Evidence for an essential role for arginyl residues for yeast phosphoglycerate kinase.

Reaction of yeast phosphoglycerate kinase with either butanedione or cyclohexanedione can result in modification of up to all 13 arginyl residues with total loss of activity; however, extrapolation to zero activity for partially modified preparations indicates that up to 7 arginyls are essential. Whereas 20 mm 3-phosphoglycerate affords partial protection of activity toward both reagents, 20 mm MgATP affords complete protection of activity and protects 2 arginyls against modification by butanedione and 1 arginyl against modification by cyclohexanedione. With butanedione the modification could be reversed with total recovery of activity, suggesting that only arginyl groups were modified, which is consistent with the amino acid analysis of the modified protein. Only at high cyclohexanedione concentrations or long reaction times was a yellow product obtained that showed loss of lysyl residues. Circular dichroism spectra show that even when all the arginyls are modified by butanedione or up to 10 modified by cyclohexanedione there is no change observed in the far or near ultraviolet, indicating that there is no detectable conformational change concomitant with modification, which is confirmed by hydrodynamic studies. It is concluded that at least one, possibly two, arginyls of yeast phosphoglycerate kinase are essential for its action on ATP.     

Quantitative proteomics for identifying biomarkers for Rabies

Introduction

Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite.

Methods

In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy.

Results and conclusion

We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and glutamate ammonia ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

Breeding for abiotic stresses for sustainable agriculture

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.     

Theory for designing nature reserves for single species

We examine the question of the optimal number of reserves that should be established to maximize the persistence of a species. We assume that the mean time to extinction of a single population increases as a power of the habitat area, that there is a certain amount of habitat to be reserved, and that the aim is to determine how this habitat is most efficiently divided. The optimal configuration depends on whether the management objective is to maximize the mean time to extinction or minimize the risk of extinction. When maximizing the mean time to extinction, the optimal number of independent reserves does not depend on the amount of available habitat for the reserve system. In contrast, the risk of extinction is minimized when individual reserves are equal to the optimal patch size, making the optimal number of reserves linearly proportional to the amount of available habitat. A model that includes dispersal and correlation in the incidence of extinction demonstrates the importance of considering the relative rate at which these two factors decrease with distance between reserves. A small number of reserves is optimal when the mean time to extinction increases rapidly with habitat area or when risks of extinction are high.     

Autophagy: for better or for worse

Autophagy is a lysosomal degradation pathway that degrades damaged or superfluous cell components into basic biomolecules, which are then recycled back into the cytosol. In this respect, autophagy drives a flow of biomolecules in a continuous degradation-regeneration cycle. Autophagy is generally considered a pro-survival mechanism protecting cells under stress or poor nutrient conditions. Current research clearly shows that autophagy fulfills numerous functions in vital biological processes. It is implicated in development, differentiation, innate and adaptive immunity, ageing and cell death. In addition, accumulating evidence demonstrates interesting links between autophagy and several human diseases and tumor development. Therefore, autophagy seems to be an important player in the life and death of cells and organisms. Despite the mounting knowledge about autophagy, the mechanisms through which the autophagic machinery regulates these diverse processes are not entirely understood. In this review, we give a comprehensive overview of the autophagic signaling pathway, its role in general cellular processes and its connection to cell death. In addition, we present a brief overview of the possible contribution of defective autophagic signaling to disease.     

Methods for Precisely Trimming Block Faces for Ultramicrotomy

Two devices are described to aid in trimming block faces of embedded tissue for ultramicrotomy. The first, a reticle to fit the ocular of a stereomicroscope, can be manufactured by the ultramicrotomist and is designed to outline the edges of the block face so that it can be trimmed to a standard size and shape with the area of interest centered in it. The second, a rectangular “trim-align” block mounted in the knife holder of the uitramicrotome, is, with the block face, aligned to the plane of sectioning, and aids in retrimming the top and bottom edges of the block face. This is the simplest trimming device yet described and the first which will, from any sort of embedded material, produce a block face with parallel top and bottom edges even if the block face is not perpendicular to the axis of the specimen holder. If the edge of the diamond knife used for sectioning is parallel to the axis of rotation of the knife holder, the block face has also been automatically aligned to the knife as a consequence of this aligning and trimming procedure. As a result, sectioning can begin immediately without further adjustments.     

Common pathways for growth and for plasticity

Cell growth and differentiation in developing tissues are, at first impression, quite different endeavors from readjusting synaptic strength during activity-dependent synaptic plasticity in mature neurons. Nevertheless, it is becoming increasingly clear that these two distinct processes share multiple intracellular signaling events. How these common pathways result in cell division (during proliferation), large-scale cellular remodeling (during differentiation) or synapse-specific changes (during synaptic plasticity) is only starting to be elucidated. Here we review the latest findings on two prototypical examples of these shared mechanisms: the Ras-PI3K pathway and the intracellular signaling elicited by neural cell adhesion molecules interacting with growth factor receptors.     

Improved methods for calculating formation constants for nucleotide-cation complexes

Two data reduction methods that can be used to calculate formation constants for nucleotidecation complexes are described. Both methods are used to analyze data obtained by an anion-exchange resin method, and either method can improve the accuracy of the calculated formation constants by more than 50%. The key to this significant improvement in accuracy is the realization that the equation for the mathematical model describing such systems is always nonlinear in terms of the formation constants and, in the general case, is higher order in the cation concentration. There are two major reasons for the improved quality of the results associated with the new model. First, successive linear extrapolations are eliminated, and error propagation is reduced. Second, all of the data are used for the simultaneous calculation of all formation constants, and the uncertainty due to random experimental errors is minimized.     

Approaches for calculating power for case-cohort studies

An approach for determining the power of a case-cohort study for a single binary exposure variable and a low failure rate was recently proposed by Cai and Zeng (2004, Biometrics 60, 1015-1024). In this article, we show that computing power for a case-cohort study using a standard case-control method yields nearly identical levels of power. An advantage of the case-control approach is that existing sample size software can be used for the calculations. We also propose an additional formula for computing the power of a case-cohort study for the situation when the event is not rare.     

The Need for a Kinetics for Biological Transport

The traditional theory of transport across capillary membranes via a laminar Poiseuille flow is shown to be invalid. It is demonstrated that the random, diffusive nature of the molecular flow and interactions with the “pore” walls play an important role in the transport process. Neither the continuum Navier-Stokes theory nor the equivalent theory of irreversible thermodynamics is adequate to treat the problem. Combination of near-continuum hydrodynamic theory, noncontinuum kinetic theory, and the theory of fluctuations provides a first step toward modeling both liquid processes in general and membrane transport processes as a specific application.     

Searching for a function for nuclear actin

The abundant cytoskeletal protein actin has numerous cytoplasmic roles. Although there are many reports of the presence of actin in the nucleus, in general they have been discounted as artifactual. However, recent work has begun to provide evidence for important roles for actin in nuclear processes ranging from chromatin remodelling to splicing. In addition, several regulators of actin polymerization are localized to the nucleus or translocate to the nucleus in a regulated manner, suggesting that there is some function of actin in the nucleus that is subject to regulation. This review discusses the evidence for actin in the nucleus and summarizes recent work suggesting that actin or actin-related proteins are involved in the regulation of nuclear processes such as chromatin remodelling.     

A Standardized Procedure for Echoencephalography and for Analyzing Echoencephalograms

Although echoencephalography is a simple, convenient and atraumatic diagnostic technique, the accuracy and reliability of this test and whether it is reproducible can be greatly influenced by the way in which the examination is performed and subsequently analyzed. Echoencephalography in 850 patients has led to the development of a standardized technique which takes into account the positioning of the patient, the application of the transducer, the identification of the midline-echo-complex, and the elimination of observer bias. Once performed the test must meet rigid standards of acceptability. If acceptable the test is analyzed according to an established format.     

A Decision-Tree Strategy for Combining Diagnostic Tests for Prediction

In the context of medical screening, various diagnostic tests have been developed for determining whether a disease is present in an individual. Similarly, in the context of toxicological screening, a variety of short-term assays have been developed to predict whether a chemical would be carcinogenic if tested in a long-term bioassay. In both contexts, it is a challenge to combine the results of several predictive tests in a way that improves on the predictivity of the individual tests. Increases in positive predictivity can be accompanied by decreases in negative predictivity, and vice versa. This article presents a decision-tree classification model for combining results from several independent short-term or diagnostic tests to quantify the likelihood of a true positive result (patient has disease, or chemical is carcinogenic). The decision-tree strategy determines the most advantageous sequence for conducting the predictive tests. The classification model is based on statistical confidence limits on the predictive probability of disease (carcinogenicity) rather than on the central estimate of the predictive probability. This model is applied to the assessment of the abilities of four short-term tests in the prediction of chemical carcinogenicity under the assumption of independence among the four tests, and is used to demonstrate a testing strategy for the application of three pancreatic cancer diagnostic tests.     

Modeling for Understanding v. Modeling for Numbers

I draw a distinction between Modeling for Numbers, which aims to address how much, when, and where questions, and Modeling for Understanding, which aims to address how and why questions. For-numbers models are often empirical, which can be more accurate than their mechanistic analogues as long as they are well calibrated and predictions are made within the domain of the calibration data. To extrapolate beyond the domain of available system-level data, for-numbers models should be mechanistic, relying on the ability to calibrate to the system components even if it is not possible to calibrate to the system itself. However, development of a mechanistic model that is reliable depends on an adequate understanding of the system. This understanding is best advanced using a for-understanding modeling approach. To address how and why questions, for-understanding models have to be mechanistic. The best of these for-understanding models are focused on specific questions, stripped of extraneous detail, and elegantly simple. Once the mechanisms are well understood, one can then decide if the benefits of incorporating the mechanism in a for-numbers model is worth the added complexity and the uncertainty associated with estimating the additional model parameters.     

Dissociation constants for dihydrofolic acid and dihydrobiopterin and implications for mechanistic models for dihydrofolate reductase

The dissociation constants (pKa) for the pteridine ring system of dihydrofolate (H2folate) have been redetermined, and those for dihydrobiopterin (H2biopterin) have been determined. Determination of the pKa for N5 of H2folate is complicated by the low solubility and instability of H2folate at pH 2-4, and other complicating factors. The initial rate of absorbance change due to degradation is a maximum at pH 2.5, and the products depend on the oxygen concentration: under aerobic conditions, (p-aminobenzoyl)glutamic acid and 7,8-dihydropterin-6-carboxaldehyde are major products. H2Biopterin is much more soluble and more stable at low pH. For protonation of N5, the pKa is 2.56 +/- 0.01 for H2biopterin and 2.59 +/- 0.03 for H2folic acid. Spectrophotometric determination of the pKa for the N3-O4 amide group of H2folate is subject to serious errors when a wavelength between 220 and 235 nm is used. These errors arise from the pH-dependent absorbance of mercaptoethanol often present in the preparation. The amide group has a pKa of 10.41 +/- 0.04 in H2biopterin and 10.85 +/- 0.04 in H2folate. The redetermined value for the pKa of N5 of H2folate has implications for mechanistic models for dihydrofolate reductase, and revised kinetic constants have been calculated for one model.     

Prospects for biopesticides for aphid control

Diseases form an important component of the natural enemy complex of aphids. The most common and obvious of these diseases are entomophthoran fungi such asErynia neoaphidis Remaudiere & Herbert,Entomophthora planchoniana Cornu,Zoophthora radicans (Brefeld) Batko andConidiobolus obscurus (Hall & Dunn) Remaudiere & Keller. The pest status of some aphids such as the pea aphid,Acyrthosiphon pisum (Harris), is considerably reduced by natural epizootics of fungal disease. However, disease may contribute little to practical control as it is mainly effective in high density populations when weather conditions are suitable. Introduction of exotic diseases for classical biological control is only rarely possible since most diseases, like their aphid hosts, are distributed world-wide. One exception was the successful introduction into Australia of a strain ofZ. radicans for control of spotted alfalfa aphid,Therioaphis trifolii (Monell) f.maculata in 1979. Attempts to manipulate entomophthoran fungi have had limited success because of problems with mass production, the fragility of the conidia and the need for suitably moist conditions. Hyphomycete fungi such asVerticillium lecanii (Zimm.) Viegas,Metarhizium anisopliae (Metsch.) Sorokin,Beauveria bassiana (Bals.) Vuill. andPaecilomyces spp. are more suitable for development as mycoinsecticides as they are cheap to mass produce and form stable conidia. “Vertalec?”, a formulation ofV. lecanii, has been sold in small quantities commercially in Britain and parts of Europe for many years and used mainly in glasshouses. Recently promising results have been obtained with use ofM. anisopliae for control of lettuce root aphid,Pemphigus bursarius (L.) in the UK. Laboratory studies on selected isolates ofB. bassiana andPaecilomyces spp. show a promising level of activity. Problems may occur with these species as they can kill aphid predators such as coccinelids. In addition, more research is needed on developing improved formulations which enable control to be achieved under low humidity conditions.     

Strategies for the prevention of antimalarial drug resistance: rationale for combination chemotherapy for malaria

Among the several 'tropical' diseases that affect humans, malarin poses special control problems due to the increasing population at risk from the disease, the difficulties in eradicating the mosquito vector in the tropics and the emergence and spread of parasite resistance to commonly used antimalarial drugs. There is both clinical experience and experimental evidence that, however effective when first introduced, the lifespan of drugs is inevitably curtailed by the emergence of resistant parasites. Resistance is the most important factor in determining the useful lifespan of antimalarial drugs. In this review, Nick White and Piero Olliaro discuss the rationale for combination chemotherapy.     

Search for the pharmacophore in prazosin for Transport-P

Partial structures of prazosin have been synthesised and tested for inhibition of Transport-P in order to identify the structural features of prazosin, which appear to be involved in binding to the putative transporter. It is shown that the pyrimidinyl 4-amino group is critically important for binding but that the 6,7-dimethoxy and 2-furoyl groups are not essential.