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1.
Cell ; 165(5): 1238-1254, 2016 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-27118425

RESUMO

Cerebral organoids, three-dimensional cultures that model organogenesis, provide a new platform to investigate human brain development. High cost, variability, and tissue heterogeneity limit their broad applications. Here, we developed a miniaturized spinning bioreactor (SpinΩ) to generate forebrain-specific organoids from human iPSCs. These organoids recapitulate key features of human cortical development, including progenitor zone organization, neurogenesis, gene expression, and, notably, a distinct human-specific outer radial glia cell layer. We also developed protocols for midbrain and hypothalamic organoids. Finally, we employed the forebrain organoid platform to model Zika virus (ZIKV) exposure. Quantitative analyses revealed preferential, productive infection of neural progenitors with either African or Asian ZIKV strains. ZIKV infection leads to increased cell death and reduced proliferation, resulting in decreased neuronal cell-layer volume resembling microcephaly. Together, our brain-region-specific organoids and SpinΩ provide an accessible and versatile platform for modeling human brain development and disease and for compound testing, including potential ZIKV antiviral drugs.


Assuntos
Encéfalo/citologia , Técnicas de Cultura de Células , Modelos Biológicos , Organoides , Zika virus/fisiologia , Reatores Biológicos , Técnicas de Cultura de Células/economia , Embrião de Mamíferos , Desenvolvimento Embrionário , Humanos , Células-Tronco Pluripotentes Induzidas , Neurogênese , Neurônios/citologia , Organoides/virologia , Infecção por Zika virus/fisiopatologia , Infecção por Zika virus/virologia
2.
Brief Bioinform ; 25(6)2024 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-39397425

RESUMO

Metabolite profiling is a powerful approach for the clinical diagnosis of complex diseases, ranging from cardiometabolic diseases, cancer, and cognitive disorders to respiratory pathologies and conditions that involve dysregulated metabolism. Because of the importance of systems-level interpretation, many methods have been developed to identify biologically significant pathways using metabolomics data. In this review, we first describe a complete metabolomics workflow (sample preparation, data acquisition, pre-processing, downstream analysis, etc.). We then comprehensively review 24 approaches capable of performing functional analysis, including those that combine metabolomics data with other types of data to investigate the disease-relevant changes at multiple omics layers. We discuss their availability, implementation, capability for pre-processing and quality control, supported omics types, embedded databases, pathway analysis methodologies, and integration techniques. We also provide a rating and evaluation of each software, focusing on their key technique, software accessibility, documentation, and user-friendliness. Following our guideline, life scientists can easily choose a suitable method depending on method rating, available data, input format, and method category. More importantly, we highlight outstanding challenges and potential solutions that need to be addressed by future research. To further assist users in executing the reviewed methods, we provide wrappers of the software packages at https://github.com/tinnlab/metabolite-pathway-review-docker.


Assuntos
Metabolômica , Software , Metabolômica/métodos , Humanos , Metaboloma , Biologia Computacional/métodos , Bases de Dados Factuais
3.
Brief Bioinform ; 25(Supplement_1)2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-39041916

RESUMO

This manuscript describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' (https://github.com/NIGMS/NIGMS-Sandbox). The module delivers learning materials on Cloud-based Consensus Pathway Analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Pathway analysis is important because it allows us to gain insights into biological mechanisms underlying conditions. But the availability of many pathway analysis methods, the requirement of coding skills, and the focus of current tools on only a few species all make it very difficult for biomedical researchers to self-learn and perform pathway analysis efficiently. Furthermore, there is a lack of tools that allow researchers to compare analysis results obtained from different experiments and different analysis methods to find consensus results. To address these challenges, we have designed a cloud-based, self-learning module that provides consensus results among established, state-of-the-art pathway analysis techniques to provide students and researchers with necessary training and example materials. The training module consists of five Jupyter Notebooks that provide complete tutorials for the following tasks: (i) process expression data, (ii) perform differential analysis, visualize and compare the results obtained from four differential analysis methods (limma, t-test, edgeR, DESeq2), (iii) process three pathway databases (GO, KEGG and Reactome), (iv) perform pathway analysis using eight methods (ORA, CAMERA, KS test, Wilcoxon test, FGSEA, GSA, SAFE and PADOG) and (v) combine results of multiple analyses. We also provide examples, source code, explanations and instructional videos for trainees to complete each Jupyter Notebook. The module supports the analysis for many model (e.g. human, mouse, fruit fly, zebra fish) and non-model species. The module is publicly available at https://github.com/NIGMS/Consensus-Pathway-Analysis-in-the-Cloud. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.


Assuntos
Computação em Nuvem , Software , Humanos , Biologia Computacional/métodos , Biologia Computacional/educação , Animais , Ontologia Genética
4.
Nucleic Acids Res ; 52(9): 4761-4783, 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38619038

RESUMO

Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).


Assuntos
Análise de Célula Única , Software , Análise de Célula Única/métodos , Humanos , Análise de Sequência de RNA/métodos , Animais , RNA-Seq/métodos , Benchmarking , Algoritmos , Perfilação da Expressão Gênica/métodos
5.
PLoS Genet ; 19(5): e1010753, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-37216404

RESUMO

Males have finite resources to spend on reproduction. Thus, males rely on a 'time investment strategy' to maximize their reproductive success. For example, male Drosophila melanogaster extends their mating duration when surrounded by conditions enriched with rivals. Here we report a different form of behavioral plasticity whereby male fruit flies exhibit a shortened duration of mating when they are sexually experienced; we refer to this plasticity as 'shorter-mating-duration (SMD)'. SMD is a plastic behavior and requires sexually dimorphic taste neurons. We identified several neurons in the male foreleg and midleg that express specific sugar and pheromone receptors. Using a cost-benefit model and behavioral experiments, we further show that SMD behavior exhibits adaptive behavioral plasticity in male flies. Thus, our study delineates the molecular and cellular basis of the sensory inputs required for SMD; this represents a plastic interval timing behavior that could serve as a model system to study how multisensory inputs converge to modify interval timing behavior for improved adaptation.


Assuntos
Drosophila melanogaster , Feromônios , Animais , Masculino , Drosophila melanogaster/genética , Paladar , Comportamento Sexual Animal/fisiologia , Reprodução , Drosophila
6.
J Biol Chem ; 300(10): 107743, 2024 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-39222680

RESUMO

Translation initiation is a highly regulated, multi-step process that is critical for efficient and accurate protein synthesis. In bacteria, initiation begins when mRNA, initiation factors, and a dedicated initiator fMet-tRNAfMet bind the small (30S) ribosomal subunit. Specific binding of fMet-tRNAfMet in the peptidyl (P) site is mediated by the inspection of the fMet moiety by initiation factor IF2 and of three conserved G-C base pairs in the tRNA anticodon stem by the 30S head domain. Tandem A-minor interactions form between 16S ribosomal RNA nucleotides A1339 and G1338 and tRNA base pairs G30-C40 and G29-C41, respectively. Swapping the G30-C40 pair of tRNAfMet with C-G (called tRNAfMet M1) reduces discrimination against the noncanonical start codon CUG in vitro, suggesting crosstalk between the gripping of the anticodon stem and recognition of the start codon. Here, we solved electron cryomicroscopy structures of Escherichia coli 70S initiation complexes containing the fMet-tRNAfMet M1 variant paired to the noncanonical CUG start codon, in the presence or absence of IF2 and the non-hydrolyzable GTP analog GDPCP, alongside structures of 70S initiation complexes containing this tRNAfMet variant paired to the canonical bacterial start codons AUG, GUG, and UUG. We find that the M1 mutation weakens A-minor interactions between tRNAfMet and 16S nucleotides A1339 and G1338, with IF2 strengthening the interaction of G1338 with the tRNA minor groove. These structures suggest how even slight changes to the recognition of the fMet-tRNAfMet anticodon stem by the ribosome can impact the start codon selection.

7.
Hum Mol Genet ; 32(2): 276-289, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-35972810

RESUMO

Somatic activating Kirsten rat sarcoma viral oncogene homologue (KRAS) mutations have been reported in patients with arteriovenous malformations. By producing LSL-Kras (G12D); Cdh5 (PAC)-CreERT2 [iEC-Kras (G12D*)] mice, we hoped to activate KRAS within vascular endothelial cells (ECs) to generate an arteriovenous malformation mouse model. Neonatal mice were treated daily with tamoxifen from postnatal (PN) days 1-3. Mortality and phenotypes varied amongst iEC-Kras (G12D*) pups, with only 31.5% surviving at PN14. Phenotypes (focal lesions, vessel dilations) developed in a consistent manner, although with unpredictable severity within multiple soft tissues (such as the brain, liver, heart and brain). Overall, iEC-Kras (G12D*) pups developed significantly larger vascular lumen areas compared with control littermates, beginning at PN8. We subsequently tested whether the MEK inhibitor trametinib could effectively alleviate lesion progression. At PN16, iEC-Kras (G12D*) pup survival improved to 76.9%, and average vessel sizes were closer to controls than in untreated and vehicle-treated mutants. In addition, trametinib treatment helped normalize iEC-Kras (G12D*) vessel morphology in PN14 brains. Thus, trametinib could act as an effective therapy for KRAS-induced vascular malformations in patients.


Assuntos
Neoplasias Pancreáticas , Proteínas Proto-Oncogênicas p21(ras) , Camundongos , Animais , Proteínas Proto-Oncogênicas p21(ras)/genética , Neoplasias Pancreáticas/genética , Células Endoteliais/patologia , Modelos Animais de Doenças , Mutação
8.
Bioinformatics ; 40(3)2024 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-38444086

RESUMO

MOTIVATION: KaMRaT is designed for processing large k-mer count tables derived from multi-sample, RNA-seq data. Its primary objective is to identify condition-specific or differentially expressed sequences, regardless of gene or transcript annotation. RESULTS: KaMRaT is implemented in C++. Major functions include scoring k-mers based on count statistics, merging overlapping k-mers into contigs and selecting k-mers based on their occurrence across specific samples. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are available via https://github.com/Transipedia/KaMRaT.


Assuntos
Algoritmos , Software , Análise de Sequência de DNA/métodos , RNA-Seq , Documentação
9.
Proc Natl Acad Sci U S A ; 119(14): e2120352119, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35357969

RESUMO

Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2'-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.


Assuntos
Proteínas de Bactérias , Metiltransferases , Mycobacterium tuberculosis , Subunidades Ribossômicas Maiores de Bactérias , Proteínas de Bactérias/química , Domínio Catalítico , Farmacorresistência Bacteriana/genética , Metiltransferases/química , Mycobacterium tuberculosis/enzimologia , Mycobacterium tuberculosis/genética , Conformação Proteica em alfa-Hélice , RNA Ribossômico 16S/química , RNA Ribossômico 23S/química , Subunidades Ribossômicas Maiores de Bactérias/química
10.
Nano Lett ; 24(38): 11839-11846, 2024 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-39268715

RESUMO

Exciton-polaritons, hybrid light-matter excitations arising from the strong coupling between excitons in semiconductors and photons in photonic nanostructures, are crucial for exploring the physics of quantum fluids of light and developing all-optical devices. Achieving room temperature propagation of polaritons with a large excitonic fraction is challenging but vital, e.g., for nonlinear light transport. We report on room temperature propagation of exciton-polaritons in a metasurface made from a subwavelength lattice of perovskite pillars. The large Rabi splitting, much greater than the optical phonon energy, decouples the lower polariton band from the phonon bath of the perovskite. These cooled polaritons, in combination with the high group velocity achieved through the metasurface design, enable long-range propagation, exceeding hundreds of micrometers even with an 80% excitonic component. Furthermore, the design of the metasurface introduces an original mechanism for unidirectional propagation through polarization control, suggesting a new avenue for the development of advanced polaritonic devices.

11.
Biophys J ; 123(13): 1896-1902, 2024 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-38850024

RESUMO

The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the ordering of hydrocarbon chains and the packing of lipids. Many eukaryotes synthesize sterols, which are uniquely capable of modulating the lipid order to decouple membrane stability from fluidity. Ancient sterol analogs known as hopanoids are found in many bacteria and proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. In this work, simulations, monolayer experiments, and cellular assays show that hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid acyl chain. We find that cholesterol and diplopterol's methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterol's constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest that cholesterol's broader lipid-ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.


Assuntos
Fosfolipídeos , Esteróis , Esteróis/química , Esteróis/metabolismo , Fosfolipídeos/química , Fosfolipídeos/metabolismo , Triterpenos/química , Triterpenos/metabolismo , Colesterol/química , Colesterol/metabolismo
12.
BMC Bioinformatics ; 25(1): 31, 2024 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-38233808

RESUMO

Analyzing the interactions of circular RNAs (circRNAs) is a crucial step in understanding their functional impacts. While there are numerous visualization tools available for investigating circRNA interaction networks, these tools are typically limited to known circRNAs from specific databases. Moreover, these existing tools usually require complex installation procedures which can be time-consuming and challenging for users. There is a lack of a user-friendly web application that facilitates interactive exploration and visualization of circRNA interaction networks. CircNetVis is an interactive online web application to enhance the analysis of human/mouse circRNA interactions. The tool allows three different input formats of circRNAs including circRNA IDs from CircBase, circRNA coordinates (chromosome, start position, end position), and circRNA sequences in the FASTA format. It integrates multiple interaction networks for visualization and investigation of the interplay between circRNA, microRNAs, mRNAs and RNA binding proteins. CircNetVis also enables users to interactively explore the interactions of unknown circRNAs which are not reported from previous databases. The tool can generate interactive plots and allows users to save results as output files for offline usage. CircNetVis is implemented as a web application using R-shiny and freely available for academic use at https://www.meb.ki.se/shiny/truvu/CircNetVis/ .


Assuntos
MicroRNAs , RNA Circular , Humanos , Camundongos , Animais , MicroRNAs/genética , MicroRNAs/metabolismo , RNA Mensageiro/genética , Software , Bases de Dados Factuais , Redes Reguladoras de Genes
13.
J Biol Chem ; 299(4): 104608, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36924943

RESUMO

Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein-coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and, from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNALys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.


Assuntos
Anticódon , Códon , RNA Ribossômico , Ribossomos , Anticódon/química , Anticódon/genética , Anticódon/metabolismo , Códon/química , Códon/genética , Códon/metabolismo , Conformação de Ácido Nucleico , Nucleotídeos/química , Nucleotídeos/metabolismo , Biossíntese de Proteínas , Ribossomos/química , Ribossomos/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , RNA de Transferência/química , RNA de Transferência/metabolismo , Pareamento Incorreto de Bases , Modelos Moleculares , RNA Ribossômico/química , RNA Ribossômico/metabolismo
14.
J Am Chem Soc ; 146(3): 2160-2166, 2024 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-38211338

RESUMO

We synthesized two isoreticular furan-based metal-organic frameworks (MOFs), MOF-LA2-1(furan) and MOF-LA2-2(furan) with rod-like secondary building units (SBUs) featuring 1D channels, as sorbents for atmospheric water harvesting (LA = long arm). These aluminum-based MOFs demonstrated a combination of high water uptake and stability, exhibiting working capacities of 0.41 and 0.48 gwater/gMOF (under isobaric conditions of 1.70 kPa), respectively. Remarkably, both MOFs showed a negligible loss in water uptake after 165 adsorption-desorption cycles. These working capacities rival that of MOF-LA2-1(pyrazole), which has a working capacity of 0.55 gwater/gMOF. The current MOFs stand out for their high water stability, as evidenced by 165 cycles of water uptake and release. MOF-LA2-2(furan) is the first aluminum MOF to employ a double 'long arm' extension strategy, which is confirmed through single-crystal X-ray diffraction (SCXRD). The MOFs were synthesized by using a straightforward synthesis route. This study offers valuable insights into the design of durable, water-stable MOFs and underscores their potential for efficient water harvesting.

15.
Breast Cancer Res ; 26(1): 81, 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38778365

RESUMO

BACKGROUND: The proportion of patients with breast cancer and obesity is increasing. While the therapeutic landscape of breast cancer has been expanding, we lack knowledge about the potential differential efficacy of most drugs according to the body mass index (BMI). Here, we conducted a systematic review on recent clinical drug trials to document the dosing regimen of recent drugs, the reporting of BMI and the possible exclusion of patients according to BMI, other adiposity measurements and/or diabetes (leading comorbidity of obesity). We further explored whether treatment efficacy was evaluated according to BMI. METHODS: A search of Pubmed and ClinicalTrials.gov was performed to identify phase I-IV trials investigating novel systemic breast cancer treatments. Dosing regimens and exclusion based on BMI, adiposity measurements or diabetes, documentation of BMI and subgroup analyses according to BMI were assessed. RESULTS: 495 trials evaluating 26 different drugs were included. Most of the drugs (21/26, 81%) were given in a fixed dose independent of patient weight. BMI was an exclusion criterion in 3 out of 495 trials. Patients with diabetes, the leading comorbidity of obesity, were excluded in 67/495 trials (13.5%). Distribution of patients according to BMI was mentioned in 8% of the manuscripts, subgroup analysis was performed in 2 trials. No other measures of adiposity/body composition were mentioned in any of the trials. Retrospective analyses on the impact of BMI were performed in 6 trials. CONCLUSIONS: Patient adiposity is hardly considered as most novel drug treatments are given in a fixed dose. BMI is generally not reported in recent trials and few secondary analyses are performed. Given the prevalence of patients with obesity and the impact obesity can have on pharmacokinetics and cancer biology, more attention should be given by investigators and study sponsors to reporting patient's BMI and evaluating its impact on treatment efficacy and toxicity.


Assuntos
Índice de Massa Corporal , Neoplasias da Mama , Ensaios Clínicos como Assunto , Obesidade , Humanos , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/epidemiologia , Feminino , Obesidade/complicações , Obesidade/epidemiologia , Antineoplásicos/uso terapêutico , Resultado do Tratamento
16.
Emerg Infect Dis ; 30(7): 1410-1415, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38916572

RESUMO

Since May 2023, a novel combination of neuraminidase mutations, I223V + S247N, has been detected in influenza A(H1N1)pdm09 viruses collected in countries spanning 5 continents, mostly in Europe (67/101). The viruses belong to 2 phylogenetically distinct groups and display ≈13-fold reduced inhibition by oseltamivir while retaining normal susceptibility to other antiviral drugs.


Assuntos
Antivirais , Farmacorresistência Viral , Vírus da Influenza A Subtipo H1N1 , Influenza Humana , Neuraminidase , Oseltamivir , Filogenia , Oseltamivir/farmacologia , Oseltamivir/uso terapêutico , Vírus da Influenza A Subtipo H1N1/efeitos dos fármacos , Vírus da Influenza A Subtipo H1N1/genética , Humanos , Antivirais/farmacologia , Antivirais/uso terapêutico , Influenza Humana/virologia , Influenza Humana/tratamento farmacológico , Influenza Humana/epidemiologia , Neuraminidase/antagonistas & inibidores , Neuraminidase/genética , Farmacorresistência Viral/genética , Mutação
17.
Emerg Infect Dis ; 30(11): 2303-2312, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39378870

RESUMO

Since 2013, a total of 167 human infections with swine-origin (variant) influenza A viruses of A(H1N1)v, A(H1N2)v, and A(H3N2)v subtypes have been reported in the United States. Analysis of 147 genome sequences revealed that nearly all had S31N substitution, an M2 channel blocker-resistance marker, whereas neuraminidase inhibitor-resistance markers were not found. Two viruses had a polymerase acidic substitution (I38M or E199G) associated with decreased susceptibility to baloxavir, an inhibitor of viral cap-dependent endonuclease (CEN). Using phenotypic assays, we established subtype-specific susceptibility baselines for neuraminidase and CEN inhibitors. When compared with either baseline or CEN-sequence-matched controls, only the I38M substitution decreased baloxavir susceptibility, by 27-fold. Human monoclonal antibodies FI6v3 and CR9114 targeting the hemagglutinin's stem showed variable (0.03 to >10 µg/mL) neutralizing activity toward variant viruses, even within the same clade. Methodology and interpretation of laboratory data described in this study provide information for risk assessment and decision-making on therapeutic control measures.


Assuntos
Antivirais , Farmacorresistência Viral , Influenza Humana , Humanos , Antivirais/farmacologia , Antivirais/uso terapêutico , Influenza Humana/virologia , Influenza Humana/epidemiologia , Influenza Humana/tratamento farmacológico , Farmacorresistência Viral/genética , Estados Unidos/epidemiologia , Animais , Suínos , Vírus da Influenza A Subtipo H1N1/efeitos dos fármacos , Vírus da Influenza A Subtipo H1N1/genética , Dibenzotiepinas , Morfolinas/farmacologia , Vírus da Influenza A/efeitos dos fármacos , Vírus da Influenza A/genética , Vírus da Influenza A Subtipo H3N2/efeitos dos fármacos , Vírus da Influenza A Subtipo H3N2/genética , Piridonas/farmacologia , Triazinas/farmacologia , Vírus da Influenza A Subtipo H1N2/genética , Vírus da Influenza A Subtipo H1N2/efeitos dos fármacos
18.
Brief Bioinform ; 23(6)2022 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-36252928

RESUMO

Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method's practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.


Assuntos
Genômica , Proteômica , Genômica/métodos , Transcriptoma , Biomarcadores
19.
Ann Surg Oncol ; 31(9): 5804-5814, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38851638

RESUMO

BACKGROUND: This study aimed to compare the benefits and safety of microwave scissors-based sutureless laparoscopic partial nephrectomy (MSLPN) with those of conventional open partial nephrectomy (cOPN). METHODS: Each kidney in nine pigs underwent MSLPN using microwave scissors (MWS) via transperitoneal laparoscopy or cOPN via retroperitoneal open laparotomy. The kidney's lower and upper poles were resected under temporary hilar-clamping. The renal calyces exposed during renal resections were sealed and transected using MWS in MSLPN and were sutured in cOPN. For MWS, the generator's power output was 60 W. Data on procedure time (PT), ischemic time (IT), blood loss (BL), normal nephron loss (NNL), and extravasation during retrograde pyelogram were compared between the two techniques. RESULTS: The authors successfully performed 22 MSLPNs and 10 cOPNs. Compared with cOPN, MSLPN was associated with significantly lower PT (median, 9.2 vs 13.0 min; p = 0.026), IT (median, 5.9 vs 9.0 min; p < 0.001), BL (median, 14.4 vs 38.3 mL; p = 0.043), and NNL (median, 7.6 vs 9.4 mm; p = 0.004). However, the extravasation rate was higher in the MSLPN group than in the cOPN group (54.5 % [n = 12] vs 30.0 % [n = 3]), albeit without a significant difference (p = 0.265). Pelvic stenosis occurred in one MSLPN procedure that involved deep lower pole resection near the kidney hilum. CONCLUSIONS: The study data show that MSLPN can improve intraoperative outcomes while reducing technical demands for selected patients with non-hilar-localized renal tumors. However, renal calyces, if violated, should be additionally sutured to prevent urine leakage.


Assuntos
Laparoscopia , Micro-Ondas , Nefrectomia , Animais , Nefrectomia/métodos , Laparoscopia/métodos , Suínos , Micro-Ondas/uso terapêutico , Complicações Pós-Operatórias/etiologia , Neoplasias Renais/cirurgia , Neoplasias Renais/patologia , Duração da Cirurgia , Feminino , Instrumentos Cirúrgicos
20.
Chem Senses ; 492024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-38877790

RESUMO

SCENTinel, a rapid smell test designed to screen for olfactory disorders, including anosmia (no ability to smell an odor) and parosmia (distorted sense of smell), measures 4 components of olfactory function: detection, intensity, identification, and pleasantness. Each test card contains one of 9 odorant mixtures. Some people born with genetic insensitivities to specific odorants (i.e. specific anosmia) may fail the test if they cannot smell an odorant but otherwise have a normal sense of smell. However, using odorant mixtures has largely been found to prevent this from happening. To better understand whether genetic differences affect SCENTinel test results, we asked genetically informative adult participants (twins or triplets, N = 630; singletons, N = 370) to complete the SCENTinel test. A subset of twins (n = 304) also provided a saliva sample for genotyping. We examined data for differences between the 9 possible SCENTinel odors; effects of age, sex, and race on SCENTinel performance, test-retest variability; and heritability using both structured equation modeling and SNP-based statistical methods. None of these strategies provided evidence for specific anosmia for any of the odors, but ratings of pleasantness were, in part, genetically determined (h2 = 0.40) and were nominally associated with alleles of odorant receptors (e.g. OR2T33 and OR1G1; P < 0.001). These results provide evidence that using odorant mixtures protected against effects of specific anosmia for ratings of intensity but that ratings of pleasantness showed effects of inheritance, possibly informed by olfactory receptor genotypes.


Assuntos
Odorantes , Olfato , Humanos , Feminino , Masculino , Adulto , Odorantes/análise , Olfato/fisiologia , Pessoa de Meia-Idade , Transtornos do Olfato/diagnóstico , Transtornos do Olfato/genética , Adulto Jovem , Percepção Olfatória , Idoso , Genótipo , Anosmia/diagnóstico , Anosmia/genética
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