Length control of extended protein structures in bacteria and bacteriophages

The length of the tail of bacteriophages is controlled by a protein which acts as a molecular ruler. The needle of the injectisome, which is assembled by the polymerization of subunits that are exported through the nascent injectisome, is functionally related to the tail of bacteriophages. Interestingly, its length is controlled by a protein, which is itself exported and acts as a molecular ruler that is coupled to a substrate specificity switch. The bacterial flagellum is evolutionarily related to the injectisome. The length of the hook is also controlled by a secreted protein. This protein acts as a substrate specificity switch and, possibly, also as a ruler.     

Pollen as food and medicine—A review

Pollen, the male gametophyte of flowering plants, is a high energy material, which is collected by insects and stored as food reserve. Pollen has been used traditionally by humans for religious purposes and as supplementary food. Pollen is a concentrated, energy and vitamin rich food that in contemporary times is not only consumed as a dietary component, but also is used in alternative medical treatments. Pollen has potential imporiance as a supplementary and survival food, and for conditioning of athletes. Pollen has been used medically in prostatitis, bleeding stomach ulcers and some infectious diseases, although such use has been questioned by the medical profession. Pollen may also be used for treatment and prevention of the high-altitude-sickness syndrome. Because some individuals are allergic to pollen, and various pollen species contain specific allergens, individual sensitivities must be tested before pollen is used as a treatment or as a supplementary food.     

Is a genome a codeword of an error-correcting code?

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.     

Bone remodeling of diaphyseal surfaces by torsional loads: theoretical predictions

A theory of surface bone remodeling is extended to include the effects of shearing strains as well as normal strains. It is shown that the surface velocity can only depend upon the square of shearing strains, but that it can be linear as well as quadratic in the normal strains. The theory is applied to predict the surface bone remodeling in the diaphysis of a long bone under combined axial and torsional loading. In the general case the diaphysis of the long bone is modeled as a hollow thin-walled cylinder of arbitrary cross-section and, in a special case, as a right circular thin-walled tube. It is shown here that if a thin-walled right circular cylinder capable of surface remodeling is subjected to an axial compressive load and a twisting torque, then the effect of increasing the torque is the same as the effect of decreasing the axial compressive load, namely the mean radius of the cross-section increases and the wall width thins. Conversely, the effect of reducing the torque is the same as the effect of increasing the axial compressive load, namely the mean radius of the cross-section decreases and the wall width thickens.     

Role of autophagy in bone and muscle biology

Autophagy in eukaryotic cells is a constitutive process and functions as a homeostatic mechanism; it is up-regulated in response to specific stress stimuli such as starvation, hypoxia and as oxidative stress. In addition to playing a crucial role in adaptive responses to different stimuli, autophagy is also required for intracellular quality control. This second aspect is important to prevent the activation of pathological processes. Autophagy also plays a central role in cellular development and differentiation because it is involved in the regulation of energetic balance. This final aspect is critical for maintaining proper bone and muscle function as well as to prevent any pathological changes. Therefore, identifying new molecular targets involved in autophagy is critical to assure a good quality of life.     

Bone breaking stress as a function of weight bearing in bipedal rats

The effect of bipedal stance on the breaking stress in compression of rat femora is investigated as a function of animal weight. It is shown that the breaking stress is a linear function of body weight, bone density and specific calcium content of the femur. In all cases investigated, bipedal femora are shown to have a higher breaking stress than controls. It is concluded that there is a continuous change in the quality as well as the quantity of bone in the rat femur with age and that the increased strength of bone material found in bipedal animals compared to controls as well as large animals as compared to small ones, cannot be explained on the basis of bone mineral content alone.     

The Taxon as an Ontological Problem

Although the term taxon is one of the most common concepts in biology, a range of its meanings cannot be comprehended by an universal definition. Usually, biologists construe their knowledge of “the same” taxon by substantially different interpretations, so they find themselves in need either to justify this “multiplication of taxon essences”, or to surmount their plurality unifying its interpretations into a single explanation of what a taxon is. In both cases, an ontological status (“reality”) of that taxon is questioned. Therefore, discrepancy between universality of the taxon concept in biology and unavoidable plurality of its interpretations can be regarded as a source of problem of the taxon ontology. The present work aims to clarify the premises of this discrepancy using phenomenological approach. Three ways of the taxon positing (as a class, as a place in the world, and as a individualized body) have been distinguished. Taxon as a class is established by common essence that is shared by a set of living beings. These living beings are regarded as speculative objects beyond an idea of the world, i.e. as objects of the experimental science. A question about ontology of taxon as a class refers to the scholastic problem of universalia; its status can be defined within the scope of the nominalism/realism opposition. Taxon as a place of common appearance of the specimens is regarded in the context of the etiological relations unifying various entities into the entire world. Taxon as a place refers to a certain position in the Natural System that is construed as an etiological map of the world. In this case a specimen of a living being is known as a curiosity, i.e. representant of its relationships as well as of the place of its origin. Ontological status of a taxon as a place is to be clarified within the framework of the natural/artificial opposition. The positing of a taxon as a collective body marked off by limits of joint survival of living beings is characteristic for biology in the strict sense which arose in the very beginning of the 19 century. A taxon as a body established by the techniques of disciplinary power sensu M. Foucault extended from the human bodies to bodies of other living beings. The ontological status of a taxon as a collective body can be defined within the scope of the wild/domesticated opposition. Therefore, the discrepancy between the universality of the taxon concept and the plurality of its interpretations is underlayed by interpenetration of three distinct modi of taxon establishing. Distinguishing between these three modi can clarify sources of ontological problems concerned with the term taxon in each case when they arise.     

巴西人参化学成分和药理活性研究进展

巴西人参原产于南美洲,当地人把它当做具有壮阳、增强体质等作用的草药。巴西人参已在我国广西、浙江等地引种栽培成功,现代研究发现,其主要含有三萜和三萜皂苷类、甾体类等多种化学成分,具有抗肿瘤、抗炎、保护胃黏膜等药理活性。本文通过对近年来巴西人参的研究情况进行综述,阐明已有的化学物质基础和药理作用,为其进一步的深入研究和开发提供理论依据。     

巴西人参化学成分和药理活性研究进展

巴西人参原产于南美洲,当地人把它当做具有壮阳、增强体质等作用的草药。巴西人参已在我国广西、浙江等地引种栽培成功,现代研究发现,其主要含有三萜和三萜皂苷类、甾体类等多种化学成分,具有抗肿瘤、抗炎、保护胃黏膜等药理活性。本文通过对近年来巴西人参的研究情况进行综述,阐明已有的化学物质基础和药理作用,为其进一步的深入研究和开发提供理论依据。     

Development of a novel fluorometric assay for nitric oxide utilizing sesamol and its application to analysis of nitric oxide‐releasing drugs

Nitric oxide (NO) is related to various physiological effects as well as to numerous diseases caused by accentuation of NO production. Measurement of NO in cells and tissues is difficult as NO readily reacts with other molecules; furthermore, its half‐life as a radical is fleeting. Currently, many NO pharmaceuticals are marketed as therapeutic agents for ischemic disease. Consequently, the identification of NO radicals and determination of generation rate from pharmaceuticals is very important when the effect of the medicinal supply is estimated. In this study, we developed a fluorometric assay for NO employing sesamol (3,4‐methylenedioxyphenol) as a fluorometric substrate. Sesamol is converted to a fluorescent derivative (ex. 365 nm, em. 447 nm), which is dimmer in the presence of NO. The detection limit of NO with this method is 400 fmol; moreover, NO generated from drugs can be measured. Copyright © 2009 John Wiley & Sons, Ltd.     

Under the volcano,or pheochromocytoma revisited

Pheochromocytoma is a well-defined clinical entity often remembered in clinical practice, but seldom encountered. Rather often, however, these patients are initially referred to a cardiologist and then a correct diagnosis is important because this disease is curable and may otherwise be lethal. Somehow clinical signs and symptoms are embedded in a sort of subconscious memory but specific knowledge is rather limited as far as, for example, the pathophysiological background is concerned. Perhaps this has something to do with the fact that already in 1922 a syndrome of paroxysmal hypertension associated with an adrenal medullary tumour was reported and that its nature and clinicopathological manifestations were described as early as the 1950s. Nevertheless it is not amiss to shed some new light upon old and established views not only for the better of our patients but as a catalyst for the motivation in search of coherence as well. The patient presented here pairs a very unusual case with unusual features. The pathophysiology is revealed with the closely monitored sequence of events. At a time where the medical professional leans heavily on test results and sophisticated technology it is refreshing to see how basic diagnostic tools pay off in clarifying and understanding as well.     

A possible involvement of glutathione in the detoxication of sulfite

Inorganic sulfite may be detoxified by conversion to S-sulfocysteine. We demonstrate this conversion by a series of enzyme-catalyzed steps as follows. Inorganic sulfite reacts with glutathione disulfide by a thiol transferase catalyzed reaction as previously demonstrated. The S-sulfoglutathione formed is then converted by gamma-glutamyltranspeptidase to S-sulfocysteinylglycine and the latter finally hydrolyzed to S-sulfocysteine by a renal dipeptidase. S-Sulfoglutathione is a substrate for gamma-glutamyl-transpeptidase as effective as glutathione itself. Furthermore, S-sulfocysteinylglycine is cleaved as efficiently as cysteinylglycine by a renal dipeptidase at high substrate concentrations but somewhat less efficiently at low substrate concentrations.     

Numerical simulation of the flow field and mass transport pattern within the coronary artery

In this study, the steady and pulsatile flow field with mass transport analysis in an anatomically correct model of coronary artery is simulated numerically using a specific patient data from a 64-multislice computed tomography scanner. It is assumed that the blood flow is laminar and that the Navier-Stokes equations of motion are applied. Downstream of the bifurcation, a strong skewing occurs towards the flow divider walls as a result of branching. For the low-density lipoprotein (LDL) transport analysis where a specific boundary condition at the arterial walls is applied, LDL is generally elevated at locations where shear stress distribution is low, but it does not co-locate at whole domain. This numerical simulation gives an insight, as well as detailed quantitative data, of haemodynamic conditions in the left coronary artery as well as mass transfer patterns for a specific patient.     

Significance levels in complex inheritance.

A LOD score >=3 is necessary but not sufficient to make a linkage test reliable, and this applies to complex inheritance as well as to major loci. Factors that affect this threshold are considered here. A LOD score as small as 2 is suggestive but is unreliable except as confirmation of either a significant linkage or a strong candidate locus. A threshold as great as 4 is unnecessarily conservative if multipoint tests are used sensibly. Marker density is not a major factor, and biases in the evaluation of LOD scores-especially inadequate allowance for estimation of nuisance parameters in multiple models-are paramount. Allelic association increases resolution for oligogenes within a candidate region and remains the only practical method to locate polygenes. The method sketched here combines multipoint linkage and allelic association to test efficiently for a regional candidate locus.     

Recent advances on biological difructose anhydride III production using inulase II from inulin

Difructose anhydride III (DFA III), the smallest cyclic disaccharide, consists of two fructose residues. DFA III is a hydrolysate of inulin and is rarely found in nature. Industrial interest in DFA III as a low-calorie sugar substitute is increasing. The present review describes the properties and physiological functions of DFA III as well as its commercial importance. Focus is also given on the biological production of DFA III from inulin, which contains enzyme resources, inulase II properties, and the capacity for mass DFA III production. Inulase II as an industrial enzyme and its molecular evolution are discussed as well. The aim is to better understand commercial-scale DFA III production as a food product.     

ONTOLOGY OR PHENOMENOLOGY? HOW THE LVAD CHALLENGES THE EUTHANASIA DEBATE

This article deals with the euthanasia debate in light of new life‐sustaining technologies such as the left ventricular assist device (LVAD). The question arises: does the switching off of a LVAD by a doctor upon the request of a patient amount to active or passive euthanasia, i.e. to ‘killing’ or to ‘letting die’? The answer hinges on whether the device is to be regarded as a proper part of the patient's body or as something external. We usually regard the switching off of an internal device as killing, whereas the deactivation of an external device is seen as ‘letting die’. The case is notoriously difficult to decide for hybrid devices such as LVADs, which are partly inside and partly outside the patient's body. Additionally, on a methodological level, I will argue that the ‘ontological’ arguments from analogy given for both sides are problematic. Given the impasse facing the ontological arguments, complementary phenomenological arguments deserve closer inspection. In particular, we should consider whether phenomenologically the LVAD is perceived as a body part or as an external device. I will support the thesis that the deactivation of a LVAD is to be regarded as passive euthanasia if the device is not perceived by the patient as a part of the body proper.     

The minimal genome paradox

The concept of a 'minimal genome' has appeared as an attempt to answer the question what the minimum number of genes or minimum amount of DNA to support life is. Since bacteria are cells bearing the smallest genomes, it has been generally accepted that the minimal genome must belong to a bacterial species. Currently the most popular chromosome in studies on a minimal genome belongs to Mycoplasma genitalium, a parasite bacterium whose total genetic material is as small as approximately 580 kb. However, the problem is how we define life, and thus also a minimal genome. M. genitalium is a parasite and requires substances provided by its host. Therefore, if a genome of a parasite can be considered as a minimal genome, why not to consider genomes of bacteriophages? Going further, bacterial plasmids could be considered as minimal genomes. The smallest known DNA region playing the function of the origin of replication, which is sufficient for plasmid survival in natural habitats, is as short as 32 base pairs. However, such a small DNA molecule could not form a circular form and be replicated by cellular enzymes. These facts may lead to an ostensibly paradoxical conclusion that the size of a minimal genome is restricted by the physical size of a DNA molecule able to replicate rather, than by the amount of genetic information.