Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 130
Filtrar
1.
Nat Commun ; 15(1): 788, 2024 Jan 26.
Artigo em Inglês | MEDLINE | ID: mdl-38278785

RESUMO

In neurodegenerative diseases, polymorphism and supramolecular assembly of ß-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-ß 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.


Assuntos
Peptídeos beta-Amiloides , Amiloide , Amiloide/química , Temperatura
2.
Inorg Chem ; 63(6): 2899-2908, 2024 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-38127051

RESUMO

The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-ß bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-ß peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.

3.
Chembiochem ; 22(7): 1292-1301, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33238068

RESUMO

Many bacteria, such as Pseudomonas aeruginosa, regulate phenotypic switching in a population density-dependent manner through a phenomenon known as quorum sensing (QS). For Gram-negative bacteria, QS relies on the synthesis, transmission, and perception of low-molecular-weight signal molecules that are predominantly N-acyl-l-homoserine lactones (AHLs). Efforts to disrupt AHL-mediated QS have largely focused on the development of synthetic AHL analogues (SAHLAs) that are structurally similar to native AHLs. However, like AHLs, these molecules tend to be hydrophobic and are poorly soluble under aqueous conditions. Water-soluble macrocycles, such as cyclodextrins (CDs), that encapsulate hydrophobic guests have long been used by both the agricultural and pharmaceutical industries to overcome the solubility issues associated with hydrophobic compounds of interest. Conveniently, CDs have also demonstrated anti-AHL-mediated QS effects. Here, using fluorescence spectroscopy, NMR spectrometry, and mass spectrometry, we evaluate the affinity of SAHLAs, as well as their hydrolysis products, for ß-CD inclusion. We also evaluated the ability of these complexes to inhibit wild-type P. aeruginosa virulence in a Caenorhabditis elegans host infection study, for the first time. Our efforts confirm the potential of ß-CDs for the improved delivery of SAHLAs at the host/microbial interface, expanding the utility of this approach as a strategy for probing and controlling QS.


Assuntos
Acil-Butirolactonas/química , Portadores de Fármacos/química , Percepção de Quorum , beta-Ciclodextrinas/química , Acil-Butirolactonas/síntese química , Acil-Butirolactonas/farmacologia , Animais , Caenorhabditis elegans/crescimento & desenvolvimento , Caenorhabditis elegans/microbiologia , Óvulo/efeitos dos fármacos , Óvulo/microbiologia , Pseudomonas aeruginosa/patogenicidade , Pseudomonas aeruginosa/fisiologia , Percepção de Quorum/efeitos dos fármacos , Virulência
4.
Pathogens ; 9(12)2020 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-33255203

RESUMO

Iron homeostasis offers a significant bacterial vulnerability because pathogens obtain essential iron from their mammalian hosts, but host-defenses maintain vanishingly low levels of free iron. Although pathogens have evolved mechanisms to procure host-iron, these depend on well-regulated iron homeostasis. To disrupt iron homeostasis, our work has targeted iron mobilization from the iron storage protein bacterioferritin (BfrB) by blocking a required interaction with its cognate ferredoxin partner (Bfd). The blockade of the BfrB-Bfd complex by deletion of the bfd gene (Δbfd) causes iron to irreversibly accumulate in BfrB. In this study we used mass spectrometry and NMR spectroscopy to compare the proteomic response and the levels of key intracellular metabolites between wild type (wt) and isogenic ΔbfdP. aeruginosa strains. We find that the irreversible accumulation of unusable iron in BfrB leads to acute intracellular iron limitation, even if the culture media is iron-sufficient. Importantly, the iron limitation and concomitant iron metabolism dysregulation trigger a cascade of events that lead to broader metabolic homeostasis disruption, which includes sulfur limitation, phenazine-mediated oxidative stress, suboptimal amino acid synthesis and altered carbon metabolism.

5.
Dis Model Mech ; 13(10)2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-32859697

RESUMO

The conserved B-subunit of succinate dehydrogenase (SDH) participates in the tricarboxylic acid cycle (TCA) cycle and mitochondrial electron transport. The Arg230His mutation in SDHB causes heritable pheochromocytoma/paraganglioma (PPGL). In Caenorhabditiselegans, we generated an in vivo PPGL model (SDHB-1 Arg244His; equivalent to human Arg230His), which manifests delayed development, shortened lifespan, attenuated ATP production and reduced mitochondrial number. Although succinate is elevated in both missense and null sdhb-1(gk165) mutants, transcriptomic comparison suggests very different causal mechanisms that are supported by metabolic analysis, whereby only Arg244His (not null) worms demonstrate elevated lactate/pyruvate levels, pointing to a missense-induced, Warburg-like aberrant glycolysis. In silico predictions of the SDHA-B dimer structure demonstrate that Arg230His modifies the catalytic cleft despite the latter's remoteness from the mutation site. We hypothesize that the Arg230His SDHB mutation rewires metabolism, reminiscent of metabolic reprogramming in cancer. Our tractable model provides a novel tool to investigate the metastatic propensity of this familial cancer and our approach could illuminate wider SDH pathology.This article has an associated First Person interview with the first author of the paper.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Proteínas Ferro-Enxofre/genética , Proteínas Mitocondriais/genética , Mutação/genética , Paraganglioma/genética , Succinato Desidrogenase/genética , Trifosfato de Adenosina/biossíntese , Sequência de Aminoácidos , Animais , Proteínas de Caenorhabditis elegans/química , Ciclo do Ácido Cítrico/genética , Sequência Conservada , Modelos Animais de Doenças , Perfilação da Expressão Gênica , Glicólise/genética , Humanos , Proteínas Ferro-Enxofre/química , L-Lactato Desidrogenase/antagonistas & inibidores , L-Lactato Desidrogenase/metabolismo , Mitocôndrias/metabolismo , Proteínas Mitocondriais/química , Fenótipo , Subunidades Proteicas/genética , Interferência de RNA , Succinato Desidrogenase/química
6.
Genes Immun ; 21(4): 260-262, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32606316

RESUMO

Cystic fibrosis (CF) is one of the most common autosomal recessive life-limiting conditions affecting Caucasians. The resulting defect in the cystic fibrosis transmembrane conductance regulator protein (CFTR) results in defective chloride and bicarbonate secretion, as well as dysregulation of epithelial sodium channels (ENaC). These changes bring about defective mucociliary clearance, reduced airway surface liquid and an exaggerated proinflammatory response driven, in part, by infection. In this short article we explore the overlap in the pathophysiology of CF and COVID-19 infection and discuss how understanding the interaction between both diseases may shed light on future treatments.


Assuntos
Infecções por Coronavirus/metabolismo , Fibrose Cística/metabolismo , Pneumonia Viral/metabolismo , Enzima de Conversão de Angiotensina 2 , Animais , COVID-19 , Infecções por Coronavirus/complicações , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Fibrose Cística/complicações , Fibrose Cística/tratamento farmacológico , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Citocinas/metabolismo , Humanos , Pandemias , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/complicações , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia
7.
Elife ; 92020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-32118580

RESUMO

Previously, we showed that serum and monocytes from patients with CF exhibit an enhanced NLRP3-inflammasome signature with increased IL-18, IL-1ß, caspase-1 activity and ASC speck release (Scambler et al. eLife 2019). Here we show that CFTR modulators down regulate this exaggerated proinflammatory response following LPS/ATP stimulation. In vitro application of ivacaftor/lumacaftor or ivacaftor/tezacaftor to CF monocytes showed a significant reduction in IL-18, whereas IL-1ß was only reduced with ivacaftor/tezacaftor. Thirteen adults starting ivacaftor/lumacaftor and eight starting ivacaftor/tezacaftor were assessed over three months. Serum IL-18 and TNF decreased significantly with treatments, but IL-1ß only declined following ivacaftor/tezacaftor. In (LPS/ATP-stimulated) PBMCs, IL-18/TNF/caspase-1 were all significantly decreased and IL-10 was increased with both combinations. Ivacaftor/tezacaftor alone showed a significant reduction in IL-1ß and pro-IL-1ß mRNA. This study demonstrates that these CFTR modulator combinations have potent anti-inflammatory properties, in addition to their ability to stimulate CFTR function, which could contribute to improved clinical outcomes.


Assuntos
Aminofenóis/uso terapêutico , Aminopiridinas/uso terapêutico , Benzodioxóis/uso terapêutico , Regulador de Condutância Transmembrana em Fibrose Cística/efeitos dos fármacos , Fibrose Cística/metabolismo , Indóis/uso terapêutico , Inflamação/metabolismo , Quinolonas/uso terapêutico , Adulto , Aminofenóis/administração & dosagem , Aminopiridinas/administração & dosagem , Benzodioxóis/administração & dosagem , Fibrose Cística/tratamento farmacológico , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Citocinas/metabolismo , Regulação para Baixo , Quimioterapia Combinada , Feminino , Humanos , Indóis/administração & dosagem , Inflamação/dietoterapia , Interleucina-18/sangue , Interleucina-1beta/sangue , Masculino , Monócitos/efeitos dos fármacos , Monócitos/metabolismo , Quinolonas/administração & dosagem , Fator de Necrose Tumoral alfa/sangue , Adulto Jovem
8.
Biomolecules ; 10(3)2020 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-32164257

RESUMO

The expression of functional, folded, and isotopically enriched membrane proteins is an enduring bottleneck for nuclear magnetic resonance (NMR) studies. Indeed, historically, protein yield optimization has been insufficient to allow NMR analysis of many complex Eukaryotic membrane proteins. However, recent work has found that manipulation of plasmid codons improves the odds of successful NMR-friendly protein production. In the last decade, numerous studies showed that matching codon usage patterns in recombinant gene sequences to those in the native sequence is positively correlated with increased protein yield. This phenomenon, dubbed codon harmonization, may be a powerful tool in optimizing recombinant expression of difficult-to-produce membrane proteins for structural studies. Here, we apply this technique to an inward rectifier K+ Channel (Kir) 3.1-KirBac1.3 chimera. Kir3.1 falls within the G protein-coupled inward rectifier K+ (GIRK) channel family, thus NMR studies may inform on the nuances of GIRK gating action in the presence and absence of its G Protein, lipid, and small molecule ligands. In our hands, harmonized plasmids increase protein yield nearly two-fold compared to the traditional 'fully codon optimized' construct. We then employ a fluorescence-based functional assay and solid-state NMR correlation spectroscopy to show the final protein product is folded and functional.


Assuntos
Canais de Potássio Corretores do Fluxo de Internalização Acoplados a Proteínas G , Dobramento de Proteína , Proteínas Recombinantes de Fusão , Escherichia coli/genética , Escherichia coli/metabolismo , Canais de Potássio Corretores do Fluxo de Internalização Acoplados a Proteínas G/biossíntese , Canais de Potássio Corretores do Fluxo de Internalização Acoplados a Proteínas G/química , Canais de Potássio Corretores do Fluxo de Internalização Acoplados a Proteínas G/genética , Humanos , Ressonância Magnética Nuclear Biomolecular , Proteínas Recombinantes de Fusão/biossíntese , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética
9.
Nanoscale ; 12(7): 4506-4518, 2020 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-32039428

RESUMO

Self-assembling peptides have garnered an increasing amount of interest as a functional biomaterial for medical and biotechnological applications. Recently, ß-sheet peptide designs utilizing complementary pairs of peptides composed of charged amino acids positioned to impart co-assembly behavior have expanded the portfolio of peptide aggregate structures. Structural characterization of these charge-complementary peptide co-assemblies has been limited. Thus, it is not known how the complementary peptides organize on the molecular level. Through a combination of solid-state NMR measurements and discontinuous molecular dynamics simulations, we investigate the molecular organization of King-Webb peptide nanofibers. KW+ and KW- peptides co-assemble into near stoichiometric two-component ß-sheet structures as observed by computational simulations and 13C-13C dipolar couplings. A majority of ß-strands are aligned with antiparallel nearest neighbors within the ß-sheet as previously suggested by Fourier transform infrared spectroscopy measurements. Surprisingly, however, a significant proportion of ß-strand neighbors are parallel. While charge-complementary peptides were previously assumed to organize in an ideal (AB)n pattern, dipolar recoupling measurements on isotopically diluted nanofiber samples reveal a non-negligible amount of self-associated (AA and BB) pairs. Furthermore, computational simulations predict these different structures can coexist within the same nanofiber. Our results highlight structural disorder at the molecular level in a charge-complementary peptide system with implications on co-assembling peptide designs.


Assuntos
Nanofibras/química , Peptídeos/química , Conformação Proteica em Folha beta , Espectroscopia de Infravermelho com Transformada de Fourier
10.
Pathol Oncol Res ; 26(1): 49-61, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31993913

RESUMO

Metastasis suppressor genes (MSGs) inhibit different biological processes during metastatic progression without globally influencing development of the primary tumor. The first MSG, NM23 (non-metastatic clone 23, isoform H1) or now called NME1 (stands for non-metastatic) was identified some decades ago. Since then, ten human NM23 paralogs forming two groups have been discovered. Group I NM23 genes encode enzymes with evolutionarily highly conserved nucleoside diphosphate kinase (NDPK) activity. In this review we summarize how results from NDPKs in model organisms converged on human NM23 studies. Next, we examine the role of NM23-H1 and its homologs within the metastatic cascade, e.g. cell migration and invasion, proliferation and apoptosis. NM23-H1 homologs are well known inhibitors of cell migration. Drosophila studies revealed that AWD, the fly counterpart of NM23-H1 is a negative regulator of cell motility by modulating endocytosis of chemotactic receptors on the surface of migrating cells in cooperation with Shibire/Dynamin; this mechanism has been recently confirmed by human studies. NM23-H1 inhibits proliferation of tumor cells by phosphorylating the MAPK scaffold, kinase suppressor of Ras (KSR), resulting in suppression of MAPK signalling. This mechanism was also observed with the C. elegans homolog, NDK-1, albeit with an inverse effect on MAPK activation. Both NM23-H1 and NDK-1 promote apoptotic cell death. In addition, NDK-1, NM23-H1 and their mouse counterpart NM23-M1 were shown to promote phagocytosis in an evolutionarily conserved manner. In summary, inhibition of cell migration and proliferation, alongside actions in apoptosis and phagocytosis are all mechanisms through which NM23-H1 acts against metastatic progression.


Assuntos
Nucleosídeo NM23 Difosfato Quinases/metabolismo , Metástase Neoplásica/patologia , Animais , Apoptose , Movimento Celular , Proliferação de Células , Humanos , Nucleosídeo NM23 Difosfato Quinases/genética , Invasividade Neoplásica , Metástase Neoplásica/genética , Núcleosídeo-Difosfato Quinase/genética , Núcleosídeo-Difosfato Quinase/metabolismo , Fagocitose
11.
Angew Chem Int Ed Engl ; 59(1): 358-363, 2020 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-31617300

RESUMO

Proteinaceous plaques associated with neurodegenerative diseases contain many biopolymers including the polyanions glycosaminoglycans and nucleic acids. Polyanion-induced amyloid fibrillation has been implicated in disease etiology, but structural models for amyloid/nucleic acid co-assemblies remain limited. Here we constrain nucleic acid/peptide interactions with model peptides that exploit electrostatic complementarity and define a novel amyloid/nucleic acid co-assembly. The structure provides a model for nucleic acid/amyloid co-assembly as well as insight into the energetic determinants involved in templating amyloid assembly.


Assuntos
Amiloide/química , Ácidos Nucleicos Peptídicos/química , Humanos , Modelos Moleculares , Eletricidade Estática
12.
J Am Chem Soc ; 142(1): 502-511, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31814397

RESUMO

Substituted triphenylamine (TPA) radical cations show great potential as oxidants and as spin-containing units in polymer magnets. Their properties can be further tuned by supramolecular assembly. Here, we examine how the properties of photogenerated radical cations, intrinsic to TPA macrocycles, are altered upon their self-assembly into one-dimensional columns. These macrocycles consist of two TPAs and two methylene ureas, which drive the assembly into porous organic materials. Advantageously, upon activation the crystals can undergo guest exchange in a single-crystal-to-single-crystal transformation generating a series of isoskeletal host-guest complexes whose properties can be directly compared. Photoinduced electron transfer, initiated using 365 nm light-emitting diodes, affords radicals at room temperature as observed by electron paramagnetic resonance (EPR) spectroscopy. The line shape of the EPR spectra and the quantity of radicals can be modulated by both polarity and heavy atom inclusion of the encapsulated guest. These photogenerated radicals are persistent, with half-lives between 1 and 7 d and display no degradation upon radical decay. Re-irradiation of the samples can restore the radical concentration back to a similar maximum concentration, a feature that is reproducible over several cycles. EPR simulations of a representative spectrum indicate two species, one containing two N hyperfine interactions and an additional broad signal with no resolvable hyperfine interaction. Intriguingly, TPA analogues without bromine substitution also exhibit similar quantities of photogenerated radicals, suggesting that supramolecular strategies can enable more flexibility in stable TPA radical structures. These studies will help guide the development of new photoactive materials.

13.
Mol Biol Rep ; 46(6): 6187-6195, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31486977

RESUMO

Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.


Assuntos
Antílopes/genética , Variação Genética , Genoma Mitocondrial , Genômica , Animais , Antílopes/classificação , Composição de Bases , Evolução Molecular , Genes Mitocondriais , Genética Populacional , Genômica/métodos , Índia , Filogenia
14.
FASEB J ; 33(10): 11606-11614, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31242766

RESUMO

Phagocytosis of various targets, such as apoptotic cells or opsonized pathogens, by macrophages is coordinated by a complex signaling network initiated by distinct phagocytic receptors. Despite the different initial signaling pathways, each pathway ends up regulating the actin cytoskeletal network, phagosome formation and closure, and phagosome maturation leading to degradation of the engulfed particle. Herein, we describe a new phagocytic function for the nucleoside diphosphate kinase 1 (NDK-1), the nematode counterpart of the first identified metastasis inhibitor NM23-H1 (nonmetastatic clone number 23) nonmetastatic clone number 23 or nonmetastatic isoform 1 (NME1). We reveal by coimmunoprecipitation, Duolink proximity ligation assay, and mass spectrometry that NDK-1/NME1 works in a complex with DYN-1/Dynamin (Caenorhabditis elegans/human homolog proteins), which is essential for engulfment and phagosome maturation. Time-lapse microscopy shows that NDK-1 is expressed on phagosomal surfaces during cell corpse clearance in the same time window as DYN-1. Silencing of NM23-M1 in mouse bone marrow-derived macrophages resulted in decreased phagocytosis of apoptotic thymocytes. In human macrophages, NM23-H1 and Dynamin are corecruited at sites of phagosome formation in F-actin-rich cups. In addition, NM23-H1 was required for efficient phagocytosis. Together, our data demonstrate that NDK-1/NME1 is an evolutionarily conserved element of successful phagocytosis.-Farkas, Z., Petric, M., Liu, X., Herit, F., Rajnavölgyi, É., Szondy, Z., Budai, Z., Orbán, T. I., Sándor, S., Mehta, A., Bajtay, Z., Kovács, T., Jung, S. Y., Afaq Shakir, M., Qin, J., Zhou, Z., Niedergang, F., Boissan, M., Takács-Vellai, K. The nucleoside diphosphate kinase NDK-1/NME1 promotes phagocytosis in concert with DYN-1/dynamin.


Assuntos
Proteínas de Caenorhabditis elegans/metabolismo , Dinaminas/metabolismo , Nucleosídeo NM23 Difosfato Quinases/metabolismo , Fagocitose/fisiologia , Actinas/metabolismo , Animais , Apoptose/fisiologia , Caenorhabditis elegans/metabolismo , Células Cultivadas , Humanos , Leucócitos Mononucleares/metabolismo , Macrófagos/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Fagossomos/metabolismo , Transdução de Sinais/fisiologia
15.
Angew Chem Int Ed Engl ; 58(13): 4210-4216, 2019 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-30672073

RESUMO

Solid-state NMR measurements coupled with density functional theory (DFT) calculations demonstrate how hydrogen positions can be refined in a crystalline system. The precision afforded by rotational-echo double-resonance (REDOR) NMR to interrogate 13 C-1 H distances is exploited along with DFT determinations of the 13 C tensor of carbonates (CO3 2- ). Nearby 1 H nuclei perturb the axial symmetry of the carbonate sites in the hydrated carbonate mineral, hydromagnesite [4 MgCO3 ⋅Mg(OH)2 ⋅4 H2 O]. A match between the calculated structure and solid-state NMR was found by testing multiple semi-local and dispersion-corrected DFT functionals and applying them to optimize atom positions, starting from X-ray diffraction (XRD)-determined atomic coordinates. This was validated by comparing calculated to experimental 13 C{1 H} REDOR and 13 C chemical shift anisotropy (CSA) tensor values. The results show that the combination of solid-state NMR, XRD, and DFT can improve structure refinement for hydrated materials.

16.
Anim Biotechnol ; 30(3): 193-201, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30522381

RESUMO

Musk deer are of high conservation priority owing to poaching pressure because of its musk pod. Representation of musk deer status using genetics is poorly documented in India, and it is not confirmed as to how many species of musk deer are present. We characterize for the first time, the genetic diversity of musk deer from Uttarakhand using Cytochrome Oxidase sub-unit (COI) gene (486 bp) and compared with the data available for other species. Results revealed the presence of six haplotypes in the Uttarakhand population amongst 17 sequences. Of these, 12 sequences shared the single haplotype. The intra-species sequences divergence was 0.003-0.017, whereas divergence with other species of musk deer was 0.071-0.081. Bayesian phylogenetic tree revealed that samples from Uttarakhand formed a separate clade with respect to other species of musk deer, whereas three species distributed in China clustered in the same clade and showed low sequences divergence, i.e., 0.002-0.061. Because of different ecomorph reported, we suggest using the barcoding based approach for inter and intra-species distinction and delineating species boundaries across the range for effective conservation. Besides, systematic classification, DNA barcoding would also help in dealing wildlife offence cases for disposal of the legal report in court.


Assuntos
Complexo IV da Cadeia de Transporte de Elétrons/genética , Variação Genética , Ruminantes/genética , Animais , Teorema de Bayes , Espécies em Perigo de Extinção , Geografia , Haplótipos , Índia , Filogenia , Ruminantes/classificação
17.
Sci Total Environ ; 647: 1256-1265, 2019 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-30180334

RESUMO

Research over the last decade on emerging trace organic contaminants in aquatic systems has largely focused on sources such as treated wastewaters in high income countries, with relatively few studies relating to wastewater sources of these contaminants in low and middle income countries. We undertook a longitudinal survey of the Ahar River for a number of emerging organic contaminants (including pharmaceuticals, hormones, personal care products and industrial chemicals) which flows through the city of Udaipur, India. Udaipur is a city of approximately 450,000 people with no wastewater treatment occurring at the time of this survey. We found the concentrations of many of the contaminants within the river water were similar to those commonly reported in untreated wastewater in high income countries. For example, concentrations of pharmaceuticals, such as carbamazepine, antibiotics and non-steroidal anti-inflammatory drugs, ranged up to 1900 ng/L. Other organic contaminants, such as steroid estrogens (up to 124 ng/L), steroid androgens (up to 1560 ng/L), benzotriazoles (up to 11 µg/L), DEET (up to 390 ng/L), BPA (up to 300 ng/L) and caffeine (up to 37.5 µg/L), were all similar to previously reported concentrations in wastewaters in high income countries. An assessment of the population densities in the watersheds feeding into the river showed increasing population density of a watershed led to a corresponding downstream increase in the concentrations of the organic contaminants, with quantifiable concentrations still present up to 10 km downstream of the areas directly adjacent to the highest population densities. Overall, this study highlights how a relatively clean river can be contaminated by untreated wastewater released from an urban centre.

18.
PLoS One ; 13(7): e0199815, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29985939

RESUMO

Patient registry data are commonly collected as annual snapshots that need to be amalgamated to understand the longitudinal progress of each patient. However, patient identifiers can either change or may not be available for legal reasons when longitudinal data are collated from patients living in different countries. Here, we apply astronomical statistical matching techniques to link individual patient records that can be used where identifiers are absent or to validate uncertain identifiers. We adopt a Bayesian model framework used for probabilistically linking records in astronomy. We adapt this and validate it across blinded, annually collected data. This is a high-quality (Danish) sub-set of data held in the European Cystic Fibrosis Society Patient Registry (ECFSPR). Our initial experiments achieved a precision of 0.990 at a recall value of 0.987. However, detailed investigation of the discrepancies uncovered typing errors in 27 of the identifiers in the original Danish sub-set. After fixing these errors to create a new gold standard our algorithm correctly linked individual records across years achieving a precision of 0.997 at a recall value of 0.987 without recourse to identifiers. Our Bayesian framework provides the probability of whether a pair of records belong to the same patient. Unlike other record linkage approaches, our algorithm can also use physical models, such as body mass index curves, as prior information for record linkage. We have shown our framework can create longitudinal samples where none existed and validate pre-existing patient identifiers. We have demonstrated that in this specific case this automated approach is better than the existing identifiers.


Assuntos
Fibrose Cística/epidemiologia , Conjuntos de Dados como Assunto/normas , Sistema de Registros , Teorema de Bayes , Confiabilidade dos Dados , Humanos
19.
Mitochondrial DNA B Resour ; 3(1): 250-255, 2018 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-33474133

RESUMO

DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra- and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra- and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.

20.
Lab Invest ; 98(2): 182-189, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-28920944

RESUMO

Abnormal regulation of cell migration and altered rearrangement of the cytoskeleton are fundamental properties of metastatic cells. The first identified metastasis suppressor NM23-H1, which displays nucleoside-diphosphate kinase (NDPK) activity is involved in these processes. NM23-H1 inhibits the migratory and invasive potential of some cancer cells. Correspondingly, numerous invasive cancer cell lines (eg, breast, colon, oral, hepatocellular carcinoma, and melanoma) display low endogenous NM23 levels. In this review, we summarize mechanisms, which are linked to the anti-metastatic activity of NM23. In human cancer cell lines NM23-H1 was shown to regulate cytoskeleton dynamics through inactivation of Rho/Rac-type GTPases. The Drosophila melanogaster NM23 homolog abnormal wing disc (AWD) controls tracheal and border cell migration. The molecular function of AWD is well characterized in both processes as a GTP supplier of Shi/Dynamin whereby AWD regulates the level of chemotactic receptors on the surface of migrating cells through receptor internalization, by its endocytic function. Our group studied the role of the sole group I NDPK, NDK-1 in distal tip cell (DTC) migration in Caenorhabditis elegans. In the absence of NDK-1 the migration of DTCs is incomplete. A half dosage of NDPK as present in ndk-1 (+/-) heterozygotes results in extra turns and overshoots of migrating gonad arms. Conversely, an elevated NDPK level also leads to incomplete gonadal migration owing to a premature stop of DTCs in the third phase of migration, where NDK-1 acts. We propose that NDK-1 exerts a dosage-dependent effect on the migration of DTCs. Our data derived from DTC migration in C. elegans is consistent with data on AWD's function in Drosophila. The combined data suggest that NDPK enzymes control the availability of surface receptors to regulate cell-sensing cues during cell migration. The dosage of NDPKs may be a coupling factor in cell migration by modulating the efficiency of receptor recycling.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Caenorhabditis elegans/genética , Movimento Celular/genética , Mutação , Nucleosídeo NM23 Difosfato Quinases/genética , Animais , Caenorhabditis elegans/enzimologia , Proteínas de Caenorhabditis elegans/metabolismo , Heterozigoto , Humanos , Nucleosídeo NM23 Difosfato Quinases/metabolismo , Transdução de Sinais/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA