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Biomedical subjects

E de Boer

Publications and source records attributed to E de Boer.

At least 19 recordsLinked to original sources
PubMed1995

TBP binding and the rate of transcription initiation from the human beta-globin gene.

DNA-protein interaction studies in vitro revealed several factors binding over the TATA box and the region of transcription initiation (cap) site of the human beta-globin promoter; TATA binding protein TBP at -30, Sp1 at -19, GATA-1 at -12 and +5, YY1 at -9 and a novel factor C1 over the site of initiation (-4 to +7). Point mutants which specifically abolish the binding of each of these proteins were tested in a beta-globin locus control region (LCR) construct which allows quantitative comparisons at physiological levels of transcription. Only mutants which drastically affect the binding of TBP resulted in decreased levels of transcription. A threshold value of TBP binding of 15-30% of wild type was sufficient to give normal levels of transcription. This indicates that the association of TF IID with the TATA box is not limiting in the rate of initiation of transcription.

Animals↗
PubMed1995

The "inverse problem" solved for a three-dimensional model of the cochlea. I. Analysis.

With nonactive cochlear models of the "classical" type, it is impossible to stimulate the characteristic type of frequency selectivity that is revealed by modern mechanical measurements of the motion of the basilar membrane (BM). Locally active models of the cochlea have been proposed to alleviate this problem but it remains uncertain whether the real cochlea is active in this sense. The present study was undertaken to investigate this subject in a more general and systematic way than has hitherto been done. The "inverse" problem is solved for a three-dimensional (3-D) model and a procedure is developed for recovering the BM impedance needed to stimulate the given BM response function. In the present paper the theoretical basis of the procedure is presented, and an analysis is given of the validity of the method and the errors involved. It is shown why the inverse problem is "ill-posed" and why the results of our procedure are more accurate in the region of the response peak than in the more basal region of the model. The latter finding serves to delimit the domain within which results of an inverse procedure (for instance, in the short- or long-wave approximation) are to be judged. In a subsequent paper the technique developed will be applied to actual data sets from the literature on mechanical BM measurements.

Auditory Perception↗
PubMed1995

The "inverse problem" solved for a three-dimensional model of the cochlea. II. Application to experimental data sets.

With "classical" nonactive models of the cochlea it is impossible to simulate the degree of frequency selectivity that is revealed by modern mechanical measurements of the motion of the basilar membrane (BM). Locally active models have been proposed to alleviate this problem, but it remains uncertain whether the actual cochlea is active in this sense. In the first paper of this series [E. de Boer, J. Acoust. Soc. Am. 98, 896-903 (1995)], the "inverse" problem is solved for a (classical) three-dimensional model and a procedure is developed for recovering the BM impedance needed to simulate a given BM response function. It was found that the results of this procedure will be more accurate in the region of the response peak than in the more basal region of the model. In the present paper the same procedure is applied to data of recent mechanical experiments. For the peak region the outcome is unequivocal: Recent measurement results can only be simulated by the classical model when it is made locally active. Resynthesis of the model response, on the basis of the recovered BM impedance, confirms the validity of the method in the peak region and strengthens this conclusion.

Auditory Perception↗
PubMed1995

On equivalence of locally active models of the cochlea.

In the literature on locally active models of the cochlea several forms of the model have been worked out in which elements of the organ of Corti are assumed to produce acoustical energy. In these models use is made of a secondary resonance or a place-dependent delay to achieve activity over a limited part of the length of the basilar membrane, and outer hair cells are postulated as sources of energy production. In the present paper it will be shown that several of these models are formally equivalent. That means that they can be reduced to a standard form, and that the only difference resides in the choice and meaning of the parameters. The results of the analysis serve to facilitate the analysis of function and structure in cochlear models containing sources of local activity. In particular, questions of positive versus negative feedback, and the parts played by resonance and impedance-level differences can be resolved unambiguously. The treatment can be extended to models with higher dimensionality, and can also serve to obtain insight in nonlinear phenomena occurring in cochlear models.

Basilar Membrane↗
PubMed1994

Two-tone suppression in a locally active nonlinear model of the cochlea.

In auditory nerve, inner-hair cell and basilar-membrane responses, it has been found that the response to one tone can be suppressed by another tone. This phenomenon, called two-tone suppression, is examined on the level of the basilar membrane with a locally active long-wave model of the cochlea in which the active mechanism is nonlinear. The model is solved in the frequency domain by means of a quasi-linear solution method. Several phenomena, such as difference in growth of suppression for low-side and high-side suppressors and critical dependence of the phase of the probe response on suppressor parameters, have been replicated. The attenuation hypothesis which states that the presence of a suppressor has the same effect on the probe response as attenuation of probe level is shown to be insufficient in explaining the experimental data. This model, in which suppression is simply reduction of power amplification due to saturation of the active mechanism, is more successful in this respect.

Auditory Perception↗
PubMed1993

Self-suppression in a locally active nonlinear model of the cochlea: a quasilinear approach.

Mechanical input-output functions of the cochlea for pure-tone stimuli are nonlinear for frequencies around the characteristic frequency. To simulate these functions, a long-wave model of the cochlea containing a saturating pressure generator (located at the site of the outer hair cells) is solved in the frequency domain with a quasilinear method. In this method distortion products in the basilar-membrane (BM) response are treated as perturbations and the nonlinear pressure waveform is approximated by the first-order Fourier component. Because the saturating pressure generator forms part of a feedback loop the solution of the model is achieved in a number of iteration steps. Model results show flattening of the BM response at higher input pressures; this property, called self-suppression, is due to saturation of the pressure generator. The resulting input-output functions display the main features of experimental curves. The third-order distortion product in the BM velocity is always more than 25 dB below the primary BM velocity and does not influence the results of the computation; this justifies the use of the quasilinear method.

Acoustic Impedance Tests↗
PubMed1992

[Enterohemorrhagic Escherichia coli O157:H7, an underestimated food pathogen? A literature review].

Escherichia coli O157:H7 has recently been recognised as a human pathogen involved in outbreaks and sporadic cases of food-borne diseases in North America and Great Britain. At present, less is known about the significance of E. coli O157:H7 as a cause of food-borne diseases in the Netherlands. This article will review current literature about this serotype, which is a predominant representative of the enterohaemorrhagic E. coli (EHEC) group. Biochemical features, toxins, pathogenesis, clinical characteristics, epidemiology and methods of isolation will also be discussed.

Animals↗
PubMed1992

Evaluation of the MPN, Anderson-Baird-Parker, Petrifilm E. coli and Fluorocult ECD method for enumeration of Escherichia coli in foods of animal origin.

Commercially available beta-D-glucuronidase (GUR) based methods, Petrifilm E. coli (PEC) and Fluorocult ECD (FECD), and ISO standard MPN and Anderson-Baird-Parker (ABP) procedures were evaluated for routine enumeration of E. coli in naturally contaminated foods of animal origin. The methods concerned were classifiable in a sequence of best qualities for: production, MPN > ABP = PEC = FECD; costs, FECD > ABP = PEC > MPN; time per measurement, ABP = PEC = FECD > MPN; practical use, PEC > FECD > ABP > MPN; detection at low contamination, MPN > ABP = PEC > FECD. The ABP and PEC method appeared useful for routine counting of E. coli in raw meat, poultry and meat products, whereas the MPN procedure turned out to be more sensitive, however, impractical and considerably more expensive. The FECD method was inexpensive although suitable for the enumeration of E. coli at higher contamination level (> 50 cfu/g). The indole and MUG indicators both applied to demonstrate E. coli with the ABP or FECD method proved to be equal in specificity.

Colony Count, Microbial↗
PubMed1992

Isolation of Yersinia enterocolitica from foods.

Many selective enrichment and plating media for the isolation of Yersinia enterocolitica from foods are described. However, at present no single isolation procedure is available for the recovery of all pathogenic strains of Yersinia enterocolitica. Cold enrichment in phosphate-buffered saline plus 1% sorbitol and 0.15% bile salts (PBSSB) and two-step enrichment with tryptone soy broth (TSB) and bile oxalate sorbose (BOS) broth are very efficient methods for the recovery of a wide spectrum of serotypes of Y. enterocolitica. Enrichment in irgasan ticarcillin chlorate (ITC) broth was found to be the most efficient method for the recovery of strains of serotype 0:3, which is the most common clinical serotype of Y. enterocolitica in Europe. Post-enrichment alkali treatment often results in higher isolation rates. Cefsulodin irgasan novobiocin (CIN) agar and Salmonella-Shigella deoxycholate calcium chloride (SSDC) agar are the most commonly used plating media. For the recovery of serotype 0:8 strains, the common clinical isolates in North America, enrichment in BOS and plating on CIN seems the most efficient procedure. Selection of the proper enrichment procedure will depend on the bio/serotypes of Yersinia spp. sought and on the type of food to be examined. The use of more than one medium for both enrichment and plating will result in higher recovery rates of Yersinia spp. from foods. Parallel use of the following two isolation procedures is recommended. (1) Enrichment in ITC for 2 days at 24 degrees C; plating on SSDC agar (2 days at 30 degrees C). (2) Pre-enrichment in TSB for 1 day at 24 degrees C; enrichment in BOS for 5 days at 24 degrees C; alkali treatment (mixing 0.5 ml enriched broth with 4.5 ml of 0.5% KOH in 0.5% NaCl for 5 s); plating on CIN agar (2 days at 24 degrees C).

Culture Media↗
PubMed1991

[Pork meat as a source of pathogenic Yersinia enterocolitica].

During a period of eight months, samples of carcasses, tonsils, tongues and rectal swabs were taken in four pig slaughter halls. Porcine head meat was sampled in a meat products factory and samples of minced pork were taken in butcher's shops. Pathogenic strains of Yersinia enterocolitica (serological groups O:3, O:9 and O:5.27) were isolated from 36 (42 per cent) of 86 porcine tonsils, 8 (20 per cent) of 40 tongues, 17 (17 per cent) of 100 rectal swabs and from 4 (1 per cent) of 400 pork samples. Pathogenic strains of Yersinia were not isolated from samples of 210 pig carcasses and from 20 samples of porcine head meat. These results confirm that pigs are an important reservoir of pathogenic Y. enterocolitica. However, contamination of carcasses during the process of slaughter with Yersinia from either faecal material or from the tonsillary region does not seem to occur frequently, which may also explain the low rate of contamination with pathogenic Y. enterocolitica observed in pork. As pork is rarely contaminated with pathogenic Y. enterocolitica, the possibilities for growth of these organisms in raw pork are limited, the minimum infective dose is probably high and pork is usually not eaten raw, it is not likely that pork is an important source of yersiniosis in the Netherlands.

Animals↗
PubMed1991

Recovery of Listeria monocytogenes on selective agar media in a collaborative study using reference samples.

Sixteen laboratories compared counts of Listeria monocytogenes in reference samples using Blood agar, Palcam(y) agar and Oxford agar. Significant differences were found between laboratories. The mean counts on Blood agar were significantly higher than on Palcam(y) or Oxford agar. The mean counts on Palcamy agar were somewhat higher than on Oxford agar (only after 48 h incubation), but no significant difference was found. Addition of egg yolk to Palcam agar seems to be beneficial for the recovery of sublethally injured cells. Recovery of L. monocytogenes was higher after 48 h incubation for all media tested.

Agar↗
PubMed1991

Slaughter pigs and pork as a source of human pathogenic Yersinia enterocolitica.

Pathogenic Yersinia enterocolitica strains (serogroups 0:3;0:9 and 0:5.27) were isolated from 36 (42%) of 86 porcine tonsils, 8 (20%) of 40 tongues, 17 (17%) of 100 rectal swabs and from 4 (1%) of 400 pork samples. Pathogenic Yersinia strains were not isolated from samples of 210 pig carcasses and from 20 samples of porcine head meat. These results confirm that pigs are an important reservoir of pathogenic Y. enterocolitica. However, contamination of carcasses during the slaughtering process with Yersinia from either faecal material or from the tonsillary region does not seem to occur frequently and this may also explain the low contamination rate of pathogenic Y. enterocolitica found for pork. For the isolation of pathogenic Y. enterocolitica strains from foods, enrichment in irgasan-ticarcillin-chlorate broth (ITC) and isolation on SS-deoxycholate-calcium agar (SSDC) is recommended.

Animals↗
PubMed1990

On ringing limits of the auditory periphery.

In classical hearing theory frequency and time have been treated as nearly independent acoustical dimensions. In this paper the interaction between temporal and spectral aspects is studied. An important determinant in this respect is the filtering of auditory stimuli in the cochlea. A view of auditory filtering that is balanced in frequency and time is obtained from the 'reverse-correlation function', abbreviated: revcor function. This function is derived from the response of an auditory-nerve fibre to a white-noise sound stimulus. It is a useful descriptor of peripheral filtering for a wide class of stimuli in which effects of nonlinear distortion are of minor importance. Measured revcor functions can be approximated by a standard mathematical function of which the parameters have a clear meaning. For these functions the spread in time and in frequency are uniquely related to one another. This relation is carried over to the case of cochlear filtering and applied to two important cases: stimulation by signals with small and with large amplitude variations. The results turn out to be markedly different in these two cases. In the final section the relevance of the results to various other fields of auditory research is discussed.

Acoustic Stimulation↗
PubMed1990

Can shape deformations of the organ of Corti influence the travelling wave in the cochlea?

Via their motile reactions outer hair cells may produce oscillatory power or amplify the fluid waves in the cochlea. When the cells move or change their lengths, the organ of Corti (OC) will change its shape. This paper describes the consequences of such shape changes for the physics of cochlear waves. The assertions posed are based on a mathematical derivation but the major conclusions can be grasped without following the mathematics in detail. There are two basic types of OC deformations. In the first type the net cross-sectional area of the OC is periodically varying, in the second type--the central subject of this paper--is is not. It is shown that for the latter type of OC shape deformation there is no interaction with the cochlear fluids, at least for long waves. Hence, in this case the outer hair cells cannot amplify cochlear waves. The other type of OC deformation has a better coupling with the cochlear waves. However, much of the pressure developed by oscillating hair cells is spent in the 'wrong' way, namely, by squeezing fluid lengthwise through the narrow channel of the OC. Therefore, in this mode power transfer from cochlear hair cells to cochlear fluids (and from there to the basilar membrane) would be very inefficient.

Animals↗