated from Polymethyl Methacrylate (PMMA) substrates using laser ablation, this device circumvents the need for cleanroom facilities. Prior to fabrication, rigorous optimization of the device's design was carried out through computational simulations conducted in COMSOL Multiphysics. To gauge its performance, chitosan microparticles were employed as a test case. The results were notably promising, achieving a precision of 96.14 %. This quantitative metric underscores the device's precision and effectiveness in size-based particle separation. This low-cost and accessible microfluidic separator offers a pragmatic solution for laboratories and researchers seeking precise control over particle sizes, without the constraints of expensive manufacturing environments. This innovation not only mitigates the limitations tied to traditional cleanroom-based fabrication but also widens the horizons for various applications within the realms of chemistry and biology.

17.
Dent J (Basel) ; 11(11)2023 Oct 24.
Article in English | MEDLINE | ID: mdl-37999009

ABSTRACT

Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, collectively recognized as periodontopathogens within the red complex, have been extensively studied in clinical samples collected from individuals with periodontitis. A lab-on-a-chip (LOC) is a miniature mechanism that integrates various laboratory operations onto a single microchip or a small-scale platform. This systematic review evaluates the application of LOC technology in identifying microorganisms from the red complex. This study adhered to PRISMA recommendations, and the review process encompassed several databases. In the electronic search, a total of 58 reports were found, and ultimately, 10 studies were considered relevant for inclusion. All these studies described effective, rapid, and reliable LOC systems for detecting and amplifying P. gingivalis, T. forsythia, and T. denticola. Compared to traditional methods, the LOC approach demonstrated minimal reagent requirements. Additionally, the results indicated that the amplification process took approximately 2 to 8 min, while detection could be completed in as little as 2 min and 40 s, resulting in a total experimental duration of around 11 min. Integrating miniaturization, speed, accuracy, and automation within microchip platforms makes them promising tools for detecting and amplifying microorganisms associated with the red complex in periodontal diseases.

18.
Int J Mol Sci ; 24(22)2023 Nov 08.
Article in English | MEDLINE | ID: mdl-38003288

ABSTRACT

We describe a strategy for the development of a rational approach of neoplastic disease therapy based on the demonstration that scale-free networks are susceptible to specific attacks directed against its connective hubs. This strategy involves the (i) selection of up-regulated hubs of connectivity in the tumors interactome, (ii) drug repurposing of these hubs, (iii) RNA silencing of non-druggable hubs, (iv) in vitro hub validation, (v) tumor-on-a-chip, (vi) in vivo validation, and (vii) clinical trial. Hubs are protein targets that are assessed as targets for rational therapy of cancer in the context of personalized oncology. We confirmed the existence of a negative correlation between malignant cell aggressivity and the target number needed for specific drugs or RNA interference (RNAi) to maximize the benefit to the patient's overall survival. Interestingly, we found that some additional proteins not generally targeted by drug treatments might justify the addition of inhibitors designed against them in order to improve therapeutic outcomes. However, many proteins are not druggable, or the available pharmacopeia for these targets is limited, which justifies a therapy based on encapsulated RNAi.


Subject(s)
Neoplasms , Protein Interaction Mapping , Humans , Neoplasms/drug therapy , Neoplasms/genetics
19.
PeerJ ; 11: e16347, 2023.
Article in English | MEDLINE | ID: mdl-37941933

ABSTRACT

Background: The psyllid, Bactericera cockerelli, is an insect vector of 'Candidatus Liberibacter' causing "Zebra chip" disease that affects potato and other Solanaceae crops worldwide. In the present study, we analyzed the bacterial communities associated with the insect vector Bactericera cockerelli central haplotype of tomato crop fields in four regions from Mexico. Methods: PCR was used to amplify the mitochondrial cytochrome oxidase I gene (mtCOI) and then analyze the single nucleotide polymorphisms (SNP) and phylogenetic analysis for haplotype identification of the isolated B. cockerelli. Moreover, we carried out the microbial diversity analysis of several B. cockerelli collected from four regions of Mexico through the NGS sequencing of 16S rRNA V3 region. Finally, Wolbachia was detected by the wsp gene PCR amplification, which is the B. cockerelli facultative symbiont. Also we were able to confirm the relationship with several Wolbachia strains by phylogenetic analysis. Results: Our results pointed that B. cockerelli collected in the four locations from Mexico (Central Mexico: Queretaro, and Northern Mexico: Sinaloa, Coahuila, and Nuevo Leon) were identified, such as the central haplotype. Analyses of the parameters of the composition, relative abundance, and diversity (Shannon index: 1.328 ± 0.472; Simpson index 0.582 ± 0.167), showing a notably relatively few microbial species in B. cockerelli. Analyses identified various facultative symbionts, particularly the Wolbachia (Rickettsiales: Anaplasmataceae) with a relative abundance higher. In contrast, the genera of Sodalis and 'Candidatus Carsonella' (Gammaproteobacteria: Oceanospirillales: Halomonadaceae) were identified with a relatively low abundance. On the other hand, the relative abundance for the genus 'Candidatus Liberibacter' was higher only for some of the locations analyzed. PCR amplification of a fragment of the gene encoding a surface protein (wsp) of Wolbachia and phylogenetic analysis corroborated the presence of this bacterium in the central haplotype. Beta-diversity analysis revealed that the presence of the genus 'Candidatus Liberibacter' influences the microbiota structure of this psyllid species. Conclusions: Our data support that the members with the highest representation in microbial community of B. cockerelli central haplotype, comprise their obligate symbiont, Carsonella, and facultative symbionts. We also found evidence that among the factors analyzed, the presence of the plant pathogen affects the structure and composition of the bacterial community associated with B. cockerelli.


Subject(s)
Hemiptera , Solanum lycopersicum , Animals , Haplotypes , RNA, Ribosomal, 16S/genetics , Hemiptera/genetics , Phylogeny , Mexico , Bacteria/genetics , Liberibacter/genetics , Crops, Agricultural/genetics
20.
Medicina (Kaunas) ; 59(10)2023 Sep 26.
Article in English | MEDLINE | ID: mdl-37893437

ABSTRACT

Background and Objectives: Staphylococcus aureus is a prevalent bacterium capable of inducing various infections, including skin and soft tissue infections, bloodstream infections, pneumonia, and surgical site infections. The emergence of antimicrobial resistance in S. aureus, particularly methicillin-resistant S. aureus, has raised substantial concerns within global healthcare settings. Prior to antibiotic prescription, the ideal approach is antimicrobial susceptibility testing (AST); however, this is frequently perceived as excessively complex and time-intensive. Lab-on-a-chip (LOC) technology holds promise in addressing these challenges and advancing fundamental microbiological research while also aiding in the development of therapeutic strategies. This systematic review aims to evaluate the potential utility of LOC for AST of S. aureus. Materials and Methods: This study adhered to the PRISMA guidelines. Various databases, including SCOPUS, PubMed/MEDLINE, SCIELO, and LILACS, in addition to gray literature sources, were employed in the review process. Results: Sixteen studies were included in this systematic review. All these studies detailed the effectiveness, rapidity, and predictability of LOC systems for assessing S. aureus susceptibility to various antibiotics. When comparing the LOC approach to traditional manual methods, it was evident that LOC requires a minimal quantity of reagents. Furthermore, most studies reported that the entire LOC procedure took 10 min to 7 h, with results being equally accurate as those obtained through traditional AST protocols. Conclusions: The potential application of LOC for AST of S. aureus is emphasized by its ability to provide rapid access to minimum inhibitory concentration data, which can substantially aid in selecting the most suitable antibiotics and dosages for treating challenging infections caused by this microorganism. Moreover, the rapid AST facilitated by LOC holds promise for enhancing the appropriateness and efficacy of therapy in clinical settings.


Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Humans , Staphylococcus aureus , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Staphylococcal Infections/drug therapy , Lab-On-A-Chip Devices
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