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1.
PLoS Genet ; 19(8): e1010885, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37603562

RESUMEN

Regulation of the microtubule cytoskeleton is crucial for the development and maintenance of neuronal architecture, and recent studies have highlighted the significance of regulated RNA processing in the establishment and maintenance of neural circuits. In a genetic screen conducted using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1/mbl-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. Our findings demonstrate that mbl-1 is required cell-autonomously for axon growth and proper synapse positioning in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 leads to increased microtubule dynamics and mixed orientation of microtubules in the anterior neurite of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and reduction of gentle touch sensation in mbl-1 mutant. Our data also revealed that mbl-1 is genetically epistatic to mec-7 (ß tubulin) and mec-12 (α tubulin) in regulating axon growth. Furthermore, mbl-1 is epistatic to sad-1, an ortholog of BRSK/Brain specific-serine/threonine kinase and a known regulator of synaptic machinery, for synapse formation at the correct location of the PLM neurite. Notably, the immunoprecipitation of MBL-1 resulted in the co-purification of mec-7, mec-12, and sad-1 mRNAs, suggesting a direct interaction between MBL-1 and these transcripts. Additionally, mbl-1 mutants exhibited reduced levels and stability of mec-7 and mec-12 transcripts. Our study establishes a previously unknown link between RNA-binding proteins and cytoskeletal machinery, highlighting their crucial roles in the development and maintenance of the nervous system.


Asunto(s)
Caenorhabditis elegans , Tubulina (Proteína) , Animales , Tubulina (Proteína)/genética , Caenorhabditis elegans/genética , ARN Mensajero , Citoesqueleto/genética , Microtúbulos/genética , Neuronas
2.
PLoS Genet ; 18(3): e1010127, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35344539

RESUMEN

Neurons are vulnerable to physical insults, which compromise the integrity of both dendrites and axons. Although several molecular pathways of axon regeneration are identified, our knowledge of dendrite regeneration is limited. To understand the mechanisms of dendrite regeneration, we used the PVD neurons in C. elegans with stereotyped branched dendrites. Using femtosecond laser, we severed the primary dendrites and axon of this neuron. After severing the primary dendrites near the cell body, we observed sprouting of new branches from the proximal site within 6 hours, which regrew further with time in an unstereotyped manner. This was accompanied by reconnection between the proximal and distal dendrites, and fusion among the higher-order branches as reported before. We quantified the regeneration pattern into three aspects-territory length, number of branches, and fusion phenomena. Axonal injury causes a retraction of the severed end followed by a Dual leucine zipper kinase-1 (DLK-1) dependent regrowth from the severed end. We tested the roles of the major axon regeneration signalling hubs such as DLK-1-RPM-1, cAMP elevation, let-7 miRNA, AKT-1, Phosphatidylserine (PS) exposure/PS in dendrite regeneration. We found that neither dendrite regrowth nor fusion was affected by the axon injury pathway molecules. Surprisingly, we found that the RAC GTPase, CED-10 and its upstream GEF, TIAM-1 play a cell-autonomous role in dendrite regeneration. Additionally, the function of CED-10 in epidermal cell is critical for post-dendrotomy fusion phenomena. This work describes a novel regulatory mechanism of dendrite regeneration and provides a framework for understanding the cellular mechanism of dendrite regeneration using PVD neuron as a model system.


Asunto(s)
Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Proteína 1 de Invasión e Inducción de Metástasis del Linfoma-T , Proteínas de Unión al GTP rac , Animales , Axones/metabolismo , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Dendritas/metabolismo , GTP Fosfohidrolasas/metabolismo , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/metabolismo , Quinasas Quinasa Quinasa PAM/genética , Regeneración Nerviosa/genética , Factores de Intercambio de Guanina Nucleótido Rho/metabolismo , Proteína 1 de Invasión e Inducción de Metástasis del Linfoma-T/metabolismo , Proteínas de Unión al GTP rac/genética , Proteínas de Unión al GTP rac/metabolismo
3.
Development ; 148(11)2021 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-34109380

RESUMEN

The adult nervous system has a limited capacity to regenerate after accidental damage. Post-injury functional restoration requires proper targeting of the injured axon to its postsynaptic cell. Although the initial response to axonal injury has been studied in great detail, it is rather unclear what controls the re-establishment of a functional connection. Using the posterior lateral microtubule neuron in Caenorhabditis elegans, we found that after axotomy, the regrowth from the proximal stump towards the ventral side and accumulation of presynaptic machinery along the ventral nerve cord correlated to the functional recovery. We found that the loss of insulin receptor DAF-2 promoted 'ventral targeting' in a DAF-16-dependent manner. We further showed that coordinated activities of DAF-16 in neuron and muscle promoted 'ventral targeting'. In response to axotomy, expression of the Netrin receptor UNC-40 was upregulated in the injured neuron in a DAF-16-dependent manner. In contrast, the DAF-2-DAF-16 axis contributed to the age-related decline in Netrin expression in muscle. Therefore, our study revealed an important role for insulin signaling in regulating the axon guidance molecules during the functional rewiring process.


Asunto(s)
Axones/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/metabolismo , Moléculas de Adhesión Celular/metabolismo , Factores de Transcripción Forkhead/metabolismo , Netrinas/metabolismo , Animales , Orientación del Axón , Proteínas de Caenorhabditis elegans/genética , Moléculas de Adhesión Celular/genética , Factores de Transcripción Forkhead/genética , Regulación de la Expresión Génica , Microtúbulos/metabolismo , Factores de Crecimiento Nervioso/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Receptores de Netrina/metabolismo , Netrinas/genética , Neuronas/metabolismo , Transducción de Señal
4.
PLoS Genet ; 17(2): e1009346, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33524034

RESUMEN

Ethanol is a widely used drug, excessive consumption of which could lead to medical conditions with diverse symptoms. Ethanol abuse causes dysfunction of memory, attention, speech and locomotion across species. Dopamine signaling plays an essential role in ethanol dependent behaviors in animals ranging from C. elegans to humans. We devised an ethanol dependent assay in which mutants in the dopamine autoreceptor, dop-2, displayed a unique sedative locomotory behavior causing the animals to move in circles while dragging the posterior half of their body. Here, we identify the posterior dopaminergic sensory neuron as being essential to modulate this behavior. We further demonstrate that in dop-2 mutants, ethanol exposure increases dopamine secretion and functions in a DVA interneuron dependent manner. DVA releases the neuropeptide NLP-12 that is known to function through cholinergic motor neurons and affect movement. Thus, DOP-2 modulates dopamine levels at the synapse and regulates alcohol induced movement through NLP-12.


Asunto(s)
Caenorhabditis elegans/efectos de los fármacos , Neuronas Dopaminérgicas/efectos de los fármacos , Etanol/farmacología , Transmisión Sináptica/efectos de los fármacos , Animales , Caenorhabditis elegans/genética , Caenorhabditis elegans/fisiología , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/fisiología , Depresores del Sistema Nervioso Central/farmacología , Dopamina/metabolismo , Neuronas Dopaminérgicas/fisiología , Humanos , Locomoción/efectos de los fármacos , Neuronas Motoras/efectos de los fármacos , Neuronas Motoras/fisiología , Mutación , Neuropéptidos/metabolismo , Receptores de Dopamina D2/genética , Receptores de Dopamina D2/fisiología , Transducción de Señal/efectos de los fármacos
5.
J Am Chem Soc ; 145(26): 14307-14315, 2023 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-37341421

RESUMEN

The catalytic versatility of pentacoordinated iron is highlighted by the broad range of natural and engineered activities of heme enzymes such as cytochrome P450s, which position a porphyrin cofactor coordinating a central iron atom below an open substrate binding pocket. This catalytic prowess has inspired efforts to design de novo helical bundle scaffolds that bind porphyrin cofactors. However, such designs lack the large open substrate binding pocket of P450s, and hence, the range of chemical transformations accessible is limited. Here, with the goal of combining the advantages of the P450 catalytic site geometry with the almost unlimited customizability of de novo protein design, we design a high-affinity heme-binding protein, dnHEM1, with an axial histidine ligand, a vacant coordination site for generating reactive intermediates, and a tunable distal pocket for substrate binding. A 1.6 Å X-ray crystal structure of dnHEM1 reveals excellent agreement to the design model with key features programmed as intended. The incorporation of distal pocket substitutions converted dnHEM1 into a proficient peroxidase with a stable neutral ferryl intermediate. In parallel, dnHEM1 was redesigned to generate enantiocomplementary carbene transferases for styrene cyclopropanation (up to 93% isolated yield, 5000 turnovers, 97:3 e.r.) by reconfiguring the distal pocket to accommodate calculated transition state models. Our approach now enables the custom design of enzymes containing cofactors adjacent to binding pockets with an almost unlimited variety of shapes and functionalities.


Asunto(s)
Hemo , Porfirinas , Hemo/química , Metales , Sistema Enzimático del Citocromo P-450/metabolismo , Hierro/química , Porfirinas/química , Sitios de Unión
6.
Am J Obstet Gynecol ; 228(2): 224.e1-224.e16, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-35952840

RESUMEN

BACKGROUND: Prenatal omega-3 fatty acid supplementation, particularly docosahexaenoic acid and eicosapentaenoic acid, has been associated with greater birthweight in clinical trials; however, its effect on fetal growth throughout gestation is unknown. OBJECTIVE: This study aimed to examine the association between first-trimester docosahexaenoic acid and eicosapentaenoic acid supplementation and growth trajectories of estimated fetal weight and specific fetal biometrics measured longitudinally from the second trimester of pregnancy to delivery. STUDY DESIGN: In a multisite, prospective cohort of racially diverse, low-risk pregnant women, we used secondary data analysis to examine fetal growth trajectories in relation to self-reported (yes or no) first-trimester docosahexaenoic acid and eicosapentaenoic acid supplementation. Fetal ultrasonographic measurements, including abdominal circumference, biparietal diameter, femur length, head circumference, and humerus length, were measured at enrollment (8-13 weeks) and up to 5 follow-up visits. Estimated fetal weight and head circumference-to-abdominal circumference ratio (a measure of growth symmetry) were calculated. Fetal growth trajectories were modeled for each measure using a linear mixed model with cubic splines. If significant differences in fetal growth trajectories between groups were observed (global P<.05), weekly comparisons were performed to determine when in gestation these differences emerged. Analyses were adjusted for maternal sociodemographics, parity, infant sex, total energy consumption, and diet quality score. All analyses were repeated using dietary docosahexaenoic acid and eicosapentaenoic acid intake, dichotomized at the recommended cutoff for pregnant and lactating women (≥0.25 vs <0.25 g/d), among women who did not report supplement intake in the first trimester of pregnancy were repeated. RESULTS: Among 1535 women, 143 (9%) reported docosahexaenoic acid and eicosapentaenoic acid supplementation in the first trimester of pregnancy. Overall, first-trimester docosahexaenoic acid and eicosapentaenoic acid supplementation was associated with statistically significant differences (P-value <.05) in fetal growth trajectories during pregnancy. Specifically, estimated fetal weight was larger among women with docosahexaenoic acid and eicosapentaenoic acid supplementation than among those without supplementation (global P=.028) with significant weekly differences in median estimated fetal weight most apparent between 38 to 41 weeks of gestation (median estimated fetal weight difference at 40 weeks of gestation, 114 g). Differences in fetal growth trajectories for abdominal circumference (P=.003), head circumference (P=.003), and head circumference-to-abdominal circumference ratio (P=.0004) were also identified by supplementation status. In weekly comparisons, docosahexaenoic acid and eicosapentaenoic acid supplement use was associated with larger median abdominal circumference (changed from 2 to 9 mm) in midpregnancy onward (19 to 41 weeks), larger median head circumference between 30 to 33 weeks of gestation, and smaller median head circumference-to-abdominal circumference ratio in the second and third trimesters of pregnancy. There was no specific weekly difference in fetal femur length or humerus length by docosahexaenoic acid and eicosapentaenoic acid supplementation. First-trimester dietary sources of docosahexaenoic acid and eicosapentaenoic acid among women with no first-trimester docosahexaenoic acid and eicosapentaenoic acid supplementation (n=1392) were associated with differences in fetal biparietal diameter (P=.043), but not other metrics of fetal growth. At the recommended dietary docosahexaenoic acid and eicosapentaenoic acid levels compared with below-recommended levels, biparietal diameter was larger between 38 to 41 weeks of gestation. CONCLUSION: In this racially diverse pregnancy cohort, first-trimester docosahexaenoic acid and eicosapentaenoic acid supplementation was associated with significant increases in fetal growth, specifically greater estimated fetal abdominal circumference in the second and third trimesters of pregnancy.


Asunto(s)
Ácidos Grasos Omega-3 , Embarazo , Femenino , Humanos , Peso Fetal , Primer Trimestre del Embarazo , Ácidos Docosahexaenoicos , Ácido Eicosapentaenoico , Estudios Prospectivos , Lactancia , Desarrollo Fetal , Suplementos Dietéticos , Ultrasonografía Prenatal
7.
Stat Med ; 41(9): 1555-1572, 2022 04 30.
Artículo en Inglés | MEDLINE | ID: mdl-35040178

RESUMEN

Often both aggregate data (AD) studies and individual participant data (IPD) studies are available for specific treatments. Combining these two sources of data could improve the overall meta-analytic estimates of treatment effects. Moreover, often for some studies with AD, the associated IPD maybe available, albeit at some extra effort or cost to the analyst. We propose a method for combining treatment effects across trials when the response is from the exponential family of distribution and hence a generalized linear model structure can be used. We consider the case when treatment effects are fixed and common across studies. Using the proposed combination method, we study the relative efficiency of analyzing all IPD studies vs combining various percentages of AD and IPD studies. For many different models, design constraints under which the AD estimators are the IPD estimators, and hence fully efficient, are known. For such models, we advocate a selection procedure that chooses AD studies over IPD studies in a manner that force least departure from design constraints and hence ensures an efficient combined AD and IPD estimator.


Asunto(s)
Proyectos de Investigación , Interpretación Estadística de Datos , Humanos , Modelos Lineales , Metaanálisis como Asunto
8.
Muscle Nerve ; 63(2): 181-191, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33150975

RESUMEN

BACKGROUND: Quantifying associations between genetic mutations and loss of ambulation (LoA) among males diagnosed with childhood-onset dystrophinopathy is important for understanding variation in disease progression and may be useful in clinical trial design. METHODS: Genetic and clinical data from the Muscular Dystrophy Surveillance, Tracking, and Research Network for 358 males born and diagnosed from 1982 to 2011 were analyzed. LoA was defined as the age at which independent ambulation ceased. Genetic mutations were defined by overall type (deletion/duplication/point mutation) and among deletions, those amenable to exon-skipping therapy (exons 8, 20, 44-46, 51-53) and another group. Cox proportional hazards regression modeling was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS: Mutation type did not predict time to LoA. Controlling for corticosteroids, Exons 8 (HR = 0.22; 95% CI = 0.08, 0.63) and 44 (HR = 0.30; 95% CI = 0.12, 0.78) were associated with delayed LoA compared to other exon deletions. CONCLUSIONS: Delayed LoA in males with mutations amenable to exon-skipping therapy is consistent with previous studies. These findings suggest that clinical trials including exon 8 and 44 skippable males should consider mutation information prior to randomization.


Asunto(s)
Distrofina/genética , Limitación de la Movilidad , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/fisiopatología , Adolescente , Corticoesteroides/uso terapéutico , Niño , Deambulación Dependiente , Progresión de la Enfermedad , Exones , Duplicación de Gen , Humanos , Masculino , Distrofia Muscular de Duchenne/tratamiento farmacológico , Mutación Puntual , Modelos de Riesgos Proporcionales , Eliminación de Secuencia , Silla de Ruedas
9.
Chemistry ; 26(28): 6240-6246, 2020 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-32201996

RESUMEN

Hybrid protein-organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe-Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species FeI Fe0 when incorporated within streptavidin compared to the biotinylated catalyst in solution.

10.
Methods ; 159-160: 146-156, 2019 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-30769100

RESUMEN

Transcribing RNA polymerase II (RNAPII) is decorated by a plethora of post-translational modifications that mark different stages of transcription. One important modification is RNAPII ubiquitylation, which occurs in response to numerous different stimuli that cause RNAPII stalling, such as DNA damaging agents, RNAPII inhibitors, or depletion of the nucleotide pool. Stalled RNAPII triggers a so-called "last resort pathway", which involves RNAPII poly-ubiquitylation and proteasome-mediated degradation. Different approaches have been described to study RNAPII poly-ubiquitylation and degradation, each method with its own advantages and caveats. Here, we describe optimised strategies for detecting ubiquitylated RNAPII and studying its degradation, but these protocols are suitable for studying other ubiquitylated proteins as well.


Asunto(s)
ARN Polimerasa II/análisis , ARN Polimerasa II/metabolismo , Ubiquitinación , Animales , Daño del ADN , Humanos , Mamíferos/genética , Mamíferos/metabolismo , Complejo de la Endopetidasa Proteasomal/metabolismo , Proteolisis , ARN Polimerasa II/antagonistas & inhibidores , ARN Polimerasa II/genética , Transcripción Genética , Rayos Ultravioleta , Levaduras/enzimología , Levaduras/genética , Levaduras/metabolismo
11.
Proc Natl Acad Sci U S A ; 114(47): E10206-E10215, 2017 11 21.
Artículo en Inglés | MEDLINE | ID: mdl-29109254

RESUMEN

Neuronal injury often leads to devastating consequences such as loss of senses or locomotion. Restoration of function after injury relies on whether the injured axons can find their target cells. Although fusion between injured proximal axon and distal fragment has been observed in many organisms, its functional significance is not clear. Here, using Caenorhabditis elegans mechanosensory neurons, we address this question. Using two femtosecond lasers simultaneously, we could scan and sever posterior lateral microtubule neurons [posterior lateral microtubules (PLMs)] on both sides of the worm. We showed that axotomy of both PLMs leads to a dramatic loss of posterior touch sensation. During the regenerative phase, only axons that fuse to their distal counterparts contribute to functional recovery. Loss of let-7 miRNA promotes functional restoration in both larval and adult stages. In the L4 stage, loss of let-7 increases fusion events by increasing the mRNA level of one of the cell-recognition molecules, CED-7. The ability to establish cytoplasmic continuity between the proximal and distal ends declines with age. Loss of let-7 overcomes this barrier by promoting axonal transport and enrichment of the EFF-1 fusogen at the growing tip of cut processes. Our data reveal the functional property of a regenerating neuron.


Asunto(s)
Transportadoras de Casetes de Unión a ATP/metabolismo , Axones/fisiología , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/fisiología , Caenorhabditis elegans/fisiología , Glicoproteínas de Membrana/fisiología , MicroARNs/metabolismo , Regeneración Nerviosa/genética , Células Receptoras Sensoriales/fisiología , Animales , Transporte Axonal/fisiología , Axotomía , Citoplasma/fisiología , Microtúbulos/fisiología , Tacto
13.
Biochim Biophys Acta ; 1857(5): 598-603, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26375327

RESUMEN

Bioinspired, protein-based molecular catalysts utilizing base metals at the active are emerging as a promising avenue to sustainable hydrogen production. The protein matrix modulates the intrinsic reactivity of organometallic active sites by tuning second-sphere and long-range interactions. Here, we show that swapping Co-Protoporphyrin IX for Fe-Protoporphyrin IX in cytochrome b562 results in an efficient catalyst for photoinduced proton reduction to molecular hydrogen. Further, the activity of wild type Co-cyt b562 can be modulated by a factor of 2.5 by exchanging the coordinating methionine with alanine or aspartic acid. The observed turnover numbers (TON) range between 125 and 305, and correlate well with the redox potential of the Co-cyt b562 mutants. The photosensitized system catalyzes proton reduction with high efficiency even under an aerobic atmosphere, implicating its use for biotechnological applications. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.


Asunto(s)
Grupo Citocromo b , Proteínas de Escherichia coli , Hidrógeno/metabolismo , Ingeniería de Proteínas/métodos , Catálisis , Dominio Catalítico/genética , Cobalto/química , Cobalto/metabolismo , Grupo Citocromo b/química , Grupo Citocromo b/genética , Grupo Citocromo b/metabolismo , Citocromos c/química , Citocromos c/genética , Citocromos c/metabolismo , Escherichia coli/enzimología , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Hidrogenasas/química , Hidrogenasas/genética , Hidrogenasas/metabolismo , Hierro/química , Hierro/metabolismo , Modelos Moleculares , Mutagénesis , Unión Proteica/genética , Protoporfirinas/química , Protoporfirinas/metabolismo , Biología Sintética/métodos
14.
Biometrics ; 72(1): 299-302, 2016 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26393800

RESUMEN

In the context of group testing screening, McMahan, Tebbs, and Bilder (2012, Biometrics 68, 287-296) proposed a two-stage procedure in a heterogenous population in the presence of misclassification. In earlier work published in Biometrics, Kim, Hudgens, Dreyfuss, Westreich, and Pilcher (2007, Biometrics 63, 1152-1162) also proposed group testing algorithms in a homogeneous population with misclassification. In both cases, the authors evaluated performance of the algorithms based on the expected number of tests per person, with the optimal design being defined by minimizing this quantity. The purpose of this article is to show that although the expected number of tests per person is an appropriate evaluation criteria for group testing when there is no misclassification, it may be problematic when there is misclassification. Specifically, a valid criterion needs to take into account the amount of correct classification and not just the number of tests. We propose, a more suitable objective function that accounts for not only the expected number of tests, but also the expected number of correct classifications. We then show how using this objective function that accounts for correct classification is important for design when considering group testing under misclassification. We also present novel analytical results which characterize the optimal Dorfman (1943) design under the misclassification.


Asunto(s)
Algoritmos , Artefactos , Biometría/métodos , Infecciones por Chlamydia/epidemiología , Interpretación Estadística de Datos , Gonorrea/epidemiología , Infecciones por VIH/diagnóstico , Infecciones por VIH/epidemiología , Tamizaje Masivo/métodos , Vigilancia de la Población/métodos , Medición de Riesgo/métodos , Humanos
15.
Biophys J ; 109(5): 1038-48, 2015 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-26331261

RESUMEN

We provide the first direct experimental comparison, to our knowledge, between the internal dynamics of calcitonin-gene-related peptide (CGRP) and amylin (islet amyloid polypeptide, IAPP), two intrinsically disordered proteins of the calcitonin peptide family. Our end-to-end contact formation measurements reveal that in aqueous solution (i.e., in the absence of structure-inducing organic solvents) CGRP preferentially populates conformations with short end-to-end distances. However, the end-to-end distance of CGRP is larger than that of IAPP. We find that electrostatic interactions can account for such a difference. At variance with previous reports on the secondary structure of CGRP, we find that the end-to-end distance of the peptide increases with decreasing pH and salt concentration, due to Coulomb repulsion by charged residues. Interestingly, our data show that the reconfiguration dynamics of CGRP is significantly slower than that of human IAPP in water but not in denaturant, providing experimental evidence for roughness in the energy landscape, or internal friction, in these peptides. The data reported here provide both structural and dynamical information that can be used to validate results from molecular simulations of calcitonin family peptides in aqueous solution.


Asunto(s)
Péptido Relacionado con Gen de Calcitonina/química , Péptido Relacionado con Gen de Calcitonina/metabolismo , Proteínas Intrínsecamente Desordenadas/química , Proteínas Intrínsecamente Desordenadas/metabolismo , Polipéptido Amiloide de los Islotes Pancreáticos/química , Polipéptido Amiloide de los Islotes Pancreáticos/metabolismo , Secuencia de Aminoácidos , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Electricidad Estática
16.
J Proteome Res ; 14(1): 183-92, 2015 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-25285964

RESUMEN

Chemical interactions have posed a big challenge in toxicity characterization and human health risk assessment of environmental mixtures. To characterize the impacts of chemical interactions on protein and cytotoxicity responses to environmental mixtures, we established a systems biology approach integrating proteomics, bioinformatics, statistics, and computational toxicology to measure expression or phosphorylation levels of 21 critical toxicity pathway regulators and 445 downstream proteins in human BEAS-2B cells treated with 4 concentrations of nickel, 2 concentrations each of cadmium and chromium, as well as 12 defined binary and 8 defined ternary mixtures of these metals in vitro. Multivariate statistical analysis and mathematical modeling of the metal-mediated proteomic response patterns showed a high correlation between changes in protein expression or phosphorylation and cellular toxic responses to both individual metals and metal mixtures. Of the identified correlated proteins, only a small set of proteins including HIF-1α is likely to be responsible for selective cytotoxic responses to different metals and metals mixtures. Furthermore, support vector machine learning was utilized to computationally predict protein responses to uncharacterized metal mixtures using experimentally generated protein response profiles corresponding to known metal mixtures. This study provides a novel proteomic approach for characterization and prediction of toxicities of metal and other chemical mixtures.


Asunto(s)
Cadmio/toxicidad , Cromo/toxicidad , Contaminantes Ambientales/toxicidad , Níquel/toxicidad , Proteoma/metabolismo , Apoptosis/efectos de los fármacos , Línea Celular , Análisis por Conglomerados , Relación Dosis-Respuesta a Droga , Interacciones Farmacológicas , Expresión Génica/efectos de los fármacos , Gluconeogénesis/efectos de los fármacos , Glucólisis/efectos de los fármacos , Humanos , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Fosforilación , Procesamiento Proteico-Postraduccional , Proteoma/genética , Proteómica , Medición de Riesgo
17.
Biopolymers ; 104(4): 412-8, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25808361

RESUMEN

iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.


Asunto(s)
Proteínas Hierro-Azufre/química , Hierro/química , Péptidos/química , Azufre/química , Transporte de Electrón
18.
J Biopharm Stat ; 25(6): 1234-46, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25372337

RESUMEN

For the statistical validation of surrogate endpoints, an alternative formulation is proposed for testing Prentice's fourth criterion, under a bivariate normal model. In such a setup, the criterion involves inference concerning an appropriate regression parameter, and the criterion holds if the regression parameter is zero. Testing such a null hypothesis has been criticized in the literature since it can only be used to reject a poor surrogate, and not to validate a good surrogate. In order to circumvent this, an equivalence hypothesis is formulated for the regression parameter, namely the hypothesis that the parameter is equivalent to zero. Such an equivalence hypothesis is formulated as an alternative hypothesis, so that the surrogate endpoint is statistically validated when the null hypothesis is rejected. Confidence intervals for the regression parameter and tests for the equivalence hypothesis are proposed using bootstrap methods and small sample asymptotics, and their performances are numerically evaluated and recommendations are made. The choice of the equivalence margin is a regulatory issue that needs to be addressed. The proposed equivalence testing formulation is also adopted for other parameters that have been proposed in the literature on surrogate endpoint validation, namely, the relative effect and proportion explained.


Asunto(s)
Determinación de Punto Final/estadística & datos numéricos , Algoritmos , Intervalos de Confianza , Interpretación Estadística de Datos , Humanos , Funciones de Verosimilitud , Modelos Estadísticos , Reproducibilidad de los Resultados , Equivalencia Terapéutica
19.
J Am Chem Soc ; 136(49): 17343-9, 2014 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-25437708

RESUMEN

[Fe-S] clusters, nature's modular electron transfer units, are often arranged in chains that support long-range electron transfer. Despite considerable interest, the design of biomimetic artificial systems emulating multicluster-binding proteins, with the final goal of integrating them in man-made oxidoreductases, remains elusive. Here, we report a novel bis-[4Fe-4S] cluster binding protein, DSD-Fdm, in which the two clusters are positioned within a distance of 12 Å, compatible with the electronic coupling necessary for efficient electron transfer. The design exploits the structural repeat of coiled coils as well as the symmetry of the starting scaffold, a homodimeric helical protein (DSD). In total, eight hydrophobic residues in the core of DSD were replaced by eight cysteine residues that serve as ligands to the [4Fe-4S] clusters. Incorporation of two [4Fe-4S] clusters proceeds with high yield. The two [4Fe-4S] clusters are located in the hydrophobic core of the helical bundle as characterized by various biophysical techniques. The secondary structure of the apo and holo proteins is conserved; further, the incorporation of clusters results in stabilization of the protein with respect to chemical denaturation. Most importantly, this de novo designed protein can mimic the function of natural ferredoxins: we show here that reduced DSD-Fdm transfers electrons to cytochrome c, thus generating the reduced cyt c stoichiometrically.


Asunto(s)
Ferredoxinas/química , Transporte de Electrón , Ferredoxinas/síntesis química , Modelos Moleculares , Conformación Proteica , Estabilidad Proteica
20.
Dalton Trans ; 2024 Oct 30.
Artículo en Inglés | MEDLINE | ID: mdl-39479915

RESUMEN

The development of active therapeutic agents to treat highly metastatic cancer while minimizing damage to healthy cells is of utmost importance. Due to potential antioxidant properties, hydroxycinnamic acid derivatives (caffeic acid and p-coumaric acids) were found to inhibit highly metastatic breast cancer cell growth both in vitro and in vivo without much effect on normal cells. Especially due to the structure-activity relationships, ester and amide derivatives of hydroxycinnamic acids are reported to gain much higher radical scavenging ability than their naked hydroxycinnamic acid analogs like caffeic acid and p-coumaric acid. These results prompted us to design a set of ligands by incorporating an amide moiety on caffeic acid and p-coumaric acid to achieve the least toxicity towards healthy cell lines. Further, the Cu(II) complexes of amide-coupled caffeic acid and p-coumaric acid ligands have been explored for their therapeutic activity on triple-negative breast cancer and other cancer cells like colon, and prostate cancer. The Cu(II) complexes (4 & 5) were characterized by UV-Vis spectroscopy, FTIR, and X-band EPR spectroscopy. The trigonal bipyramidal geometry of complexes was confirmed by the X-band EPR spectra recorded in solution state at liquid N2 temperature. The purity of the complexes was determined by elemental analysis and HPLC traces. Initially, Calf thymus DNA (ct-DNA) binding studies with the complexes were explored. The results suggested the complexes (4 & 5) bind majorly through an intercalative mode of binding with ct-DNA, whereas no significant binding was observed for the bare organic ligands (2 & 3). The intercalation binding modes of 4 and 5 were further supported by UV-visible spectroscopy, ct-DNA melting point analysis, and CD spectroscopy. Moreover, these complexes showed better activity towards cisplatin-resistant TNBC cell lines (4T1, a TNBC cell line derived from the mammary gland tissue of a mouse). The combination of antioxidants and Cu(II) as the metal center made the complexes more cytotoxic toward cancer cell lines (4T1) (IC50 ∼ 3.5 ± 2.5 µM) and the least toxic toward healthy cells (L929) (IC50 ∼ 15 ± 5 µM). Finally, the mechanism of cell death was studied using JC-1 staining and a cell colony formation assay. These studies might help in designing safer anticancer drugs for treating more aggressive types of cancer.

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