Molecular Footprints Research Articles

Molecular footprints reveal the impact of the protective HLA-A*03 allele in hepatitis C virus infection

Background and aimsCD8 T cells are central to the control of hepatitis C virus (HCV) although the key features of a successful CD8 T cell response remain to be defined....

Assembly of Chiral Amino-Acids at Surfaces from a Single Molecule Perspective: Proline on Cu(110)

We present a molecule-by-molecule mapping of an amino-acid monolayer on a Cu(110) surface in which individual molecular configuration, bonding and adsorption footprints are identified. This detailed mapping provides direct evidence that the (4 × 2) structures of enantiopure and racemic proline are governed by a strict heterochiral adsorption footprint template. For the racemic system this has an interesting consequence, namely that it leads to a 2-D random solid solution, a situation that is rarely encountered in 3-D.

Evolutionary and Structural Features of the C2, V3 and C3 Envelope Regions Underlying the Differences in HIV-1 and HIV-2 Biology and Infection

BackgroundUnlike in HIV-1 infection, the majority of HIV-2 patients produce broadly reactive neutralizing antibodies, control viral replication and survive as elite controllers. The identification of the molecular, structural and evolutionary footprints underlying these very distinct immunological and clinical outcomes may lead to the development of new strategies for the prevention and treatment of HIV infection.Methodology/Principal FindingsWe performed a side-by-side molecular, evolutionary and structural comparison of the C2, V3 and C3 envelope regions from HIV-1 and HIV-2. These regions contain major antigenic targets and are important for receptor binding. In HIV-2, these regions also have immune modulatory properties. We found that these regions are significantly more variable in HIV-1 than in HIV-2. Within each virus, C3 is the most entropic region followed by either C2 (HIV-2) or V3 (HIV-1). The C3 region is well exposed in the HIV-2 envelope and is under strong diversifying selection suggesting that, like in HIV-1, it may harbour neutralizing epitopes. Notably, however, extreme diversification of C2 and C3 seems to be deleterious for HIV-2 and prevent its transmission. Computer modelling simulations showed that in HIV-2 the V3 loop is much less exposed than C2 and C3 and has a retractile conformation due to a physical interaction with both C2 and C3. The concealed and conserved nature of V3 in the HIV-2 is consistent with its lack of immunodominancy in vivo and with its role in preventing immune activation. In contrast, HIV-1 had an extended and accessible V3 loop that is consistent with its immunodominant and neutralizing nature.Conclusions/SignificanceWe identify significant structural and functional constrains to the diversification and evolution of C2, V3 and C3 in the HIV-2 envelope but not in HIV-1. These studies highlight fundamental differences in the biology and infection of HIV-1 and HIV-2 and in their mode of interaction with the human immune system and may inform new vaccine and therapeutic interventions against these viruses.

Targeted imaging and therapy of brain cancer using theranostic nanoparticles.

The past decade has seen momentous development in brain cancer research in terms of novel imaging-assisted surgeries, molecularly targeted drug-based treatment regimens or adjuvant therapies and in our understanding of molecular footprints of initiation and progression of malignancy. However, mortality due to brain cancer has essentially remained unchanged in the last three decades. Thus, paradigm-changing diagnostic and therapeutic reagents are urgently needed. Nanotheranostic platforms are powerful tools for imaging and treatment of cancer. Multifunctionality of these nanovehicles offers a number of advantages over conventional agents. These include targeting to a diseased site thereby minimizing systemic toxicity, the ability to solubilize hydrophobic or labile drugs leading to improved pharmacokinetics and their potential to image, treat and predict therapeutic response. In this article, we will discuss the application of newer theranostic nanoparticles in targeted brain cancer imaging and treatment.

Mapping Complex Chiral Adlayers: A Truly Random 2-D Solid Solution of (RS)-3-Pyrroline-2-Carboxylic Acid on Cu(110)

The characterization of chiral molecular adlayers remains a considerable challenge, ultimately requiring detailed knowledge of the molecular chirality, the chemical form, molecular orientation, and interaction with the surface for each molecule within the assembly. In this work, we show that the (4 x 2) organization of a racemic mixture of the amino acid derivative 3-pyrroline-2-carboxylic acid (PCA) on Cu(110) may be analyzed at the single-molecule level in which the molecular chirality and adsorption footprints of each molecule are identified. Such a detailed mapping reveals the surprising outcome that within the racemic (4 x 2) organization the adlayer does not form either the 2-D racemic compound or racemic conglomerate. Instead, both the molecular chirality and adsorption footprints are randomly distributed, creating a truly random solid solution in which both molecular chirality and footprint chirality are scrambled.

Accessibility in Calix[8]arene-Bound Gold Nanoparticles: Crucial Role of Induced-Fit Binding

Metal nanoparticles bound with polymeric and oligomeric ligands are commonly employed in areas where accessibility to the underlying metal is critical, such as in catalysis. Developing a fundamental understanding of molecular-scale factors that control accessibility to the metal surface in these systems enables approaches for ligand design. Here, we implement a comparative synthetic approach to investigate the role of an induced-fit binding mechanism on accessibility, which reduces to elucidating the correlation between ligand flexibility and accessibility. Four nm gold nanoparticles are bound with a calix[8]arene phosphine ligand in the comparative series 3a−c, and ligand molecular footprints of ∼230 A2/calix[8]arene are measured on the gold surface using UV−vis spectroscopy of the surface plasmon resonance absorption band. Ligand flexibility in CDCl3 solution is characterized using variable-temperature 1H NMR spectroscopy, and results demonstrate 3c to be the most rigid of all three ligands. This is fur...

Molecular Footprints of Local Adaptation in Two Mediterranean Conifers

This study combines neutrality tests and environmental correlations to identify nonneutral patterns of evolution in candidate genes related to drought stress in two closely related Mediterranean conifers, Pinus pinaster Ait. and P. halepensis Mill. Based on previous studies, we selected twelve amplicons covering six candidate genes that were sequenced in a large sample spanning the full range of these two species. Neutrality tests relatively robust to demography (DHEW compound test and maximum likelihood multilocus Hudson-Kreitman-Aguadé test) were used to detect selection events at different temporal scales. Environmental associations between variation at candidate genes and climatic variables were also examined. These combined approaches detected distinct genes that may be targeted by selection, most of them specific to only one of the two conifers, despite their recent divergence (<10 Ma). An exception was 4-coumarate: CoA ligase, a gene involved in the production of various important secondary products that appeared to play a role in local adaptation processes of both pines. Another remarkable result was that all significant environmental correlations involved temperature indices, highlighting the importance of this climatic factor as a selective driver on Mediterranean pines. The ability to detect natural selection at the DNA sequence level depends on the nature and the strength of the selection events, on the timescale at which they occurred, and on the sensitivity of the methods to other evolutionary forces that can mimic selection (e.g., demography and population structure). Using complementary approaches can help to capture different aspects of the evolutionary processes that govern molecular variation at both intra- and interspecific levels.

UNRAVELING CRYPTIC RETICULATE RELATIONSHIPS AND THE ORIGIN OF ORPHAN HYBRID DISJUNCT POPULATIONS INNARCISSUS

Evolutionary consequences of natural hybridization between species may vary so drastically depending on spatial, genetic, and ecological factors that multiple approaches are required to uncover them. To unravel the evolutionary history of a controversial hybrid (Narcissus x perezlarae), here we use four approaches: DNA sequences from five regions (four organellar, one nuclear), cytological studies (chromosome counts and genome size), crossing experiments, and niche modeling. We conclude that (1) it actually consists of two different hybrid taxa, N.xperezlarae s.s. (N. cavanillesii x N. miniatus) and N.xalentejanus (N. cavanillesii x N. serotinus); (2) both have been formed several times independently, that is, polytopically; (3) N. cavanillesii was the mother progenitor in most hybridization events. We also address the origin of orphan hybrid populations of N.xperezlarae in eastern Spain, hundreds of kilometers away from N. cavanillesii. Although long-distance dispersal of already formed hybrids cannot be completely rejected, extirpation of N. cavanillesii via demographic competition is a more likely explanation. Low-reproductive barriers to fertilization by foreign pollen in N. cavanillesii, molecular footprints of the former presence of this species in the area, active asexual propagation by bulbs in N.xperezlarae, and overlapping ecological niches are consistent with the extirpation scenario.

Molecular footprints of a germinal center derivation of human IgM+(IgD+)CD27+ B cells and the dynamics of memory B cell generation

The origin of IgM+CD27+ B lymphocytes with mutated IgV genes, which account for ∼20% of human peripheral blood (PB) B cells, is controversially discussed. A generation in a primary diversification pathway, in T cell–independent immune responses, or in T cell–dependent germinal center (GC) reactions has been proposed. We show here that IgM+IgD+CD27+ and IgM+IgD−/lowCD27+ B cell subsets carry, like class-switched memory B cells, mutations in the Bcl6 gene as a genetic trait of a GC experience. Moreover, the identification of PB IgM+IgD+CD27+ B cells clonally related to GC-derived IgG+ memory B cells with shared and distinct IgV gene mutations demonstrates the GC origin also of the former subset. These findings provide genetic evidence for a GC derivation of somatically mutated IgM+ B cells and indicate that adult humans harbor a large population of IgM+IgD+ post-GC memory B cells. Furthermore, the analysis revealed that a highly diverse and often very large population of memory B cells is generated from a given GC B cell clone, and that (preferentially IgM) memory B cells are generated already early in the GC reaction. This provides novel insights into the dynamics of GC reactions and the generation of a memory B cell repertoire.

Tuning Selectivity in Adsorption on Composite Chiral Surfaces

Designing the structure of enantioselective adsorbents is a difficult task. In this work we propose a simple theoretical method of optimization of selectivity in adsorption on a model chiral surface composed of inert and active sites. Our approach is based on using the molecular footprints of the adsorbing enantiomers to find the optimal arrangement of active sites on the surface. In particular, we use a Monte Carlo search algorithm to predict the spatial distribution of active sites leading to the highest enantioselectivity. Additionally, we present the results of grand canonical Monte Carlo simulations performed for the equilibrium adsorption of enantiomers from a racemic mixture on the surfaces obtained using the MC approach. The optimal pattern of the active sites is dependent on the footprint of the chiral molecule as well as on the pressure under which the separation is performed.

A quantitative genotype algorithm reflecting H5N1 Avian influenza niches

Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza prevention and control. Most of the current methods that are available are based on multiple sequence alignment and phylogenetic tree construction, which are time consuming and limited by the number of taxa. Arbitrarily defining genotypes further complicates the interpretation of genotyping results. In this study, we describe a quantitative influenza genotyping algorithm based on the theory of quasispecies. First, the complete composition vector (CCV) was utilized to calculate the pairwise evolutionary distance between genotypes. Next, Hierarchical Bayesian Modeling using the Gibbs Sampling algorithm was applied to identify the segment genotype threshold, which is used to identify influenza segment genotype through a modularity calculation. The viral genotype was defined by combining eight segment genotypes based on the genetic reassortment feature of influenza A viruses. We applied this method for H5N1 avian influenza viruses and identified 107 niches among 283 viruses with a complete genome set. The diversity of viral genotypes, and their correlation with geographic locations suggests that these viruses form local niches after being introduced to a new ecological environment through poultry trade or bird migration. This novel method allows us to define genotypes in a robust, quantitative as well as hierarchical manner. Supplementary data are available at Bioinformatics online.

Genetic Analysis of Helicobacter pylori Strain Populations Colonizing the Stomach at Different Times Postinfection

Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.

Porphyrin Dyads Bearing Carbon Tethers for Studies of High-Density Molecular Charge Storage on Silicon Surfaces

Redox-active molecules that afford high charge density upon attachment to an electroactive surface are of interest for use in molecular-based information-storage applications. One strategy for increasing charge density is to covalently link a second redox center to the first in an architecture that uses the vertical dimension in essentially the same molecular footprint. Toward this end, a set of four new porphyrin dyads have been prepared and characterized. Each dyad consists of two zinc porphyrins, an intervening linker (p-phenylene or 4,4'-diphenylethyne), and a surface attachment group (ethynyl or triallyl group). The porphyrin dyads were attached to an electroactive Si(100) surface and interrogated via electrochemical and FTIR techniques. The charge density obtainable for the ethynyl-functionalized porphyrin dyads is approximately double that observed for an analogously functionalized monomer, whereas that for the triallyl-functionalized dyads is at most 40% larger. These results indicate that the molecular footprint of the former dyads is similar to that of a monomer while that of the latter dyads is larger. For both the ethynyl- and triallyl-functionalized porphyrin dyads, higher charge densities (smaller molecular footprints) are obtained for the molecules containing the 4,4'-diphenylethyne versus the p-phenylene linker. This feature is attributed to the enhanced torsional flexibility of the former linker compared with that of the latter, which affords better packed monolayers. The FTIR studies indicate that the adsorption geometry of all the dyads is qualitatively similar and similar to that of monomers. However, the dyads containing the 4,4'-diphenylethyne linker sit somewhat more upright on the surface than those containing the p-phenylene linker, generally consistent with the smaller molecular footprint for the former dyads. Collectively, the high surface charge density (34-58 muC.cm(-)(2)) of the porphyrin dyads makes these constructs viable candidates for molecular-information-storage applications.

What does tumour necrosis factor excess do to the immune system long term?

Members of the tumour necrosis factor (TNF)/TNF-receptor (TNF-R) superfamily coordinate the immune response at multiple levels. For example, TNF, LTα, LTβ and RANKL provide signals required for lymphoid neogenesis, CD27,...

From Molecular Footprints of Disease to New Therapeutic Interventions in Diabetic Nephropathy: A Detective Story

Oxidative tissue damage in vivo is a complex phenomenon involving many factors and pathways. Proteins are particularly attractive targets for oxidative products analysis in order to understand better the physiopathology of human diseases. Protein modifications serve as footprints of biochemical processes. They also help ascertain the mechanism of anti-oxidative action of medical drugs and further search for novel agents that inhibit efficiently oxidative protein damage. Several drugs already used clinically interfere with oxidative protein damage through different mechanisms characteristic of their chemical structure. This review delineates the oxidative protein modifications existing in diabetic nephropathy and their regression in association with renoprotective anti-hypertensive agents. Our hypothetical approach will require further testing. Nevertheless, the insights gained on the biochemistry of protein modifications open new avenues towards the development of new classes of renoprotective agents for diabetic nephropathy.

From Molecular Footprints of Disease to New Therapeutic Interventions in Diabetic Nephropathy

Proteins are particularly attractive targets for product analysis, which is used to understand pathology. Protein modifications, such as advanced glycation end products (AGEs), serve as footprints of biochemical processes and also help in the search for novel agents that efficiently inhibit protein damage. Interestingly, several medical agents that are used clinically interfere with oxidative protein damage through different mechanisms characteristic of their chemical structures. We recently found that angiotensin II receptor blockers (ARBs) and angiotensin converting enzyme inhibitors (ACEIs) lower the in vitro formation of the AGEs pentosidine and carboxymethyllysine. Their inhibition for AGE formation is more striking than aminoguanidine. Unlike aminoguanidine, ARBs and ACEIs do not trap reactive carbonyl precursors of AGEs. Rather, they inhibit AGE formation, possibly as a result of their potent ability to scavenge hydroxyl radicals and to chelate the transition metals necessary for the Fenton reaction. We tested their AGE-lowering ability in vivo in a unique type-2 diabetic model with nephropathic SHR/NDmcr-cp rats, which exhibits the metabolic syndrome (obesity, hyperglycemia, hyperlipidemia, hyperinsulinemia) in addition to hypertension. Obesity and associated metabolic derangements, in addition to hypertension, markedly accelerate renal injury. Expectedly, correction of hyperglycemia and hyperinsulinemia partially but significantly improves renal injury. A low-calorie diet greatly improves renal injury despite persistent hypertension. Among antihypertensive agents, ARBs, unlike nifedipine and atenolol, are renoprotective despite persistent metabolic syndrome, but their action is independent of blood pressure lowering and is observed in a dose-dependent manner despite the complete blockade of angiotensin II receptor. Interestingly, the improvement of renal injury by ARBs as well as a low-calorie diet is associated with a significant reduction in local oxidative stress and AGE formation in the kidney. During the characterization of the AGE-lowering profile of our chemical compound libraries ( approximately 2000), we identified several inhibitors of oxidative stress and advanced glycation. They are indeed renoprotective, independently of correction of hypertension and metabolic syndrome, in experimental diabetic nephropathy and other nephritis models. Altogether, our data are in good agreement with the recent therapeutic concept for diabetic nephropathy that multiple risk factor interventions are critical in the treatment of diabetic renal injury, and further implicate a therapeutic potential of inhibition of oxidative stress and advanced glycation.

Molecular footprints of human lung cancer progression.

Lung cancer is the leading cause of cancer-related death in the world. To understand the molecular processes and pathways of, and contributing factors to lung cancer progression, genetic alterations in various progression stages of lung cancer cells have been studied, since these alterations can be regarded as molecular footprints representing the individual processes of multistage lung carcinogenesis. The results indicate that defects in both the p53 and RB/p16 pathways are essential for the malignant transformation of lung epithelial cells. Several other genes, such as K-ras, PTEN and MYO18B, are genetically altered less frequently than p53 and RB/p16 in lung cancer cells, suggesting that alterations in these genes are associated with further malignant progression or unique phenotypes in a subset of lung cancer cells. However, it is still unclear what genes control the metastatic potential of lung cancer cells. Further analyses of molecular footprints in lung cancer cells, in particular in the cells of metastatic sites, will give us valuable information to fully understand the process of lung cancer progression, and to find novel ways of controlling it. Molecular footprints at the sites of p53 mutations and p16 deletions further indicate that DNA repair activities for G:C to T:A transversion and non-homologous end-joining of DNA double-strand breaks play important roles in the accumulation of genetic alterations in lung cancer cells. Thus, identification of environmental as well as genetic factors inducing or suppressing the occurrence of such alterations would be a clue to find novel ways of lung cancer prevention.

TP53 mutations in workers exposed to occupational carcinogens.

In some cases, evidence exists that exogenous carcinogenic exposures contribute to the mutation spectrum of the TP53 gene (p53) in human cancers. Although the clearest examples come from dietary and environmental sources, only a restricted number of papers have concentrated specifically on TP53 mutations in tumors from workers exposed to occupational carcinogens. In populations exposed to dietary aflatoxin B1 with liver cancer (AFB1) and ultraviolet (UV)-radiation with skin cancer, a single specific-looking TP53 mutation has been described in some of the tumors. Whether these fingerprints in the TP53 gene can be used to reveal an occupational etiology remains to be shown. In other cases, although differences in the TP53 mutation spectrum exist, they are more diffuse and difficult to interpret at this point. For instance, cigarette smoking seems to induce long-lasting molecular footprints in TP53. However, their use to rule out other occupational exposures as etiological factors in occupational cancers is still very questionable, especially due to the putative synergistic effects of cigarette smoke with other carcinogens. Although interesting implications of possible typical mutation spectra among cancers with other occupational etiologies exist, the data are scanty and await further development of TP53 mutation databases.

Epigenetic gene silencing in cancer initiation and progression

Hypermethylation of CpG islands, an epigenetic event that is not accompanied by changes in DNA sequence, represents an alternative mechanism to deletions or mutations to inactivate tumor suppressor genes. Recent evidence supports the notion that CpG island hypermethylation, by silencing key cancer-related genes, plays a major causal role in cancer. However, a long-standing issue in the field is the sequence of molecular events leading to epigenetic gene silencing. A new model has been proposed that chromatin remodeling, as a result of histone deacetylation and methylation, is the primary event in abrogating transcriptional initiation; subsequently, CpG island hypermethylation establishes a permanent state of gene silencing. Accumulating evidence indicates that CpG island hypermethylation is an early event in cancer development and, in some cases, may precede the neoplastic process. Because of their heritable nature, hypermethylated CpG islands leave ‘molecular footprints’ in evolving cancer cells and can be used as molecular markers to reconstruct epigenetic progression during tumorigenesis. Furthermore, hypermethylated CpG islands are proving to be useful for molecular classification of different cancer types.

Steady-State Fluorescence-Based Investigation of the Interaction between Protected Thiols and Gold Nanoparticles

The first demonstration of thioester and thiocarbonate binding to gold is provided via steady-state fluorescence spectroscopy of probe molecule adsorption onto a nanoparticle surface. Both thioester 1 and thiocarbonate 2 bind noncovalently to gold from aqueous solution, with 2 possessing a greater affinity for the gold surface relative to 1. The surface-bound molecules assemble into high packing densities comprising molecular footprints of 24.5 ± 1.0 Å2 per molecule. Both 1 and 2 deprotect catalytically on the gold surface to yield hydrolysis products and surface-bound thiolate. This process is thermally activated and can be described by an Arrhenius-type expression with activation energies of 14.0 and 16.7 kcal/mol for 1 and 2, respectively. The results presented herein demonstrate the role of gold in catalyzing thioester and thiocarbonate hydrolysis and diversify the synthetic repertoire of organosulfur functional groups that can be used for binding to gold.