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1.
EMBO J ; 41(17): e109205, 2022 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-35880301

RESUMO

Patient-derived organoids and cellular spheroids recapitulate tissue physiology with remarkable fidelity. We investigated how engagement with a reconstituted basement membrane in three dimensions (3D) supports the polarized, stress resilient tissue phenotype of mammary epithelial spheroids. Cells interacting with reconstituted basement membrane in 3D had reduced levels of total and actin-associated filamin and decreased cortical actin tension that increased plasma membrane protrusions to promote negative plasma membrane curvature and plasma membrane protein associations linked to protein secretion. By contrast, cells engaging a reconstituted basement membrane in 2D had high cortical actin tension that forced filamin unfolding and endoplasmic reticulum (ER) associations. Enhanced filamin-ER interactions increased levels of PKR-like ER kinase effectors and ER-plasma membrane contact sites that compromised calcium homeostasis and diminished cell viability. Consequently, cells with decreased cortical actin tension had reduced ER stress and survived better. Consistently, cortical actin tension in cellular spheroids regulated polarized basement membrane membrane deposition and sensitivity to exogenous stress. The findings implicate cortical actin tension-mediated filamin unfolding in ER function and underscore the importance of tissue mechanics in organoid homeostasis.


Assuntos
Actinas , Retículo Endoplasmático , Actinas/metabolismo , Retículo Endoplasmático/metabolismo , Estresse do Retículo Endoplasmático , Células Epiteliais/metabolismo , Filaminas/metabolismo , Fenótipo
2.
Nature ; 579(7799): 427-432, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32132707

RESUMO

In mammalian cells, mitochondrial dysfunction triggers the integrated stress response, in which the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) results in the induction of the transcription factor ATF41-3. However, how mitochondrial stress is relayed to ATF4 is unknown. Here we show that HRI is the eIF2α kinase that is necessary and sufficient for this relay. In a genome-wide CRISPR interference screen, we identified factors upstream of HRI: OMA1, a mitochondrial stress-activated protease; and DELE1, a little-characterized protein that we found was associated with the inner mitochondrial membrane. Mitochondrial stress stimulates OMA1-dependent cleavage of DELE1 and leads to the accumulation of DELE1 in the cytosol, where it interacts with HRI and activates the eIF2α kinase activity of HRI. In addition, DELE1 is required for ATF4 translation downstream of eIF2α phosphorylation. Blockade of the OMA1-DELE1-HRI pathway triggers an alternative response in which specific molecular chaperones are induced. The OMA1-DELE1-HRI pathway therefore represents a potential therapeutic target that could enable fine-tuning of the integrated stress response for beneficial outcomes in diseases that involve mitochondrial dysfunction.


Assuntos
Citosol/metabolismo , Metaloendopeptidases/metabolismo , Mitocôndrias/metabolismo , Mitocôndrias/patologia , Proteínas Mitocondriais/metabolismo , Estresse Fisiológico , eIF-2 Quinase/metabolismo , Fator 4 Ativador da Transcrição/biossíntese , Fator 4 Ativador da Transcrição/metabolismo , Sistemas CRISPR-Cas , Linhagem Celular , Citosol/enzimologia , Ativação Enzimática , Fator de Iniciação 2 em Eucariotos/metabolismo , Humanos , Masculino , Proteínas Mitocondriais/química , Chaperonas Moleculares/metabolismo , Fosforilação , Ligação Proteica
3.
Nature ; 583(7818): 845-851, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32699415

RESUMO

Malignant transformation of cells typically involves several genetic lesions, whose combined activity gives rise to cancer1. Here we analyse 1,148 patient-derived B-cell leukaemia (B-ALL) samples, and find that individual mutations do not promote leukaemogenesis unless they converge on one single oncogenic pathway that is characteristic of the differentiation stage of transformed B cells. Mutations that are not aligned with this central oncogenic driver activate divergent pathways and subvert transformation. Oncogenic lesions in B-ALL frequently mimic signalling through cytokine receptors at the pro-B-cell stage (via activation of the signal-transduction protein STAT5)2-4 or pre-B-cell receptors in more mature cells (via activation of the protein kinase ERK)5-8. STAT5- and ERK-activating lesions are found frequently, but occur together in only around 3% of cases (P = 2.2 × 10-16). Single-cell mutation and phospho-protein analyses reveal the segregation of oncogenic STAT5 and ERK activation to competing clones. STAT5 and ERK engage opposing biochemical and transcriptional programs that are orchestrated by the transcription factors MYC and BCL6, respectively. Genetic reactivation of the divergent (suppressed) pathway comes at the expense of the principal oncogenic driver and reverses transformation. Conversely, deletion of divergent pathway components accelerates leukaemogenesis. Thus, persistence of divergent signalling pathways represents a powerful barrier to transformation, while convergence on one principal driver defines a central event in leukaemia initiation. Pharmacological reactivation of suppressed divergent circuits synergizes strongly with inhibition of the principal oncogenic driver. Hence, reactivation of divergent pathways can be leveraged as a previously unrecognized strategy to enhance treatment responses.


Assuntos
Linfócitos B/citologia , Linfócitos B/metabolismo , Transformação Celular Neoplásica , Leucemia de Células B/metabolismo , Leucemia de Células B/patologia , Transdução de Sinais , Animais , Linfócitos B/patologia , Linhagem Celular Tumoral , Ativação Enzimática , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Feminino , Humanos , Camundongos , Proteína Tirosina Fosfatase não Receptora Tipo 6/metabolismo , Proteínas Proto-Oncogênicas c-bcl-6/metabolismo , Proteínas Proto-Oncogênicas c-myc/metabolismo , Fator de Transcrição STAT5/metabolismo
4.
Nature ; 588(7838): 491-497, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33149299

RESUMO

Interferon-induced transmembrane protein 3 (IFITM3) has previously been identified as an endosomal protein that blocks viral infection1-3. Here we studied clinical cohorts of patients with B cell leukaemia and lymphoma, and identified IFITM3 as a strong predictor of poor outcome. In normal resting B cells, IFITM3 was minimally expressed and mainly localized in endosomes. However, engagement of the B cell receptor (BCR) induced both expression of IFITM3 and phosphorylation of this protein at Tyr20, which resulted in the accumulation of IFITM3 at the cell surface. In B cell leukaemia, oncogenic kinases phosphorylate IFITM3 at Tyr20, which causes constitutive localization of this protein at the plasma membrane. In a mouse model, Ifitm3-/- naive B cells developed in normal numbers; however, the formation of germinal centres and the production of antigen-specific antibodies were compromised. Oncogenes that induce the development of leukaemia and lymphoma did not transform Ifitm3-/- B cells. Conversely, the phosphomimetic IFITM3(Y20E) mutant induced oncogenic PI3K signalling and initiated the transformation of premalignant B cells. Mechanistic experiments revealed that IFITM3 functions as a PIP3 scaffold and central amplifier of PI3K signalling. The amplification of PI3K signals depends on IFITM3 using two lysine residues (Lys83 and Lys104) in its conserved intracellular loop as a scaffold for the accumulation of PIP3. In Ifitm3-/- B cells, lipid rafts were depleted of PIP3, which resulted in the defective expression of over 60 lipid-raft-associated surface receptors, and impaired BCR signalling and cellular adhesion. We conclude that the phosphorylation of IFITM3 that occurs after B cells encounter antigen induces a dynamic switch from antiviral effector functions in endosomes to a PI3K amplification loop at the cell surface. IFITM3-dependent amplification of PI3K signalling, which in part acts downstream of the BCR, is critical for the rapid expansion of B cells with high affinity to antigen. In addition, multiple oncogenes depend on IFITM3 to assemble PIP3-dependent signalling complexes and amplify PI3K signalling for malignant transformation.


Assuntos
Linfócitos B/metabolismo , Proteínas de Membrana/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Fosfatos de Fosfatidilinositol/metabolismo , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais , Animais , Antígenos CD19/metabolismo , Linfócitos B/enzimologia , Linfócitos B/imunologia , Linfócitos B/patologia , Transformação Celular Neoplásica , Feminino , Centro Germinativo/citologia , Centro Germinativo/imunologia , Centro Germinativo/patologia , Humanos , Integrinas/metabolismo , Microdomínios da Membrana/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos NOD , Modelos Moleculares , Fosforilação , Receptores de Antígenos de Linfócitos B/metabolismo
5.
J Biol Chem ; 300(2): 105630, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38199568

RESUMO

Sterile alpha and toll/interleukin receptor motif-containing 1 (SARM1) is a critical regulator of axon degeneration that acts through hydrolysis of NAD+ following injury. Recent work has defined the mechanisms underlying SARM1's catalytic activity and advanced our understanding of SARM1 function in axons, yet the role of SARM1 signaling in other compartments of neurons is still not well understood. Here, we show in cultured hippocampal neurons that endogenous SARM1 is present in axons, dendrites, and cell bodies and that direct activation of SARM1 by the neurotoxin Vacor causes not just axon degeneration, but degeneration of all neuronal compartments. In contrast to the axon degeneration pathway defined in dorsal root ganglia, SARM1-dependent hippocampal axon degeneration in vitro is not sensitive to inhibition of calpain proteases. Dendrite degeneration downstream of SARM1 in hippocampal neurons is dependent on calpain 2, a calpain protease isotype enriched in dendrites in this cell type. In summary, these data indicate SARM1 plays a critical role in neurodegeneration outside of axons and elucidates divergent pathways leading to degeneration in hippocampal axons and dendrites.


Assuntos
Proteínas do Domínio Armadillo , Proteínas do Citoesqueleto , Neurônios , Animais , Camundongos , Proteínas do Domínio Armadillo/genética , Proteínas do Domínio Armadillo/metabolismo , Axônios/metabolismo , Calpaína/metabolismo , Proteínas do Citoesqueleto/metabolismo , Dendritos/metabolismo , Neurônios/metabolismo , Transdução de Sinais
6.
Nucleic Acids Res ; 51(D1): D418-D427, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36350672

RESUMO

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.


Assuntos
Bases de Dados de Proteínas , Humanos , Sequência de Aminoácidos , Inteligência Artificial , Internet , Proteínas/química , Software
7.
Cytotherapy ; 26(7): 729-738, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38466264

RESUMO

BACKGROUND AIMS: Chimeric antigen receptor T (CAR-T) cells are a remarkably efficacious, highly promising and rapidly evolving strategy in the field of immuno-oncology. The precision of these targeted cellular therapies is driven by the specificity of the antigen recognition element (the "binder") encoded in the CAR. This binder redirects these immune effector cells precisely toward a defined antigen on the surface of cancer cells, leading to T-cell receptor-independent tumor lysis. Currently, for tumor targeting most CAR-T cells are designed using single-chain variable fragments (scFvs) derived from murine or human immunoglobulins. However, there are several emerging alternative binder modalities that are finding increasing utility for improved CAR function beyond scFvs. METHODS: Here we review the most recent developments in the use of non-canonical protein binding domains in CAR design, including nanobodies, DARPins, natural ligands, and de novo-designed protein elements. RESULTS: Overall, we describe how new protein binder formats, with their unique structural properties and mechanisms of action, may possess key advantages over traditional scFv CAR designs. CONCLUSIONS: These alternative binder designs may contribute to enhanced CAR-T therapeutic options and, ultimately, improved outcomes for cancer patients.


Assuntos
Imunoterapia Adotiva , Neoplasias , Receptores de Antígenos Quiméricos , Humanos , Receptores de Antígenos Quiméricos/imunologia , Imunoterapia Adotiva/métodos , Animais , Neoplasias/terapia , Neoplasias/imunologia , Linfócitos T/imunologia , Anticorpos de Cadeia Única/imunologia , Receptores de Antígenos de Linfócitos T/imunologia , Receptores de Antígenos de Linfócitos T/metabolismo , Antígenos de Neoplasias/imunologia , Anticorpos de Domínio Único/imunologia
8.
Br J Haematol ; 201(5): 935-939, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36846905

RESUMO

The CD38-targeting monoclonal antibodies (CD38 mAbs) are well-established therapies in multiple myeloma (MM), but responses to treatment are not always deep or durable. Natural killer (NK) cells deficient in Fc epsilon receptor gamma subunits, known as g-NK cells, are found in higher numbers among individuals exposed to cytomegalovirus (CMV) and are able to potentiate the efficacy of daratumumab in vivo. Here, we present a single-centre, retrospective analysis of 136 patients with MM with known CMV serostatus who received a regimen containing a CD38 mAb (93.4% daratumumab and 6.6% isatuximab). CMV seropositivity was associated with an increased overall response rate to treatment regimens containing a CD38 mAb (odds ratio 2.65, 95% confidence interval [CI] 1.17-6.02). However, CMV serostatus was associated with shorter time to treatment failure in a multivariate Cox model (7.8 vs. 8.8 months in the CMV-seropositive vs. CMV-seronegative groups respectively, log-rank p = 0.18, hazard ratio 1.98, 95% CI 1.25-3.12). Our data suggest that CMV seropositivity may predict better response to CD38 mAbs, although this did not correspond to longer time to treatment failure. Larger studies directly quantitating g-NK cells are required to fully understand their effect on CD38 mAb efficacy in MM.


Assuntos
Infecções por Citomegalovirus , Mieloma Múltiplo , Humanos , Mieloma Múltiplo/tratamento farmacológico , Estudos Retrospectivos , Citomegalovirus , ADP-Ribosil Ciclase 1 , Anticorpos Monoclonais/uso terapêutico , Anticorpos Monoclonais/farmacologia , Infecções por Citomegalovirus/tratamento farmacológico
9.
Biochem Biophys Res Commun ; 666: 61-67, 2023 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-37178506

RESUMO

The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVß3 and α5ß1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVß3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.


Assuntos
COVID-19 , Humanos , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/genética , Asparagina , Integrina alfaVbeta3
10.
Nat Chem Biol ; 17(10): 1065-1074, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34168367

RESUMO

The clinical benefits of pan-mTOR active-site inhibitors are limited by toxicity and relief of feedback inhibition of receptor expression. To address these limitations, we designed a series of compounds that selectively inhibit mTORC1 and not mTORC2. These 'bi-steric inhibitors' comprise a rapamycin-like core moiety covalently linked to an mTOR active-site inhibitor. Structural modification of these components modulated their affinities for their binding sites on mTOR and the selectivity of the bi-steric compound. mTORC1-selective compounds potently inhibited 4EBP1 phosphorylation and caused regressions of breast cancer xenografts. Inhibition of 4EBP1 phosphorylation was sufficient to block cancer cell growth and was necessary for maximal antitumor activity. At mTORC1-selective doses, these compounds do not alter glucose tolerance, nor do they relieve AKT-dependent feedback inhibition of HER3. Thus, in preclinical models, selective inhibitors of mTORC1 potently inhibit tumor growth while causing less toxicity and receptor reactivation as compared to pan-mTOR inhibitors.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Desenho de Fármacos , Alvo Mecanístico do Complexo 1 de Rapamicina/antagonistas & inibidores , Neoplasias da Mama/tratamento farmacológico , Linhagem Celular Tumoral , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Humanos , Alvo Mecanístico do Complexo 1 de Rapamicina/genética , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismo , Relação Estrutura-Atividade
11.
Am J Med Genet A ; 191(4): 1077-1082, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36574751

RESUMO

TRAPPC9 loss-of-function biallelic variants are associated with an autosomal recessive intellectual disability syndrome (Online Mendelian Inheritance of Man no. 613192), also characterized by microcephaly, hypertelorism, obesity, growth delay, and behavioral differences. Here, we describe an 8-year-old Hispanic female with neurodevelopmental disorder, partial epilepsy, microcephaly, bilateral cleft lip and alveolus, growth delay, and dysmorphic features. She had abnormal myelination, mega cisterna magna, and colpocephaly on brain magnetic resonance imaging (MRI). Microarray showed a single ~146 Mb region of homozygosity (ROH) encompassing all of Chromosome 8, consistent with uniparental isodisomy (UPD). Exome sequencing performed in-house did not identify single nucleotide variants to explain her phenotype. Algorithms developed in-house and further evaluation of BAM files revealed a homozygous deletion overlapping Exon 2 in TRAPPC9 within the ROH. Subsequent del/dup analyses with exon-level oligo array confirmed a likely pathogenic deletion in TRAPPC9 (NM_031466.5): arr[GRCh37] 8q24.3(141460661_141461780)x0. Our case highlights the implications of downstream analyses from UPD/ROH given the increased risk for AR conditions, the strengths of combining orthologous molecular methods to establish a diagnosis and further delineates the TRAPPC9-related phenotype in an individual of Hispanic ancestry.


Assuntos
Deficiência Intelectual , Microcefalia , Feminino , Humanos , Dissomia Uniparental , Microcefalia/genética , Homozigoto , Deleção de Sequência , Deficiência Intelectual/genética
12.
Phys Chem Chem Phys ; 25(19): 13708-13715, 2023 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-37158223

RESUMO

The manuscript details various simple LCR circuits to explain the experimentally observed surface plasmon resonance behavior of spherical metal nanoparticles. The results of the circuit's performance simulated using standard software like "QUCS" show similarity with SPR results in the literature, thus successfully explaining the size-effect, the influence of the surrounding dielectric medium and the proximity effect of densely packed metal nanoparticles. The study also explains these material dependent observations in terms of circuital parameters. This opens an avenue to detail the exact role of the material parameters in the influence of the surrounding dielectric medium and the proximity effect.

13.
Nucleic Acids Res ; 49(D1): D344-D354, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33156333

RESUMO

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.


Assuntos
Bases de Dados de Proteínas , Proteínas/química , Sequência de Aminoácidos , COVID-19/metabolismo , Internet , Anotação de Sequência Molecular , Domínios Proteicos , Mapas de Interação de Proteínas , SARS-CoV-2/metabolismo , Alinhamento de Sequência
14.
Proc Natl Acad Sci U S A ; 117(45): 28046-28055, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33093202

RESUMO

An essential mechanism for severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here, we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest-affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human immunoglobulin crystallizable fragment (Fc) domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2-pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50s) in the 10- to 100-ng/mL range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-using coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be predesigned for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated from convalescent patients.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , Antivirais/química , Desenho de Fármacos , Engenharia de Proteínas/métodos , Glicoproteína da Espícula de Coronavírus/metabolismo , Enzima de Conversão de Angiotensina 2/química , Enzima de Conversão de Angiotensina 2/genética , Antivirais/metabolismo , Sítios de Ligação , Células HEK293 , Humanos , Simulação de Acoplamento Molecular , Mutação , Biblioteca de Peptídeos , Ligação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae , Glicoproteína da Espícula de Coronavírus/química
15.
Environ Monit Assess ; 195(9): 1041, 2023 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-37589780

RESUMO

The growing concerns surrounding water supply, driven by factors such as population growth and industrialization, have highlighted the need for accurate estimation of streamflow at the river basin level. To achieve this, rainfall-runoff models are widely employed as valuable tools in watershed management. For this specific study, two modelling approaches were employed: the Soil and Water Assessment Tool (SWAT) model and a set of eight artificial intelligence (AI) models. The AI models consisted of seven data-driven approaches, namely k-nearest neighbour regression, support vector regression, linear regression, artificial neural networks, random forest regression, XGBoost, and Histogram-based Gradient Boost regression. Additionally, a deep learning model known as Long Short-Term Memory (LSTM) was also utilized. The study focused on monthly streamflow modelling in the Murredu River basin, with a calibration period from 1999 to 2003 and a validation period from 2004 to 2005, spanning a total of 7 years from 1999 to 2005. The results indicated that all nine models were generally suitable for simulating the rainfall-runoff process, with the LSTM model demonstrating exceptional performance in both the calibration (R2 is 0.97 and NSE is 0.96) and validation (R2 is 0.97 and NSE is 0.92) periods. Its high coefficient of determination (R2) and Nash-Sutcliffe efficiency (NSE) values indicated its superior ability to accurately model the rainfall-runoff relationship. While the other models also produced satisfactory results, the findings suggest that selecting the most efficient model, such as the LSTM model, could significantly contribute to the effective management and planning of sustainable water resources in the Murredu watershed.


Assuntos
Inteligência Artificial , Monitoramento Ambiental , Índia , Solo , Água
16.
J Med Virol ; 94(9): 4181-4192, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35575289

RESUMO

Cleavage of the severe respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein has been demonstrated to contribute to viral-cell fusion and syncytia formation. Studies have shown that variants of concern (VOC) and variants of interest (VOI) show differing membrane fusion capacity. Mutations near cleavage motifs, such as the S1/S2 and S2' sites, may alter interactions with host proteases and, thus, the potential for fusion. The biochemical basis for the differences in interactions with host proteases for the VOC/VOI spike proteins has not yet been explored. Using sequence and structure-based bioinformatics, mutations near the VOC/VOI spike protein cleavage sites were inspected for their structural effects. All mutations found at the S1/S2 sites were predicted to increase affinity to the furin protease but not TMPRSS2. Mutations at the spike residue P681 in several strains, such P681R in the Delta strain, resulted in the disruption of a proline-directed kinase phosphorylation motif at the S1/S2 site, which may lessen the impact of phosphorylation for these variants. However, the unique N679K mutation in the Omicron strain was found to increase the propensity for O-linked glycosylation at the S1/S2 cleavage site, which may prevent recognition by proteases. Such glycosylation in the Omicron strain may hinder entry at the cell surface and, thus, decrease syncytia formation and induce cell entry through the endocytic pathway as has been shown in previous studies. Further experimental work is needed to confirm the effect of mutations and posttranslational modifications on SARS-CoV-2 spike protein cleavage sites.


Assuntos
SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Glicosilação , Mutação , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/genética
18.
Eur Spine J ; 31(12): 3251-3261, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36322212

RESUMO

PURPOSE: Epidural corticosteroid injections (ESI) are a mainstay of nonoperative treatment for patients with lumbar spine pathology. Recent literature evaluating infection risk following ESI after elective orthopedic surgery has produced conflicting evidence. Our primary objective was to review the literature and provide a larger meta-analysis analyzing the temporal effects of steroid injections on the risk of infection following lumbar spine surgery. METHODS: We conducted a query of the PubMed, Embase, and Scopus databases from inception until April 1, 2022 for studies evaluating the risk of infection in the setting of prior spinal steroid injections in patients undergoing lumbar spine decompression or fusion. Three meta-analyses were conducted, (1) comparing ESI within 30-days of surgery to control, (2) comparing ESI within 30-days to ESI between 1 and 3 months preoperatively, and (3) comparing any history of ESI prior to surgery to control. Tests of proportions were utilized for all comparisons between groups. Study heterogeneity was assessed via forest plots, and publication bias was assessed quantiatively via funnel plots and qualitatively with the Newcastle-Ottawa Scale. RESULTS: Nine total studies were included, five of which demonstrated an association between ESI and postoperative infection, while four found no association. Comparison of weighted means demonstrated no significant difference in infection rates between the 30-days ESI group and control group (2.67% vs. 1.69%, p = 0.144), 30-days ESI group and the > 30-days ESI group (2.34% vs. 1.66%, p = 0.1655), or total ESI group and the control group (1.99% vs. 1.70%, p = 0.544). Heterogeneity was low for all comparisons following sensitivity analyses. CONCLUSION: Current evidence does not implicate preoperative ESI in postoperative infection rates following lumbar fusion or decompression. Operative treatment should not be delayed due to preoperative steroid injections based on current evidence. There remains a paucity of high-quality data in the literature evaluating the impact of preoperative ESI on postoperative infection rates. LEVEL OF EVIDENCE: II.


Assuntos
Região Lombossacral , Esteroides , Humanos , Esteroides/efeitos adversos , Região Lombossacral/cirurgia , Injeções Epidurais/efeitos adversos , Vértebras Lombares/cirurgia , Descompressão Cirúrgica/efeitos adversos , Complicações Pós-Operatórias/etiologia
19.
Proc Natl Acad Sci U S A ; 116(26): 13026-13035, 2019 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-31182586

RESUMO

Pancreatic cancer typically spreads rapidly and has poor survival rates. Here, we report that the calcium-activated chloride channel TMEM16A is a biomarker for pancreatic cancer with a poor prognosis. TMEM16A is up-regulated in 75% of cases of pancreatic cancer and high levels of TMEM16A expression are correlated with low patient survival probability. TMEM16A up-regulation is associated with the ligand-dependent EGFR signaling pathway. In vitro, TMEM16A is required for EGF-induced store-operated calcium entry essential for pancreatic cancer cell migration. TMEM16A also has a profound impact on phosphoproteome remodeling upon EGF stimulation. Moreover, molecular actors identified in this TMEM16A-dependent EGFR-induced calcium signaling pathway form a gene set that makes it possible not only to distinguish neuro-endocrine tumors from other forms of pancreatic cancer, but also to subdivide the latter into three clusters with distinct genetic profiles that could reflect their molecular underpinning.


Assuntos
Anoctamina-1/metabolismo , Biomarcadores Tumorais/metabolismo , Sinalização do Cálcio , Carcinoma Ductal Pancreático/patologia , Fator de Crescimento Epidérmico/metabolismo , Proteínas de Neoplasias/metabolismo , Neoplasias Pancreáticas/patologia , Anoctamina-1/genética , Carcinoma Ductal Pancreático/diagnóstico , Carcinoma Ductal Pancreático/mortalidade , Linhagem Celular Tumoral , Movimento Celular , Conjuntos de Dados como Assunto , Diagnóstico Diferencial , Receptores ErbB/metabolismo , Células HEK293 , Humanos , Proteínas de Neoplasias/genética , Pâncreas/patologia , Neoplasias Pancreáticas/diagnóstico , Neoplasias Pancreáticas/mortalidade , Prognóstico , RNA Interferente Pequeno/metabolismo , RNA-Seq , Taxa de Sobrevida , Regulação para Cima
20.
Analyst ; 146(8): 2542-2549, 2021 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-33899057

RESUMO

We describe and characterize a dual-channel incoherent broadband cavity-enhanced absorption spectrometer (DC-IBBCEAS) for the sensitive measurements of NOx: the sum of nitrogen monoxide (NO) and nitrogen dioxide (NO2) in the atmosphere. The instrument employs two 1 m long optical cavities, with air being extracted from a common sampling line. The first channel (cavity-1) spans 340-380 nm and the second channel (cavity-2) spans the 405-460 nm spectral range, both measuring NO2 simultaneously. High absorption cross-sections of NO2 in both channels are effectively utilized for its sensitive quantification. NO is quantified by titrating it with ozone to NO2 in channel-2, where the difference of NO2 measured from that in channel-1 corresponds to the NO concentration in the sampled air. The instrument offers 1-ppb detection sensitivity for both NO and NO2 with a maximum possible uncertainty of ∼9%. The use of close yet different spectral regions in the two channels readily extended measurements to a broader range without compromising its sensitivity to NOx quantification. This would extend the DC-IBBCEAS applicability to simultaneously monitor interfering species with significant absorption cross-sections in the region in either channel, such as glyoxal (CHOCHO), methylglyoxal (CH3COCHO), and nitrous acid (HONO).

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