Ghost Bands Research Articles

Appearance of ghost bands in gel electrophoresis depending on agarose concentration.

Standard agarose gel electrophoresis is a widely used method to analyse diversity of nucleic acids. Certain conditions, however, may give rise to artefactual bands. We report on artefactual bands frequently occurring, especially when partially homologous nucleic acids, such as splicing variants of DNA transcripts, are analysed simultaneously. Interestingly, to some extent agarose concentration may influence the occurrence of artefactual bands.

Quartz Vein Formation and Deformation during Porphyry Cu Deposit Formation: A Microstructural and Geochemical Analysis of the Butte, Montana, Ore Deposit

Abstract Hydrothermal quartz veins from the Butte deposit display euhedral and mottled cathodoluminescent (CL) textures that reflect the growth and deformation history of quartz crystals. A CL-euhedral texture consists of oscillatory dark-light zonations that record primary precipitation from an aqueous fluid. The origin of a CL-mottled texture, which consists of irregularly distributed dark and light portions, is less clear. Previous work showed that in some veins, CL-euhedral and CL-mottled crystals coexist, but the processes leading to their formation and coexistence were unknown. We find that CL-mottled crystals occur predominantly along the wall rock fracture surface and in vein centers and that CL-euhedral cockscomb quartz protrudes from the mottled layers along the wall rock. We infer that the mottled crystals formed by strain-induced recrystallization that was preferentially accommodated by the rheologically weaker layers of noncockscomb quartz because cockscomb crystals are in hard glide orientations relative to adjacent noncockscomb layers. During strain, crystals in noncockscomb layers that are not initially susceptible to slip can rotate in their deforming matrix until they deform plastically. Some of the CL-mottled crystals exhibit a relict CL-euhedral texture (“ghost bands”) whereby bright bands have been blurred and deformed owing to Ti redistribution facilitated by grain boundary migration. The edges of some CL-euhedral crystals become CL-mottled by localized grain boundary migration along adjacent crystals that do not align perfectly. Throughout the veins, CL-mottled crystals are randomly oriented, indicating that small deviatoric stresses were sufficient to drive recrystallization and mobilization of trace elements. Ti concentrations in CL-mottled crystals (23-47 ppm Ti; mean of 31 ppm) overlap those of CL-euhedral dark growth bands (16-40 ppm Ti; mean of 25 ppm Ti) in neighboring CL-euhedral crystals. Average Ti concentrations in CL-mottled quartz and CL-euhedral dark growth bands correspond to temperature estimates of 600°C (31 ppm Ti; CL-mottled) and 619°C (25 ppm Ti; dark bands), which are in good agreement with previous quartz precipitation temperature estimates based on independent thermobarometers. We conclude that recrystallization resets CL-mottled Ti concentrations close to the equilibrium value for the conditions of deformation and that CL-dark growth bands record near-equilibrium Ti concentrations. Recognition of widespread quartz recrystallization in porphyry Cu deposits underscores the significant role that strain plays in deposit formation. Individual veins host crystals that preserve conditions of primary growth and other crystals that preserve conditions of deformation and thermal overprint. Textural information is key to accurately interpreting trace element data and identifying different stages of vein formation. Our suggestion that CL-dark bands are the best candidates for near-equilibrium growth will aid the interpretation of trace element zoning in other hydrothermal systems.

Notes on the Field Identification of the Intricate Satyr, Hermeuptychia intricata (Nymphalidae), and Its Ecology in South Carolina

Due to strong morphological similarities, the Intricate Satyr Hermeuptychia intricata has been difficult for lepidopterists to visually differentiate from the Carolina Satyr Hermeuptychia sosybius since the former's discovery in 2014. The historical confusion between the two species has resulted in a dearth of information on the ecology and life history of the less abundant and more narrowly distributed H. intricata. I observed adults and larvae of both species in the field at five sites across three counties in the coastal plain of South Carolina, USA. Hermeuptychia intricata exhibited subtle but notable differences in both preferred habitat and behavior that are useful in field identification. Both species utilize various species of Rosette Grasses, Dichanthelium spp., as larval food sources. Larvae of the two species are extremely similar in appearance with only a slight difference in overall hue. Pupae appear identical save for the absence of an abdominal spot in H. intricata. The ghost band phenomenon and the sinuous band gap feature appear to be unreliable diagnostics but, with further research, may prove useful characteristics for identifying female H. intricata and H. sosybius, respectively. A better understanding of the ecology and life history of the cryptic H. intricata, as well as enhanced methods for its field identification, can facilitate the future study and conservation of the species.

Potential Second-Harmonic Ghost Bands in Fourier Transform Infrared (FT-IR) Difference Spectroscopy of Proteins.

Fourier transform infrared (FT-IR) difference absorption spectroscopy is a common method for studying the structural and dynamical aspects behind protein function. In particular, the 2800-1800 cm-1 spectral range has been used to obtain information about internal (deuterated) water molecules, as well as site-specific details about cysteine residues and chemically modified and artificial amino acids. Here, we report on the presence of ghost bands in cryogenic light-induced FT-IR difference spectra of the protein bacteriorhodopsin. The presence of these ghost bands can be particularly problematic in the 2800-1900 cm-1 region, showing intensities similar to O-D vibrations from water molecules. We demonstrate that they arise from second harmonics from genuine chromophore bands located in the 1400-850 cm-1 region, generated by double-modulation artifacts caused from reflections of the IR beam at the sample and at the cryostat windows back to the interferometer (inter-reflections). The second-harmonic ghost bands can be physically removed by placing an optical filter of suitable cutoff in the beam path, but at the cost of losing part of the multiplexing advantage of FT-IR spectroscopy. We explored alternatives to the use of optical filters. Tilting the cryostat windows was effective in reducing the intensity of the second harmonic artifacts but tilting the sample windows was not, presumably by their close proximity to the focal point of the IR beam. We also introduce a simple numerical post-processing approach that can partially, but not fully, correct for second-harmonic ghost bands in FT-IR difference spectra.

A weird DNA band in PCR and its cause

Abstract Purpose: Polymerase chain reaction (PCR) has been widely used in biological experiments. Sometimes, the PCR product can not go out of the sample groove in agarose gel. Such DNA band was called ghost band in

Doğu Karadeniz Bölgesi Hepatit C Hastalarında Hepatit C Virusu Genotiplerinin Belirlenmesi

Hepatitis C virus (HCV), the major cause of transfusion-associated hepatitis, is an important public health problem in the world as well as in Turkey. HCV is grouped as six distinct genotypes and a large number of closely-related subtypes. Genotyping of HCV is an important tool for providing epidemiological data, prediction of prognosis, and optimization of antiviral therapy. This study was carried out to determine the distribution of HCV genotypes in hepatitis C patients residing in different provinces of the Eastern Black Sea Region, Turkey. A total of 304 HCV-RNA positive cases (151 male, 153 female; age range: 11-93 years, mean age: 55.2 ± 13.3 years) who were admitted to the Molecular Microbiology Unit of Department of Medical Microbiology, Karadeniz Technical University Faculty of Medicine, between January 2009 to December 2012, were included in the study. HCV genotypes were detected in plasma samples of the patients by using commercial assays [INNO-LiPA HCV II (Innogenetics, Belgium) or Abbott RealTime HCV Genotype II (Abbott Molecular Inc, USA)]. Due to the ambiguous genotyping results in some samples with these methods, an in-house multiplex polymerase chain reaction (PCR) assay with genotype-specific primers was also used in the study. Similar to the previous reports from Turkey, our results showed that four HCV genotypes (1, 2, 3, and 4) prevailed in the Eastern Black Sea Region and the predominant genotype and subtype were genotype 1 (92.8%) and 1b (87.5%), respectively. Distribution of genotypes were observed to vary according to the province. Prevalences of subtype 1a, genotype 2, 3, and 4 were noted as 5.3%, 1.6%, 4.9%, and 0.7%, respectively. Furthermore, the samples from Giresun, Gumushane and Bayburt provinces, which are relatively less immigrated, had higher genotype 1, and the prevalence rates in the region was affected by the presence of non-citizen residents. This study is the first report on distribution of HCV genotypes in chronic hepatitis C patients living in the provinces of Eastern Black Sea Region. Moreover, genotype-specific multiplex PCR assay could be useful in resolving certain methodological problems such as "ghost bands" encountered in line probe assay (LiPA) and multiple genotypes (including genotype 4) observed in real-time PCR during the characterization of HCV genotypes seen in Turkey.

Accounting for scattering and reabsorption in the analysis of luminescence spectra of nanoparticles

An algorithm and a program are developed allowing the correction of experimentally measured luminescence spectra of nanocomposite materials with the aim to determine the luminescence spectra of the nanoparticles or of the local regions of the sample. The optical characteristics of CdS nanoparticles synthesised in a high-pressure polyethylene and in the orthoxylene solution are studied. It is shown that the luminescence spectra of the nanoparticles differ from those experimentally observed due to the scattering and reabsorption in the samples. In the region of wavelengths 500 — 550 nm a ghost band may arise due to the scattering and reabsorption of the luminescence in the sample near the edge of the CdS absorption band.

Control of pH during plasmid preparation by alkaline lysis of Escherichia coli

Alkaline lysis of Escherichia coli is usually the method of choice for plasmid preparation, but ‘‘ghost bands” of denatured supercoiled DNA can result if the pH is too high or the period of lysis is too long. By replacing the usual sodium hydroxide lysis solution with an arginine buffer prepared in the range of pH 11.4 to 12.0, we were able to stabilize the pH during lysis and obtain plasmid that is suitably pure for restriction digestion and DNA sequencing.

A rapid and sensitive method to detect specific human lymphocyte antigen (HLA) class II alleles associated with celiac disease

Celiac disease (CD) is a complex disorder triggered by gluten affecting genetically predisposed individuals. More than 90% of patients carry human lymphocyte antigen (HLA)-DQ2 (DQA1*05, DQB1*02) and/or HLA-DQ8 (DQA1*03, DQB1*0302). We propose the use of the DQ-CD Typing kit that allows identification of the HLA class II alleles (DQA1*0201,*03,*05, DQB1*02,*0302, DRB1*03,*04,*07) selected to be informative in the CD risk evaluation and of a second kit, namely DQ-CD Zygosis, for DQB1*02 homozygosity determination. The study was performed on a cohort of 100 individuals previously HLA typed with commercial kits. Fresh blood or previously extracted DNA was amplified in a unique PCR program using allele-specific primers and visualized on agarose gel. DNA amplification yielded strong and clear products without non specific signals or ghost bands. All the samples showed the expected alleles in accordance with the previous HLA typing. The DQ-CD Typing and Zygosis kits are fast, simple, economical and accurate tools that can be used to determinate the HLA-DQ2/DQ8 status in laboratory practice addressed for the diagnosis of CD. Molecular HLA testing is considered a valid support in the confirmation/exclusion of CD, especially in high-risk groups, such as CD relatives, or when serological and histological data are ambiguous.

Quantification of shell banding polymorphism in the East African tree snail Sitala jenynsi (Pulmonata: Ariophantidae)

In eastern Africa, populations of the tree snail Sitala jenynsi are monomorphic, dimorphic or trimorphic for the width of the upper brown band on their shells.We measured the variation in the width of this band in several populations and analysed it using two mutually verifiable methods: arithmetical probability paper and regressions of log-transformed shell metrics. The demarcations of the three morphs in areas of spatial overlap between the band-width states have been defined. We recognized existence of type I narrow-banding which associates monomorphism, and type II narrow-banding, medium banding and wide-banding forms which associate polymorphism. We have also quantified the variation in three other characters, two of which are also polymorphic: a lower pigmented band and an upper unpigmented ‘ghost band’. The evolutionary implications of the findings are discussed. Continued use of varietal names to describe the banding polymorphism of S. jenynsi is recommended, in preference to the multidimensional colour pattern notation commonly applied to gastropods.

Quantification of shell banding polymorphism in the East African tree snail Sitala jenynsi (Pulmonata: Ariophantidae)

In eastern Africa, populations of the tree snail Sitala jenynsi are monomorphic, dimorphic or trimorphic for the width of the upper brown band on their shells. We measured the variation in the width of this band in several populations and analysed it using two mutually verifiable methods: arithmetical probability paper and regressions of log-transformed shell metrics. The demarcations of the three morphs in areas of spatial overlap between the band-width states have been defined. We recognized existence of type I narrow-banding which associates monomorphism, and type II narrow-banding, medium banding and wide-banding forms which associate polymorphism. We have also quantified the variation in three other characters, two of which are also polymorphic: a lower pigmented band and an upper unpigmented 'ghost band'. The evolutionary implications of the findings are discussed. Continued use of varietal names to describe the banding polymorphism of S. jenynsi is recommended, in preference to the multidimensional colour pattern notation commonly applied to gastropods.

Purification and Identification of Proteins That Bind to the Hereditary Persistence of Fetal Hemoglobin –198 Mutation in the γ-Globin Gene Promoter

Expression of the gamma-globin gene is silenced in adult humans. However, certain point mutations in the gamma-globin gene promoter are capable of maintaining expression of this gene during adult erythropoiesis, a condition called non-deletion hereditary persistence of fetal hemoglobin (HPFH). Among these, the British form of HPFH carrying a T-->C point mutation at position -198 of the Agamma-globin gene promoter results in 4-10% fetal hemoglobin in heterozygotes. In this study, we used nuclear extracts from murine erythroleukemia cells to purify a protein complex that binds the HPFH -198 gamma-globin gene promoter. Members of this protein complex were identified by mass spectrometry and include DNMT1, the transcriptional coactivator p52, the protein SNEV, and RAP74 (the largest subunit of the general transcription factor IIF). Sp1, which was previously considered responsible for HPFH -198 gamma-globin gene activation, was not identified. The potential role of these proteins in the reactivation and/or maintenance of gamma-globin gene expression in the adult transcriptional environment is discussed.

A Database for Norm-Conserving Pseudopotential (NCPS2K): Application to Rare Gas Atoms

A norm-conserving pseudopotential database (NCPS95) and updated version NCPS97 have been available since 1995. NCPS97 has been updated to NCPS2K and will be distributed by CD-R media. In the updated version (NCPS2K), new numerical pseudopotential data for the rare gas atoms (He, Ne, Ar, Kr, Xe, Rn) and Ba and At have been prepared. In addition, some pseudopotentials in NCPS97 have been updated and retained. In this database, lattice properties and the absence of ghost bands in the electronic band structures are checked.

Norm-conserving pseudopotential database (NCPS97)

Norm-conserving pseudopotential database (NCPS95) was prepared in 1995. This database is distributed by CD-R media. NCPS95 is updated in order to be available for 5d transition metals etc. In this database, lattice properties and electronic band structures without ghost bands are checked.

The cardiac transcription factors Nkx2-5 and GATA-4 are mutual cofactors.

The tissue-restricted GATA-4 transcription factor and Nkx2-5 homeodomain protein are two early markers of precardiac cells. Both are essential for heart formation, but neither can initiate cardiogenesis. Overexpression of GATA-4 or Nkx2-5 enhances cardiac development in committed precursors, suggesting each interacts with a cardiac cofactor. We tested whether GATA-4 and Nkx2-5 are cofactors for each other by using transcription and binding assays with the cardiac atrial natriuretic factor (ANF) promoter_the only known target for Nkx2-5. Co-expression of GATA-4 and Nkx2-5 resulted in synergistic activation of the ANF promoter in heterologous cells. The synergy involves physical Nkx2-5-GATA-4 interaction, seen in vitro and in vivo, which maps to the C-terminal zinc finger of GATA-4 and a C-terminus extension; similarly, a C-terminally extended homeodomain of Nkx2-5 is required for GATA-4 binding. Structure/function studies suggest that binding of GATA-4 to the C-terminus autorepressive domain of Nkx2-5 may induce a conformational change that unmasks Nkx2-5 activation domains. GATA-6 cannot substitute for GATA-4 for interaction with Nkx2-5. This interaction may impart functional specificity to GATA factors and provide cooperative crosstalk between two pathways critical for early cardiogenesis. Given the co-expression of GATA proteins and NK2 class members in other tissues, the GATA/Nkx partnership may represent a paradigm for transcription factor interaction during organogenesis.

Methods and reagents: Eliminating ghost bands from plasmid preps

Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methds-reagnts, available on the internet. This month's column updates the discussion of a ghost DNA band that continues to haunt netters. For details on how to partake in the newsgroup, see the accompanying box.

Angle-resolved photoemission spectroscopy study of the superconducting gap anisotropy in Bi2Sr2CaCu2O8+x.

We report measurements of the momentum dependence of the superconducting gap in Bi_2Sr_2CaCu_2O_{8+x} (Bi2212) with angle-resolved photoemission spectroscopy using a dense sampling of the Brillouin zone in the vicinity of the Fermi surface. In the Y quadrant of the zone, where there are no complications from ghost bands caused by the superlattice, we find a gap function consistent within error bars to the form cos(k_x)-cos(k_y) expected for a d-wave order parameter. Similar results are found in the X quadrant with the photon polarization chosen to enhance main band emission over that due to ghost bands.

Analytical evaluation of the purity of commercial preparations of Cibacron Blue F3GA and related dyes

The composition and purity of three commercial preparations of the widely used affinity chromatography ligand Cibacron Blue F3GA have been evaluated by TLC and by paired-ion reversed-phase HPLC and were found to contain several chromophoric species. Stepwise synthesis of the reported dye structure showed that only one commercial preparation contained any actual Cibacron Blue F3GA, and that it was present only in minor amounts. In all three preparations the major component appears to be the dichlorotriazinyl precursor of Cibacron Blue F3GA. Commercial samples of the related dyes Procion Blue MX-3G and Procion Blue MX-R are also highly heterogeneous. In addition, our experiments suggest that TLC results must be evaluated carefully to ensure that catalytic surface activity of alumina and silica has not created ghost bands.

Interaction of phloretin with the anion transport protein of the red blood cell membrane

Phloretin is an inhibitor of anion exchange and glucose and urea transport in human red cells. Equilibrium binding and kinetic studies indicate that phloretin binds to band 3, a major integral protein of the red cell membrane. Equilibrium phloretin binding has been found to be competitive with the binding of the anion transport inhibitor, 4,4′-dibenzamido-2,2′-disulfonic stilbene (DBDS), which binds specifically to band 3. The apparent binding (dissociation) constant of phloretin to red cell ghost band 3 in 28.5 mM citrate buffer, pH 7.4, 25°C, determined from equilibrium binding competition, is 1.8 ± 0.1 μM . Stopped-flow kinetic studies show that phloretin decreases the rate of DBDS binding to band 3 in a purely competitive manner, with an apparent phloretin inhibition constant of 1.6 ± 0.4 μM . The pH dependence of equilibrium binding studies show that it is the charged, anionic form of phloretin that competes with DBDS binding, with an apparent phloretin inhibition constant of 1.4 μM. The phloretin binding and inhibition constants determined by equilibrium binding, kinetic and pH studies are all similar to the inhibition constant of phloretin for anion exchange. These studies suggest that phloretin inhibits anion exchange in red cells by a specific interaction between phloretin and band 3.