Class Of Sites Research Articles

Candida albicans exhibit two classes of cell surface binding sites for serum albumin defined by their affinity, abundance and prospective role in interkingdom signalling.

Serum albumin binding to the yeast form of Candida albicans is described. Two populations of binding site are identified using two complementary spectroscopic techniques: an extrinsic fluorescent probe, 3-hexa-decanoyl-7-hydrocoumarin ([HEXCO) added to the C. albicans yeast cell surface that records the electrostatic surface potential and so responds to the surface binding of serum albumin and secondly a light scattering technique that reveals how albumin modulates aggregation of the yeast population. The albumin binding sites are found to possess different binding affinities and relative abundance leading to different total binding capacities. These are characterized as a receptor population with high affinity binding (Kd ~ 17 μM) but relatively low abundance and a separate population with high abundance but much lower affinity (Kd ~ 364 μM). The low-affinity binding sites are shown to be associated with the yeast cell aggregation. These values are found be dependent on the C. albicans strain and the nature of the culture media; some examples of these effects are explored. The possible physiological consequences of the presence of these sites are speculated in terms of evading the host’s immune response, biofilm formation and possible interkingdom signaling processes.

The comparison of botanical composition and the condition and health class of different rangeland sites in forest ecosystem

In this study conducted in Erzurum province's Oltu district Kırdağı location during 2015, 2016 and 2017 concerning the above forest, forest interior and forest edge rangeland sites, the botanical composition of rangeland sites, canopy coverage rate, rangeland condition scores, and comparison of the condition of rangeland and the health class were emphasized. According to the results, although the grass and legume rations in the forest edge rangeland was lower, the others families? ratio was higher than that of the other sites. Hence, it was determined that the ratio of canopy coverage rate was higher in the forest top rangelandsite compared to other sites. Consequently, the health class of the rangeland is in the risky class in the forest edge site. Rangeland status class, which is a comparison of vegetation for climax, was found to be weak in this site. As a result, these values clearly indicate that the forest edge rangeland was seriously damaged compared to the other sites.

PH and NaCl effects on the interactions between safranal and whey protein isolate

The molecular binding between whey protein isolate (WPI) and safranal, as a function of pH (4–9) and NaCl concentration (0–0.5 M), was studied using headspace solid phase micro-extraction coupled with gas chromatography (HS-SPME/GC) and fluorescence spectroscopy. Structural changes of WPI were also investigated using 3D-fluorescence and circular dichroism spectroscopies. Elucidation of the binding properties of WPI and safranal using HS-SPME/GC showed that pH 9 and 0.5 M NaCl favored the binding constant (Ka) being equal to 2.3 × 103 and 2.3 × 103 M−1, respectively. In addition, WPI had a single class of binding site for safranal with all conditions, except at pH 5 with two classes of binding sites. Structural studies of WPI using dynamic light scattering and atomic force microscopy showed its aggregation at pH 4, which could be a consequence of associations of whey proteins. WPI had looser secondary and tertiary structures with acidic (pH 4 and 5) and basic (pH 9) conditions compared with pH 7.2 and 6; as well as at 0.1 and 0.3 M NaCl compared with other NaCl concentrations. Both the secondary and tertiary structures of WPI were affected by complexation with safranal, with various solvent conditions. WPI could be introduced as a promising safranal carrier in dairy products with different pH and ionic strengths.

Revisiting the notion of deleterious sweeps.

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites-both in the presence and absence of interference amongst deleterious mutations-and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of FST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.

Landscape of allele-specific transcription factor binding in the human genome

Sequence variants in gene regulatory regions alter gene expression and contribute to phenotypes of individual cells and the whole organism, including disease susceptibility and progression. Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Differential transcription factor binding in heterozygous genomic loci provides a natural source of information on such regulatory variants. We present a novel approach to call the allele-specific transcription factor binding events at single-nucleotide variants in ChIP-Seq data, taking into account the joint contribution of aneuploidy and local copy number variation, that is estimated directly from variant calls. We have conducted a meta-analysis of more than 7 thousand ChIP-Seq experiments and assembled the database of allele-specific binding events listing more than half a million entries at nearly 270 thousand single-nucleotide polymorphisms for several hundred human transcription factors and cell types. These polymorphisms are enriched for associations with phenotypes of medical relevance and often overlap eQTLs, making candidates for causality by linking variants with molecular mechanisms. Specifically, there is a special class of switching sites, where different transcription factors preferably bind alternative alleles, thus revealing allele-specific rewiring of molecular circuitry.

Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling.

SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines, yet is frequently mutated in human cancer. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by SHP099. The dynamics of phosphotyrosine abundance at more than 400 tyrosine residues reveal six distinct response signatures following SHP099 treatment and washout. Remarkably, in addition to newly identified substrate sites on proteins such as occludin, ARHGAP35, and PLCγ2, another class of sites shows reduced phosphotyrosine abundance upon SHP2 inhibition. Sites of decreased phospho-abundance are enriched on proteins with two nearby phosphotyrosine residues, which can be directly protected from dephosphorylation by the paired SH2 domains of SHP2 itself. These findings highlight the distinct roles of the scaffolding and catalytic activities of SHP2 in effecting a transmembrane signaling response.

Academic Social Networking Sites: An Evaluation exploratory study

Academic social networking sites ASNs are a class of sites that seek to create a series of scientific and academic groupings and the formation of relationships between members with respect to research interests and intertwining tendencies of scientific publishing processes as a means for this. Social networks have affected the way we get to the latest articles and scientific outputs, as well as to To generate links and links between researchers and scientists, and the purpose of this study is to compare five of the most popular academic social networking sites (Research Portal, Academia.edu, Mendeley, Orcid, and Zotero) based on this with a preparation and design with me to evaluate sites Subject of study. The list includes 201 sub criteria distributed into 12 main categories. The study concluded that the study sites lack the navigation and navigation services, filtering services, filtering results, and search and browsing features, as is the case in most sites in the study that do not provide all the fields of research, and they do not complete the features of displaying data so that these sites do not provide all categories of content for download Moreover, none of the sites are given alternative measurements and sufficient analytical features, as well to this, the beneficiaries' interface for these sites needs to be improved to attract their users, which use the sites The sites lack text display features, and you cannot use by renewing the privacy settings, study sites Offer the lowest possible services to the users.

Heparin Binding to Resting and Activated Platelets

AbstractHeparin inhibits platelet function and can cause thrombocytopenia. In an effort to understand these phenomena, we have measured the binding of (3H)-heparin to resting and stimulated platelets. In platelet-rich plasma, a single class of saturable heparin binding sites was observed (apparent dissociation constant [kd] ~ 0.55μg/mL, R ~ 0.059 μg/109 cells). In gel-filtered platelets, a similar class of sites was present but with a greater binding capacity (apparent kd1 ~ 0.56 μg/mL, R ~ 0.44 μg/109 cells). Gel-filtered platelets that had been stimulated with thrombin displayed two classes of binding sites: a high-affinity class (apparent kd1 ~1.1 μg/mL, R1 ~ 0.39 μg/109 cells) corresponding to that of the unstimulated cells, and a low-affinity class (apparent kd2 ~13 μg/mL, R2 ~ 2.2 μg/109 cells). Heparin binding was also increased in platelet-rich plasma when the cells had been stimulated by adenosine diphosphate (ADP) to release, but not when ADP caused primary aggregation without release. Binding was not dependent on extracellular calcium, nor was it reduced by monoclonal antibodies to platelet membrane glycoproteins la/Ila, lb, llb/llla, or IV. Because the apparent dissociation constant of the high-affinity sites (~0.55 μg/mL) falls in the range of heparin concentrations achieved clinically, these binding sites may be involved in the platelet dysfunction and immune-mediated thrombocytopenia associated with therapeutic heparin. The low-affinity, high-capacity class of sites, which appears after cell stimulation, may participate in the process of platelet adhesion.

Isolating the Contributions of Specific Network Sites to the Diffuse Vibrational Spectrum of Interfacial Water with Isotopomer-Selective Spectroscopy of Cold Clusters.

Decoding the structural information contained in the interfacial vibrational spectrum of water requires understanding how the spectral signatures of individual water molecules respond to their local hydrogen bonding environments. In this study, we isolated the contributions for the five classes of sites that differ according to the number of donor (D) and acceptor (A) hydrogen bonds that characterize each site. These patterns were measured by exploiting the unique properties of the water cluster cage structures formed in the gas phase upon hydration of a series of cations M+·(H2O)n (M = Li, Na, Cs, NH4, CH3NH3, H3O, and n = 5, 20-22). This selection of ions was chosen to systematically express the A, AD, AAD, ADD, and AADD hydrogen bonding motifs. The spectral signatures of each site were measured using two-color, IR-IR isotopomer-selective photofragmentation vibrational spectroscopy of the cryogenically cooled, mass selected cluster ions in which a single intact H2O is introduced without isotopic scrambling, an important advantage afforded by the cluster regime. The resulting patterns provide an unprecedented picture of the intrinsic line shapes and spectral complexities associated with excitation of the individual OH groups, as well as the correlation between the frequencies of the two OH groups on the same water molecule, as a function of network site. The properties of the surrounding water network that govern this frequency map are evaluated by dissecting electronic structure calculations that explore how changes in the nearby network structures, both within and beyond the first hydration shell, affect the local frequency of an OH oscillator. The qualitative trends are recovered with a simple model that correlates the OH frequency with the network-modulated local electron density in the center of the OH bond.

The Deposition of History in Prehistory: Copper Objects on Sites and in the Landscape

A variable proportion of finds from the Neolithic and Chalcolithic of ‘Old Europe’ has come from places outside settlements, cemeteries, production sites, ritual sites, or caves. Such finds tend to be described as ‘chance/isolated/single/stray’ finds or, when in groups, as ‘hoards’. The frequent, modernist cause invoked for these finds is that they were either ‘hidden’ in times of mortal danger, represented a ‘gift to the gods’, or simply ‘lost’. One reason for these explanatory shortcomings is the over-attention to the types of objects deposited in the landscape and the frequent lack of attention to the often-distinctive place of deposition. We believe that we have misnamed, overlooked, or not accurately characterised an entire class of sites, which we term ‘landscape deposition sites’, whose defining feature was the transformation of a place by the deposition of a significant object or group of objects to create a qualitatively different place. The creation of such landscape deposit sites varied in time and space throughout Old Europe, but all sites were affected by this new dimension of the extended cultural domain.In this article, we consider the interpretations of metal deposition in North-west Europe and the light they shed on an earlier and geographically different region. The primary aim of this paper is an exploration of the variable relationships between landscape deposit sites and the coeval finds made in special deposits in settlements and cemeteries in the 5th and 4th millenniabc, which will lead to proposed new interpretations of landscape deposition sites.

Two classes of active transcription sites and their roles in developmental regulation

The expression of genes encoding powerful developmental regulators is exquisitely controlled, often at multiple levels. Here, we investigate developmental expression of three conserved genes, Caenorhabditis elegans mpk-1, lag-1, and lag-3/sel-8, which encode homologs of ERK/MAPK and core components of the Notch-dependent transcription complex, respectively. We use single-molecule FISH (smFISH) and MATLAB to visualize and quantify nuclear nascent transcripts and cytoplasmic mRNAs as a function of position along the germline developmental axis. Using differentially labeled probes, one spanning an exceptionally long first intron and the other spanning exons, we identify two classes of active transcription sites (ATS). The iATS class, for "incomplete" ATS, harbors only partial nascent transcripts; the cATS class, for "complete" ATS, harbors full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis. For example, most mpk-1 ATS are iATS in hermaphrodite germline stem cells, but most are cATS in differentiating stem cell daughters. Thus, mpk-1 ATS class frequencies switch in a graded manner as stem cell daughters begin differentiation. Importantly, the patterns of ATS class frequency are gene-, stage-, and sex-specific, and cATS frequency strongly correlates with transcriptional output. Although the molecular mechanism underlying ATS classes is not understood, their primary difference is the extent of transcriptional progression. To generate only partial nascent transcripts in iATS, progression must be slowed, paused, or aborted midway through the gene. We propose that regulation of ATS class can be a critical mode of developmental gene regulation.

Tailoring the Health-Promoting Potential of Protein Hydrolysate Derived from Fish Wastes and Flavonoids from Yellow Onion Skins: From Binding Mechanisms to Microencapsulated Functional Ingredients.

This study focuses on combining different bioprocessing tools in order to develop an in-depth engineering approach for enhancing the biological properties of two valuable food by-products, namely fish waste and yellow onion skins, in a single new bioactive formulation. Bone tissue from phytophagous carp (Hypophthalmichthys molitrix) was used to obtain bioactive peptides through papain-assisted hydrolysis. The peptides with molecular weight lower than 3 kDa were characterized through MALDI-ToF/ToF mass spectrometry and bioinformatics tools. As a prerequisite for microencapsulation, the ability of these peptides to bind the flavonoids extracted from yellow onion skins was further tested through fluorescence quenching measurements. The results obtained demonstrate a considerable binding potency with a binding value of 106 and also the presence of one single or one class of binding site during the interaction process of flavonoids with peptides, in which the main forces involved are hydrogen bonds and van der Waals interactions. In the freeze-drying microencapsulation process, an efficiency for total flavonoids of 88.68 ± 2.37% was obtained, considering the total flavonoids and total polyphenols from the powder of 75.72 ± 2.58 quercetin equivalents/g dry weight (DW) and 97.32 ± 2.80 gallic acid equivalents/g DW, respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test on the L929 cell line cultivated in the presence of different concentrations of microencapsulated samples (0.05–1.5 mg/mL) proved no sign of cytotoxicity, the cell viability being over 80% for all the samples.

Characteristics of Dolutegravir and Bictegravir Plasma Protein Binding: a First Approach for the Study of Pharmacologic Sanctuaries.

This study aimed to characterize in vitro dolutegravir (DTG) and bictegravir (BIC) binding. They had a preferential binding to human serum albumin (HSA) with two classes of albumin sites. Human alpha-1-acid glycoprotein (HAAG) binding of DTG and BIC showed an atypical nonlinear binding. The low-affinity site on HSA, the main plasma binding protein, suggests that the high protein binding rate should not impair passive diffusion.

Kinetic, spectroscopic, and molecular docking studies on the inhibition of membrane-bound polyphenol oxidase from Granny Smith apples (Malus domestica Borkh.)

We investigated the inhibitory effect and binding mechanism of four selected compounds (ascorbic acid, l-cysteine, glutathione, and citric acid) on membrane-bound polyphenol oxidases (mPPO) using spectroscopic and molecular docking techniques. Kinetic analysis demonstrated that these inhibitors reversibly inhibited the mPPO activity. Fluorescence spectroscopy revealed that the intrinsic fluorescence intensity of mPPO was quenched by inhibitors with a single class of the inhibition site on mPPO. Amino acid residues His 180, His 201, His 366, Cys 184, Glu 328, and Asn 333 were the important binding sites in the active center. These sites were identified using molecular docking techniques. Our findings suggested that the inhibitors were allosterically bound to the active center of mPPO through hydrogen bonds and ion contacts. This study provides new insights into the active site residues responsible for catalyzing mPPO and provides applicable information about the design of mPPO inhibitors.

Decoding the epitranscriptional landscape from native RNA sequences.

Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing.

Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs, and nascent polypeptide structure is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.

Inhibition of Tyrosinase by Mercury Chloride: Spectroscopic and Docking Studies.

Inorganic mercury compounds have been used in skin-lightening products since ancient times. Although a previous study demonstrated that mercury impeded the transfer of Cu2+ to the apotyrosinase, the effect of mercury on tyrosinase is still unclear. In the present study, the mechanism of mercury chloride (HgCl2) induced inactivation of tyrosinase was investigated for the first time. The IC50 values were 29.97 and 77.93 μmol/L for monophenolase and diphenolase, respectively. A kinetic analysis revealed that HgCl2 inhibited tyrosinase activity in an irreversible non-competitive manner. The strong intrinsic fluorescence quenching suggested that the formation of the HgCl2-tyrosinase complex induced conformational changes of the enzyme, and HgCl2 had only one single binding site or a single class of binding site on tyrosinase. The molecular docking and further experiments demonstrated that HgCl2 bound to the amino residuals (His) in the catalytic center of tyrosinase. To our knowledge, these findings presented in this paper were the first evidence of the direct interactions between HgCl2 and tyrosinase, which provided a deep understanding of the inhibition mechanism of mercury on tyrosinase.

Abstract DL-1: Essential Genes and Cistromes in Breast Cancer

Abstract Steroid hormones mediate critical lineage-specific developmental and physiologic responses. While estrogen is required for normal breast development, the genes regulated by estrogen and the genomic targets of the estrogen receptor (ER) are altered in ER+ breast cancers. The requirement of most breast cancers for estrogen has led to the development of endocrine therapies that block ER action. While initial endocrine interventions are successful, in the advanced disease setting resistance to ER-targeted therapy almost invariably arises. As with other targeted therapies, gain of function mutations play a significant role in the development of therapeutic resistance to ER directed treatments in breast cancer. In addition, pathways downstream of ER are activated in cases in which ER itself is not genetically altered suggesting that these pathways remain essential. Activation of these pathways may depend on mutations in other transcription factors involved in steroid receptor networks or chromatin modifying enzymes involved in transcriptional regulation mediated by ER. These mutations may be present in the protein coding regions of the genes or in the cis-regulatory elements regulating expression of key genes in the pathways. Renewed success in targeting ER and promising advances in inhibiting the activity of the chromatin modifying enzymes provides new opportunities for the treatment of patients with breast cancer. Using genome-wide CRISPR-Cas9 knockout screens we have identified the genes essential for hormone-dependent breast cancer growth including key genes in the receptor-centered transcriptional networks. Although large sets transcription factor binding sites or cistromes have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR-Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of more than 10,000 FOXA1 and CTCF binding sites in breast cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed two classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at TAD boundaries and display distinct characteristics. Using regression methods trained on the screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts non-coding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given transcription factor and can inform the development of predictive models of cistrome function. In addition, defining the essential cistrome may shed light on the noncoding regions of the genome most likely to harbor oncogenic driver mutations. Citation Format: M Brown. Essential Genes and Cistromes in Breast Cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr DL-1.

Defect activation and annihilation in CIGS solar cells: an operando x-ray microscopy study

The efficiency of thin-film solar cells with a Cu( Gax)Se2 absorber is limited by nanoscopic inhomogeneities and defects. Traditional characterization methods are challenged by the multi-scale evaluation of the performance at defects that are buried in the device structures. Multi-modal x-ray microscopy offers a unique tool-set to probe the performance in fully assembled solar cells, and to correlate the performance with composition down to the micro- and nanoscale. We applied this approach to the mapping of temperature-dependent recombination for Cu( Gax)Se2 solar cells with different absorber grain sizes, evaluating the same areas from room temperature to . It was found that poor performing areas in the large-grain sample are correlated with a Cu-deficient phase, whereas defects in the small-grain sample are not correlated with the distribution of Cu. In both samples, classes of recombination sites were identified, where defects were activated or annihilated by temperature. More generally, the methodology of combined operando and in situ x-ray microscopy was established at the physical limit of spatial resolution given by the device itself. As proof-of-principle, the measurement of nanoscopic current generation in a solar cell is demonstrated with applied bias voltage and bias light.

Endoplasmic reticulum contact sites regulate the dynamics of membraneless organelles.

Tethered interactions between the endoplasmic reticulum (ER) and other membrane-bound organelles allow for efficient transfer of ions and/or macromolecules and provide a platform for organelle fission. Here, we describe an unconventional interface between membraneless ribonucleoprotein granules, such as processing bodies (P-bodies, or PBs) and stress granules, and the ER membrane. We found that PBs are tethered at molecular distances to the ER in human cells in a tunable fashion. ER-PB contact and PB biogenesis were modulated by altering PB composition, ER shape, or ER translational capacity. Furthermore, ER contact sites defined the position where PB and stress granule fission occurs. We thus suggest that the ER plays a fundamental role in regulating the assembly and disassembly of membraneless organelles.