Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 22
Filtrar
1.
Mol Microbiol ; 120(1): 75-90, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37330636

RESUMO

Spx is a global transcriptional regulator that orchestrates the Bacillus subtilis response to disulfide stress. The YjbH (SpxH) protein adapts Spx for ClpXP-mediated degradation, playing a critical role in the regulation of the cellular Spx levels. Upon stress, YjbH forms aggregates by a yet unknown mechanism, resulting in increased Spx levels due to reduced proteolysis. Here, we studied how individual cells use the Spx-YjbH system to respond to disulfide stress. We show, using fluorescent reporters, a correlation between the Spx levels and the amount of YjbH, as well as a transient growth inhibition upon disulfide stress. The in vivo dynamics and inheritance of YjbH aggregates are characterized by a bipolar distribution over time and appear to be entropy-driven by nucleoid exclusion. Moreover, we reveal that the population following disulfide stress is highly heterogenous in terms of aggregate load and that the aggregate load has strong implications for cellular fitness. We propose that the observed heterogeneity could be a mechanism to ensure population survival during stress. Finally, we find that the two YjbH domains (DsbA-like domain and winged-helix domain) contribute to its aggregation function, and show that the aggregation of the DsbA-like domain is conserved among other studied orthologs, whereas important differences are observed for the winged-helix domain.


Assuntos
Bacillus subtilis , Dissulfetos , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Dissulfetos/metabolismo , Proteínas de Bactérias/metabolismo , Endopeptidase Clp/metabolismo , Regulação Bacteriana da Expressão Gênica
2.
J Membr Biol ; 256(2): 137-145, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36331589

RESUMO

Nucleus is at the center stage of cellular drama orchestrated in the life of a cell and the nucleoplasm is surrounded by a double membranous compartment constituting the Nuclear membrane/envelope (NE) that separates it from the cytoplasm in nucleated cells. The initial understanding of the NE was that of a border security entity between the nucleus and the cytoplasm, separating gene regulation and transcription in the nucleus from translation in the cytoplasm. However, the discovery of a wide array of inherited diseases caused by mutations in genes encoding proteins that reside or interact with NE diverted the interest into deciphering the lipid-protein-rich environment of the NE. Today, the NE is considered a dynamic organelle which forms a functional linkage between the nucleus and the rest of the cell. The exposure of NE to constant mechanical constraints by its connectivity to the large polymer network of the lamina and chromatin on one side, and to the cytoskeleton on the other side results, in a variety of shape changes. We discuss two such deformation, the formation of nuclear blebs and nucleoplasmic reticulum (NER). Although the protein and the lipid composition of NE comprises a small fraction of the total lipid-protein load of the cell, the ability to define the lipid-protein composition of Inner nuclear membrane (INM) and Outer nuclear membrane (ONM) with precision is crucial for obtaining a deeper mechanistic understanding of their lipid-protein interaction and the various signaling pathways that are triggered by them. In addition, this allows us to further understand the direct and indirect roles of NE machinery in the chromosomal organization and gene regulation.


Assuntos
Núcleo Celular , Membrana Nuclear , Membrana Nuclear/metabolismo , Núcleo Celular/metabolismo , Citoplasma/metabolismo , Citoesqueleto/metabolismo , Lipídeos
3.
Environ Res ; 237(Pt 1): 116905, 2023 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-37597831

RESUMO

Membranes are receiving significant attention to remove emerging organic micropollutants (OMPs) from wastewater and natural water sources. Herein, we report the facile preparation of a novel thin-film nanocomposite (TFN) membrane with high permeability and efficient removal of OMPs. ZnO nanoparticles were first synthesized using the co-precipitation method and functionalized with N1-(3-Trimethoxysilylpropyl)diethylenetriamine to make the surface rich with amine groups and then synthesized nanomaterials were covalently cross-linked into the active layer during the interfacial polymerization (IP) process. The performance of the membranes containing the cross-linked ZnO was significantly better than the non-cross-linked ZnO NPs containing membranes. Adding multiple hydrophilic groups and entities on the surface significantly decreased the contact angle (from ∼60° to 20°). SEM images confirmed the uniform presence and homogeneous distribution of the functionalized NPs throughout the entire membrane surface. Zeta potential measurements showed the modified membranes have a lower negative charge than the pristine membranes. Filtration studies revealed a significant increase in permeability ascribed to the creation of nanochannels in the membrane's active layer. The modified membranes outperformed commercial NF membranes in removing four common OMPs with rejection efficiencies of ∼30%, 64%, 60%, and 70% for Sulfamethoxazole, Amitriptyline, Omeprazole, and Loperamide HCl, respectively. The higher removal efficiency was attributed to the weakened hydrophobic interactions due to the presence of hydrophilic moieties and a stronger size exclusion effect. Moreover, the modified membranes showed high resistance to bacterial adhesion in static conditions.

4.
J Pathol ; 255(3): 232-242, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34346511

RESUMO

Deep neural networks (DNNs) that predict mutational status from H&E slides of cancers can enable inexpensive and timely precision oncology. Although expert knowledge is reliable for annotating regions informative of malignancy and other known histologic patterns (strong supervision), it is unreliable for identifying regions informative of mutational status. This poses a serious impediment to obtaining higher prognostic accuracy and discovering new knowledge of pathobiology. We used a weakly supervised learning technique to train a DNN to predict BRAF V600E mutational status, determined using DNA testing, in H&E-stained images of thyroid cancer tissue without regional annotations. Our discovery cohort was a tissue microarray of only 85 patients from a single hospital. On a large independent external cohort of 444 patients from other hospitals, the trained model gave an area under the receiver operating characteristic curve of 0.98 (95% CI 0.97-1.00), which is much higher than the previously reported results for detecting any mutation using H&E by DNNs trained using strong supervision. We also developed a visualization technique that can automatically highlight regions the DNN found most informative for predicting mutational status. Our visualization is spatially granular and highly specific in highlighting strong negative and positive regions and moves us toward explainable artificial intelligence. Using t-tests, we confirmed that the proportions of follicular or papillary histology and oncocytic cytology, as noted for each patient by a pathologist who was blinded to the mutational status, were significantly different between mutated and wildtype patients. However, based solely on these features noted by the pathologist, a logistic regression classifier gave an average area under the receiver operating characteristic curve of 0.78 in five-fold cross-validation, which is much lower than that obtained using the DNN. These results highlight the potential of weakly supervised learning for training DNN models for problems where the informative visual patterns and their locations are not known a priori. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Assuntos
Redes Neurais de Computação , Proteínas Proto-Oncogênicas B-raf/genética , Neoplasias da Glândula Tireoide/genética , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Coloração e Rotulagem
5.
Mol Microbiol ; 114(5): 839-856, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32738827

RESUMO

In bacteria, ParABS systems and structural maintenance of chromosome (SMC) condensin-like complexes are important for chromosome segregation and organization. The rod-shaped Myxococcus xanthus cells have a unique chromosome arrangement in which a scaffold composed of the BacNOP bactofilins and PadC positions the essential ParB∙parS segregation complexes and the DNA segregation ATPase ParA in the subpolar regions. We identify the Smc and ScpAB subunits of the SMC complex in M. xanthus and demonstrate that SMC is conditionally essential, with Δsmc or ΔscpAB mutants being temperature sensitive. Inactivation of SMC caused defects in chromosome segregation and organization. Lack of the BacNOP/PadC scaffold also caused chromosome segregation defects but this scaffold is not essential for viability. Inactivation of SMC was synthetic lethal with lack of the BacNOP/PadC scaffold. Lack of SMC interfered with formation of the BacNOP/PadC scaffold while lack of this scaffold did not interfere with chromosome association by SMC. Altogether, our data support that three systems function together to enable chromosome segregation in M. xanthus. ParABS constitutes the basic and essential machinery. SMC and the BacNOP/PadC scaffold have different yet redundant roles in chromosome segregation with SMC supporting individualization of daughter chromosomes and BacNOP/PadC making the ParABS system operate more robustly.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Ciclo Celular/metabolismo , Segregação de Cromossomos/fisiologia , Myxococcus xanthus/metabolismo , Adenosina Trifosfatases/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/fisiologia , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/fisiologia , Segregação de Cromossomos/genética , Cromossomos Bacterianos/metabolismo , DNA Bacteriano/metabolismo , Proteínas de Ligação a DNA , Complexos Multiproteicos , Myxococcus xanthus/genética , Ligação Proteica
6.
Soft Matter ; 13(15): 2866-2875, 2017 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-28352880

RESUMO

The high interfacial activity of protein-polymer conjugates has inspired their use as stabilizers for Pickering emulsions, resulting in many interesting applications such as synthesis of templated micro-compartments and protocells or vehicles for drug and gene delivery. In this study we report, for the first time, the stabilization of Pickering emulsions with conjugates of a genetically modified transmembrane protein, ferric hydroxamate uptake protein component A (FhuA). The lysine residues of FhuA with open pore (FhuA ΔCVFtev) were modified to attach an initiator and consequently controlled radical polymerization (CRP) carried out via the grafting-from technique. The resulting conjugates of FhuA ΔCVFtev with poly(N-isopropylacrylamide) (PNIPAAm) and poly((2-dimethylamino)ethyl methacrylate) (PDMAEMA), the so-called building blocks based on transmembrane proteins (BBTP), have been shown to engender larger structures. The properties such as pH-responsivity, temperature-responsivity and interfacial activity of the BBTP were analyzed using UV-Vis spectrophotometry and pendant drop tensiometry. The BBTP were then utilized for the synthesis of highly stable Pickering emulsions, which could remain non-coalesced for well over a month. A new UV-crosslinkable monomer was synthesized and copolymerized with NIPAAm from the protein. The emulsion droplets, upon crosslinking of polymer chains, yielded micro-compartments. Fluorescence microscopy proved that these compartments are of micrometer scale, while cryo-scanning electron microscopy and scanning force microscopy analysis yielded a thickness in the range of 11.1 ± 0.6 to 38.0 ± 18.2 nm for the stabilizing layer of the conjugates. Such micro-compartments would prove to be beneficial in drug delivery applications, owing to the possibility of using the channel of the transmembrane protein as a gate and the smart polymer chains as trigger switches to tune the behavior of the capsules.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Nanoestruturas/química , Polímeros/química , Concentração de Íons de Hidrogênio , Lisina , Modelos Moleculares , Domínios Proteicos , Temperatura
7.
Mol Membr Biol ; 33(6-8): 125-137, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-29189113

RESUMO

Outer membrane vesicles (OMVs) (∼50-250 nm in diameter) are produced by both pathogenic and nonpathogenic bacteria as a canonical end product of secretion. In this review, we focus on the OMVs produced by gram-negative bacteria. We provide an overview of the OMV structure, various factors regulating their production, and their role in modulating host immune response using a few representative examples. In light of the importance of the diverse cargoes carried by OMVs, we discuss the different modes of their entry into the host cell and advances in the high-throughput detection of these OMVs. A conspicuous application of OMVs lies in the field of vaccination; we discuss its success in immunization against human diseases such as pertussis, meningitis, shigellosis and aqua-farming endangering diseases like edwardsiellosis.

8.
Mol Cancer ; 14: 76, 2015 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-25890053

RESUMO

p66Shc, a member of the ShcA (Src homologous- collagen homologue) adaptor protein family, is one of the three isoforms of this family along with p46Shc and p52Shc. p66Shc, a 66 kDa protein is different from the other isoforms of the ShcA family. p66Shc is the longest isoform of the ShcA family. p66Shc has an additional CH domain at the N-terminal, called the CH2 domain, which is not not present in the other isoforms. This CH2 domain contains a very crucial S36 residue which is phosphorylated in response to oxidative stress and plays a role in apoptosis. Whereas p52Shc and p46Shc are ubiquitously expressed, p66Shc shows constrained expression. This adaptor protein has been shown to be involved in mediating and executing the post effects of oxidative stress and increasing body of evidence is pinpointing to its role in carcinogenesis as well. It shows proto-oncogenic as well as pro-apoptotic properties. This multitasking protein is involved in regulating different networks of cell signaling. On one hand it shows an increased expression profile in different cancers, has a positive role in cell proliferation and migration, whereas on the other hand it promotes apoptosis under oxidative stress conditions by acting as a sensor of ROS (Reactive Oxygen Species). This paradoxical role of p66Shc could be attributed to its involvement in ROS production, as ROS is known to both induce cell proliferation as well as apoptosis. p66Shc by regulating intracellular ROS levels plays a crucial role in regulating longevity and cell senescence. These multi-faceted properties of p66Shc make it a perfect candidate protein for further studies in various cancers and aging related diseases. p66Shc can be targeted in terms of it being used as a possible therapeutic target in various diseases. This review focuses on p66Shc and highlights its role in promoting apoptosis via different cell signaling networks, its role in cell proliferation, along with its presence and role in different forms of cancers.


Assuntos
Apoptose , Proteínas Adaptadoras da Sinalização Shc/metabolismo , Proliferação de Células , Humanos , Neoplasias/metabolismo , Neoplasias/patologia , Espécies Reativas de Oxigênio/metabolismo , Transdução de Sinais
9.
Chem Asian J ; 19(9): e202400074, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38545693

RESUMO

This work demonstrates the use of jute stick extract as a reducing and stabilizing agent for the synthesis of spherical gold nanoparticles (AuNPs). In UV-Vis spectroscopy, peak at 550 nm was used to confirm the formation of AuNPs. The spherical surface morphology of AuNPs was determined through SEM and TEM analysis. While XRD investigation revealed the crystallinity of the prepared AuNPs. To ensure the biocompatibility of synthesized AuNPs, a bacterial investigation was conducted with negative results towards bacterial strain. The, modified FTO with AuNPs were able to detect glucose in CV analysis and the constructed sensor displayed a wide linear range of 50 µM to 40 mM with a detection limit of 20 µM. Scan rate analysis was performed to determine the charge transfer coefficient (0.42) and Tafel slope (102 mV/decade). Furthermore, the interfacial surface mechanism is illustrated to understand the interaction of glucose with the electrode surface in an alkaline medium and the product formation through the dehydrogenation and hydrolysis process. The prepared sensor also showed good stability, reproducibility, and anti-interference capabilities. In the case of real sample analysis, we used a blood serum sample. A low RSD value (<10 %) suggests the practical use of AuNPs/FTO in real-life applications.


Assuntos
Técnicas Biossensoriais , Técnicas Eletroquímicas , Eletrodos , Flúor , Ouro , Nanopartículas Metálicas , Compostos de Estanho , Ouro/química , Nanopartículas Metálicas/química , Flúor/química , Compostos de Estanho/química , Materiais Biocompatíveis/química , Materiais Biocompatíveis/síntese química , Glucose/análise , Propriedades de Superfície , Humanos , Glicemia/análise , Tamanho da Partícula
11.
Front Microbiol ; 14: 1227210, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37771703

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are chemicals that are released into the environment during activities of the petroleum industry. The bioaccumulation, carcinogenic and mutagenic potential of PAHs necessitates the bioremediation of these contaminants. However, bioremediation of PAHs has a number of limitations including the inability of a single microbe to degrade all of the PAH fraction's environmental constituents. Therefore, a different paradigm, employing microalgal-bacterial consortium (MBC), may be used to effectively remove PAHs contaminants. In this type of interaction, the microalgae and bacteria species in the consortium work together in a way that enhances the overall performance of the MBC. Bacterial species in the consortium provide essential nutrients or growth factors by degrading toxic substances and provide these to microalgae, while the microalgae species provide organic carbon for the bacterial species to grow. For the first time, the ability of Gonium pectorale (G. pectorale) microalgae to break down phenanthrene (PHE) and anthracene (ANT) was investigated. Phenanthrene was shown to be more effectively degraded by G. pectorale (98%) as compared to Bacillus licheniformis (B. licheniformis) 19%. Similarly, G. pectorale has effectively degrade anthracene (98%) as compared with B. licheniformis (45%). The consortia of G. pectorale and B. licheniformis has shown a slight increase in the degradation of PHE (96%) and ANT (99%). Our findings show that B. licheniformis did not inhibit the growth of G. pectorale and in the consortia has effectively eliminated the PAHs from the media. Therefore G. pectorale has a tremendous potential to remove PAHs from the polluted environment. Future research will be conducted to assess Gonium's capacity to eliminate PAHs that exhibit high molar masses than that of PHE and ANT.

12.
J Bacteriol ; 194(3): 702-7, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22101845

RESUMO

The ultrastructural functions of the electron-dense glycopeptidolipid-containing outermost layer (OL), the arabinogalactan-mycolic acid-containing electron-transparent layer (ETL), and the electron-dense peptidoglycan layer (PGL) of the mycobacterial cell wall in septal growth and constriction are not clear. Therefore, using transmission electron microscopy, we studied the participation of the three layers in septal growth and constriction in the fast-growing saprophytic species Mycobacterium smegmatis and the slow-growing pathogenic species Mycobacterium xenopi and Mycobacterium tuberculosis in order to document the processes in a comprehensive and comparative manner and to find out whether the processes are conserved across different mycobacterial species. A complete septal partition is formed first by the fresh synthesis of the septal PGL (S-PGL) and septal ETL (S-ETL) from the envelope PGL (E-PGL) in M. smegmatis and M. xenopi. The S-ETL is not continuous with the envelope ETL (E-ETL) due to the presence of the E-PGL between them. The E-PGL disappears, and the S-ETL becomes continuous with the E-ETL, when the OL begins to grow and invaginate into the S-ETL for constriction. However, in M. tuberculosis, the S-PGL and S-ETL grow from the E-PGL and E-ETL, respectively, without a separation between the E-ETL and S-ETL by the E-PGL, in contrast to the process in M. smegmatis and M. xenopi. Subsequent growth and invagination of the OL into the S-ETL of the septal partition initiates and completes septal constriction in M. tuberculosis. A model for the conserved sequential process of mycobacterial septation, in which the formation of a complete septal partition is followed by constriction, is presented. The probable physiological significance of the process is discussed. The ultrastructural features of septation and constriction in mycobacteria are unusually different from those in the well-studied organisms Escherichia coli and Bacillus subtilis.


Assuntos
Membrana Celular/ultraestrutura , Parede Celular/ultraestrutura , Mycobacterium smegmatis/ultraestrutura , Mycobacterium tuberculosis/ultraestrutura , Membrana Celular/metabolismo , Parede Celular/metabolismo , Mycobacterium/crescimento & desenvolvimento , Mycobacterium/metabolismo , Mycobacterium/ultraestrutura , Mycobacterium smegmatis/crescimento & desenvolvimento , Mycobacterium smegmatis/metabolismo , Mycobacterium tuberculosis/crescimento & desenvolvimento , Mycobacterium tuberculosis/metabolismo , Peptidoglicano/metabolismo
13.
Front Microbiol ; 13: 920117, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36338044

RESUMO

Bacteria regulate FtsZ protein levels through transcriptional and translational mechanisms for proper cell division. A cis-antisense RNA, StfZ, produced from the ftsA-ftsZ intergenic region, was proposed to regulate FtsZ level in Escherichia coli. However, its structural identity remained unknown. In this study, we determined the complete sequence of StfZ and identified the isoforms and its promoters. We find that under native physiological conditions, StfZ is expressed at a 1:6 ratio of StfZ:ftsZ mRNA at all growth phases from three promoters as three isoforms of 366, 474, and 552 nt RNAs. Overexpression of StfZ reduces FtsZ protein level, increases cell length, and blocks cell division without affecting the ftsZ mRNA stability. We did not find differential expression of StfZ under the stress conditions of heat shock, cold shock, or oxidative stress, or at any growth phase. These data indicated that the cis-encoded StfZ antisense RNA to ftsZ mRNA may be involved in the fine tuning of ftsZ mRNA levels available for translation as per the growth-phase-specific requirement at all phases of growth and cell division.

14.
Curr Microbiol ; 62(5): 1581-9, 2011 May.
Artigo em Inglês | MEDLINE | ID: mdl-21336990

RESUMO

Bacterial FtsE gene codes for the ATP-binding protein, FtsE, which in complex with the transmembrane protein, FtsX, participates in diverse cellular processes. Therefore, regulated expression of FtsE and FtsX might be critical to the human pathogen, Mycobacterium tuberculosis, under stress conditions. Although ftsX gene of M. tuberculosis (MtftsX) is known to be transcribed from a promoter inside the upstream gene, ftsE, the transcriptional status of ftsE gene of M. tuberculosis (MtftsE) remains unknown. Therefore, the authors initiated transcriptional analyses of MtftsE, using total RNA from M. tuberculosis cells that were grown under stress conditions, which the pathogen is exposed to, in granuloma in tuberculosis patients. Primer extension experiments showed the presence of putative transcripts, T1, T2, T3, and T4. T1 originated from the intergenic region between the upstream gene, MRA_3135, and MtftsE. T2 and T3 were found initiated from within MRA_3135. T4 was transcribed from a region upstream of MRA_3135. RT-PCR confirmed co-transcription of MRA_3135 and MtftsE. The cloned putative promoter regions for T1, T2, and T3 elicited transcriptional activity in Mycobacterium smegmatis transformants. T1, T2, and T3, but no new transcript, were present in the M. tuberculosis cells that were grown under the stress conditions, which the pathogen is exposed to in granuloma in tuberculosis patients. It showed lack of modulation of MtftsE transcripts under the stress conditions tested, indicating that ftsE may not have a stress response-specific function in M. tuberculosis.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Mycobacterium tuberculosis/genética , Transcrição Gênica , Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Bactérias/metabolismo , Sequência de Bases , DNA Intergênico , Humanos , Dados de Sequência Molecular , Mycobacterium tuberculosis/isolamento & purificação , Mycobacterium tuberculosis/metabolismo , Regiões Promotoras Genéticas , Tuberculose/microbiologia
15.
J Pathol Inform ; 11: 19, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33033656

RESUMO

CONTEXT: Several therapeutically important mutations in cancers are economically detected using immunohistochemistry (IHC), which highlights the overexpression of specific antigens associated with the mutation. However, IHC panels can be imprecise and relatively expensive in low-income settings. On the other hand, although hematoxylin and eosin (H&E) staining used to visualize the general tissue morphology is a routine and low cost, it does not highlight any specific antigen or mutation. AIMS: Using the human epidermal growth factor receptor 2 (HER2) mutation in breast cancer as an example, we strengthen the case for cost-effective detection and screening of overexpression of HER2 protein in H&E-stained tissue. SETTINGS AND DESIGN: We use computational methods that reliably detect subtle morphological changes associated with the over-expression of mutation-specific proteins directly from H&E images. SUBJECTS AND METHODS: We trained a classification pipeline to determine HER2 overexpression status of H&E stained whole slide images. Our training dataset was derived from a single hospital containing 26 (11 HER2+ and 15 HER2-) cases. We tested the classification pipeline on 26 (8 HER2+ and 18 HER2-) held-out cases from the same hospital and 45 independent cases (23 HER2+ and 22 HER2-) from the TCGA-BRCA cohort. The pipeline was composed of a stain separation module and three deep neural network modules in tandem for robustness and interpretability. STATISTICAL ANALYSIS USED: We evaluate our trained model through area under the curve (AUC)-receiver operating characteristic. RESULTS: Our pipeline achieved an AUC of 0.82 (confidence interval [CI]: 0.65-0.98) on held-out cases and an AUC of 0.76 (CI: 0.61-0.89) on the independent dataset from TCGA. We also demonstrate the region-level correspondence of HER2 overexpression between a patient's IHC and H&E serial sections. CONCLUSIONS: Our work strengthens the case for automatically quantifying the overexpression of mutation-specific proteins in H&E-stained digital pathology, and it highlights the importance of multi-stage machine learning pipelines for added robustness and interpretability.

16.
IEEE Trans Med Imaging ; 39(5): 1380-1391, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-31647422

RESUMO

Generalized nucleus segmentation techniques can contribute greatly to reducing the time to develop and validate visual biomarkers for new digital pathology datasets. We summarize the results of MoNuSeg 2018 Challenge whose objective was to develop generalizable nuclei segmentation techniques in digital pathology. The challenge was an official satellite event of the MICCAI 2018 conference in which 32 teams with more than 80 participants from geographically diverse institutes participated. Contestants were given a training set with 30 images from seven organs with annotations of 21,623 individual nuclei. A test dataset with 14 images taken from seven organs, including two organs that did not appear in the training set was released without annotations. Entries were evaluated based on average aggregated Jaccard index (AJI) on the test set to prioritize accurate instance segmentation as opposed to mere semantic segmentation. More than half the teams that completed the challenge outperformed a previous baseline. Among the trends observed that contributed to increased accuracy were the use of color normalization as well as heavy data augmentation. Additionally, fully convolutional networks inspired by variants of U-Net, FCN, and Mask-RCNN were popularly used, typically based on ResNet or VGG base architectures. Watershed segmentation on predicted semantic segmentation maps was a popular post-processing strategy. Several of the top techniques compared favorably to an individual human annotator and can be used with confidence for nuclear morphometrics.


Assuntos
Processamento de Imagem Assistida por Computador , Redes Neurais de Computação , Núcleo Celular , Humanos
17.
Chem Commun (Camb) ; 55(38): 5431-5434, 2019 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-30916680

RESUMO

Downstream processing to obtain enantiopure compounds from a racemic mixture relies mainly on crystallization. Natural transporters can specifically translocate enantiomers through membranes. Here a ß-barrel transmembrane protein FhuA is re-engineered into a chiral channel protein (FhuAF4) to resolve racemic mixtures of d-/l-arginine. The engineered FhuAF4 variant exhibits an enantioselectivity (E-value) of 1.92 and an enantiomeric excess percentage (ee%) of 23.91 at 52.39% conversion. OmniChange mutant libraries at the computationally identified "filter-regions" likely help to identify FhuA variants for enantiomeric separation of other compounds.


Assuntos
Arginina/química , Arginina/isolamento & purificação , Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Nanoestruturas , Engenharia de Proteínas , Estereoisomerismo
18.
Biomaterials ; 107: 115-23, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27614163

RESUMO

The research on protein-polymer conjugates by grafting from the surface of proteins has gained significant interest in the last decade. While there are many studies with globular proteins, membrane proteins have remained untouched to the best of our knowledge. In this study, we established the conjugate formation with a class of transmembrane proteins and grow polymer chains from the ferric hydroxamate uptake protein component A (FhuA; a ß-barrel transmembrane protein of Escherichia coli). As the lysine residues of naturally occurring FhuA are distributed over the whole protein, FhuA was reengineered to have up to 11 lysines, distributed symmetrically in a rim on the membrane exposed side (outside) of the protein channel and exclusively above the hydrophobic region. Reengineering of FhuA ensures a polymer growth only on the outside of the ß-barrel and prevents blockage of the channel as a result of the polymerization. A water-soluble initiator for controlled radical polymerization (CRP) was consecutively linked to the lysine residues of FhuA and N-isopropylacrylamide (NIPAAm) polymerized under copper-mediated CRP conditions. The conjugate formation was analyzed by using MALDI-ToF mass spectrometry, SDS-PAGE, circular dichroism spectroscopy, analytical ultracentrifugation, dynamic light scattering, transmission electron microscopy and size exclusion chromatography. Such conjugates combine the specific functions of the transmembrane proteins, like maintaining membrane potential gradients or translocation of substrates with the unique properties of synthetic polymers such as temperature and pH stimuli handles. FhuA-PNIPAAm conjugates will serve as functional nanosized building blocks for applications in targeted drug delivery, self-assembly systems, functional membranes and transmembrane protein gated nanoreactors.


Assuntos
Resinas Acrílicas/química , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/ultraestrutura , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/ultraestrutura , Bicamadas Lipídicas/química , Nanoporos/ultraestrutura , Engenharia de Proteínas/métodos , Proteínas da Membrana Bacteriana Externa/genética , Proteínas de Escherichia coli/genética , Conformação Molecular , Relação Estrutura-Atividade
19.
J Clin Diagn Res ; 8(9): RD01-2, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25386502

RESUMO

Intracranial dermoid cysts are rare tumours which usually occur in the midline. Sylvian fissure is a very unusual site for this lesion. This case presents a patient with unruptured dermoid cyst in the left sylvian fissure who was operated successfully without any residual deficit.

20.
Artigo | IMSEAR | ID: sea-201549

RESUMO

Background: ‘Sanitary labourers’ are known by different names such as ‘Health Labourers’, ‘Manual Scavengers’ garbage man, trash man etc. They are mainly involved in street cleaning, waste carrying, drainage and toilet cleaning in the cities. Intake of alcohol and tobacco products is prevalent to cope with the inhuman task of cleaning filthy sewage, and as a modality to forget their health problems. The aim of the present cross-sectional study was to find out the association of dental problems with tobacco abuse among the study population.Methods: The study population included 610, 122 from each zone of Allahabad city through “Proportionate stratified random sampling”. The study subjects was interviewed and examined, Dental problems were assessed by taking history, doing a clinical examination, reviewing past medical records.Results: Dental problems were found to be higher in prevalence among “exclusive smokers”, “combined abuser” and “exclusive tobacco” chewers as compared to “non abuser”. Dental caries were found to be higher in prevalence among the entire three abusers group as compared to “non abusers”. Missed teeth were found to higher in prevalence among “combined abuser” and “exclusive tobacco chewers” group as compared to “non abusers”. Enamel erosion was found to be higher among “exclusive tobacco chewers” group as compared to “non abusers”. All these finding were found to be statistically significant.Conclusions: Dental problems were found to be more prevalent among tobacco abusers than non abusers.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA