Molecular Terms Research Articles

Hypoxia in Atherogenesis.

The anoxemia theory proposes that an imbalance between the demand for and supply of oxygen in the arterial wall is a key factor in the development of atherosclerosis. There is now substantial evidence that there are regions within the atherosclerotic plaque in which profound hypoxia exists; this may fundamentally change the function, metabolism, and responses of many of the cell types found within the developing plaque and whether the plaque will evolve into a stable or unstable phenotype. Hypoxia is characterized in molecular terms by the stabilization of hypoxia-inducible factor (HIF) 1α, a subunit of the heterodimeric nuclear transcriptional factor HIF-1 and a master regulator of oxygen homeostasis. The expression of HIF-1 is localized to perivascular tissues, inflammatory macrophages, and smooth muscle cells adjacent to the necrotic core of atherosclerotic lesions and regulates several genes that are important to vascular function including vascular endothelial growth factor, nitric oxide synthase, endothelin-1, and erythropoietin. This review summarizes the effects of hypoxia on the functions of cells involved in atherogenesis and the evidence for its potential importance from experimental models and clinical studies.

Comprehensive profiling of metaplastic breast carcinomas reveals frequent overexpression of programmed death-ligand 1

AimsMetaplastic breast carcinoma (MBC) is a rare subtype of breast carcinoma less responsive to conventional chemotherapy than ductal carcinoma. In molecular terms, MBCs usually cluster with triple-negative breast cancers (TNBCs),...

Characterization of the interactions between human high-molecular-mass kininogen and cell wall proteins of pathogenic yeasts, Candida tropicalis

Candida tropicalis is one of the most frequent causes of serious disseminated candidiasis in human patients infected by non-albicans Candida species, but still relatively little is known about its virulence mechanisms. In our current study, the interactions between the cell surface of this species and a multifunctional human protein - high-molecular-mass kininogen (HK), an important component of the plasma contact system involved in the development of the inflammatory state - were characterized at the molecular level. The quick release of biologically active kinins from candidal cell wall-adsorbed HK was presented and the HK-binding ability was assigned to several cell wall-associated proteins. The predicted hyphally regulated cell wall protein (Hyr) and some housekeeping enzymes exposed at the cell surface (known as "moonlighting proteins") were found to be the major HK binders. Accordingly, after purification of selected proteins, the dissociation constants of the complexes of HK with Hyr, enolase, and phosphoglycerate mutase were determined using surface plasmon resonance measurements, yielding the values of 2.20 × 10(-7) M, 1.42 × 10(-7) M, and 5.81 × 10(-7) M, respectively. Therefore, in this work, for the first time, the interactions between C. tropicalis cell wall proteins and HK were characterized in molecular terms. Our findings may be useful for designing more effective prevention and treatment approaches against infections caused by this dangerous fungal pathogen.

Stabilization of lifted hydrogen jet diffusion flame in a vitiated co-flow: Effects of jet and coflow velocities, coflow temperature and mixing

The present paper reports on the numerical investigation of lifted turbulent jet flames with H2/N2 fuel issuing into a vitiated coflow of lean combustion products of H2/air using conditional moment closure method (CMC). A 2D axisymmetric formulation has been used for the predictions of fluid flow, while CMC equations are solved with detailed chemistry to represent the turbulence–chemistry interaction. Simulations are carried out for different coflow temperatures, jet and coflow velocities in order to investigate the impact on the flame lift-off height as well as on the flame stabilization. Furthermore, the role of conditional velocity models on the flame has also been investigated. In addition, the effect of mixing is investigated over a range of coflow temperatures and the stabilization mechanism is determined from the analysis of the transport budgets. It is found that the lift-off height is highly sensitive to the coflow temperature, while the predicted lift-off height using the mixing model constant, i.e., CΦ = 4, is found to be the closest to the experimental results. For all the coflow temperatures, the balance is found between the chemical, axial convection and molecular diffusion terms while the contribution from axial and radial diffusion is negligible, thus indicating auto-ignition as the flame stabilization mechanism.

HOW AD-SPECIFIC ARE AD-LIKE MRI BIOMARKERS?

Alzheimer’s disease is currently defined in molecular terms as the association of cortical amyloid and hyper-phosphorilated tau deposition. MRI biomarkers for AD capture neurodegenerative phenomena related to tissue loss, axonal damage, and synaptic loss but are blind to the underlying molecular pathology. On the other hand, neurodegenerative phenomena but not molecular pathology are closely related to clinical symptoms. Survey of the literature on structural MRI, diffusion MRI, and functional networks at rest including personal and international studies. Non topographic structural MRI markers are sensitive to AD even at the pre-dementia MCI stage, while diffusion and functional network markers at the asymptomatic stage. Topographic information enhance specificity, but is complicated by the heterogeneity of the topography of molecular pathology in AD (e.g. early onset AD being more often neocortical and late onset limbic). The association of MRI with molecular biomarkers also enhances specificity to very high figures at the MCI stage (>90%). The specificity of MRI AD-like biomarkers lies in their topography. Enhancement of specificity can be achieved through the association with either molecular markers or different MRI markers.

The Origin of Life from Quantum Vacuum, Water and Polar Molecules

In contemporary established biology life is almost exclusively treated as a molecular phenomenon. Therefore the mystery of the origin of life is sought in molecular terms and processes. But according to certain advanced researches and considerations, life has also other essential ingredients: active information and a special electrodynamic state of the liquid living matter characterized by coherent domains interspersed by the non-coherent ones. Coherent domains are the product of interaction of water molecules with the vacuum electromagnetic field; life has thus a special electromagnetic nature that is bound to the quantum vacuum field. This characteristic should also form the basis of the pre-biotic evolution, the phase of more or less organized liquid systems that leads from non-life to life. In this view water as an ensemble (not as an aggregate of molecules) replaces the famous DNA molecule in its importance and is seen as an active medium where the principle of active information can begin with its triumphant march from inanimate liquid systems up to contemporary highly organized organisms.

Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades.

The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.

New Method of Rigorous Modeling and CFD Simulation for Methanol—Steam Reforming in Packed-Bed Reactors

A comprehensive dynamic mathematical model was developed to analyze methanol−steam reforming in catalytic packed-bed reactor. The contributions of all molecular and convective terms of momentum, heat, and mass transfer were taken into consideration, with the inclusion of effectiveness factor. Effects of two predominant parameters: particle size and the wall heat flux on the reactor performance for the methanol−steam reforming were examined. It was revealed that by increasing the average particle size from 700 to 3200 µm, which corresponded to porosity values of 0.4 and 0.6, the effectiveness factor decreased by nearly 80% and subsequently the overall methanol conversion decreased by around 74%. Besides, through a set of organized simulation runs, it was discovered that with increasing the dimensionless wall heat flux from 0 to 0.2 Wm−1 K−1, the methanol conversion was enhanced by 87%.

A comparative examination of density functional performance against the ISOL24/11 isomerization energy benchmark

The isomerization energy (ΔisomE) performance of a wide range of density functionals was tested against the set of 24 individual intramolecular reactions collectively comprising the ISOL24/11 benchmark database. Among 50 non-dispersion corrected functionals examined, the M06-2X single-component density functional offered the best estimation capacity, yielding a mean unsigned error (MUE) of 2.4kcal/mol. The addition of molecular mechanics dispersion-like terms to the M06-2X functional offers minimal improvement in its capacity to reliably estimate isomerization energies, whereas the choice of basis set played a significant role. Triple zeta Dunning, Ahlrichs, and Pople basis sets offer effectively equivalent ΔisomE performance, modestly better than double zeta equivalent basis sets, with ΔisomE performance subsequently rapidly declining at basis set sizes below this level. Among a reduced set of dispersion corrected functionals considered, the APFD functional displayed ΔisomE performance (MUE=1.8kcal/mol) superior to both the non-dispersion corrected M06-2X functional and the wB97X-D and PBE0-D3 dispersion corrected functionals (1.9kcal/mol). At this accuracy, the APFD functional is competitive with computationally expensive high-accuracy methods such as MC3MPWB and MC3MPW and nearing that of composite methods and dispersion corrected double-hybrid density functionals.

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification.

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.

Learning from the Uncontrollable

Research papers are usually revisionist histories, imagined accounts driven by impeccable logic and unbroken experimental success, which in no way reflect the slowness, messiness, and serendipity of real life in the lab. To give a different hopefully more balanced perspective than what is often told, I want to tell you the story behind some of the discoveries that shaped my early career.“In reality, of course, I had stumbled on the control by complete accident.”

Differential proteome and phosphoproteome may impact cell signaling in the corpus callosum of schizophrenia patients

Schizophrenia is a multifactorial disease in both clinical and molecular terms. Thus, depicting the molecular aspects of the disease will contribute to the understanding of its biochemical mechanisms and consequently may lead to the development of new treatment strategies. The protein phosphorylation/dephosphorylation switch acts as the main mechanism for regulating cellular signaling. Moreover, approximately onethird of human proteins are phosphorylable. Thus, identifying proteins differentially phosphorylated in schizophrenia postmortem brains may improve our understanding of the molecular basis of brain function in this disease. Hence, we quantified the phosphoproteome of corpus callosum samples collected post mortem from schizophrenia patients and healthy controls. We used state-of-the-art, bottom-up shotgun mass spectrometry in a two-dimensional liquid chromatography-tandem mass spectrometry setup in the MSE mode with label-free quantification. We identified 60,634 peptides, belonging to 3283 proteins. Of these, 68 proteins were differentially phosphorylated, and 56 were differentially expressed.These proteins are mostly involved in signaling pathways, such as ephrin B and ciliary neurotrophic factor signaling. The data presented here are novel because this was the very first phosphoproteome analysis of schizophrenia brains. They support the important role of glial cells, especially astrocytes, in schizophrenia and help to further the understanding of the molecular aspects of this disease. Our findings indicate a need for further studies on cell signaling, which might shape the development of treatment strategies.

Protein side chain conformation predictions with an MMGBSA energy function.

The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc.

ALFY-Controlled DVL3 Autophagy Regulates Wnt Signaling, Determining Human Brain Size.

Primary microcephaly is a congenital neurodevelopmental disorder of reduced head circumference and brain volume, with fewer neurons in the cortex of the developing brain due to premature transition between symmetrical and asymmetrical cellular division of the neuronal stem cell layer during neurogenesis. We now show through linkage analysis and whole exome sequencing, that a dominant mutation in ALFY, encoding an autophagy scaffold protein, causes human primary microcephaly. We demonstrate the dominant effect of the mutation in drosophila: transgenic flies harboring the human mutant allele display small brain volume, recapitulating the disease phenotype. Moreover, eye-specific expression of human mutant ALFY causes rough eye phenotype. In molecular terms, we demonstrate that normally ALFY attenuates the canonical Wnt signaling pathway via autophagy-dependent removal specifically of aggregates of DVL3 and not of Dvl1 or Dvl2. Thus, autophagic attenuation of Wnt signaling through removal of Dvl3 aggregates by ALFY acts in determining human brain size.

Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be(II) complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid.

A method designed to investigate, on a fundamental level, the origin of relative stability of molecular systems using Be(II) complexes with nitrilotriacetic acid (NTA) and nitrilotri-3-propionic acid (NTPA) is described. It makes use of the primary and molecular fragment energy terms as defined in the IQA/F (Interacting Quantum Atoms/Fragments) framework. An extensive classical-type investigation, focused on single descriptors (bond length, density at critical point, the size of metal ion or coordination ring, interaction energy between Be(II) and a donor atom, etc.) showed that it is not possible to explain the experimental trend. The proposed methodology is fundamentally different in that it accounts for the total energy contributions coming from all atoms of selected molecular fragments, and monitors changes in defined energy terms (e.g., fragment deformation, inter- and intra-fragment interaction) on complex formation. By decomposing combined energy terms we identified the origin of relative stability of Be(II) (NTA) and Be(II) (NTPA) complexes. We found that the sum of coordination bonds' strength, as measured by interaction energies between Be(II) ion and donor atoms, favours Be(II) (NTA) but the binding energy of Be(II) ion to the entire ligand correlates well with experimental trend. Surprisingly, the origin of Be(II) (NTPA) being more stable is due to less severe repulsive interactions with the backbone of NTPA (C and H-atoms). This general purpose protocol can be employed not only to investigate the origin of relative stability of any molecular system (e.g., metal complexes) but, in principle, can be used as a predictive tool for, e.g., explaining reaction mechanism. © 2016 Wiley Periodicals, Inc.

Clustering of Microarray Data to Identify Enriched Go Terms of Genes in Severe Asthma Dataset using Gene Enrichment Analy

Objective: The main objective of the research paper is to identify gene enrichment analysis of clustered genes from asthma microarray dataset that are clustered using k-means clustering algorithm. The enrichment analysis is used to assign biological meaning to some group of genes and in this paper the gene enrichment analysis is done using Gene Ontology terms. Method: The proposed research work consists of two-fold task: clustering gene expression profile using K-Means clustering algorithm; conducting Gene Enrichment Analysis using Gene Ontology (GO) to identify the enriched GO terms in each cluster with respect to specific set of Molecular Functions, Biological Processes and Cellular Components; Gene Ontology is used to provide external validation for the clusters to determine if the genes in a cluster belong to the specific functionalities. The most significant or enriched GO terms are extracted based on P-Value metric and the most enriched GO terms are visualized for genes in each cluster by using graph. Finding: The asthma microarray dataset contains 41,000 genes and out of that only 9,425 genes are considered for clustering process after preprocessing task. The series of preprocessing tasks certainly helpful to improve and predicts the accurate results. The experimental result of the research work produces the 3 sets of clusters and the first cluster set with 4 clusters have the number of genes 1720, 2636, 2458 and 2611 respectively. Similarly, the other two cluster sets numbers of genes are identified. The gene enrichment analysis is conducted for each cluster in the cluster set based on top most significant molecular functions GO terms enriched in each cluster. The most significant GO terms have been identified based on the P-value metric and associations among top most significant GO terms are visualized in each cluster.

Abstract P3-07-47: Comprehensive profiling of metaplastic breast carcinoma reveals frequent over-expression of PD-L1

Abstract Background: Metaplastic breast carcinoma (MBC) is a rare subtype of breast carcinoma less responsive to conventional chemotherapy relative to usual breast carcinomas (UBCs) such as ductal and lobular subtype. In molecular terms MBC usually clusters with triple negative breast cancer (TNBC), but MBCs portray a worse prognosis in comparison to TNBCs. Published studies investigating MBCs for specific biomarkers of therapy response are rare and limited by the methodological approaches. Methods: This study included 132 patients with 38 histologically confirmed MBCs and 94 UBCs. Amongst the 94 UBCSs, 44 were estrogen receptor positive, 33 were triple negative and 17 were HER2 positive. Direct sequencing analysis was performed on genomic DNA isolated from formalin-fixed paraffin-embedded tissue (FFPE) using the Illumina MiSeq Next Generation Sequencing platform (NGS). Immunohistochemistry for PD-L1 (SP142, Spring Bioscience), PD-1 (NAT105, Ventana) and EGFR (31G7, Life Technologies) was performed using automated procedures. Additionally, mutation analysis for EGFRvIII was performed on RNA extracted from FFPE tissue. Results: At the genomic level, numerous cases of MBC had multiple genomic alterations with the most frequent genetic mutation in TP53 gene (14/24), similar to the TNBC controls (17/33). BRCA1 mutations were detected in 2/10 cases. Potentially actionable mutations were rare and included PIK3CA gene. Importantly, PD-L1 expression on cancer cells was detected in significantly higher proportion of MBCs (37%) than in the UBC cohort (6%) or TNBC control (14%) (p=3.7x10-5 and p=0.03, respectively). PD-1 positive tumors infiltrating lymphocytes (TILS) varied greatly in MBC (0 to >50/mm2). Over-expression of EGFR was frequent in MBCs (62%); however no mutations in the gene including EGFRvIII were detected. Conclusion: Comprehensive profiling of a large cohort of this rare carcinoma highlighted predominance of TP53 mutations, wild type EGFR gene expression, a distinct increase in proportion of PD-L1 expression in carcinoma cells, and PD-1 expression in TILS. The latter properties can be exploited in clinical trials utilizing immune check point inhibitors. Citation Format: Gatalica Z, Joneja U, Ghazalpour A, Swensen J, Feldman R, Cai F, Chen W, Xiao N, Reddy S, Palazzo J. Comprehensive profiling of metaplastic breast carcinoma reveals frequent over-expression of PD-L1. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-47.

Evaluation of the relative stabilities of two non-IPR isomers of Sm@C76

ABSTRACTDensity-functional theory calculations are presented for two low-energy Sm@C76 isomers with the isolated-pentagon rule (IPR) violating cages. The relative isomeric populations at high temperatures are evaluated using the calculated molecular terms and relationships to observations are discussed. It is shown that the observed Sm@C2v(19138)-C76 species can be computed as the major isomer if the encapsulate motions are treated as relatively restricted. With the restriction conjecture, the major isomer is about two times more populated than the minor Sm@C1(17459)-C76 endohedral. The study points out the importance of symmetry considerations in stability evaluations for general nanocarbons.

Gauge-invariant expectation values of the energy of a molecule in an electromagnetic field.

In this paper, we show that the full Hamiltonian for a molecule in an electromagnetic field can be separated into a molecular Hamiltonian and a field Hamiltonian, both with gauge-invariant expectation values. The expectation value of the molecular Hamiltonian gives physically meaningful results for the energy of a molecule in a time-dependent applied field. In contrast, the usual partitioning of the full Hamiltonian into molecular and field terms introduces an arbitrary gauge-dependent potential into the molecular Hamiltonian and leaves a gauge-dependent form of the Hamiltonian for the field. With the usual partitioning of the Hamiltonian, this same problem of gauge dependence arises even in the absence of an applied field, as we show explicitly by considering a gauge transformation from zero applied field and zero external potentials to zero applied field, but non-zero external vector and scalar potentials. We resolve this problem and also remove the gauge dependence from the Hamiltonian for a molecule in a non-zero applied field and from the field Hamiltonian, by repartitioning the full Hamiltonian. It is possible to remove the gauge dependence because the interaction of the molecular charges with the gauge potential cancels identically with a gauge-dependent term in the usual form of the field Hamiltonian. We treat the electromagnetic field classically and treat the molecule quantum mechanically, but nonrelativistically. Our derivation starts from the Lagrangian for a set of charged particles and an electromagnetic field, with the particle coordinates, the vector potential, the scalar potential, and their time derivatives treated as the variables in the Lagrangian. We construct the full Hamiltonian using a Lagrange multiplier method originally suggested by Dirac, partition this Hamiltonian into a molecular term Hm and a field term Hf, and show that both Hm and Hf have gauge-independent expectation values. Any gauge may be chosen for the calculations; but following our partitioning, the expectation values of the molecular Hamiltonian are identical to those obtained directly in the Coulomb gauge. As a corollary of this result, the power absorbed by a molecule from a time-dependent, applied electromagnetic field is equal to the time derivative of the non-adiabatic term in the molecular energy, in any gauge.

Lack of Altered BECN1 Gene Expression in Iranian Patients with Acute Myeloid Leukemia

Acute myeloid leukemia (AML), one of the most prevalent leukemia types in adults, demonstrates great heterogeneity in molecular and clinical terms. Hence, there is a necessity to the mechanisms involved in AML generation in order to determine optimal treatment. This cross sectional study aimed to assess changes in BECN1 gene expression in with blood samples from 30 AML patients, compared with samples from 15 healthy persons. RNA was extracted and cDNA was synthesized and Real Time PCR applied to determine BECN1 gene expression. The results showed no significant differences in BECN1 gene expression between patients with AML and normal controls (P > 0.05). It appears that expression of BECN1 does not play a significant role in genesis of AML leukemia.