From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity

Lung adenocarcinoma accounts for ∼40% of lung cancers, the leading cause of cancer-related death worldwide, and current therapies provide only limited survival benefit. Approximately half of lung adenocarcinomas harbor mutations in TP53 (p53), making these mutants appealing targets for lung cancer therapy. As mutant p53 remains untargetable, mutant p53-dependent phenotypes represent alternative targeting opportunities, but the prevalence and therapeutic relevance of such effects (gain of function and dominant-negative activity) in lung adenocarcinoma are unclear. Through transcriptional and functional analysis of murine Kras(G12D) -p53(null) , -p53(R172H) (conformational), and -p53(R270H) (contact) mutant lung tumors, we identified genotype-independent and genotype-dependent therapeutic sensitivities. Unexpectedly, we found that wild-type p53 exerts a dominant tumor-suppressive effect on mutant tumors, as all genotypes were similarly sensitive to its restoration in vivo. These data show that the potential of p53 targeted therapies is comparable across all p53-deficient genotypes and may explain the high incidence of p53 loss of heterozygosity in mutant tumors. In contrast, mutant p53 gain of function and their associated vulnerabilities can vary according to mutation type. Notably, we identified a p53(R270H) -specific sensitivity to simvastatin in lung tumors, and the transcriptional signature that underlies this sensitivity was also present in human lung tumors, indicating that this therapeutic approach may be clinically relevant.This work was supported by the Medical Research Council

Lung tumors with distinct p53 mutations respond similarly to p53 targeted therapy but exhibit genotype-specific statin sensitivity

Lung adenocarcinoma accounts for ∼40% of lung cancers, the leading cause of cancer-related death worldwide, and current therapies provide only limited survival benefit. Approximately half of lung adenocarcinomas harbor mutations in TP53 (p53), making these mutants appealing targets for lung cancer therapy. As mutant p53 remains untargetable, mutant p53-dependent phenotypes represent alternative targeting opportunities, but the prevalence and therapeutic relevance of such effects (gain of function and dominant-negative activity) in lung adenocarcinoma are unclear. Through transcriptional and functional analysis of murine Kras(G12D) -p53(null) , -p53(R172H) (conformational), and -p53(R270H) (contact) mutant lung tumors, we identified genotype-independent and genotype-dependent therapeutic sensitivities. Unexpectedly, we found that wild-type p53 exerts a dominant tumor-suppressive effect on mutant tumors, as all genotypes were similarly sensitive to its restoration in vivo. These data show that the potential of p53 targeted therapies is comparable across all p53-deficient genotypes and may explain the high incidence of p53 loss of heterozygosity in mutant tumors. In contrast, mutant p53 gain of function and their associated vulnerabilities can vary according to mutation type. Notably, we identified a p53(R270H) -specific sensitivity to simvastatin in lung tumors, and the transcriptional signature that underlies this sensitivity was also present in human lung tumors, indicating that this therapeutic approach may be clinically relevant.This work was supported by the Medical Research Council

The regulatory mechanism of fungal elicitor-induced secondary metabolite biosynthesis in medical plants.

A wide range of external stress stimuli trigger plant cells to undergo complex network of reactions that ultimately lead to the synthesis and accumulation of secondary metabolites. Accumulation of such metabolites often occurs in plants subjected to stresses including various elicitors or signal molecules. Throughout evolution, endophytic fungi, an important constituent in the environment of medicinal plants, have known to form long-term stable and mutually beneficial symbiosis with medicinal plants. The endophytic fungal elicitor can rapidly and specifically induce the expression of specific genes in medicinal plants which can result in the activation of a series of specific secondary metabolic pathways resulting in the significant accumulation of active ingredients. Here we summarize the progress made on the mechanisms of fungal elicitor including elicitor signal recognition, signal transduction, gene expression and activation of the key enzymes and its application. This review provides guidance on studies which may be conducted to promote the efficient synthesis and accumulation of active ingredients by the endogenous fungal elicitor in medicinal plant cells, and provides new ideas and methods of studying the regulation of secondary metabolism in medicinal plants

Hysteresis-free perovskite transistor with exceptional stability through molecular cross-linking and amine-based surface passivation

This is the author accepted manuscript. The final version is available from the Royal Society of Chemistry via the DOI in this recordOrgano-metal halide perovskite field-effect transistors present serious challenges in terms of device stability and hysteresis in the current-voltage characteristics. Migration of ions located at grain boundaries and surface defects in the perovskite film are the main reasons for instability and hysteresis issues. Here, we introduce a perovskite grains molecular cross-linking approach combined with amine-based surface passivation to face these issues. Molecular cross-linking was achieved through hydrogen bond interactions between perovskite halogens and dangling bonds present at grain boundaries and a hydrophobic cross-linker, namely diethyl-(12-phosphonododecyl)phosphonate, added to the precursor solution. With our approach we obtained smooth and compact perovskite layers composed of few and tightly bound grains hence significantly suppressing the generation and migration of ions. Moreover, we obtained efficient surface passivation of the perovskite films upon surface treatment with an amine-bearing polymer, namely polyethylenimine ethoxylated. With our synergistic grain and surface passivation approach we were able to demonstrate the first perovskite transistor with complete lack of hysteresis and unprecedented stability upon continuous operation under ambient conditions. Added to the merits are its ambipolar transport of opposite carriers with balanced hole and electron mobilities of 4.02 and 3.35 cm2 V−1 s−1, respectively, its high Ion/Ioff ratio >104 and the lowest sub-thresshold swing of 267 mV dec-1 reported to date for any perovskite transistor. These remarkable achievements obtained through a cost-effective molecular cross-linking of grains combined with amine-based surface passivation in the perovskite films open new eras and pave the way for the practical application of perovskite transistors on low-cost electronic circuits.European Unio

Recombinant family 3 carbohydrate-binding module as a new additive for enhanced enzymatic saccharification of whole slurry from autohydrolyzed eucalyptus globulus wood

By-products resulting from lignocellulosics pretreatment affect the digestibility of resulting whole slurries, but this can be minimized by additives supplementation. In this work, a family 3 carbohydrate-binding module (CBM3), recombinantly produced from Escherichia coli, was used as additive in the enzymatic hydrolysis of the whole slurry from autohydrolyzed Eucalyptus globulus wood (EGW). At the higher dosage used (30 mg/gsolids), CBM3 led to an increase in glucose yield from 75 to 89%. A similar result was obtained for bovine serum albumin (BSA) (11% increase), which has a well-documented additive effect. CBM3 had no effect on the non-productive binding of enzymes, since it could not bind to EGW lignin, while it rapidly bound to cellulose, as shown by fluorescence microscopy. CBM3 is a valid additive for enhanced lignocellulosic saccharification and a valuable alternative to costly additives (e.g. polyethylene glycol) as it can be affordably produced from heterologous bacterium, thus contributing to more cost-efficient biomass valorization bioprocesses.This work was developed under the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte. The research leading to the reported results has received funding from Fundação para a Ciência e a Tecnologia (FCT) through the project MultiBiorefinery (POCI-01–0145-FEDER-016403) and through grants to C. Oliveira (SFRH/BPD/110640/2015) and D. Gomes (SFRH/BD/88623/2012).info:eu-repo/semantics/publishedVersio

Dynamic changes of cytotoxic T lymphocytes (CTLs), natural killer (NK) cells, and natural killer T (NKT) cells in patients with acute hepatitis B infection

<p>Abstract</p> <p><b>Background</b></p> <p>The goal of this study is to observe changes in HBcAg-specific cytotoxic T lymphocytes (CTLs), natural killer (NK) and natural killer T (NKT) cells from peripheral blood and to relate such changes on viral clearance and liver injury in patients with acute hepatitis B (AHB).</p> <p><b>Methods</b></p> <p>Dynamic profiles on the frequency of HLA-A0201-restricted HBcAg18-27 pentamer complex (MHC-Pentamer)-specific CTLs and lymphocyte subsets in AHB patients were analyzed in addition to liver function tests, HBV serological markers, and HBV DNA levels. ELISPOT was used to detect interferon-gamma (INF-γ) secretion in specific CTLs stimulated with known T cell epitope peptides associated with HBV surface protein, polymerase, and core protein.</p> <p><b>Results</b></p> <p>HBV-specific CTL frequencies in AHB patients were much higher than in patients with chronic hepatitis B (CHB) (p < 0.05). HBeAg and HBV DNA disappeared earlier in AHB patients with a high frequency of HBV-specific CTLs compared with those with a low frequency of HBV-specific CTLs (p = 0.001 and 0.024, respectively). INF-γ spots of effector cells stimulated by Pol575-583, Env348-357, or Core18-27 epitope peptides were significantly greater in AHB patients than in CHB patients (p < 0.01). CD3⁺CD8⁺T cell numbers in AHB patients was more than observed in the healthy control group from the first to the fourth week after admission (p <it>= </it>0.008 and 0.01, respectively); the number of CD3⁺CD8⁺T cells and frequency of HBcAg18-27-specific CTLs in AHB patients reached peak levels at the second week after admission. NK and NKT cell numbers were negatively correlated with the frequency of HBcAg-specific CTLs (<it>r </it>= -0.266, p = 0.05).</p> <p><b>Conclusions</b></p> <p>Patients with AHB possess a higher frequency of HBcAg-specific CTLs than CHB patients. The frequency of specific CTLs in AHB patients is correlated with HBeAg clearance indicating that HBV-specific CTLs play an important role in viral clearance and the self-limited process of the disease. Furthermore, NK and NKT cells are likely involved in the early, non-specific immune response to clear the virus.</p

Continuum of care in maternal, newborn and child health in Pakistan: analysis of trends and determinants from 2006 to 2012

Iqbal S, Maqsood S, Zakar R, Zakria Zakar M, Fischer F. Continuum of care in maternal, newborn and child health in Pakistan: analysis of trends and determinants from 2006 to 2012. BMC Health Services Research. 2017;17(1): 189.Background Pakistan, being a developing country, presents the dismal picture of maternal and neonatal mortality and morbidity. The majority of maternal and neonatal deaths could be avoided if Continuum of Care (CoC) is provided in a structured pathway from pregnancy to birth and to the first week of life of the newborn child. This study aimed to analyse the trends of CoC at all three levels (antenatal care, skilled delivery and postpartum care) and to identify various factors affecting the continuation in receiving CoC in Pakistan during 2006 to 2012. Methods Secondary data analysis was performed on nationally representative data from the last two iterations of Pakistan Demographic and Health Survey (PDHS), conducted during 2006/07 to 2012/13. The analysis is limited to women of the reproductive age group (15–49 years) who gave birth during the last five years preceding both surveys. This leads to a sample size of 5,724 and 7,461 respondents from PDHS 2006/07 and 2012/13 respectively. The association between CoC and several factors, including individual attributes (reproductive status), family influences, community context, as well as cultural and social values was assessed in bivariate analyses in a first step. Furthermore, odds ratios and adjusted odds ratios with 95% confidence intervals using a binary and multivariable logistic regression were calculated. Results Our research presents the trends of a composite measure of CoC including antenatal care, delivery assistance and postpartum care. The largest gap in CoC was observed at antenatal care followed by delivery and postnatal care within 48 h after delivery. Results show that CoC completion rate has increased from 15% to 27% amongst women in Pakistan over time from 2006 to 2012. Women with high age at first birth, having less number of children, with higher education, belonging to richest quintile, living in Sindh province and urban areas, having high autonomy and exposure to mass media were most likely to avail complete CoC. Conclusions The findings show that women in Pakistan still lack the CoC. This calls for attention to develop and implement tailored interventions, focusing on the needs of women in Pakistan to provide CoC in an integrated manner, involving both public and private sectors by appropriately addressing the factors hindering CoC completion rates