Enzyme structure with two catalytic sites for double-sieve selection of substrate

High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.     

Net interaction between different forms of short-term synaptic plasticity and slow-IPSPs in the hippocampus and auditory cortex

Paired-pulse plasticity is typically used to study the mechanisms underlying synaptic transmission and modulation. An important question relates to whether, under physiological conditions in which various opposing synaptic properties are acting in parallel, the net effect is facilitatory or depressive, that is, whether cells further or closer to threshold. For example, does the net sum of paired-pulse facilitation (PPF) of excitatory postsynaptic potentials (EPSPs), paired-pulse depression (PPD) of inhibitory postsynaptic potentials (IPSPs), and the hyperpolarizing slow IPSP result in depression or facilitation? Here we examine how different time-dependent properties act in parallel and examine the contribution of gamma-aminobutyric acid-B (GABAB) receptors that mediate two opposing processes, the slow IPSP and PPD of the fast IPSP. Using intracellular recordings from rat CA3 hippocampal neurons and L-II/III auditory cortex neurons, we examined the postsynaptic responses to paired-pulse stimulation (with intervals between 50 and 400 ms) of the Schaffer collaterals and white matter, respectively. Changes in the amplitude, time-to-peak (TTP), and slope of each EPSP were analyzed before and after application of the GABAB antagonist CGP-55845. In both CA3 and L-II/III neurons the peak amplitude of the second EPSP was generally depressed (further from threshold) compared with the first at the longer intervals; however, these EPSPs were generally broader and exhibited a longer TTP that could result in facilitation by enhancing temporal summation. At the short intervals CA3 neurons exhibited facilitation of the peak EPSP amplitude in the absence and presence of CGP-55845. In contrast, on average L-II/III cells did not exhibit facilitation at any interval, in the absence or presence of CGP-55845. CGP-55845 generally "erased" short-term plasticity, equalizing the peak amplitude and TTP of the first and second EPSPs at longer intervals in the hippocampus and auditory cortex. These results show that it is necessary to consider all time-dependent properties to determine whether facilitation or depression will dominate under intact pharmacological conditions. Furthermore our results suggest that GABAB-dependent properties may be the major contributor to short-term plasticity on the time scale of a few hundred milliseconds and are consistent with the hypothesis that the balance of different time-dependent processes can modulate the state of networks in a complex manner and could contribute to the generation of temporally sensitive neural responses.     

A point of view: why point-of-care places are not free marketplaces

Current wisdom holds that health care is a business and "as such must abide by market principles." Most nurses are not well enough versed in economic theories to credibly critique health care delivery decisions based on economic theories. The relationship of market principles to health care realities is described in basic terms to encourage nurses to "optimize patient care and influence health care policy." Physicians, who control all access points to the health care system, have enjoyed a 40-year market dominance that is "rapidly being replaced by insurance companies and for-profit investors." Providers' decisions to treat or not to treat are strongly influenced by whether the patient is in a fee-for-service or capitated payment environment.     

Ristocetin- and thrombin-induced platelet aggregation at physiological shear rates: differential roles for GPIb and GPIIb-IIIa receptor

We recently reported that washed platelets (WP) activated with ADP and expressing surface-bound vWF aggregated in flow through small tubes or in a cylindrical couette device at physiological shear rates of G = 300 s(-1)-1000 s(-1) in the absence of exogenous ligands, with GPIb-vWF partially, and activated GPIIb-IIIa totally required for the aggregation. We have now extended these studies to aggregation of platelets "activated" with ristocetin or thrombin. Washed platelet suspensions with added soluble vWF and ristocetin (0.3-0.75 mg/ml), or activated with thrombin (0.01-0.5 U/ml) but no added ligand, were sheared in a coaxial cylinder device at uniform shear rate, G = 1000 s(-1). The collision capture efficiency (alphaG) with which small aggregates form (= experimental/calculated initial rates of aggregation) was correlated with vWF platelet binding assessed by flow cytometry. The vWF-GPIb interaction was exclusively able to support ristocetin-mediated shear aggregation of metabolically active platelets, with very few vWF monomer equivalents bound per platelet (representing < or = 10 molecules of 10 million Da) required to yield high capture efficiencies (alphaG = 0.38+/-.02; n = 11), suggesting rapid and stable bond formations between vWF and GPIb. However, platelet surface-expressed vWF, generated by addition of thrombin to washed platelets, was found to mediate platelet aggregation with alphaG = 0.08+/-.01 (n = 6), surprisingly comparable to that previously reported for WP and ADP activation. Blocking the GPIIb-Illa receptor decreased alphaG by 95+/-3% (n =3), while a monoclonal antibody to the vWF site on GPIb caused a 49+/-7% (n = 8) decrease in alphaG. The partial role for GPIb thus appears to reflect a facilitative function for increasing contact time between flowing platelets, and allowing engagement of the GPIIb-IIa receptor to yield stable attachment.     

New dissimilarity measure for recognizing noisy subsequence trees

Tree is a data structure used to express various objects such as semistructured data and genes. When objects are represented as trees, computing tree similarity is essential for pattern recognition and retrieval. This paper considers the noisy subsequence tree recognition problem whose purpose is to recognize the original tree, given its noisy subsequence tree. Previous research on this problem relied on constrained tree edit distance to measure the dissimilarity. However, the number of relabelings must be predetermined to compute it. This paper proposes a new dissimilarity measure for this problem. Our dissimilarity measure is obtained by counting the node edit operations included in the unit‐cost tree edit distance that contribute to the matching of node labels. The number of relabelings need not be specified to compute our dissimilarity measure. Moreover, our measure achieves more accurate recognition performance and faster execution speed than the constrained tree edit distance. Our measure is also useful to solve the tree inclusion problem which is the problem of deciding whether a tree includes another tree and shows the extent of approximate tree inclusion when a tree incompletely includes another tree. © 2011 Wiley Periodicals, Inc.     

Parametric polynomial spectral factorization using the sum of roots and its application to a control design problem

This paper presents an algebraic approach to polynomial spectral factorization, an important mathematical tool in signal processing and control. The approach exploits an intriguing relationship between the theory of Gröbner bases and polynomial spectral factorization which can be observed through the sum of roots, and allows us to perform polynomial spectral factorization in the presence of real parameters. It is discussed that parametric polynomial spectral factorization enables us to express quantities such as the optimal cost in terms of parameters and the sum of roots. Furthermore an optimization method over parameters is suggested that makes use of the results from parametric polynomial spectral factorization and also employs two quantifier elimination techniques. This proposed approach is demonstrated in a numerical example of a particular control problem.     

Application of polymerase chain reaction for the correlation of Salmonella serovars recovered from greyhound feces with their diet

The polymerase chain reaction was employed to correlate Salmonella serovars isolated from fecal material of greyhounds suffering from gastroenteritis with those isolated from the diet fed to the greyhounds prior to onset of diarrhea. Kennels around the Abilene, Kansas, area were contacted and supplied with materials needed to collect a portion of the diet each day. With the onset of diarrhea, the kennels were instructed to ship the fecal material and diet from the previous 10 days to the laboratory for testing. Forty-one fecal samples and corresponding diets were screened for Salmonella, Clostridium perfringens, Campylobacter jejuni, Staphylococcus aureus, Staphylococcus intermedius, and pathogenic (piliated) Escherichia coli by direct culture using standard procedures. The fecal material was also screened for coronavirus and parvovirus using electron microscopy. Thirty-five "normal" fecal samples were screened for all of the above mentioned microorganisms as a control. In addition, the fecal material was screened for E. coli verotoxins I and II and clostridial enterotoxins. A total of 61 Salmonella isolates were recovered from the 41 samples of feces and diet submitted for testing; 31 were recovered from the feces and 30 from the diet. Four Salmonella isolates were recovered from the normal fecal samples. Results obtained by PCR, plasmid profiles, antigenic analysis, and antibiogram profiles indicated that 16 of the 31 isolates recovered from the fecal material were the same strain as that recovered from the diet.     

Diagnostic value of determining hemoglobin in cerebrospinal fluid in acute cerebral circulatory disorders

The results of hemoglobin determination in the CSF by the method of fluorescence microscopy in 195 patients speaks in favor of relative diagnostical importance of hemoglobin in the supra fall-out CSF for establishing the character of the stroke. The following circumstances testify to this fact: 1) in an artificial admixture of blood in the CSF in some cases there may be hemolysis of "passing" erythrocytes; 2) in a genuine admixture of blood, tests of hemoglobin in the centrifugate of the CSF may be negative since in some cases the transition of hemoglobin into bilirubin in the subarachmoid space occurs more rapidly than the hemolysis of erythrocytes. Thus, the hemoglobin does not accumulate in the liquid in quantities, sufficient enough to be measured by the existing methods; 3) in a large amount of artificial blood admixture, even without a hemolysis of "passing" erythrocytes the hemoglobin tests in the centrifugate of the CSF may be positive at the expense of hemoglobin of the blood plasma.     

The fluorescence behavior from SAM of dendron with rhodamine B as a center

We studied energy transfer between rhodamine B molecules centered in each corn-shaped dendrons that forms self-assembled monolayer (SAM) film on an Au substrate. A SAM film using dendron moiety as a spacer can change the distance between rhodamines depending on the size, so that the energy transfer from an initially photo-excited rhodamine to its surrounding molecules can be controlled. The absorption spectrum of a SAM film for each generation of dendron was measured to ascertain a linear correlation between the generation and the distance. Picosecond time-resolved fluorescence spectra showed clear differences in the fluorescence decay dynamics between third-generation (G3) and fourth-generation (G4) dendron SAM films. In addition, we found that “dry” or “wet” dendron SAM considerably influenced fluorescence behavior. As a result, the use of “wet” G4 SAM is suitable in preserving photo-excitation energy. This is because it gave almost equal dynamics to G4 dendron in the dilute solution and prevented deactivation by energy dissipation.