Determination of pK's of trinucleotides

pK's of trinucleotides are calculated according to the theory of Kirkwood and Westheimer for ellipsoids. In order to compare the calculated values with some experimental results, a number of trimers were prepared and their pK's were measured. The question of syn and anti conformations for monomers are discussed in light of the above considerations.     

Characterization of a human immunodeficiency virus neutralizing monoclonal antibody and mapping of the neutralizing epitope.

A monoclonal antibody was produced to the exterior envelope glycoprotein (gp120) of the human T-cell lymphotropic virus (HTLV)-IIIB isolate of the human immunodeficiency virus (HIV). This antibody binds to gp120 of HTLV-IIIB and lymphadenopathy-associated virus type 1 (LAV-1) and to the surface of HTLV-IIIB- and LAV-1-infected cells, neutralizes infection by cell-free virus, and prevents fusion of virus-infected cells. In contrast, it does not bind, or weakly binds, the envelope of four heterologous HIV isolates and does not neutralize heterologous isolates HTLV-IIIRF and HTLV-IIIMN. The antibody-binding site was mapped to a 24-amino-acid segment, using recombinant and synthetic segments of HTLV-IIIB gp120. This site is within a segment of amino acid variability known to contain the major neutralizing epitopes (S. D. Putney, T. J. Matthews, W. G. Robey, D. L. Lynn, M. Robert-Guroff, W. T. Mueller, A. J. Langlois, J. Ghrayeb, S. R. Petteway, K. J. Weinhold, P. J. Fischinger, F. Wong-Staal, R. C. Gallo, and D. P. Bolognesi, Science 234:1392-1395, 1986). These results localize an epitope of HIV type-specific neutralization and suggest that neutralizing antibodies may be effective in controlling cell-associated, as well as cell-free, virus infection.     

HMG17 protein facilitates the DNA catenation reaction catalyzed by DNA topoisomerases

HMG17 protein is shown to greatly facilitate the catention of double-stranded DNA rings catalyzed by DNA topoisomerases. Even at low DNA concentrations such that catenanes are not observable in the absence of HMG17, the addition of the protein promotes the catenation of greater than 95% of the input DNA into networks that do not enter the gel upon electrophoresis. Electron microscopy and restriction enzyme cleavage experiments indicate that these networks are large structures containing many catenated DNA rings. The HMG17-promoted DNA network formation has been observed with calf thymus type II DNA topoisomerase and the type I topoisomerases of Escherichia coli, Micrococcus luteus, and calf thymus.     

Conformational studies of two non-histone chromosomal proteins and their interactions with DNA.

The conformational properties of two non-histone chromosomal proteins (high-mobility-group proteins 1 and 2) have been studied by spectroscopic methods. The interaction of high-mobility-group protein 1 with DNA has also been studied. 1. Circular dichroism results indicate that in the presence of salt both proteins are 40-50% helical between pH 1 and 9. Above pH 9 denaturation takes place. In the absence of salt the proteins denature below pH 4. 2. Nuclear magnetic resonance spectra show the presence of ring-current shifted peaks and perturbed aromatic resonances, demonstrating that the helix formation is accompanied by specific tertiary folding. 3. Nuclear magnetic resonance spectra of compelxes between high mobility group protein 1 and DNA demonstrate that a low ionic strength a portion of the molecule rich in lysine and containing all the aromatic residues is bound to DNA, whilst a more acidic region of the chain remains free from the DNA.     

Mechanical properties of a mature biofilm from a wastewater system: from microscale to macroscale level

A fundamental understanding of biofilm mechanical stability is critical in order to describe detachment and develop biofouling control strategies. It is thus important to characterise the elastic deformation and flow behaviour of the biofilm under different modes of applied force. In this study, the mechanical properties of a mature wastewater biofilm were investigated with methods including macroscale compression and microscale indentation using atomic force microscopy (AFM). The mature biofilm was found to be mechanically isotropic at the macroscale level as its mechanical properties did not depend on the scales and modes of loading. However, the biofilm showed a tendency for mechanical inhomogeneity at the microscale level as indentation progressed deeper into the matrix. Moreover, it was observed that the adhesion force had a significant influence on the elastic properties of the biofilm at the surface, subjected to microscale tensile loading. These results are expected to inform a damage-based model for biofilm detachment.     

Relationship between myocardial bridge compression severity and haemodynamic perturbations

Objectives: This study aims to examine the alteration in coronary haemodynamics with increasing the severity of vessel compression caused by myocardial bridging (MB).

Methods: Angiography and intravascular ultrasound were performed in 10 patients with MB with varying severities of systolic compression in the left anterior descending (LAD) artery. Computer models of MB were developed and transient computational fluid dynamics simulations were performed to derive distribution of blood residence time and shear stress.

Results: With increasing the severity of bridge compression, a decreasing trend was observed in the shear stress over proximal segment whereas an increasing trend was found in the shear stress over bridge segment. When patients were divided into 2 groups based on the average systolic vessel compression in the whole cohort (%CR_ave = 27.38), patients with bridges with major systolic compression (>%CR_ave) had smaller shear stress and higher residence time in the proximal segment compared to those with bridges with minor systolic compression (<%CR_ave) (0.37?±?0.23 vs 0.69?±?0.29?Pa and 0.0037?±?0.0069 vs 0.022?±?0.0094?s). In contrast, patients with bridges with major systolic compression had greater shear stress in the bridge segment compared to those with bridges with minor systolic compression (2.49?±?2.06 vs 1.13?±?0.89?Pa). No significant difference was found in the distal shear stress of patients with bridges with major and minor systolic compression.

Conclusion: Our findings revealed a direct relationship between the severity of systolic compression of MB and haemodynamic perturbations in the proximal segment such that the increased systolic vessel compression was associated with decreased shear stress and increased blood residence time.     

Inability of Agrobacterium tumefaciens ribosomes to translate in vivo mRNAs containing non-Shine-Dalgarno translational initiators

Numerous data accumulated during the last decade have shown that the Shine-Dalgarno (SD) sequence is not a unique initiator of translation for Escherichia coli. Several other sequences, mostly of viral origin, have demonstrated their capability of either enhancing or initiating translation in vivo. A phage T7 gene 10 sequence, called "epsilon" (epsilon), has shown its high enhancing activity on translation in both Escherichia coli and Agrobacterium tumefaciens cells. In this study the epsilon, together with three other nucleotide sequences derived from the 5' non-translated regions of tobacco mosaic virus (TMV), papaya mosaic virus (PMV) and clover yellow mosaic virus (CYMV) RNAs are tested for translation initiation activity in A. tumefaciens cells. The obtained results indicate that none of them was capable of initiating translation in vivo of chloramphenicol acetyltransferase (CAT) mRNA. To determine whether their inactivity was related with structural differences in the ribosomal protein S1, the rpsA gene (coding for S1 protein in E. coli) was co-expressed in A. tumefaciens together with the cat gene placed under the translational control of the above sequences. Our results showed that the rpsA gene product did not make any of the four viral enhancers active in A. tumefaciens cells. The inability of A. tumefaciens ribosomes to translate mRNAs devoid of SD sequences indicates for a substantial difference in the ribosome structure of the two Gram negative bacteria E. coli and A. tumefaciens.     

Pilomatrixoma: a review of 346 cases

Pilomatrixoma, also known as calcifying epithelioma of Malherbe, is a benign skin neoplasm that arises from hair follicle matrix cells. Pilomatrixoma is a common skin neoplasm in the pediatric population that is often misdiagnosed as other skin conditions. This study reviews an 11-year experience at a tertiary children's hospital, examining the cause, clinical and histopathological presentation, management, and treatment outcomes of pilomatrixoma. A review of the pathology database at Children's Hospital Los Angeles revealed 346 pilomatrixomas excised from 336 patients between 1991 and 2001. The hospital charts, pathology records, and plastic surgery clinic charts were reviewed with respect to variables such as sex, age at the time of presentation, clinical and histopathological presentation, preoperative diagnosis, management, recurrence, and treatment outcome. The main presenting symptom was a hard, subcutaneous, slowly growing mass. The preoperative diagnosis was accurate and consistent with the pathological diagnosis of pilomatrixoma in only 100 cases (28.9 percent). This entity should be considered with other benign or malignant conditions in the clinical differential diagnosis of solitary firm skin nodules, especially those on the head, neck, or upper limbs. The diagnosis can generally be made with a clinical examination. Imaging studies are not required unless symptoms or the location of the lesion warrants such diagnostic assessments. The treatment of choice is surgical excision, and the recurrence rate is low.     

The aesthetic earlobe: classification of lobule ptosis on the basis of a survey of North American Caucasians

North American Caucasian male subjects (n = 59) and female subjects (n = 72) were surveyed, to investigate earlobe height preferences that could serve as guidelines for aesthetic earlobe surgical procedures and reconstructions. Subjects were asked to rank their preferences for variously shaped earlobes in life-size-scaled sketched male and female profiles. Earlobe heights were varied on the basis of previously established anatomical landmarks, including the intertragal notch, the most caudal anterior attachment of the earlobe to the cheek skin (the otobasion inferius), and the most caudal extension of the earlobe-free margin (the subaurale). While the intertragal notch-to-otobasion inferius distance (range, 5 to 20 mm) and otobasion inferius-to-subaurale distance (range, 0 to 20 mm) varied, all other facial and ear anthropometric measurements were held constant. Each of the rank orders for the female and male facial profiles completed by the female and male subjects demonstrated statistical significance, as determined by one-way analysis of variance analysis of ranks (p < 0.001 for all four groups). No difference was noted between the two sexes' rank orders for either sex (p > 0.05). Therefore, analysis of the combined male and female preferences for each sex was completed with one-way analysis of variance analysis of ranks (p < 0.001 and p < 0.001) and a post hoc Dunn's test, to delineate significant preference differences between subgroups with respect to the intertragal notch-to-otobasion inferius and otobasion inferius-to-subaurale distances. Both female and male earlobe intertragal notch-to-otobasion inferius distances were preferred at either 5, 10, or 15 mm, more so than at 20 mm (p < 0.05 for all female and male comparisons). Furthermore, both female and male earlobe otobasion inferius-to-subaurale distances were preferred, in descending order, at 5 mm > 10 mm > 0 mm > 15 mm > 20 mm (p < 0.05 for all female and male comparisons). On the basis of the findings of this survey, the first classification of earlobe ptosis (based on otobasion inferius-to-subaurale distances), as well as a criterion for earlobe pseudoptosis (intertragal notch-to-otobasion inferius distance of greater than 15 mm), is presented. These findings suggest a role for independent assessment of the lobule length with respect to its anteriorly attached cephalad component (intertragal notch-to-otobasion inferius distance) and its free-margin caudal component (otobasion inferius-to-subaurale distance).     

Gas chromatographic method for detection of urinary sucralose: application to the assessment of intestinal permeability

We developed a capillary column gas chromatography (CCGC) method for the measurement of urinary sucralose (S) and three other sugar probes including, sucrose, lactulose (L) and mannitol (M) for use in in vivo studies of intestinal permeability. We compared the capillary method with a packed column gas chromatography (PCGC) method. We also investigated a possible role for sucralose as a probe for the measurement of whole gut permeability. Sample preparation was rapid and simple. The above four sugars were detected precisely, without interference. We measured intestinal permeability using 5- and 24-h urine collections in 14 healthy volunteers. The metabolism of sugars was evaluated by incubating the intestinal bacteria with an iso-osmolar mixture of mannitol, lactulose and sucralose at 37 degrees C for 19 h. Sugar concentrations and the pH of the mixture were monitored. The use of the CCGC method improved the detection of sucralose as compared to PCGC. The average coefficient of variation decreased from 15% to 4%. It also increased the sensitivity of detection by 200-2000-fold. The GC assay was linear between sucralose concentrations of 0.2 and 40 g/l (r=1.000). Intestinal bacteria metabolized lactulose and acidified the media but did not metabolize sucralose or mannitol. The new method for the measurement of urinary sucralose permits the simultaneous quantitation of sucrose, mannitol and lactulose, and is rapid, simple, sensitive, accurate and reproducible. Because neither S nor M is metabolized by intestinal bacteria, and because only a tiny fraction of either sugar is absorbed, this pair of sugar probes appears to be available for absorption throughout the GI tract. Thus, the 24-h urinary concentrations of S and M, or the urinary S/M ratio following an oral dose of a sugar mixture, might be good markers for whole gut permeability.