The program XEASY for computer-supported NMR spectral analysis of biological macromolecules

A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of 'strips', i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of DeltaG degrees37 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within 3.2%, 6.0%, 6.8%, and 1.3 degreesC, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.

Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR

Myotonic dystrophy is caused by an expanded CTG repeat in the 3' untranslated region of the DM protein kinase (DMPK) gene. The expanded repeat triggers the nuclear retention of mutant DMPK transcripts, but the resulting underexpression of DMPK probably does not fully account for the severe phenotype. One proposed disease mechanism is that nuclear accumulation of expanded CUG repeats may interfere with nuclear function. Here we show by thermal melting and nuclease digestion studies that CUG repeats form highly stable hairpins. Furthermore, CUG repeats bind to the dsRNA-binding domain of PKR, the dsRNA-activated protein kinase. The threshold for binding to PKR is approximately 15 CUG repeats, and the affinity increases with longer repeat lengths. Finally, CUG repeats that are pathologically expanded can activate PKR in vitro. These results raise the possibility that the disease mechanism could be, in part, a gain of function by mutant DMPK transcripts that involves sequestration or activation of dsRNA binding proteins.

NMR structure of a protein kinase C-gamma phorbol-binding domain and study of protein-lipid micelle interactions

Classical protein kinase C (PKC) family members are activated by the binding of various ligands to one of several cysteine-rich domains of the enzyme. The natural agonist, diacylglycerol (DAG), and the natural product superagonist, phorbol dibutyrate (PDB), activate the enzyme to produce wide-ranging physiological effects. The second cysteine-rich (Cys2) domain of rat brain PKC-gamma was expressed and labeled with 15N and 13C, and the solution structure was determined to high resolution using multidimensional heteronuclear NMR methods. The phorbol binding site was identified by titrating this domain with phorbol-12,13-dibutyrate (PDB) in the presence of organic cosolvents. Titrations of this domain with lipid micelles, in the absence and presence of phorbols, indicate selective broadening of some resonances. The observed behavior indicates conformational exchange between bound and free states upon protein-micelle interaction. The data also suggest that half of the domain, including the phorbol site and one of the zinc sites, is capable of inserting into membranes.

Occurrence of Candida albicans in infections of endodontic origin

Microorganisms are recognized as the etiological agent for the majority of pulpal and periradicular disease. Although bacteria have been the most studied, fungi have also been associated with infected root canals. The purpose of this study was to evaluate the contents of infected root canals and aspirates of cellulitis/abscesses of endodontic origin for the presence of Candida albicans using the polymerase chain reaction (PCR). PCR primers specific for the 18S ribosomal RNA gene of C. albicans were used to survey 24 samples taken from infected root canals and 19 aspirates from periradicular infections of endodontic origins. The presence of C. albicans was detected in 5 of 24 (21%) samples taken from root canals, but none was detected in the periradicular aspirates. The results indicate that PCR is an extremely sensitive molecular method that may be used to identify C. albicans directly in samples from infections of endodontic origin.

NMR structure of oxidized Escherichia coli glutaredoxin: comparison with reduced E. coli glutaredoxin and functionally related proteins

The determination of the NMR structure of oxidized Escherichia coli glutaredoxin in aqueous solution is described, and comparisons of this structure with that of reduced E. coli glutaredoxin and the related proteins E. coli thioredoxin and T4 glutaredoxin are presented. Based on nearly complete sequence-specific 1H-NMR assignments, 804 nuclear Overhauser enhancement distance constraints and 74 dihedral angle constraints were obtained as the input for the structure calculations, for which the distance geometry program DIANA was used followed by simulated annealing with the program X-PLOR. The molecular architecture of oxidized glutaredoxin is made up of three helices and a four-stranded beta-sheet. The three-dimensional structures of oxidized and the recently described reduced glutaredoxin are very similar. Quantitative analysis of the exchange rates of 34 slowly exchanging amide protons from corresponding series of two-dimensional [15N,1H]-correlated spectra of oxidized and reduced glutaredoxin showed close agreement, indicating almost identical hydrogen-bonding patterns. Nonetheless, differences in local dynamics involving residues near the active site and the C-terminal alpha-helix were clearly manifested. Comparison of the structure of E. coli glutaredoxin with those of T4 glutaredoxin and E. coli thioredoxin showed that all three proteins have a similar overall polypeptide fold. An area of the protein surface at the active site containing Arg 8, Cys 11, Pro 12, Tyr 13, Ile 38, Thr 58, Val 59, Pro 60, Gly 71, Tyr 72, and Thr 73 is proposed as a possible site for interaction with other proteins, in particular ribonucleotide reductase. It was found that this area corresponds to previously proposed interaction sites in T4 glutaredoxin and E. coli thioredoxin. The solvent-accessible surface area at the active site of E. coli glutaredoxin showed a general trend to increase upon reduction. Only the sulfhydryl group of Cys 11 is exposed to the solvent, whereas that of Cys 14 is buried and solvent inaccessible.

Association of black-pigmented bacteria with endodontic infections

Black-pigmented bacteria (BPB) have been associated with endodontic infections. The purpose of this study was to evaluate further the presence of BPB with the clinical signs and symptoms associated with endodontic infections. Microbial samples were collected from the root canals of 40 intact teeth with necrotic pulps and apical periodontitis. Conventional laboratory methods were used for identification of the strains of BPB isolated in pure culture. In addition, the polymerase chain reaction and specific primers for 16S r-RNA genes were used to differentiate Prevotella nigrescens from Prevotella intermedia. Twenty-two (55%) samples were positive for the growth of BPB. Of those, 11 of 22 (50%) were identified as P. nigrescens, 8 of 22 (36%) were P. intermedia, 2 of 22 (9%) were Porphyromonas gingivalis, and 1 of 22 (5%) was Prevotella melaninogenica. Sixteen of the 22 root canals positive for the growth of BPB were associated with purulent drainage either from the root canal or an associated sinus tract. Statistical analysis did not show a significant relationship for the presence of BPB with clinical signs and symptoms.

No time to lose--high throughput screening to assess nanomaterial safety

Nanomaterials hold great promise for medical, technological and economical benefits. Knowledge concerning the toxicological properties of these novel materials is typically lacking. At the same time, it is becoming evident that some nanomaterials could have a toxic potential in humans and the environment. Animal based systems lack the needed capacity to cope with the abundance of novel nanomaterials being produced, and thus we have to employ in vitro methods with high throughput to manage the rush logistically and use high content readouts wherever needed in order to gain more depth of information. Towards this end, high throughput screening (HTS) and high content screening (HCS) approaches can be used to speed up the safety analysis on a scale that commensurate with the rate of expansion of new materials and new properties. The insights gained from HTS/HCS should aid in our understanding of the tenets of nanomaterial hazard at biological level as well as assist the development of safe-by-design approaches. This review aims to provide a comprehensive introduction to the HTS/HCS methodology employed for safety assessment of engineered nanomaterials (ENMs), including data analysis and prediction of potentially hazardous material properties. Given the current pace of nanomaterial development, HTS/HCS is a potentially effective means of keeping up with the rapid progress in this field--we have literally no time to lose.

Isolation and characterization of a Na+/H+ antiporter gene from the halophyte Atriplex gmelini

With a homologous gene region we successfully isolated a Na+/H+ antiporter gene from a halophytic plant, Atriplex gmelini, and named it AgNHX1. The isolated cDNA is 2607 bp in length and contains one open reading frame, which comprises 555 amino acid residues with a predicted molecular mass of 61.9 kDa. The amino acid sequence of the AgNHX1 gene showed more than 75% identity with those of the previously isolated NHX1 genes from glycophytes, Arabidopsis thaliana and Oryza sativa. The migration pattern of AgNHX1 was shown to correlate with H+-pyrophosphatase and not with P-type H+-ATPase, suggesting the localization of AgNHX1 in a vacuolar membrane. Induction of the AgNHX1 gene was observed by salt stress at both mRNA and protein levels. The expression of the AgNHX1 gene in the yeast mutant, which lacks the vacuolar-type Na+/H+ antiporter gene (NHX1) and has poor viability under the high-salt conditions, showed partial complementation of the NHX1 functions. These results suggest the important role of the AgNHX1 products for salt tolerance.

Geographical Differences in Bacteria Detected in Endodontic Infections Using Polymerase Chain Reaction

The polymerase chain reaction (PCR) is an innovative nucleic acid-based assay that has the highest sensitivity of any microbiological technique for the detection of bacteria. The purpose of this study was to use PCR to detect the presence of specific species of bacteria in samples collected from two geographical locations. Microbial samples from abscesses of endodontic origin were collected from patients in Portland, Oregon, and Rio de Janeiro, Brazil. PCRs with species-specific oligonucleotide primers for the 16S ribosomal RNA gene were used for detection of the bacteria after DNA extraction from each clinical sample. Statistical analysis revealed that there was a significant difference in detection of the bacteria between the two geographical locations for Prevotella intermedia, Prevotella nigrescens, Prevotella tannerae, Fusobacterium nucleatum, and Porphyromonas gingivalis, but not for Porphyromonas endodontalis, Fusobacterium necrophorum, and Enterococcus faecalis. These results suggest that differences in bacteria detected or cultured in studies can be associated with geographical location.

Sequence-specific 1H n.m.r. assignments and determination of the three-dimensional structure of reduced Escherichia coli glutaredoxin

The determination of the nuclear magnetic resonance structure of reduced E. coli glutaredoxin in aqueous solution is described. Based on nearly complete, sequence-specific resonance assignments, 813 nuclear Overhauser effect distance constraints and 191 dihedral angle constraints were employed as the input for the structure calculations, for which the distance geometry program DIANA was used followed by simulated annealing with the program X-PLOR. The molecular architecture of reduced glutaredoxin is made up of three helices and four-stranded beta-sheet. The first strand of the beta-sheet (residues 2 to 7) runs parallel to the second strand (32 to 37) and antiparallel to the third strand (61 to 64), and the sheet is extended in an antiparallel fashion with a fourth strand (67 to 69). The first helix with residues 13 to 28 and the last helix (71 to 83) run parallel to each other on one side of the beta-sheet, with their direction opposite to that of the two parallel beta-strands, and the helix formed by residues 44 to 53 fills space available due to the twist of the beta-sheet and the reduced length of the last two beta-strands. The active site Cys11-Pro-Tyr-Cys14 is located after the first beta-strand and occupies the latter part of the loop connecting this strand with the first helix.

Pseudomonas aeruginosa possesses homologues of mammalian phenylalanine hydroxylase and 4 alpha-carbinolamine dehydratase/DCoH as part of a three-component gene cluster

Pseudomonas aeruginosa possesses a multigene operon that includes phenylalanine hydroxylase (PhhA; phenylalanine 4-monooxygenase, EC 1.14.16.1). phhA encodes PhhA (M(r) = 30,288), phhB (M(r) = 13,333) encodes a homologue of mammalian 4 alpha-carbinolamine dehydratase/homeodomain protein transregulator, and phhC encodes an aromatic aminotransferase (M(r) = 43,237). The reading frames specifying phhB and phhC overlap by 2 bases. The P. aeruginosa PhhA appears to contain iron and is pterin dependent. Unlike the multimeric mammalian hydroxylase, the native P. aeruginosa enzyme is a monomer. The P. aeruginosa PhhA is homologous with mammalian PhhA, tryptophan hydroxylase, and tyrosine hydroxylase. Expression of PhhA from its native promoter required phhB. This may suggest a positive regulatory role for phhB, consistent with the dual catalytic and regulatory roles of the corresponding mammalian homologue.

Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA

The thermodynamic stabilities and structures of a series of RNA duplexes containing nonsymmetric tandem mismatches in the context of , where are tandem mismatches, were studied by UV melting and imino proton NMR. The contribution of one mismatch to the free energy increment for tandem mismatch formation depends on the identity of the other mismatch. Imino proton NMR indicates that this is partly because the structure of a mismatch is dependent on the adjacent mismatch. The results suggest that differences in size, shape, and hydrogen bonding of the adjacent mismatches play important roles in determining loop stability. A model for predicting stabilities of all possible tandem mismatches is proposed based on these and previous results.

Substrate ambiguity of 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases

3-Deoxy-D-manno-octulosonate 8-phosphate (KDOP) synthase and 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase catalyze similar phosphoenolpyruvate-utilizing reactions. The genome of Neisseria gonorrhoeae contains one gene encoding KDOP synthase and one gene encoding DAHP synthase. Of the two nonhomologous DAHP synthase families known, the N. gonorrhoeae protein belongs to the family I assemblage. KDOP synthase exhibited an ability to replace arabinose-5-P with either erythrose-4-P or ribose-5-P as alternative substrates. The results of periodate oxidation studies suggested that the product formed by KDOP synthase with erythrose-4-P as the substrate was 3-deoxy-D-ribo-heptulosonate 7-P, an isomer of DAHP. As expected, this product was not utilized as a substrate by dehydroquinate synthase. The significance of the ability of KDOP synthase to substitute erythrose-4-P for arabinose-5-P is (i) recognition of the possibility that the KDOP synthase might otherwise be mistaken for a species of DAHP synthase and (ii) the possibility that the broad-specificity type of KDOP synthase might be a relatively vulnerable target for antimicrobial agents which mimic the normal substrates. An analysis of sequences in the database indicates that the family I group of DAHP synthase has a previously unrecognized membership which includes the KDOP synthases. The KDOP synthases fall into a subfamily grouping which includes a small group of DAHP synthases. Thus, family I DAHP synthases separate into two subfamilies, one of which includes the KDOP synthases. The two subfamilies appear to have diverged prior to the acquisition of allosteric-control mechanisms for DAHP synthases. These allosteric control specificities are highly diverse and correlate with the presence of N-terminal extensions which lack homology with one another.

Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis

This study compared the bacterial community profiles of the microbiota associated with acute apical abscesses from Brazilian and USA patients using denaturing gradient gel electrophoresis (DGGE). DNA was extracted from purulent exudate aspirates and part of the 16S rRNA gene was amplified by polymerase chain reaction and separated by DGGE. The resulting banding patterns, which were representative of the bacterial community structures in samples from the two locations, were then compared. Distinct DGGE banding patterns were observed from different samples. Ninety-nine bands with distinct positions in the gels were detected, of which 27 were found only in the USA samples and 13 were exclusive to Brazilian samples. Four of the 59 shared bands showed very discrepant findings with regard to prevalence in the two locations. Cluster analysis of DGGE banding profiles showed a great variability in the bacterial populations associated with teeth with abscesses regardless of the geographical location. Two big clusters, one for each location, were observed. Other clusters contained a mixture of samples from the two locations. The results of the present study demonstrated a great variability in the bacterial community profiles among samples. This indicates that the bacterial communities of abscesses are unique for each individual in terms of diversity. The composition of the microbiota in some samples showed a geography-related pattern. Furthermore, several bands were exclusive for each location and others were shared by the two locations and showed great differences in prevalence.

Eclipsing Z-scan measurement of lambda/10(4) wave-front distortion

We introduce a simple modification to the Z-scan technique that results in a sensitivity enhancement that permits measurement of nonlinearly induced wave-front distortion of =lambda/10(4). This sensitivity was achieved with 10-Hz repetition-rate pulsed laser sources. Sensitivity to nonlinear absorption is also enhanced by a factor of =3. This method permits characterization of nonlinear thin films without the need for waveguiding.

Inactivation of airborne viruses using a packed bed non-thermal plasma reactor

Outbreaks of airborne infectious diseases such as measles or severe acute respiratory syndrome can cause significant public alarm. Where ventilation systems facilitate disease transmission to humans or animals, there exists a need for control measures that provide effective protection while imposing minimal pressure differential. In the present study, viral aerosols in an airstream were subjected to non-thermal plasma (NTP) exposure within a packed-bed dielectric barrier discharge reactor. Comparisons of plaque assays before and after NTP treatment found exponentially increasing inactivation of aerosolized MS2 phage with increasing applied voltage. At 30 kV and an air flow rate of 170 standard liters per minute, a greater than 2.3 log reduction of infective virus was achieved across the reactor. This reduction represented ~2 log of the MS2 inactivated and ~0.35 log physically removed in the packed bed. Increasing the air flow rate from 170 to 330 liters per minute did not significantly impact virus inactivation effectiveness. Activated carbon-based ozone filters greatly reduced residual ozone, in some cases down to background levels, while adding less than 20 Pa pressure differential to the 45 Pa differential pressure across the packed bed at the flow rate of 170 standard liters per minute.

Effect of beverage osmolality on intestinal fluid absorption during exercise

To determine how osmolality of an orally ingested fluid-replacement beverage would alter intestinal fluid absorption from the duodenum and/or jejunum during 85 min of cycle exercise (63.3 +/- 0.9% peak O2 uptake) in a cool environment (22 degreesC), seven subjects (5 men, 2 women, peak O2 uptake = 54.5 +/- 3.8 ml . kg-1 . min-1) participated in four experiments separated by 1 wk in which they ingested a water placebo (WP) or one of three 6% carbohydrate (CHO) beverages formulated to give mean osmolalities of 197, 295, or 414 mosmol/kgH2O. CHO solutions also contained 17-18 meq Na+ and 3.2 meq K+. Nasogastric and multilumen tubes were fluoroscopically positioned in the gastric antrum and duodenojejunum, respectively. Subjects ingested a total of 23 ml/kg body mass of the test solution, 20% (370 +/- 9 ml) of this volume 5 min before exercise and 10% (185 +/- 4 ml) every 10 min thereafter. By using the rate of gastric emptying as the rate of intestinal perfusion (G. P. Lambert, R. T. Chang, D. Joensen, X. Shi, R. W. Summers, H. P. Schedl, and C. V. Gisolfi. Int. J. Sports Med. 17: 48-55, 1996), intestinal absorption was determined by segmental perfusion from the duodenum (0-25 cm) and jejunum (25-50 cm). There were no differences (P > 0.05) in gastric emptying (mean 18.1 +/- 1.3 ml/min) or total fluid absorption (802 +/- 109, 650 +/- 52, 674 +/- 62, and 633 +/- 74 ml . 50 cm-1 . h-1 for WP, hypo-, iso-, and hypertonic solutions, respectively) among beverages; but WP was absorbed faster (P < 0.05) from the duodenum than in the jejunum. Of the total volume of fluid ingested, 82 +/- 14, 74 +/- 6, 76 +/- 5, and 68 +/- 7% were absorbed for WP, hypo-, iso-, and hypertonic beverages, respectively. There were no differences in urine production or percent change in plasma volume among solutions. We conclude that total fluid absorption of 6% CHO-electrolyte beverages from the duodenojejunum during exercise, within the osmotic range studied, is not different from WP.

Fructose transport mechanisms in humans

BACKGROUND & AIMS

The possible mechanisms of fructose transport are diffusion, a disaccharidase-related transport system, and glucose-facilitated fructose transport. However, these mechanisms in the human small intestine have not been systematically examined. This study was designed to investigate the mechanisms of fructose transport in the human duodenojejunum.

METHODS

A triple-lumen tube was fluoroscopically positioned in the duodenojejunum of 7 men. Nine carbohydrate-electrolyte solutions were perfused at the rate of 15 mL/min. Acarbose and lactulose were used to examine the disaccharidase-related transport system and glucose-facilitated fructose transport, respectively.

RESULTS

Fructose absorption was greater (P < 0.05) from fructose-glucose (FruGlu) and fructose-glucose-acarbose (FruGluA) solutions than from fructose-mannitol (FruMann) and fructose-mannitol-acarbose (FruMannA) solutions, but there was no difference between FruGlu and FruGluA solutions. A sucrose solution produced greater (P < 0.05) sucrose absorption than a sucrose-acarbose solution. Lactulose absorption (0.016-0.039 mmol.h-1.cm-1) was observed from solutions containing glucose or sucrose. Water absorption was not different among sucrose, FruGlu, and glucose solutions. FruMann solution produced net water secretion. These data suggest that free fructose and glucose transport were not inhibited by acarbose and that the presence of glucose induced lactulose absorption and enhanced fructose absorption.

CONCLUSIONS

Fructose is transported transcellularly by facilitated diffusion and paracellularly (based on lactulose transport) via glucose-activated solution drag. In the human small intestine, free fructose and glucose transport does not occur via the disaccharidase system.

Isolation and identification of Prevotella tannerae from endodontic infections

Black-pigmented bacteria are often isolated from endodontic infections. Five strains of black-pigmented bacteria isolated from endodontic infections could not be identified in our laboratory. The purpose of this study was to sequence the 16S rRNA gene of the five unknown isolates and identify the organisms. The 16S rRNA genes from the unknown organisms were cloned, sequenced, and determined to be Prevotella tannerae. In addition, samples from endodontic infections were surveyed for the presence of the organism. When 118 samples from endodontic infections were examined using polymerase chain reaction with specific primers for P. tannerae, 60% of the samples were positive for the presence of the organism. This suggests that P. tannerae is commonly present in endodontic infections and could be a potential pathogen.

Absorption from different intestinal segments during exercise

This study evaluated intestinal absorption from the first 75 cm of the proximal small intestine during 85 min of cycle exercise [63.6 +/- 0.7% peak O2 consumption (VO2 peak)] while subjects ingested either an isotonic carbohydrate-electrolyte beverage (CHO-E) or a water placebo (WP). The CHO-E beverage contained 117 mM (4%) sucrose, 111 mM (2%) glucose, 18 meq Na+, and 3 meq K+. The two experiments were performed a week apart by seven subjects (6 men and 1 woman; mean VO2 peak = 53.5 +/- 6.5 ml . kg-1 . min-1). Nasogastric and multilumen tubes were fluoroscopically positioned in the gastric antrum and duodenojejunum, respectively. Subjects ingested 23 ml/kg body weight of the test solution, 20% (383 +/- 11 ml) of this volume 5 min before exercise and 10% (191 +/- 5 ml) every 10 min thereafter. By using the rate of gastric emptying (18.1 +/- 1.1 vs. 19.2 +/- 0. 7 ml/min for WP and CHO-E, respectively) as the rate of intestinal perfusion, intestinal absorption was determined by segmental perfusion from the duodenum (0-25 cm) and jejunum (25-50 and 50-75 cm). Water flux was different (P < 0.05) between solutions in the 0- to 25- and 25- to 50-cm segments for WP vs. CHO-E (30.7 +/- 2.7 vs. 15.0 +/- 2.9 and 3.8 +/- 1.1 vs. 11.9 +/- 3.3 ml . cm-1 . h-1, respectively). Furthermore, water flux differed (P < 0.05) for WP in a comparison of the 0- to 25- to the 25- to 50-cm segment. Total solute flux (TSF) was not significantly different among segments for a given solution or between solutions for a given segment. There was no difference between trials for percent change in plasma volume. These results indicate that 1) fluid absorption in the proximal small intestine depends on the segment studied and 2) solution composition can significantly effect water absorption rate in different intestinal segments.

Comparison of cleavage site specificity of gelatinases A and B using collagenous peptides

The gelatinases (type IV collagenases) are members of the matrix metalloproteinase family that not only have a high degree of structural homology but are known to be nearly identical in their digestion profile against macromolecular substrates. We have shown previously that the preferred cleavage sites in the hydrolysis of type I gelatin, catalyzed by gelatinase A (72 kDa type IV collagenase), are bracketed by hydroxyproline in the P5 and P5' positions. In this report, a kinetic investigation using a series of collagenous dodecylpeptides in which the P5 and P5' hydroxyprolines were systematically varied and used as substrates for recombinant human gelatinase A, we show that replacement with either proline or alanine always resulted in increased Km. In contrast, substitution of the hydroxylated amino acids tyrosine and serine at P5 and P5' reduced the Km significantly, indicating that the hydroxyl moiety of the hydroxyproline is the functional group responsible for favorable enzyme-substrate affinity. This was shown by the kcat/Km ratio, which was doubled by the substitution of serine in that site. Cleavage of the same series of dodecylpeptides by recombinant human gelatinase B (92 kDa type IV collagenase) showed a very different kinetic profile for which no patterns were discernible. In subsequent comparisons of the two enzymes, it was found that gelatinase B cleaved the thiopeptolide substrate AcProLeuGly-S-LeuGly-OC2H5 at double the velocity of gelatinase A. In contrast, gelatinase A digested type I gelatin about 2.5-times faster than gelatinase B. SDS-PAGE analysis of gelatin cleavage products showed different patterns of product peptides for each enzyme. Further comparisons of the proteinases using synthetic peptide substrates with variations in size and in substituents at the P2' site again showed marked kinetic differences. Although these two matrix metalloproteinases seem similar in that they are both gelatinolytic and can degrade a nearly identical battery of macromolecular matrix components including type IV collagen, it is clear from these results that they are very different enzymatically. Since the regulatory portions of gelatinases A and B differ markedly, it has been assumed that the enzymes serve the same function, but respond to different stimuli. The differences in substrate specificity described herein suggest that their proposed physiological roles may require reevaluation.

Large libraries reveal diverse solutions to an RNA recognition problem

RNA loops that adopt a characteristic GNRA "tetraloop" fold are common in natural RNAs. Here, we have used in vitro selection by means of mRNA-peptide fusions to select peptides that bind an example of this RNA loop motif. Starting with the RNA recognition domain from the lambda N protein, we have constructed libraries containing 150, 1,600, and 9 trillion different peptide sequences as mRNA-peptide fusions and isolated those capable of high-affinity RNA binding. These selections have resulted in more than 80 different peptides that bind the same RNA loop. The highest affinity peptides exhibit low nanomolar dissociation constants as well as the ability to discriminate RNA hairpins differing by a single loop nucleotide. Thus, our work demonstrates that numerous, chemically distinct solutions exist for a particular RNA recognition problem.

Optimization of optical limiting devices based on excited-state absorption

Limiting devices protect sensitive optical elements from laser-induced damage (LID). Passive devices use focusing optics to concentrate the light through a nonlinear optical (NLO) element (or elements) to reduce the limiting threshold. Unfortunately, these NLO elements may themselves undergo LID for high inputs, restricting the useful dynamic range (DR). Recently, efforts at optimizing this DR have focused on distributing the NLO material along the propagation path z of a focused beam, resulting in different portions of the device (in z) exhibiting NLO response at different inputs. For example, nonlinear absorbers closer to the lens, i.e., upstream, protect device elements downstream near the focal plane. This results in an undesirable increase in the threshold, although the lowest threshold is always obtained with the final element at focus. Thus there is a compromise between DR and threshold. This compromise is determined by the material. We concentrate on reverse saturable absorber (RSA) materials (molecules exhibiting larger excited-state than ground-state absorption). We look at both tandem devices and devices in which the concentration of the NLO material is allowed to spatially vary in z. These latter devices require solid-state hosts. The damage threshold of currently available solid-state hosts is too low to allow known RSA materials to reach their maximum absorption, which occurs when all molecules are in their excited state. This is demonstrated by approximate analytical methods as well as by a full numerical solution of the nonlinear wave propagation equation over extremely large distances in z (up to 10(3)Z(0), where Z(0) is the Rayleigh range of the focused beam). The numerical calculations, based on a one-dimensional fast Fourier transform, indicate that proper inclusion of diffraction reduces the effectiveness of reverse saturable absorption for limiting, sometimes by more than a factor of 10. Liquid-based devices have higher damage thresholds (damage occurs to the cuvette wall) and, thus, larger nonlinear absorption. However, RSA material in liquid hosts may suffer from larger thermal lensing.

Cloning, expression and chromosome localization of porcine adiponectin and adiponectin receptors genes

Adiponectin is a cytokine secreted specifically by adipocytes that has been proposed to enhance insulin sensitivity and prevent atherosclerosis. Adiponectin receptors (adipoR1 and adipoR2) are recently found in mice which act as receptors for globular and full-length adiponectin to mediate the fatty-acid oxidation and glucose uptake in muscle and liver. The primary goal of this study was to examine chromosome localization of porcine adiponectin and adiponectin receptors and the gene expression pattern in various tissues of pigs of the three genes. Radiation hybrid mapping demonstrated that porcine adiponectin, adipoR1 and adipoR2 were located to chromosome13q36-41, 10p11 and 5q25, in the regions that were syntenic to the homologs of human genes, respectively. Semi-quantitative RT-PCR showed that porcine adiponectin mRNA was specifically expressed in adipose tissue and porcine adipoR1 and adipoR2 mRNA were ubiquitously expressed in many tissues except brain. Comparison to adipoR2 mRNA which was highly expressed in liver, heart, kidney, adipose tissues and lung, adipoR1 mRNA was expressed at relatively high levels in porcine muscle, leukocytes and epididymis. Our data provide basic molecular information useful for the further investigation on the function of the three genes.