The Ribosome Filter Redux

The ribosome filter hypothesis postulates that ribosomes are not simply translation machines but also function as regulatory elements that differentially affect or filter the translation of particular mRNAs. On the basis of new information, we take the opportunity here to review the ribosome filter hypothesis, suggest specific mechanisms of action, and discuss recent examples from the literature that support it.     

A Kalman filtering approach to the representation of kinematic quantities by the hippocampal-entorhinal complex

Several regions of the brain which represent kinematic quantities are grouped under a single state-estimator framework. A theoretic effort is made to predict the activity of each cell population as a function of time using a simple state estimator (the Kalman filter). Three brain regions are considered in detail: the parietal cortex (reaching cells), the hippocampus (place cells and head-direction cells), and the entorhinal cortex (grid cells). For the reaching cell and place cell examples, we compute the perceived probability distributions of objects in the environment as a function of the observations. For the grid cell example, we show that the elastic behavior of the grids observed in experiments arises naturally from the Kalman filter. To our knowledge, the application of a tensor Kalman filter to grid cells is completely novel.     

基于决策森林特征基因的两种识别方法

应用DNA芯片可获得成千上万个基因的表达谱数据。寻找对疾病有鉴别力的特征基因 ,滤掉与疾病无关的基因是基因表达谱数据分析的关键问题。利用决策森林方法的集成优势 ,提出基于决策森林的两种特征基因识别方法。该方法先由决策森林按照一定的显著性水平滤掉大部分与疾病类别无关的基因 ,然后采用统计频数法和扰动法 ,根据所选特征对分类的贡献程度对初选的特征基因作更加精细地选择。最后 ,选用神经网络作为外部分类器对所选的特征基因子集进行评价 ,将提出的方法应用于 4 0例结肠癌组织与 2 2例正常组织中 2 0 0 0个基因的表达谱实验数据。结果表明 :上述两种方法选出的特征基因均具有较高的疾病鉴别能力 ,均可获得最优特征基因子集 ,基于决策森林的统计频数法优于扰动法。     

Filter assay technique and quench-flow experiments: examples of receptor-mediated transmembrane ion-exchange measured with membrane vesicles.

Modifications to a quench-flow apparatus are described which allow a rapid, in-line filter assay with immediate washing, in conditions to give minimum background. A design for an effluent spout is presented, which decelerates the liquid by a large factor, prevents splashes, limits the area of the filter exposed to the sample and allows an immediate wash over a larger area. A design for a filter assay funnel for general use is also presented. These devices feature minimal contact of the funnels with the filter disc. Examples are given in which in-line filtration was used to follow transmembrane ion flux in membrane vesicle preparations. In measurements of transmembrane flux with membrane vesicles and radioisotope the filter assay background can be resolved into three components. These are, (1) the uptake of radioactivity by the filter, (2) the radioactivity inside the vesicles not taking part in the specific measurement and (3) the occlusion of radioactivity in aggregated membrane particles on the filter. These different components depend on the conditions in different ways. Techniques for minimizing the background in filter assays are discussed. The importance of rapid filtration and immediate washing is demonstrated. The examples given illustrate that the function of the acetylcholine receptor from E. electricus is not affected by diisopropylfluorophosphate in the conditions used, and that added GABA is not removed from solution in a brain membrane preparation by the GABA uptake mechanisms in the short times of the experiments.     

How does environmental variation translate into biological processes?

Birth and death rates, as so many other biological processes, are usually not linearly related to environmental variation. Common examples of non-linear response forms include unimodal "optimum-type" responses and various saturating responses. These responses filter the signal coming from the environment to a corresponding biological process. We explored how different types of environmental signal may be transformed to a biological process. We were interested in the effect of the filter on modulation of (1) the variance of the signal, on (2) the variance-covariance structure between the signal and the filtered signal, and on (3) the match between the power spectra of the signal and the filtered signal. We found that the filters will change the frequency distribution (mean, variance, modality) of the signal. Especially symmetric filters that have a single peak of optimum will change signal structure so that there either exists or does not exist a correlation between the signal and the filtered signal. When the correlation exists it may be either positive or negative depending on the signal's mode relative to the filter structure. Also, the power spectrum properties of the signal may be dramatically transformed after passing the filter, e.g., blue noise can turn into red noise. Our results strongly suggest that studies on the influence of external signals on biological processes, such as population dynamics, should explicitly consider how the signal is transferred to biological processes.     

Wiener filtration versus averaging of evoked responses

The extraction of the evoked potential by the Wiener filtration technique is performed to compare it with classical averaging. It is well known that the Wiener filter supplies the least square error estimate. On the other hand, it is apparent that this error substantially depends on the choice of the lengths of interstimulation intervals. Artificially simulated examples are processed by both techniques, averaging and Wiener filtration, to show that the proper choice of the interstimulating intervals is much more relevant for decreasing the estimate error than in helping us make the decision which of these methods should be used.     

Spectro-temporal interpretation of activity patterns of auditory neurons

Sensory receptors transform an external sensory stimulus into an internal neural activity pattern. This mapping is studied through its inverse. An earlier paper showed that within the context of a neuron model composed of a linear filter followed by an exponential pulse generator and a Gaussian stimulus ensemble a unique "most plausible" first-order stimulus estimate can be constructed. This method, applicable only to neurons showing phase-lock, is extended to neurons without phase-lock. In this situation second-order spectro-temporal stimulus estimates are produced; examples are given from simulation. The method is applied to activity of neurons in the auditory system of the frog.     

测定细胞内自由钙的显微荧光光度计的研制和应用

以ＸＳＪ－２型荧光显微镜为基础,建立了测定细胞内自由钙的显微荧光光度计,为建立这套装置,对荧光显微镜主要作了如下改动：首先,为提供稳定的激光光源,交流汞灯被换成直流氙灯;其次光路中安装了镶有两块干涉滤色片的激发滤色片转盘,使生物样品交地被两种不同波长的光激发。整套装置的运转在微机控制下,在这套装置上,成功地用Ｆｕｒａ－２测定了细胞内自由钙变化,文中提供了应用实例。     

Optimal foraging and feeding mode shifts in fishes

Synopsis Most optimal foraging models for fishes are based on particulate feeding behavior. But many obligate planktivores also filter zooplankton. I suggest that feeding mode shifts (e.g. from particulate feeding to filtering) may be predictable from the costs and benefits of foraging in various modes. Quantitative examples of feeding mode shifts in three species of fishes (northern anchovy, pacific mackerel and alewife) from 3 different families support this hypothesis. Feeding mode shifts seem to depend on relative profitability of each mode, but improvements in model predictions will need to include the effects of spatial and temporal patchiness on encounter rates of prey of various sizes.     

Estimating ultraviolet radiation at the earth's surface

Surface ultraviolet (UV) irradiance depends not only on stratospheric ozone amounts, but also varies with time and date, latitude, cloud amount and aerosol load. Any assessment of the effect of stratospheric ozone depletion on surface UV irradiance must take into consideration all of the above parameters. Measurements in the UV-B region may be accomplished using filter and detector combinations which mimic a biological response curve. However there are uncertainties such as in determining the exact filter response and in the cosine error of the detector. The UV-A region lacks a strong ozone absorption band and approaches which relate measured UV-A irradiance to measured global irradiance show promise. Theoretical models have been derived which calculate spectral UV irradiance in cloudless and cloudy conditions. Results show that cloud transmissivities increase as wavelength increases; however, there is a strong dependence on cloud type. In the absence of surface observations of clouds, satellite data may be used to map UV-A and UV-B irradiance in a region, and this approach is illustrated using two specific examples.     

Diagnosis of inborn errors of metabolism using filter paper urine,urease treatment,isotope dilution and gas chromatography–mass spectrometry

This review will be concerned primarily with a practical yet comprehensive diagnostic procedure for the diagnosis or even mass screening of a variety of metabolic disorders. This rapid, highly sensitive procedure offers possibilities for clinical chemistry laboratories to extend their diagnostic capacity to new areas of metabolic disorders. The diagnostic procedure consists of the use of urine or filter paper urine, preincubation of urine with urease, stable isotope dilution, and gas chromatography–mass spectrometry. Sample preparation from urine or filter paper urine, creatinine determination, stable isotope-labeled compounds used, and GC–MS measurement conditions are described. Not only organic acids or polar ones but also amino acids, sugars, polyols, purines, pyrimidines and other compounds are simultaneously analyzed and quantified. In this review, a pilot study for screening of 22 target diseases in newborns we are conducting in Japan is described. A neonate with presymptomatic propionic acidemia was detected among 10,000 neonates in the pilot study. The metabolic profiles of patients with ornithine carbamoyl transferase deficiency, fructose-1,6-bisphosphatase deficiency or succinic semialdehyde dehydrogenase deficiency obtained by this method are presented as examples. They were compared to those obtained by the conventional solvent extraction methods or by the tandem mass spectrometric method currently done with dried filter blood spots. The highly sensitive, specific and comprehensive features of our procedure are also demonstrated by its use in establishing the chemical diagnosis of pyrimidine degradation defects in order to prevent side effects of pyrimidine analogs such as 5-flurouracil, and the differential diagnosis of three types of homocystinuria, orotic aciduria, uraciluria and other urea cycle disorders. Evaluation of the effects of liver transplantation or nutritional conditions such as folate deficiency in patients with inborn errors of metabolism is also described.     

Performance of inhomogeneous and anisotropic filters in the visual system

Inhomogeneous and anisotropic processing stages developed in the visual system during evolution in order to match a (certainly highly complex) biological optimality criterion. As the examples presented in this paper show, scenes viewed can be separated stages such as processing of the central area of the picture field in a wide band fashion, where each detail is percieved and the contrasts are amplified. This requires good illumination as the amplification is small. At the periphery the amplification is higher which favors twilight vision. Especially the sensitivity for moving patterns is highly developed and a band pass prefilter requires only spatially narrow band channels in the course of further processing. Direction specific filter stages make it possible to solve special problems such as the reconstruction of a form from an illuminance distribution.     

Semi-automated high throughput combinatorial solid-phase organic synthesis.

A semi-automated technique for massive parallel solid-phase organic synthesis based on a "split only" strategy is described. Two different types of purpose-oriented reaction vessels are used. The initial steps are performed in domino blocks, and the resin-bound intermediates then split into wells of a micro plate for the last combinatorial step. The domino block is a reaction block for manual and semi-automatic parallel solid-phase organic synthesis that simplifies liquid exchange and integrates common synthetic steps. The synthesis in micro plates does not use any filter for separation of resin beads from the supernatant liquid, and allows high throughput parallel synthesis on solid phase to be performed. This technique, documented on examples of diverse disubstituted benzenes, includes the use of gaseous cleavage in the last synthetic step and allows the synthesis of thousands of compounds per day in mg quantities.     

UVB-based mate-choice cues used by females of the jumping spider Phintella vittata

Although there are numerous examples of animals having photoreceptors sensitive to UVA (315-400 nm) [1] and relying on UVA-based mate-choice cues [2-5], here we provide the first evidence of an animal using UVB (280-315 nm) for intraspecific communication. An earlier study showed that Phintella vittata, a jumping spider (Salticidae) from China, reflects UVB [6]. By performing six series of binary mate-choice experiments in which we varied lighting conditions with filters (UVB+ [no filter] versus UVB-, UVB+ versus ND1, UVB+ versus ND2, UVB- versus ND1, UVB- versus ND2, and UVB- versus UVA-), we show that significantly more UVB + males than UVB- males are chosen by females as preferred mates. Female preference for UVB-reflective males is not affected by differences in brightness or by UVA.     

Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis

The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein-protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody-antigen complexes and 14 enzyme-inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near-native solutions were ranked first or second in all but two enzyme-inhibitor complexes. Less success was encountered for antibody-antigen complexes, but in all cases studied, the more complete free energy evaluation was able to identify native and near-native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody-antigen complexes and resulted in a native and near-native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody-antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible.     

Reactions chimiques couplees considerees en tant que filtres passe-bande

An investigation is made as to whether or not the existence of a band-pass filter function, analogous to that in electronics, can be proved from the fundamental laws of chemical kinetics. The problem is important for better understanding of the preference of certain biological rhythms to others. It is shown with simple examples that such behavior is possible for a number of systems of coupled chemical reactions far enough from the thermodynamic equilibrium. It is of interest to generalize this behavior since it could conceivably play a role in the transmission of “usable information” in biology.