Detection of Babesia bigemina infection: use of a DNA probe - a review

The development of a repetitive DNA probe for Babesia bigemina was reviewed. The original plasmid (p(Bbi)16) contained an insert of B. bigemina DNA of approximately 6.3 kb. This probe has been evaluated for specificityand analytical sensitivity by dot hybridization with isolates from Mexico, the Caribbean region and Kenya. A partial restriction map has been constructed and insert fragments have been subcloned and utilized as specific DNA probes. A comparison of 32P labelled and non-radioactive DNA probes was presented. Non-radioctive detection systems that have been used include digoxigenin dUTP incorporation, and detection by colorimetric substrate methods. Derivatives from the original DNA probe have been utilized to detect B. bigemina infection in a) experimentally inoculated cattle, b) field exposed cattle, c) infected Boophilus microplus ticks, and d) the development of a PCR amplification system.

Evaluation of a colorimetric Babesia bigemina-DNA probe within an epidemiological survey

An epidemiological survey was conducted in south east Mexico, in an effort to establish the serological reactivity and carrier status to Babesia bigemina of an indigenous cattle population. The prevalance was obtained through the Indirect Fluorescent Antibody Test (IFAT), using an in vitro culture-derived B. bigemina antigen. A specific, digoxigenin-coupled, ~6kb B. bigemina-DNA probe (BBDP), was used to indicate the presence of the parasite. Serum samples from 925 animals of all ages, were obtained within the three regions (I, II, III) of the state of Yucatan and tested by IFAT. In addition, whole blood samples draw from 136 of the same animals of region II were analyzed using the BBDP. Positive IFAT (IFAT+) reactions were observed in 531 sera for a 57% overall prevalence. Regional values were: I = 157 + (56%), II = 266 + (68%) and III = 108 + (42%). Only 32 (23%) of the blood samples tested with BBDP showed distinctive hybridization signal, in contrast with 100 (73%) IFAT + animals. The responses distribution for IFAT vs. BBDP was: +/+ 23, +/- 77, -/+ 9 and -/- 27 respectively. It was found that the analytical sinsitivity of BBDP appears to be low for its utilization is widespread epidemiological surveys. It was considered, however, that the colorimetric probe mifht to be useful to safely detect transmission prone carriers, since it is able to detect parasitemias as low as 0.001%.

An oligonucleotide probe derived from kDNA minirepeats is specific for Leishmania (Viannia)

Sequence analysis of Leishmania (Viannia) kDNA minicircles and analysis of multiple sequence alignments of the conserved region (minirepeats) of five distinct minicircles from L. (V.) braziliensis species with corresponding sequences derived from other dermotropic leishmanias indicated the presence of a sub-genus specific sequence. An oligonucleotide bearing this sequence was designed and used as a molecular probe, being able to recognize solely the sub-genus Viannia species in hybridization experiments. A dendrogram reflecting the homologies among the minirepeat sequences was constructed. Sequence clustering was obtained corresponding to the traditional classification based on similarity of biochemical, biological and parasitological characteristics of these Leishmania species, distinguishing the Old World dermotropic leishmanias, the New World dermotropic leishmanias of the sub-genus Leishmania and of the sub-genus Viannia.

A novel study of copy number variations in Hirschsprung disease using the multiple ligation-dependent probe amplification (MLPA) technique.

BACKGROUND Hirschsprung disease (HSCR) is a congenital malformation of the hindgut produced by a disruption in neural crest cell migration during embryonic development. HSCR has a complex genetic etiology and mutations in several genes, mainly the RET proto-oncogene, have been related to the disease. There is a clear predominance of missense/nonsense mutations in these genes whereas copy number variations (CNVs) have been seldom described, probably due to the limitations of conventional techniques usually employed for mutational analysis. METHODS In this study we have aimed to analyze the presence of CNVs in some HSCR genes (RET, EDN3, GDNF and ZFHX1B) using the Multiple Ligation-dependent Probe Amplification (MLPA) approach. RESULTS Two alterations in the MLPA profiles of RET and EDN3 were detected, but a detailed inspection showed that the decrease in the corresponding dosages were due to point mutations affecting the hybridization probes regions. CONCLUSION Our results indicate that CNVs of the gene coding regions analyzed here are not a common molecular cause of Hirschsprung disease. However, further studies are required to determine the presence of CNVs affecting non-coding regulatory regions, as well as other candidate genes.

A novel interferon-gamma regulated human melanoma-associated antigen, gp33-38, defined by monoclonal antibody Me14-D12. II. Molecular cloning of a genomic probe.

The human Me14-D12 antigen is a cell surface glycoprotein regulated by interferon-gamma (IFN-gamma) on tumor cell lines of neuroectodermal origin. It consists of two non-convalently linked subunits with apparent mol. wt sizes of 33,000 and 38,000. Here we describe the molecular cloning of a genomic probe for the Me14-D12 gene using the gene transfer approach. Mouse Ltk- cells were stably cotransfected with human genomic DNA and the Herpes Simplex virus thymidine kinase (TK) gene. Primary and secondary transfectants expressing the Me14-D12 antigen were isolated after selection in HAT medium by repeated sorting on a fluorescence activated cell sorter (FACS). A recombinant phage harboring a 14.3 kb insert of human DNA was isolated from a genomic library made from a positive secondary transfectant cell line. A specific probe derived from the phage DNA insert allowed the identification of two mRNAs of 3.5 kb and 2.2 kb in primary and secondary L cell transfectants, as well as in human melanoma cell lines expressing the Me14-D12 antigen. The regulation of Me14-D12 antigen by INF-gamma was retained in the L cell transfectants and could be detected both at the level of protein and mRNA expression.

An improved synthesis of dansylated α-galactosylceramide and its use as a fluorescent probe for the monitoring of glycolipid uptake by cells.

A highly efficient synthesis of the biologically important fluorescent probe dansyl α-GalCer is presented. Key in our strategy is the incorporation of the fluorescent dansyl group at an early stage in the synthesis to facilitate in the monitoring and purification of intermediates via TLC and flash column chromatography, respectively, and the use of a high yielding α-selective glycosylation reaction between the phytosphingosine lipid and a galactosyl iodide donor. The ability of dansyl α-GalCer to activate iNKT cells and to serve as a fluorescent marker for the uptake of glycolipid by dendritic cells is also presented.

Prediction of subcutaneous fatty acid composition from ham of CLA fed boars and gilts using a NIRS fiber optic probe

The aim of this work was the use of NIR technology by direct application of a fiber optic probe on back fat to analyze the fatty acid composition of CLA fed boars and gilts. 265 animals were fed 3 different diets and the fatty acid profile of back fat from Gluteus medius was analyzed using gas chromatography and FT-NIR. Spectra were acquired using a Bruker Optics Matrix-F duplex spectrometer equipped with a fiber optic probe (IN-268-2). Oleic and stearic fatty acids were predicted accurately; myristic, vaccenic and linoleic fatty acids were predicted with lower accuracy, while palmitic and α-linolenic fatty acids were poorly predicted. The relative percentage of fatty acids and NIR spectra showed differences in fatty acid composition of back fat from pigs fed CLA which increased the relative percentage of SFA and PUFA while MUFA decreased. Results suggest that a NIR fiber optic probe can be used to predict total saturated and unsaturated fatty acid composition, as well as the percentage of stearic and oleic. NIR showed potential as a rapid and easily implemented method to discriminate carcasses from animals fed different diets.

Sampling and TDR probe insertion in the determination of the volumetric soil water content

Volumetric soil water content (theta) can be evaluated in the field by direct or indirect methods. Among the direct, the gravimetric method is regarded as highly reliable and thus often preferred. Its main disadvantages are that sampling and laboratory procedures are labor intensive, and that the method is destructive, which makes resampling of a same point impossible. Recently, the time domain reflectometry (TDR) technique has become a widely used indirect, non-destructive method to evaluate theta. In this study, evaluations of the apparent dielectric number of soils (epsilon) and samplings for the gravimetrical determination of the volumetric soil water content (thetaGrav) were carried out at four sites of a Xanthic Ferralsol in Manaus - Brazil. With the obtained epsilon values, theta was estimated using empirical equations (thetaTDR), and compared with thetaGrav derived from disturbed and undisturbed samples. The main objective of this study was the comparison of thetaTDR estimates of horizontally as well as vertically inserted probes with the thetaGrav values determined by disturbed and undisturbed samples. Results showed that thetaTDR estimates of vertically inserted probes and the average of horizontally measured layers were only slightly and insignificantly different. However, significant differences were found between the thetaTDR estimates of different equations and between disturbed and undisturbed samples in the thetaGrav determinations. The use of the theoretical Knight et al. model, which permits an evaluation of the soil volume assessed by TDR probes, is also discussed. It was concluded that the TDR technique, when properly calibrated, permits in situ, nondestructive measurements of q in Xanthic Ferralsols of similar accuracy as the gravimetric method.

Oral administration of a low dose of midazolam (75 microg) as an in vivo probe for CYP3A activity.

OBJECTIVE: We investigated whether the oral administration of a low dose (75 micro g) of midazolam, a CYP3A probe, can be used to measure the in vivo CYP3A activity. METHODS: Plasma concentrations of midazolam, 1'OH-midazolam and 4'OH-midazolam were measured after the oral administration of 7.5 mg and 75 micro g midazolam in 13 healthy subjects without medication, in four subjects pretreated for 2 days with ketoconazole (200 mg b.i.d.), a CYP3A inhibitor, and in four subjects pretreated for 4 days with rifampicin (450 mg q.d.), a CYP3A inducer. RESULTS: After oral administration of 75 micro g midazolam, the 30-min total (unconjugated + conjugated) 1'OH-midazolam/midazolam ratios measured in the groups without co-medication, with ketoconazole and with rifampicin were (mean+/-SD): 6.23+/-2.61, 0.79+/-0.39 and 56.1+/-12.4, respectively. No side effects were reported by the subjects taking this low dose of midazolam. Good correlations were observed between the 30-min total 1'OH-midazolam/midazolam ratio and midazolam clearance in the group without co-medication (r(2)=0.64, P<0.001) and in the three groups taken together (r(2)=0.91, P<0.0001). Good correlations were also observed between midazolam plasma levels and midazolam clearance, measured between 1.5 h and 4 h. CONCLUSION: A low oral dose of midazolam can be used to phenotype CYP3A, either by the determination of total 1'OH-midazolam/midazolam ratios at 30 min or by the determination of midazolam plasma levels between 1.5 h and 4 h after its administration.

Damage spreading transition in glasses: A probe for the ruggedness of the configurational landscape

We consider damage spreading transitions in the framework of mode-coupling theory. This theory describes relaxation processes in glasses in the mean-field approximation which are known to be characterized by the presence of an exponentially large number of metastable states. For systems evolving under identical but arbitrarily correlated noises, we demonstrate that there exists a critical temperature T0 which separates two different dynamical regimes depending on whether damage spreads or not in the asymptotic long-time limit. This transition exists for generic noise correlations such that the zero damage solution is stable at high temperatures, being minimal for maximal noise correlations. Although this dynamical transition depends on the type of noise correlations, we show that the asymptotic damage has the good properties of a dynamical order parameter, such as (i) independence of the initial damage; (ii) independence of the class of initial condition; and (iii) stability of the transition in the presence of asymmetric interactions which violate detailed balance. For maximally correlated noises we suggest that damage spreading occurs due to the presence of a divergent number of saddle points (as well as metastable states) in the thermodynamic limit consequence of the ruggedness of the free-energy landscape which characterizes the glassy state. These results are then compared to extensive numerical simulations of a mean-field glass model (the Bernasconi model) with Monte Carlo heat-bath dynamics. The freedom of choosing arbitrary noise correlations for Langevin dynamics makes damage spreading an interesting tool to probe the ruggedness of the configurational landscape.

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace.Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

Specific delineation of BK polyomavirus in kidney tissue with a digoxigenin-labeled DNA probe.

The detection of BK polyomavirus (BK virus, BKV) in kidney tissue is hampered by nonspecificity of antibodies suited to immunohistochemistry, and nonspecific background with in situ hybridization. The biotin-labeled DNA probe that is commercially available (Enzo Life Sciences, Inc.) shows good signal, but the intrinsic background in kidney tissue is high. We determined that the intrinsic background is due to endogenous biotin or biotin-binding activity in the renal tubular epithelium. Neither antibody blocking procedures nor an avidin/biotin block were entirely satisfactory for eliminating this background staining. We developed a digoxigenin-labeled DNA probe, and protocol, for detecting BK virus in formalin-fixed, paraffin embedded, kidney tissue obtained at autopsy. The hybridization signal is strong and there is no perceptible background staining. Eleven negative control kidneys all failed to hybridize. Conditions for low stringency hybridization may be employed, detecting both the related JC polyomavirus and BKV. Alternatively, high stringency hybridization conditions may be utilized, detecting BKV only. BK associated tubular necrosis is clearly demonstrated in two cases of BK nephritis.

Electron probe microanalysis: principles and applications

This article summarizes the basic principles of electron probe microanalysis, with examples of applications in materials science and geology that illustrate the capabilities of the technique.