Temperature-induced reversals of rotation in phycomyces

The steady state extension and rotation rates of the Phycomyces sporangiophore were measured as a function of temperature. Maximum growth occurred at 27°C; maximum rotation at 28°C. The rotation to extension ratio, a qualitative parameter of cell wall structure, is affected differently by high and low temperatures. Steady state counterclockwise rotation, as opposed to the normal clockwise rotation, was found at both high and low temperatures. The extensional and rotational responses to step changes in temperature were also measured. The conclusions are drawn that a relative decrease in the lysis rate of wall polymer is responsible for the decrease in growth rate at low temperatures, and that a relative increase in the rate of wall synthesis and cross-linking is responsible for the decrease in growth rate at high temperatures. It is suggested that reversals in rotation result from changes in the handedness of the wall's helical structure.     

Factors influencing the lignin-peroxidase-producing ability of Phanerochaete chrysosporium

The dependence of lignin peroxidase (LiP) activities on agitation was confirmed in medium A containing low vitamin and low trace element concentrations. Vigorous shaking (100 strokes·min^–1) caused a total loss of LiP activity, and detergents, having a protective effect on the enzyme activity, could not prevent a substantial reduction in enzyme activity. More important, LiP activity also depends on the maintenance media (potato dextrose agar or malt extract agar) and enzyme production media (carbon- or nitrogen-limited). High losses of LiP activity were observed by subsequent subculturing. Even storage of the inoculum on the maintenance media at 4° C, although better than subculturing, was not advisable. After long storage periods (50–75 weeks) at 4° C, LiP could not be reactivated in poor medium A, containing low amounts of vitamins and trace elements. In rich medium B, containing higher amounts of vitamins and trace elements, even after long storage periods, LiP activity was higher than when the activity was measured in poor medium A before storage.     

Factors influencing the ability of isolated cell nuclei to from gels in dilute alkali

1. Known methods for isolating cell nuclei are divided into two classes, depending on whether or not the nuclei are capable of forming gels in dilute alkali or strong saline solutions. Methods which produce nuclei that can form gels apparently prevent the action of an intramitochondrial enzyme capable of destroying the gel-forming capacity of the nuclei. Methods in the other class are believed to permit this enzyme to act on the nuclei during the isolation procedure, causing detachment of DNA from some nuclear constituent (probably protein). 2. It is shown that heating in alkaline solution and x-irradiation can destroy nuclear gels. Heating in acid or neutral solutions can destroy the capacity of isolated nuclei to form gels. 3. Chemical and biological evidence is summarized in favor of the hypothesis that DNA is normally bound firmly to some nuclear component by non-ionic linkages.     

Evolutionary simulations to detect functional lineage-specific genes

MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.     

Factors influencing the ability of nuclear localization sequence peptides to enhance nonviral gene delivery

Nonviral gene delivery is limited by inefficient transfer of DNA from the cytoplasm to the nucleus. Nuclear localization sequence (NLS) peptides have been widely used to exploit intracellular transport mechanisms and promote nuclear uptake of DNA. However, the exact conditions to successfully utilize the properties of NLS peptides are still unclear. In the present study a panel of NLS peptides that bind different transport receptors were compared for their ability to enhance nonviral gene transfer. Several factors such as method of incorporating the NLS peptide, type of NLS peptide, DNA morphology, and proper characterization of NLS peptide/DNA conjugates were identified as important considerations in utilizing NLS peptides to enhance gene transfer. In particular, it was shown that a peptide derived from human T cell leukaemia virus type 1 (HTLV) was able to effectively condense DNA into discrete particles and mediate levels of transgene expression up to 32-fold greater than polylysine-based polyplexes. This is the first study to demonstrate efficient transfection mediated by an importin beta-binding peptide based on the HTLV sequence. Promising results were also achieved with a 7-fold increase in gene expression using a NLS peptide/DNA conjugate formed by site-specific linkage of an extended SV40 peptide via a peptide nucleic acid (PNA) clamp. Altogether, the results from this study should help to define the requirements for successful NLS-enhanced transfection.     

Factors influencing the ability of Pseudomonas putida strains epI and II to degrade the organophosphate ethoprophos

Two strains of Pseudomonas putida (epI and epII), isolated previously from ethoprophos-treated soil, were able to degrade ethoprophos (10 mg 1(-1)) in a mineral salts medium plus nitrogen (MSMN) in less than 50 h with a concurrent population growth. Addition of glucose or succinate to MSMN did not influence the degrading ability of Ps. putida epI, but increased the lag phase before rapid degradation commenced with Ps. putida epII. The degrading ability of the two isolates was lost when the pesticide provided the sole source of phosphorus. Degradation of ethoprophos was most rapid when bacterial cultures were incubated at 25 and 37 degrees C. Pseudomonas putida epI was capable of completely degrading ethoprophos at a slow rate at 5 degrees C, compared with Ps. putida epII which could not completely degrade ethoprophos at the same time. Pseudomonas putida epI was capable of degrading ethoprophos when only 60 cells ml(-1) were used as initial inoculum. In contrast, Ps. putida epII was able to totally degrade ethoprophos when inoculum densities of 600 cells ml(-1) or higher were used. In general, longer lag phases accompanied the lower inoculum levels. Both isolates rapidly degraded ethoprophos in MSMN at pHs ranging from 5.5 to 7.6, but not at pH 5 or below.     

Factors influencing the ability of Listeria monocytogenes to pass through a membrane filter by active infiltration

Listeria monocytogenes infiltrated the reticulate structure of a membrane filter and passed through a filter with pore sizes of 0.45 microm and 0.2 microm in 6 to 24 h and 5 to 6 days, respectively. Flagellar motility and expansive pressure generated by the growing bacterial population were indicated as the driving forces of infiltration.     

Factors influencing final range of motion in the fingers after fractures of the hand.

We evaluated 123 patients in which we treated 150 fractured fingers primarily. Sixty-seven percent of these fractured fingers required open reduction with internal fixation; the remainder had closed reduction with internal or external fixation, or immediate arthrodeses. Active and passive range-of-motion (ROM) exercises were usually begun within 3 days after injury. The active and passive ROM of all joints of each finger in the involved hand were measured at regular intervals until no further change in ROM occurred. An associated crush injury, a flexor or extensor tendon injury, or a skin loss (each) caused a significantly more frequent decrease in the final ROM of the unfractured fingers of the same hand. An associated joint injury, more than one fracture per finger, a crush injury, a flexor or extensor tendon injury, or a skin loss (each) caused a significant decrease in the ROM of the fractured fingers. After treatment of a simple fracture, the ROM in both the fractured and the unfractured fingers was essentially normal.     

Factors influencing eating ability of old in-patients in a rehabilitation hospital in Japan

Objectives: This study was designed to determine the factors influencing eating ability of old in‐patients in a rehabilitation hospital. Design: Cross‐sectional investigation. Setting: Forty‐six in‐patients in the rehabilitation ward of Hashimoto Hospital in Kagawa Prefecture in Japan were investigated using a multi‐disciplinary approach. Main outcome measures: Age, gender, state of dentition, muscle activity of lip, cheek and tongue, biting force, salivary flow rate per a minute (SFR), masticatory ability for gummy jelly, swallowing ability, texture of meal, independency of walking (Functional Independence Measure=FIM) and ability to communicate. Results: Bivariate analysis for the relationship between surveyed items and masticatory ability (chi‐square test) identified that better masticatory ability for gummy jelly was associated with age (<85 years), gender (male), state of dentition (dentate), SFR (high), activity of lip (good), biting force (high), swallowing ability (good) and activity of communication (high). Among these items, SFR (p=0.001), gender (p=0.004), ability to communicate (p=0.005) and age (p=0.012) were found having an influence on the masticatory ability (logistic regression analysis). On the other hand, age (<85years), gender (male), SFR (high), activity of lip (good), activity of cheek (good), biting force (high), masticatory ability (good) and swallowing ability (good) had a relationship with normal texture of meal. In regression analysis, only two items, activity of lip (p=0.003) and swallowing ability (p=0.024) emerged as factors on texture of meal. Conclusions: Masticatory ability for gummy jelly was influenced by cognitive function and was excluded from the factors on the state of meal. These results suggested the limitation of evaluation using test food, so dentists should observe eating behaviour of in‐patients. In addition, dentists should pay attention to the activity of the lip and swallowing ability as well as dentition and prostheses in the rehabilitation of eating ability. As SFR was the most significant factor on masticatory ability, this emphasizes the necessity of care for dry mouth caused by side effects of multi‐medication     

Network-based model weighting to detect multiple loci influencing complex diseases

For genome-wide association studies, it has been increasingly recognized that the popular locus-by-locus search for DNA variants associated with disease susceptibility may not be effective, especially when there are interactions between or among multiple loci, for which a multi-loci search strategy may be more productive. However, even if computationally feasible, a genome-wide search over all possible multiple loci requires exploring a huge model space and making costly adjustment for multiple testing, leading to reduced statistical power. On the other hand, there are accumulating data suggesting that protein products of many disease-causing genes tend to interact with each other, or cluster in the same biological pathway. To incorporate this prior knowledge and existing data on gene networks, we propose a gene network-based method to improve statistical power over that of the exhaustive search by giving higher weights to models involving genes nearby in a network. We use simulated data under realistic scenarios, including a large-scale human protein–protein interaction network and 23 known ataxia-causing genes, to demonstrate potential gain by our proposed method when disease-genes are clustered in a network.     

Factors influencing decisions to terminate life

Abstract

The present study attempted to identify situations that would lead subjects to endorse euthanasia when no implicit assumption about the inevitability of death was made. Participants in the study were 54 males and 47 females enrolled in introductory psychology courses at the University of California, Los Angeles. Subjects indicated how likely they would be to endorse euthanasia in specific hypothetical situations for themselves and for each of their parents. When a factor analysis was conducted on the self situations, four factors were identified: (1) physical condition and pain; (2) external sanction, financial hardship, and emotional stress; (3) mental alertness; and (4) lowered expectation of recovery. A factor analysis was also conducted on the parents’ situations and four slightly different factors were obtained. The results indicate that different decisional criteria are used for self than for parents. Also, the decision to terminate another's life appears to involve the consideration of more factors than the decision to terminate one's own life. Neither sex nor religious affiliation differences were found to be related to the endorsement of euthanasia. However, a significant relationship was found between endorsement of euthanasia and low scores on a religiosity measure when subjects were divided into low and high scorers.     

Factors influencing the development of tolerance to ethanol

The influence of three parameters on the degree of acquired tolerance to ethanol was studied using goldfish as the animal model. These factors were: a) the rate of ethanol administration; b) the repeated performance of the behavioral test, and c) the prior presence of tolerance to a low dose of ethanol. Tolerance, as indicated by the increase in the ethanol brain levels associated with the loss of righting reflex (overturn test), was observed in fish exposed to 0.2, 0.4, or 0.6% (w/v) ethanol for 1 to 24 hours independently of the rate of ethanol administration. Fish exposed to 0.8% (w/v) ethanol developed tolerance only when this ethanol concentration was reached slowly (circa 3 hours). The increase in functional demand by the repeated testing of the fish and the presence of tolerance to a low dose of ethanol (0.4%) did not affect the degree of the observed tolerance in fish left to equilibrate with a 0.8% ethanol dose. The data support the suggestion that motor functions controlled by the central nervous system can adapt to a high concentration of ethanol if an adequate amount of time is allowed for this compensation to occur or if this concentration is reached slowly. Furthermore, in goldfish the degree of acquired tolerance is directly proportional to the concentration of the ethanol during the time of exposure and independent of the previous experience in alcohol solution.     

Factors influencing bacterial attachment to the ruminal epithelium in vitro

Some factors influencing bacterial attachment to the rumen epithelium were studied in vitro using mixed rumen bacteria (upper- or lower-layer bacteria formed at bacterial sediment by centrifugation), isolated from steers fed a roughage diet, and rumen epithelial cells collected from beef cattle given low-concentrate (50%; LC) and high-concentrate (90%; HC) diets. Optimal incubation conditions for bacterial attachment to rumen epithelial cells were 39 degrees C for 30 min. The bacteria isolated from the upper layer had a higher attaching activity to the LC epithelial cells than those of the lower layer. A higher degree of bacterial attachment was observed using the rumen epithelium from steers fed the LC diet rather than the HC diet (p<0.01). Ethylenediamine dihydroiodide (EDDI) added at 10 through 40 &mgr;g/ml increased bacterial attachment to the HC epithelial cells. Ammonia at 50 through 100 &mgr;g/ml positively affected bacterial attachment to both LC and HC epithelial cells. Bacterial attachment to the HC epithelial cells was enhanced (p<0.01) by the addition of a reducing agent (L-cysteine.HCl) but no increase was noted with LC cells. L- or D-lactate, volatile and unsaturated fatty acids markedly decreased bacterial attachment to rumen epithelial cells.     

Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations

N-BAR domains are protein modules that bind to and induce curvature in membranes via a charged concave surface and N-terminal amphipathic helices. Recently, molecular dynamics simulations have demonstrated that the N-BAR domain can induce a strong local curvature that matches the curvature of the BAR domain surface facing the bilayer. Here we present further molecular dynamics simulations that examine in greater detail the roles of the concave surface and amphipathic helices in driving local membrane curvature. We find that the strong curvature induction observed in our previous simulations requires the stable presentation of the charged concave surface to the membrane and is not driven by the membrane-embedded amphipathic helices. Nevertheless, without these amphipathic helices embedded in the membrane, the N-BAR domain does not maintain a close association with the bilayer, and fails to drive membrane curvature. Increasing the membrane negative charge through the addition of PIP₂ facilitates closer association with the membrane in the absence of embedded helices. At sufficiently high concentrations, amphipathic helices embedded in the membrane drive membrane curvature independently of the BAR domain.     

Trade-off between BCG vaccination and the ability to detect and treat latent tuberculosis

Policies regarding the use of the Bacille Calmette-Guérin (BCG) vaccine for tuberculosis vary greatly throughout the international community. In several countries, consideration of discontinuing universal vaccination programs is currently under way. The arguments against mass vaccination are that the effectiveness of BCG in preventing tuberculosis is uncertain and that BCG vaccination can interfere with the detection and treatment of latent tuberculosis.In this work, we pose a dynamical systems model for the population-level dynamics of tuberculosis in order to study the trade-off which occurs between vaccination and detection/treatment of latent tuberculosis. We assume that latent infection in vaccinated individuals is completely undetectable. For the case of a country with very low levels of tuberculosis, we establish analytic thresholds, via stability analysis and the basic reproductive number, which determine the optimal vaccination policy, given the effectiveness of the vaccine and the detection/treatment rate of latent tuberculosis.The results of this work suggest that it is unlikely that a country detects and treats latent tuberculosis at a high enough rate to justify the discontinuation of mass vaccination from this perspective.     

Testing human sperm chemotaxis: how to detect biased motion in population assays

Biased motion of motile cells in a concentration gradient of a chemoattractant is frequently studied on the population level. This approach has been particularly employed in human sperm chemotactic assays, where the fraction of responsive cells is low and detection of biased motion depends on subtle differences. In these assays, statistical measures such as population odds ratios of swimming directions can be employed to infer chemotactic performance. Here, we report on an improved method to assess statistical significance of experimentally determined odds ratios and discuss the strong impact of data correlations that arise from the directional persistence of sperm swimming.     

Phase-linking and the perceived motion during off-vertical axis rotation

Human off-vertical axis rotation (OVAR) in the dark typically produces perceived motion about a cone, the amplitude of which changes as a function of frequency. This perception is commonly attributed to the fact that both the OVAR and the conical motion have a gravity vector that rotates about the subject. Little-known, however, is that this rotating-gravity explanation for perceived conical motion is inconsistent with basic observations about self-motion perception: (a) that the perceived vertical moves toward alignment with the gravito-inertial acceleration (GIA) and (b) that perceived translation arises from perceived linear acceleration, as derived from the portion of the GIA not associated with gravity. Mathematically proved in this article is the fact that during OVAR these properties imply mismatched phase of perceived tilt and translation, in contrast to the common perception of matched phases which correspond to conical motion with pivot at the bottom. This result demonstrates that an additional perceptual rule is required to explain perception in OVAR. This study investigates, both analytically and computationally, the phase relationship between tilt and translation at different stimulus rates—slow (45°/s) and fast (180°/s), and the three-dimensional shape of predicted perceived motion, under different sets of hypotheses about self-motion perception. We propose that for human motion perception, there is a phase-linking of tilt and translation movements to construct a perception of one’s overall motion path. Alternative hypotheses to achieve the phase match were tested with three-dimensional computational models, comparing the output with published experimental reports. The best fit with experimental data was the hypothesis that the phase of perceived translation was linked to perceived tilt, while the perceived tilt was determined by the GIA. This hypothesis successfully predicted the bottom-pivot cone commonly reported and a reduced sense of tilt during fast OVAR. Similar considerations apply to the hilltop illusion often reported during horizontal linear oscillation. Known response properties of central neurons are consistent with this ability to phase-link translation with tilt. In addition, the competing “standard” model was mathematically proved to be unable to predict the bottom-pivot cone regardless of the values used for parameters in the model.