Structural origins of fibrin clot rheology

The origins of clot rheological behavior associated with network morphology and factor XIIIa-induced cross-linking were studied in fibrin clots. Network morphology was manipulated by varying the concentrations of fibrinogen, thrombin, and calcium ion, and cross-linking was controlled by a synthetic, active-center inhibitor of FXIIIa. Quantitative measurements of network features (fiber lengths, fiber diameters, and fiber and branching densities) were made by analyzing computerized three-dimensional models constructed from stereo pairs of scanning electron micrographs. Large fiber diameters and lengths were established only when branching was minimal, and increases in fiber length were generally associated with increases in fiber diameter. Junctions at which three fibers joined were the dominant branchpoint type. Viscoelastic properties of the clots were measured with a rheometer and were correlated with structural features of the networks. At constant fibrinogen but varying thrombin and calcium concentrations, maximal rigidities were established in samples (both cross-linked and noncross-linked) which displayed a balance between large fiber sizes and great branching. Clot rigidity was also enhanced by increasing fiber and branchpoint densities at greater fibrinogen concentrations. Network morphology is only minimally altered by the FXIIIa-catalyzed cross-linking reaction, which seems to augment clot rigidity most likely by the stiffening of existing fibers.     

In vivo analysis of fracture toughness of thyroid gland tumors

Background

Human solid tumors that are hard or firm on physical palpation are likely to be cancerous, a clinical maxim that has been successfully applied to cancer screening programs, such as breast self-examination. However, the biological relevance or prognostic significance of tumor hardness remains poorly understood. Here we present a fracture mechanics based in vivo approach for characterizing the fracture toughness of biological tissue of human thyroid gland tumors.

Methods

In a prospective study, 609 solid thyroid gland tumors were percutaneously probed using standard 25 gauge fine needles, their tissue toughness ranked on the basis of the nature and strength of the haptic force feedback cues, and subjected to standard fine needle biopsy. The tumors' toughness rankings and final cytological diagnoses were combined and analyzed. The interpreting cytopathologist was blinded to the tumors' toughness rankings.

Results

Our data showed that cancerous and noncancerous tumors displayed remarkable haptically distinguishable differences in their material toughness.

Conclusion

The qualitative method described here, though subject to some operator bias, identifies a previously unreported in vivo approach to classify fracture toughness of a solid tumor that can be correlated with malignancy, and paves the way for the development of a mechanical device that can accurately quantify the tissue toughness of a human tumor.     

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

Background  

Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos.     

Separating physical disturbance and nutrient enrichment caused by Pacific salmon in stream ecosystems

1. Pacific salmon (Oncorhynchus spp.) deliver marine‐derived nutrients to the streams in which they spawn and die, and these resource subsidies can increase the abundance of stream biota. In strong contrast, physical disturbance from salmon spawning activity can reduce the abundance of benthic organisms. Previous experimental designs have not established the relative effects of these two contrasting processes on stream organisms during a salmon run. 2. We combined manipulative and observational field studies to assess the degree of nutrient enrichment, physical disturbance, and the net effect of salmon on the abundance of benthic periphyton. Related salmon‐mediated processes were also evaluated for benthic macroinvertebrates. Mesh exclosures (2 × 2 m plots) prevented salmon from disturbing areas of the stream channel, which were compared with areas to which salmon had access. Sampling was conducted both before and during the late‐summer spawning run of pink (O. gorbushca) and chum (O. keta) salmon. 3. Streamwater nitrogen and phosphorus concentrations increased sharply with the onset of the salmon run, and highly significant positive relationships were observed between the numbers of salmon present in the stream and these dissolved nutrients. Before the salmon run, periphyton biomass (as chlorophyll a) and total macroinvertebrate abundance were very similar between control and exclosure plots. During the salmon run, exclosures departed substantially from controls, suggesting significant disturbance imparted on benthic biota. 4. Comparing exclosures before and during the salmon run enabled us to estimate the effects of salmon in the absence of direct salmon disturbance. This ‘nutrient enrichment potential’ was significant for periphyton biomass, as was a related index for macroinvertebrate abundance (although enhanced invertebrate drift into exclosures during the salmon run could also have been important). Interestingly, however, the net effect of salmon, evaluated by comparing control plots before and during the salmon run, was relatively modest for both periphyton and macroinvertebrates, suggesting that nutrient enrichment effects were largely offset by disturbance. 5. Our results illustrate the importance of isolating the specific mechanisms via which organisms affect ecosystems, and indicate that the relative magnitude of salmon nutrient enrichment and benthic disturbance determines the net effect that these ecologically important fish have on stream ecosystems.     

Basolateral K channels in an insect epithelium. Channel density, conductance, and block by barium

K channels in the basolateral membrane of insect hindgut were studied using current fluctuation analysis and microelectrodes. Locust recta were mounted in Ussing-type chambers containing Cl-free saline and cyclic AMP (cAMP). A transepithelial K current was induced by raising serosal [K] under short-circuit conditions. Adding Ba to the mucosal (luminal) side under these conditions had no effect; however, serosal Ba reversibly inhibited the short-circuit current (Isc), increased transepithelial resistance (Rt), and added a Lorentzian component to power density spectra of the Isc. A nonlinear relationship between corner frequency and serosal [Ba] was observed, which suggests that the rate constant for Ba association with basolateral channels increased as [Ba] was elevated. Microelectrode experiments revealed that the basolateral membrane hyperpolarized when Ba was added: this change in membrane potential could explain the nonlinearity of the 2 pi fc vs. [Ba] relationship if external Ba sensed about three-quarters of the basolateral membrane field. Conventional microelectrodes were used to determine the correspondence between transepithelially measured current noise and basolateral membrane conductance fluctuations, and ion-sensitive microelectrodes were used to measure intracellular K activity (acK). From the relationship between the net electrochemical potential for K across the basolateral membrane and the single channel current calculated from noise analysis, we estimate that the conductance of basolateral K channels is approximately 60 pS, and that there are approximately 180 million channels per square centimeter of tissue area.     

Restriction-map variation with the yellow-achaete-scute region in five populations of Drosophila melanogaster

It has been proposed that the degree of recombination for a genomic region will affect the level of both nucleotide heterozygosity and the density of transposable elements. Both features of genomic diversity have been examined in a number of recent reports for regions undergoing relatively normal levels of recombination in Drosophila melanogaster. In this study the genomic variation associated with yellow-achaete- scute loci located at the tip of the X chromosome is examined by six- cutter restriction mapping. In this region, as usual for regions adjacent to telomeres, crossing-over is dramatically reduced, and published studies of visible mutants indicate extremely little restriction-map variation. Eight six-cutter restriction endonucleases were used to locate sequence variation in 14- and 16.5-kb regions in 109 lines sampled from North America, Africa, and Europe. The overall level of heterozygosity is estimated as 0.29%. Nine large insertions, all presumed to be transposable elements, were observed. Base-pair heterozygosity appears to be reduced compared with regions having normal levels of recombination. The estimated heterozygosity is much higher than reported in earlier studies of restriction-map variation among visible mutations in the complex. The incidence of large insertions is not elevated compared with that in other regions of the genome. This suggests that asymmetric synapsis and exchange is not an important mechanism for the elimination of transposable elements.      

The influence of form of deposit on the phytotoxicity of MCPA, paraquat and glyphosate applied as individual drops

MCPA, paraquat and glyphosate were applied as individual drops (200–400 μm) to pot-grown plants of radish (Raphanus sativus) or wild oat (Avena fatua), using concentrations appropriate to very low volume applications of these herbicides. For a given dose per plant, herbicide activity was unaffected by concentration of MCPA or paraquat but was enhanced as the concentration of glyphosate was increased. The activity of all three herbicides on both species was affected by variation of the site of application but not by drop size. On radish the greatest activity resulted when paraquat was applied to the cotyledons, glyphosate to the interveinal areas of true leaves and MCPA to the veins of true leaves. This is discussed in relation to herbicide mobility and local toxicity following applications at high concentration.