Probe Sites Research Articles

Karyotypic characterization of melon accessions

Cucumis melo (melon) is a species from the Iberian Peninsula and is included in the family Cucurbitaceae. Despite the knowledge about the physical structure of melon chromosomes, little is known about the intraspecific karyotype diversity of the species. To study karyotype diversity in eight melon accessions, the following methods were used: Giemsa 3% staining; application of CMA 3 /DAPI fluorochromes; and location of 45S and 5S rDNA sequences by fluorescence in situ hybridization. Conventional staining analysis revealed stability in the chromo­some number, with accessions presenting 2 n = 24. There were significant variations in the mean chromosome size between accessions, ranging from 0.98 μm to 1.46 μm for accessions A26 and A18, respectively. Scott-Knott clustering distributed the accessions into two groups. GC-rich heterochromatic blocks (CMA 3 + /DAPI - ) were observed in pericentromeric regions of all chromosomes in the complement. CMA 3 + /DAPI - blocks were also lo­cated in terminal regions, being specific to satellite regions. Hybridization sites of 45S rDNA probes revealed the presence of a chromosome pair with this locus . In addition, 5S rDNA sites revealed a labeled chromosome pair. No quantitative variation was observed in rDNA sites between the accessions analyzed, indicating these markers as ideal for the verification of karyotypic stability in C . melo .

β 2-Microglobulin and Neutrophil Gelatinase-Associated Lipocalin, Potential Novel Urine Biomarkers in Periodontitis: A Cross-Sectional Study in Japanese.

Objectives Several serum biomarkers have been reported to increase in periodontitis patients as possible mediators linking periodontal inflammation to systemic diseases. However, the relationship between periodontitis and urine biomarkers is still unclear. The aim of this cross-sectional study was to investigate potential urine biomarkers of periodontitis in a Japanese population. Materials and Methods This study included 108 male subjects, and microbiological and clinical parameters were evaluated as a periodontitis marker. The correlation between nine urine biomarkers (typically used to diagnose kidney disease) and periodontal parameters was analyzed. Based on the findings, β2-microglobulin (β2-MG) and neutrophil gelatinase-associated lipocalin (NGAL) were selected for comparison and multivariate regression analysis, and the Kruskal–Wallis test followed by Bonferroni correction was used to identify differences in their concentrations between the three periodontitis groups (severe, moderate, and no/mild periodontitis). Results β 2-MG and NGAL exhibited a significant correlation with clinical parameters of periodontitis. The prevalence of clinical parameters such as bleeding on probing and number of sites with probing depth (PD) ≥ 6 mm were greater in the β2-MG high group (≥300 μg/g creatinine) than in the normal group (P=0.017 and 0.019, respectively). Multivariate regression analysis indicated that the number of sites with PD ≥ 6 mm was independently associated with urine β2-MG. Moreover, the number of sites with the clinical attachment level (CAL) ≥ 6 mm was greater in the NGAL high group (highest quartile) (P=0.041). Multivariate regression analysis showed that the number of sites with CAL ≥ 6 mm was associated independently with urine NGAL. Finally, β2-MG was significantly higher in the severe periodontitis subjects compared to the no/mild periodontitis subjects. Conclusion The significant association between urine β2-MG or NGAL and periodontitis was revealed. These biomarkers can potentially be used to screen for or diagnose periodontitis. This trial is registered with the UMIN Clinical Trials Registry UMIN000013485.

Estimating active storage of groundwater quality zones in alluvial deposits of Faisalabad area, Rechna Doab, Pakistan

The quantification and assessment of groundwater are of great significance for the urbanization and town planning in an area. The current study has been carried out for quantification and assessment of groundwater quality zones by using geo-electrical technique in Faisalabad area (73° 06′ 08″–73° 11′ 59″ E; 31° 35′ 00″–31° 40′ 39″ N) of Pakistan. Vertical electrical soundings (VES) at six locations were conducted by Schlumberger configuration up to 300-m depth of investigation. Modeling technique is used for the interpretation of apparent resistivity, and the true resistivities of various subsurface lithologies were recorded from 2.10 to 55 Ω m for the depth of investigation. Three sand-dominant aquifers were identified at depth intervals of 0–50 m, 50–100 m, and 100–300 m. The VES results are compared and calibrated with the available borehole data taken from the tube wells drilled in the vicinity of the study area. The GIS technique is applied for the preparation of water quality zonation maps. Some of the groundwater quantification parameters such as total volume of the alluvium, total volumes of the water content, and active storage are estimated through GIS applications. Top geo-electrical layer (0–50 m) is dominated by low resistivity zone (10–25 Ω m), having an active storage of 0.71 km3. Intermediate geo-electrical layer (50–100 m) comprised coarse sand with low-to-medium resistivity zone of 10–35 Ω m, showing a low active storage (1.01 km3). Deep geo-electrical layer (100–300 m) is dominant by very low resistivity zone (< 10 Ω m) in the whole area. This 200-m-thick zone is possibly an admixture of fine sand, clay, and silt, having a high active storage (4.06 km3). The quality of water deteriorates with depth, and aquifer zones saturated with marginal-to-saline groundwater are interpreted below the fresh water zone at all the probe sites. The active storage of the lower geo-electrical layer (100–300 m) indicates a huge water potential but it is trapped in medium sand and alternative layers of clay. The intermediate geo-electrical layer (50–100 m) is comparatively better in quality but has low ground water potential.

Discriminating Among Pacific Salmon, Rainbow Trout, and Atlantic Salmon Species Using Common Genetic Screening Methods

Abstract The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

Cofactor Analogues as Active Site Probes in Lysine Acetyltransferases.

Lysine acetyltransferases (KATs, also termed histone acetyltransferases, HATs) catalyze the acetylation of substrate lysine residues by employing the cofactor acetyl-coenzyme A (AcCoA), thereby providing a dynamic control mechanism of protein function. Because of their major involvement in cell development and homeostasis, small-molecule modulators of KAT activity are urgently needed to assess their therapeutic potential and for probing their underlying biology. Recent advances in the field suggest that targeting the cofactor binding site represents a promising strategy for identifying potent and selective ligands. Here, we present the synthesis of two functional cofactor-based chemical probes and their usage as mechanistic tools in a broadly applicable assay platform. A fluorescence polarization (FP)-based binding assay was combined with biolayer interferometry competition analysis and a FP competition activity immunoassay to enable easy, reliable, and profound evaluation of ligands that target the KAT cofactor binding site.

Sex Differences in Estradiol Secretion by Trigeminal Brainstem Neurons.

Estrogen status is a significant risk factor in the development of temporomandibular joint disorders (TMD). Classically, estrogen status is thought to derive mainly from ovarian sources; however, it is well known that estradiol (E2) also is synthesized by neurons in the brain. This study tested the hypothesis that E2 is produced by neurons in trigeminal subnucleus caudalis (Vc), the principal site of termination for sensory afferents that supply the temporomandibular joint (TMJ), to modify evoked responses in a model of TMJ nociception in male and female rats. Intra-TMJ injection of the small fiber excitant, allyl isothiocyanate (AIC), increased the levels of E2 collected from microdialysis probes sites at Vc of ovariectomized (OvX) female rats, ipsilateral to the stimulus, whereas males displayed no change. Dialysate levels of E2 collected from probe sites in the contralateral Vc or cerebellum in OvX rats were not affected by TMJ stimulation. Reverse dialysis of anastrozole, an aromatase (ARO) inhibitor, via the probe reduced perfusate levels of E2 in Vc. Systemic administration of letrozole, a non-steroid ARO inhibitor, for 4 days prevented TMJ-evoked increases in masseter muscle electromyography (MMemg) activity. ARO-positive neurons were distributed mainly in superficial laminae (I-III) at Vc and cell counts revealed no significant difference between OvX and male rats. Intra-TMJ injection of AIC revealed similar numbers of ARO/Fos dual-labeled neurons in OvX and male rats. By contrast, the percentage of ARO neurons co-labeled for glutamic acid decarboxylase (GAD), the biosynthetic enzyme for GABA, was greater in OvX (35%) than male rats (14%). Few ARO-positive neurons were co-labeled for estrogen receptor alpha. These data indicate that E2 is secreted continuously by Vc neurons and that acute stimulation of TMJ nociceptors evokes further secretion in a sex-dependent manner. Reduced TMJ-evoked MMemg activity after ARO inhibition suggests that locally produced E2 by Vc neurons acts via paracrine mechanisms to modify TMJ nociception in female rats.

Characterization of tolazamide binding with glycated and normal human serum albumin by using high-performance affinity chromatography

Sulfonylurea drugs are antidiabetic drugs that are utilized in the treatment of type II diabetes and often have significant binding with human serum albumin (HSA). Immobilized samples of normal or glycated HSA in affinity microcolumns were used to investigate interactions of these proteins with the sulfonylurea drug tolazamide. HPLC and frontal analysis were used to first examine the overall binding of this drug with these samples of HSA. It was found that tolazamide had two general classes of binding sites (i.e., high and low affinity) for normal and glycated HSA. The higher affinity sites had binding constants of around 4.3–6.0 × 104 M−1 for these interactions at pH 7.4 and 37 °C, while the lower affinity sites had binding strengths of 4.9–9.1 × 103 M−1. Zonal competition studies between tolazamide and probes for Sudlow sites I and II on HSA were also performed and used to provide site-specific affinities for tolazamide at these sites. A decrease of 22% in affinity was observed for tolazamide at Sudlow site I and an increase up to 58% was seen at Sudlow site II when comparing glycated HSA with normal HSA. These observed changes were compared to those of other first-generation sulfonylurea drugs, providing information on how glycation can alter the total and local binding strength of tolazamide and related compounds with HSA under levels of glycation seen in patients with diabetes.

Synthesis and Properties of Novel Fluorescence Probe Based on 1,8-Naphthalimide for Detection of Hydrogen Sulfide

Two fluorescence-enhanced probes, 4-(2,4-dinitrophenoxy)-N-(2-hydroxyethyl)-1,8-naphthalimide(NTE-1) and 4-(2,4-dinitrophenoxy)-N-(4-(2,4-dinitrophenoxy)phenyl)-1,8-naphthalimide(NTE-2), have been designed and synthesized for detection of H2S. 4-Hydroxy-1,8-naphthalimide as fluorophore in combination with 2,4-dinitrophenyl ether as H2S response site constructed the fluorescence probes. The consequences showed that both NTE-1 and NTE-2 displayed large red-shift(excess 100 nm) in absorption spectra and more than 30-fold fluorescence enhancement in response to H2S. Moreover, the dual site probe, NTE-2, displayed wider linear range between fluorescence intensity and concentration of H2S(0—40 μmol/L) compared with single site probe, which can be applied to quantitative detection of high concentration of H2S. The photoinduced electron transfer(PET) response mechanism of probe was further studied by analyzing the distributions of molecular orbital. Importantly, the probes have potential practical applications in detection of H2S.

Directly monitoring the active sites of charge transfer in heterocycles in situ and in real time.

Coherent degenerate infrared-infrared-visible sum frequency generation vibrational spectroscopy provides a powerful label-free sensitive probe for charge transfer active sites in heterocyclic molecules in situ and in real time.

Colorimetric and NIR Fluorescence Probe with Multiple Binding Sites for Distinguishing Detection of Cys/Hcy and GSH in Vivo

Although some progress has been made in distinguishing the detection of biothiols, NIR biothiol fluorescent probes for simultaneously distinguishing detection of Cys, Hcy, and GSH in vivo have not been reported. The design of these probes involves the introduction of NIR fluorophores and multiple binding sites; thus, the integrated design of probes remains a challenge. Although Cys, Hcy, and GSH have common functional groups, a sulfydryl group and an amino group, due to their differences in spatial structure, they may react with multiple binding site probes to produce different reaction products in different bonding mechanisms, resulting in different colors and fluorescent signal changes of the system. Therefore, multiple binding site fluorescent probes can realize their discrimination detection. For an NIR fluorescent probe, it is easier to realize in vivo imaging to promote the research of biothiols in clinical diagnosis. In our work, not only were multiple binding sites constructed in the compound but also NIR fluorophores were introduced. This enables the probe to not only efficiently distinguish detection of Cys/Hcy and GSH but also achieve fluorescence imaging in vivo. We believe this result is a milestone in the discrimination detection of biothiols.

Study on the interaction of fisetholz with BSA/HSA by multi-spectroscopic, cyclic voltammetric, and molecular docking technique

The interaction of fisetholz with bovine serum albumin (BSA) and human serum albumin (HSA) was investigated by multi-spectroscopic, cyclic voltammetric, and molecular docking technique. The results revealed that there was a static quenching of BSA/HSA induced by fisetholz. The binding constants (Ka) and binding sites (n) were calculated at different temperatures (293, 303, and 311 K). The enthalpy change (ΔH) were calculated to be –17.20 kJ mol−1 (BSA) and –18.28 kJ mol−1 (HSA) and the entropy change (ΔS) were calculated to be 35.41 J mol−1 (BSA) and 24.02 J mol−1 (HSA), respectively, which indicated that the interaction between fisetholz and BSA/HSA was mainly by electrostatic attraction. Based on displacement experiments using site probes, indomethacin and ibuprofen, the binding site of fisetholz to BSA/HSA was identified as sub-domain IIIA, which was further confirmed by molecular docking method. There was little effect of K+, Ca2+, Cu2+, Zn2+, and Fe3+ on fisetholz-BSA or fisetholz-HSA complex. The spectra of synchronous fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) all showed that fisetholz binding to BSA/HSA leads to secondary structures change of the two serum albumins. According to the Förster non-radiation energy transfer theory, the binding distance between fisetholz and BSA/HSA was 2.94/4.68 nm. The cyclic voltammetry as a supporting tool also indicated that fisetholz interacted with protein.Communicated by Ramaswamy H. Sarma

Novel monoamine oxidase inhibitors based on the privileged 2-imidazoline molecular framework

Series of structurally diverse 2-imidazoline derivatives have been synthesized by condensation of substituted aldehydes with ethylenediamine, Pd-catalyzed N-arylation of 2-imidazolines and by the formation of 1,2,4-oxadiazoles and benzoxazepines from 2-imidazoline-containing precursors. The 2-imidazoline derivatives were evaluated as potential inhibitors of human monoamine oxidase (MAO) A and B. Among the 2-imidazolines, good potency inhibitors were discovered with compound 9p (IC50 = 0.012 µM) being the most potent MAO-B inhibitor, while compound 9d (IC50 = 0.751 µM) was the most potent MAO-A inhibitor of the series. These potencies are in the same range as those of reference MAO inhibitors used in the clinic. Among 33 compounds evaluated, 13 exhibited IC50 values in the submicromolar range for the inhibition of an MAO isoform. It is postulated that the imidazoline moieties of some of these inhibitors may be recognized by the imidazoline I2-binding site of MAO. Good potency MAO inhibitors may be useful for the treatment of neuropsychiatric and neurodegenerative disorders such as depression and Parkinson’s disease, and future application for the treatment of prostate cancer, congestive heart failure and Alzheimer’s disease. In addition, high potency 2-imidazoline-derived MAO inhibitors may be used as potential probes for the imidazoline binding sites of the MAOs, as well as to determine alternative binding regions of imidazoline within the MAO active site.

Characterization of the binding and conformational changes of bovine serum albumin upon interaction with antihypertensive olmesartan medoxomil

The interaction of bovine serum albumin (BSA) with the olmesartan medoxomil (OLM) was investigated by different spectroscopic and linear sweep voltammetric techniques under experimentally optimised physiological conditions. The alteration of functional properties of BSA when quenched by OLM was illustrated by the continuous decrease of the fluorescence intensity of BSA upon addition of OLM. The quenching constants (Ksv) obtained were 0.71 × 104, 1.3 × 104 and 2.1 × 104 Lmol−1 at 288, 298 and 308 K respectively. The binding mechanism was dynamic type quenching. The value of K is of the order of 104, indicating that a long-lasting interaction exists between OLM and BSA. The positive values of ΔH0 and ΔS0 suggested the hydrophobic interactions play the major roles in the binding reaction. The conformational change of BSA after binding with OLM was demonstrated by the synchronous, FTIR and 3-D fluorescence spectral results. The effects of some common metal ions and site probes on binding of BSA– OLM were also investigated.

Synthesis, characterization, HSA interaction, and antibacterial activity of a new water-soluble Pt(II) complex containing the drug cephalexin

A new water-soluble platinum(II) complex, [Pt(CEX)Cl(DMSO)]Cl (CEX is cephalexin), was synthesized and characterized by physicochemical, spectroscopic, and computational methods. Multispectroscopic techniques were used to investigate the interaction of Pt(II) complex with human serum albumin (HSA) under the physiological conditions. The results of fluorescence titration indicated that the binding of the Pt(II) complex to HSA induced fluorescence quenching through static quenching mechanism with binding constant of 1.24 × 104 M−1 at 298 K. The thermodynamic parameters at different temperatures indicated that van der Waals forces, hydrogen bonds, and electrostatic forces play major roles in the stability of Pt(II) complex–HSA association. The displacement experiments using the site probes warfarin and ibuprofen substantiated that Pt(II) complex could bind to both site I and II of HSA. Furthermore, UV–Vis and fluorescence spectra were used to investigate the conformational changes of HSA molecule with the addition of Pt(II) complex. The binding constant of Pt(II) complex is more than two orders of magnitude higher than the corresponding value of cephalexin. These results indicate that the binding affinity of Pt(II) complex is stronger than the free drug. In addition, the antibacterial study showed that the MIC of platinum complex of cephalexin for variety of organisms was lower than free cephalexin.

Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements

Increases in CO2 concentration in plant leaves due to respiration in the dark and the continuing atmospheric [CO2] rise cause closing of stomatal pores, thus affecting plant-water relations globally. However, the underlying CO2/bicarbonate (CO2/HCO3-) sensing mechanisms remain unknown. [CO2] elevation in leaves triggers stomatal closure by anion efflux mediated via the SLAC1 anion channel localized in the plasma membrane of guard cells. Previous reconstitution analysis has suggested that intracellular bicarbonate ions might directly up-regulate SLAC1 channel activity. However, whether such a CO2/HCO3- regulation of SLAC1 is relevant for CO2 control of stomatal movements in planta remains unknown. Here, we computationally probe for candidate bicarbonate-interacting sites within the SLAC1 anion channel via long-timescale Gaussian accelerated molecular dynamics (GaMD) simulations. Mutations of two putative bicarbonate-interacting residues, R256 and R321, impaired the enhancement of the SLAC1 anion channel activity by CO2/HCO3- in Xenopus oocytes. Mutations of the neighboring charged amino acid K255 and residue R432 and the predicted gate residue F450 did not affect HCO3- regulation of SLAC1. Notably, gas-exchange experiments with slac1-transformed plants expressing mutated SLAC1 proteins revealed that the SLAC1 residue R256 is required for CO2 regulation of stomatal movements in planta, but not for abscisic acid (ABA)-induced stomatal closing. Patch clamp analyses of guard cells show that activation of S-type anion channels by CO2/HCO3-, but not by ABA, was impaired, indicating the relevance of R256 for CO2 signal transduction. Together, these analyses suggest that the SLAC1 anion channel is one of the physiologically relevant CO2/HCO3- sensors in guard cells.

The preparation and clinical application of diagnostic DNA microarray for the detection of pathogens in intracranial bacterial and fungal infections

The present study prepared 2 types of DNA diagnostic chips based on 16S ribosomal DNA (rDNA) and 18S-28S rDNA, and evaluated their values in the detection of pathogens in intracranial bacterial/fungal infections. A total of 14 probes of bacteria (Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Haemophilus influenza, Stenotrophomonas maltophilia, Neisseria meningitidis, Enterobacter spp., Enterococcus faecalis, Enterococcus faecium, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pneumonia and coagulase negative staphylococcus) and 4 probes of fungi (Candida albicans, Candida tropicalis, Candida glabrata and Cryptococcus neoformans), determined frequently in cerebrospinal fluid (CSF), were designed and used for preparation of microarrays. CSF samples from 88 patients with clinically suspected intracranial infection and standard strains were used to evaluate the chips. The same samples were also analyzed by culture and sequencing. The results demonstrated that the sensitivity, specificity and false-positive rate of the microarray assay compared with culture method were 100 vs. 68.3% (P<0.05), 97.1 vs. 100%, and 2.9 vs. 0%, respectively. The minimum concentration of detection with the chips was 10 cfu ml−1 for bacteria and 100 cfu ml−1 for fungi. The specificity of the probes was confirmed, and no cross-reaction was detected in the present study. Furthermore, 13 cases were positive in the microarray and negative in culture. However, 4 cases were not identified as clear pathogens and only positive in the 16S probe sites. The diagnostic DNA microarray for intracranial infections has proven to be more rapid and sensitive, and it may be a better option for clinical application than culture methods.

Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development

ABSTRACTLate onset of clinical symptoms in hepatocellular carcinoma (HCC) results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable tools that would distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed. We used the Illumina HumanMethylation450 BeadChip microarray to test whether white blood cell DNA, an easily accessible source of DNA, exhibits site-specific changes in DNA methylation in blood of diagnosed HCC patients (post-diagnostic, 24 cases, 24 controls) and in prospectively collected blood specimens of HCC patients who were cancer-free at blood collection (pre-diagnostic, 21 cases, 21 controls). Out of 22 differentially methylated loci selected for validation by pyrosequencing, 19 loci with neighbouring CpG sites (probes) were confirmed in the pre-diagnostic study group and subjected to verification in a prospective cirrhotic cohort (13 cases, 23 controls). We established for the first time 9 probes that could distinguish HBV-negative cirrhotic patients who subsequently developed HCC from those who stayed cancer-free. These probes were identified within regulatory regions of BARD1, MAGEB3, BRUNOL5, FXYD6, TET1, TSPAN5, DPPA5, KIAA1210, and LSP1. Methylation levels within DPPA5, KIAA1210, and LSP1 were higher in prospective samples from HCC cases vs. cirrhotic controls. The remaining probes were hypomethylated in cases compared with controls. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established probes have potential to be developed into a routine clinical test after validation in larger cohorts.

Plaque‐induced gingivitis: Case definition and diagnostic considerations

Clinical gingival inflammation is a well-defined site-specific condition for which several measurement systems have been proposed and validated, and epidemiological studies consistently indicate its high prevalence globally. However, it is clear that defining and grading a gingival inflammatory condition at a site level (i.e. a "gingivitis site") is completely different from defining and grading a "gingivitis case" (GC) (i.e. a patient affected by gingivitis), and that a "gingivitis site" does not necessarily mean a "GC". The purpose of the present review is to summarize the evidence on clinical, biochemical, microbiologic, genetic markers as well as symptoms associated with plaque-induced gingivitis and to propose a set of criteria to define GC. A universally accepted case definition for gingivitis would provide the necessary information to enable oral health professionals to assess the effectiveness of their prevention strategies and treatment regimens; help set priorities for therapeutic actions/programs by health care providers; and undertake surveillance. Based on available methods to assess gingival inflammation, GC could be simply, objectively and accurately identified and graded using bleeding on probing score (BOP%) CONCLUSIONS: A patient with intact periodontium would be diagnosed as a GC according to a BOP score ≥ 10%, further classified as localized (BOP score ≥ 10% and ≤30%) or generalized (BOP score>30%). The proposed classification may also apply to patients with a reduced periodontium, where a GC would characterize a patient with attachment loss and BOP score ≥ 10%, but without BOP in any site probing ≥4mm in depth.

Plaque-induced gingivitis: Case definition and diagnostic considerations.

Clinical gingival inflammation is a well-defined site-specific condition for which several measurement systems have been proposed and validated, and epidemiological studies consistently indicate its high prevalence globally. However, it is clear that defining and grading a gingival inflammatory condition at a site level (i.e. a "gingivitis site") is completely different from defining and grading a "gingivitis case" (GC) (i.e. a patient affected by gingivitis), and that a "gingivitis site" does not necessarily mean a "GC". The purpose of the present review is to summarize the evidence on clinical, biochemical, microbiologic, genetic markers as well as symptoms associated with plaque-induced gingivitis and to propose a set of criteria to define GC. A universally accepted case definition for gingivitis would provide the necessary information to enable oral health professionals to assess the effectiveness of their prevention strategies and treatment regimens; help set priorities for therapeutic actions/programs by health care providers; and undertake surveillance. Based on available methods to assess gingival inflammation, GC could be simply, objectively and accurately identified and graded using bleeding on probing score (BOP%) CONCLUSIONS: A patient with intact periodontium would be diagnosed as a GC according to a BOP score ≥ 10%, further classified as localized (BOP score ≥ 10% and ≤30%) or generalized (BOP score>30%). The proposed classification may also apply to patients with a reduced periodontium, where a GC would characterize a patient with attachment loss and BOP score ≥ 10%, but without BOP in any site probing ≥4mm in depth.

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes.

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.